Broadening the Scope of Nanopublications

In this paper, we present an approach for extending the existing concept of nanopublications --- tiny entities of scientific results in RDF representation --- to broaden their application range. The proposed extension uses English sentences to represent informal and underspecified scientific claims. These sentences follow a syntactic and semantic scheme that we call AIDA (Atomic, Independent, Declarative, Absolute), which provides a uniform and succinct representation of scientific assertions. Such AIDA nanopublications are compatible with the existing nanopublication concept and enjoy most of its advantages such as information sharing, interlinking of scientific findings, and detailed attribution, while being more flexible and applicable to a much wider range of scientific results. We show that users are able to create AIDA sentences for given scientific results quickly and at high quality, and that it is feasible to automatically extract and interlink AIDA nanopublications from existing unstructured data sources. To demonstrate our approach, a web-based interface is introduced, which also exemplifies the use of nanopublications for non-scientific content, including meta-nanopublications that describe other nanopublications.Comment: To appear in the Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013

Friends or Foes? Emerging Impacts of Biological Toxins

Toxins are substances produced from biological sources (e.g., animal, plants, microorganisms) that have deleterious effects on a living organism. Despite the obvious health concerns of being exposed to toxins, they are having substantial positive impacts in a number of industrial sectors. Several toxin-derived products are approved for clinical, veterinary, or agrochemical uses. This review sets out the case for toxins as ‘friends’ that are providing the basis of novel medicines, insecticides, and even nucleic acid sequencing technologies. We also discuss emerging toxins (‘foes’) that are becoming increasingly prevalent in a range of contexts through climate change and the globalisation of food supply chains and that ultimately pose a risk to health

Are metabolic equivalents (METS) an accurate method for estimating change in peak oxygen consumption after cardiac rehabilitation?

Background: Maximal cardiopulmonary exercise testing (CPET) is the “gold standard” method of determining Vo2peak. When CPET is unavailable, VO2peak and metabolic equivalents (METs) are estimated from treadmill or cycle ergometer workloads. UK cardiac rehabilitation programmes (CR) use estimated METs to report changes in cardiorespiratory fitness (CRF). However, the accuracy of determining changes in VO2peak based on changes in estimated METs is not known. Methods: 27 patients with coronary heart disease (88.9% male; age 59.5 ± 10.0 years, body mass index 29.6 ± 3.8 kg.m-2) performed maximal CPET before and after an exercise based CR intervention. VO2peak was directly determined using ventilatory gas exchange data and was also estimated using the American College of Sports Medicine (ACSM) leg cycling equation for METs. Agreement between changes in directly determined VO2peak and VO2peak estimated from METs was tested using Bland-Altman limits of agreement (LoA), and intraclass correlation coefficients. Results: Directly determined VO2peak did not increase significantly following CR (0.5 ml.kg-1.min-1 (2.7%); p=0.332). In contrast, estimated VO2peak increased significantly (0.4 METs; 1.4 ml.kg-1.min-1; 6.7%; p=0.006). The mean bias for estimated VO2peak versus directly-determined VO2peak was 0.7 ml.kg-1.min-1 (LoA -4.7 to 5.9 ml.kg-1.min-1). Aerobic efficiency, (ΔVO2/ΔWR slope) was significantly associated with estimated VO2peak measurement error. Conclusion: Changes in estimated VO2peak determined using the ACSM equation for leg cycling are not accurate surrogates for directly determined changes in VO2peak. Reporting mean CRF changes using estimated METs may over-estimate the efficacy of CR and lead to a different interpretation of study findings compared to directly determined VO2peak

Oral health of the prehistoric Rima Rau cave burials, Atiu, Cook Islands.

The human skeletal remains buried in the cave of Rima Rau on the island of Atiu, have long been a subject of speculation as to their origins. Oral histories of a massacre, battle, famine and cannibal feast surround the sacred site. The local Atiuan community invited a group of bioarchaeologists from the University of Otago to help shed light on the people buried in the cave. We examined nearly 600 skeletal elements and 400 teeth, which represent at least 38 adults and 8 infants and children. This research is the assessment of their oral health, a first for a prehistoric Cook Island population. Oral health was within the range of other tropical Pacific skeletal assemblages, for dental caries, antemortem tooth loss, and supragingival calculus, with low rates of periodontal disease and periapical cavities. Degeneration of the temporomandibular joint was high and this was associated with enamel chipping, possibly linked to diet. Enamel defect prevalence indicates sex-specific health differences, but the population was robust with a good proportion who survived to adulthood despite periods of early childhood stress. Through the consideration of a skeletal census and oral health indicators, we begin to describe the burials in the cave

Added value of frailty and social support in predicting risk of 30-day unplanned re-admission or death for patients with heart failure: an analysis from OPERA-HF

Background: Models for predicting the outcome of patients hospitalized for heart failure (HF) rarely take a holistic view. We assessed the ability of measures of frailty and social support in addition to demographic, clinical, imaging and laboratory variables to predict short-term outcome for patients discharged after a hospitalization for HF. Methods: OPERA-HF is a prospective observational cohort, enrolling patients hospitalized for HF in a single center in Hull, UK. Variables were combined in a logistic regression model after multiple imputation of missing data to predict the composite outcome of death or readmission at 30 days. Comparisons were made to a model using clinical variables alone. The discriminative performance of each model was internally validated with bootstrap re-sampling. Results: 1094 patients were included (mean age 77 [interquartile range 68–83] years; 40% women; 56% with moderate to severe left ventricular systolic dysfunction) of whom 213 (19%) had an unplanned re-admission and 60 (5%) died within 30 days. For the composite outcome, a model containing clinical variables alone had an area under the receiver-operating characteristic curve (AUC) of 0.68 [95% CI 0.64–0.72]. Adding marital status, support from family and measures of physical frailty increased the AUC (p < 0.05) to 0.70 [95% CI 0.66–0.74]. Conclusions: Measures of physical frailty and social support improve prediction of 30-day outcome after an admission for HF but predicting near-term events remains imperfect. Further external validation and improvement of the model is required

Semiseparable integral operators and explicit solution of an inverse problem for the skew-self-adjoint Dirac-type system

Inverse problem to recover the skew-self-adjoint Dirac-type system from the generalized Weyl matrix function is treated in the paper. Sufficient conditions under which the unique solution of the inverse problem exists, are formulated in terms of the Weyl function and a procedure to solve the inverse problem is given. The case of the generalized Weyl functions of the form $\phi(\lambda)\exp\{-2i\lambda D\}$, where $\phi$ is a strictly proper rational matrix function and $D=D^* \geq 0$ is a diagonal matrix, is treated in greater detail. Explicit formulas for the inversion of the corresponding semiseparable integral operators and recovery of the Dirac-type system are obtained for this case

Optimizing the fast Rydberg quantum gate

The fast phase gate scheme, in which the qubits are atoms confined in sites of an optical lattice, and gate operations are mediated by excitation of Rydberg states, was proposed by Jaksch et al. Phys. Rev. Lett. 85, 2208 (2000). A potential source of decoherence in this system derives from motional heating, which occurs if the ground and Rydberg states of the atom move in different optical lattice potentials. We propose to minimize this effect by choosing the lattice photon frequency \omega so that the ground and Rydberg states have the same frequency-dependent polarizability \alpha(omega). The results are presented for the case of Rb.Comment: 5 pages, submitted to PR

Dark soliton states of Bose-Einstein condensates in anisotropic traps

Dark soliton states of Bose-Einstein condensates in harmonic traps are studied both analytically and computationally by the direct solution of the Gross-Pitaevskii equation in three dimensions. The ground and self-consistent excited states are found numerically by relaxation in imaginary time. The energy of a stationary soliton in a harmonic trap is shown to be independent of density and geometry for large numbers of atoms. Large amplitude field modulation at a frequency resonant with the energy of a dark soliton is found to give rise to a state with multiple vortices. The Bogoliubov excitation spectrum of the soliton state contains complex frequencies, which disappear for sufficiently small numbers of atoms or large transverse confinement. The relationship between these complex modes and the snake instability is investigated numerically by propagation in real time.Comment: 11 pages, 8 embedded figures (two in color

Routine exercise-based cardiac rehabilitation does not increase aerobic fitness: A CARE CR study

Background Recent evidence suggests that routine exercise-based cardiac rehabilitation (CR) may not lead to a substantial increase in estimated peak oxygen uptake (V̇O2peak). This could reduce the potential benefits of CR and explain why CR no longer improves patient survival in recent studies. We aimed to determine whether routine exercise-based CR increases V̇O2peak using gold-standard maximal cardiopulmonary exercise testing (CPET), and to quantify the exercise training stimulus which might be insufficient in patients undertaking CR. Methods We studied the effects of a routine, twice weekly, exercise-based CR programme for eight weeks (intervention group) compared with abstention from supervised exercise training (control group) in patients with coronary heart disease. The primary outcome was V̇O2peak measured using CPET. We also measured changes in body composition using dual X-ray absorptiometry, carotid intima-media thickness, hs-CRP and N-terminal pro B-type natriuretic peptide at baseline, 10 weeks and one year. We also calculated the Calibre 5-year all-cause mortality risk score. Results Seventy patients (age 63.1 SD10.0 years; BMI 29.2 SD4.0 kg·m−2; 86% male) were recruited (n = 48 intervention; n = 22 controls). The mean aerobic exercise training duration was 23 min per training session, and the mean exercise training intensity was 45.9% of heart rate reserve. V̇O2peak was 23·3 ml·kg-1·min−1 at baseline, and there were no changes in V̇O2peak between groups at any time point. The intervention had no effect on any of the secondary endpoints. Conclusion Routine CR does not lead to an increase in V̇O2peak and is unlikely to improve long-term outcomes