Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed

Online unit clustering in higher dimensions

We revisit the online Unit Clustering and Unit Covering problems in higher dimensions: Given a set of $n$ points in a metric space, that arrive one by one, Unit Clustering asks to partition the points into the minimum number of clusters (subsets) of diameter at most one; while Unit Covering asks to cover all points by the minimum number of balls of unit radius. In this paper, we work in $\mathbb{R}^d$ using the $L_\infty$ norm. We show that the competitive ratio of any online algorithm (deterministic or randomized) for Unit Clustering must depend on the dimension $d$. We also give a randomized online algorithm with competitive ratio $O(d^2)$ for Unit Clustering}of integer points (i.e., points in $\mathbb{Z}^d$, $d\in \mathbb{N}$, under $L_{\infty}$ norm). We show that the competitive ratio of any deterministic online algorithm for Unit Covering is at least $2^d$. This ratio is the best possible, as it can be attained by a simple deterministic algorithm that assigns points to a predefined set of unit cubes. We complement these results with some additional lower bounds for related problems in higher dimensions.Comment: 15 pages, 4 figures. A preliminary version appeared in the Proceedings of the 15th Workshop on Approximation and Online Algorithms (WAOA 2017

Survival gains needed to offset persistent adverse treatment effects in localised prostate cancer

BACKGROUND: Men diagnosed with localised prostate cancer (LPC) face difficult choices between treatment options that can cause persistent problems with sexual, urinary and bowel function. Controlled trial evidence about the survival benefits of the full range of treatment alternatives is limited, and patients' views on the survival gains that might justify these problems have not been quantified. METHODS: A discrete choice experiment (DCE) was administered in a random subsample (n=357, stratified by treatment) of a population-based sample (n=1381) of men, recurrence-free 3 years after diagnosis of LPC, and 65 age-matched controls (without prostate cancer). Survival gains needed to justify persistent problems were estimated by substituting side effect and survival parameters from the DCE into an equation for compensating variation (adapted from welfare economics). RESULTS: Median (2.5, 97.5 centiles) survival benefits needed to justify severe erectile dysfunction and severe loss of libido were 4.0 (3.4, 4.6) and 5.0 (4.9, 5.2) months. These problems were common, particularly after androgen deprivation therapy (ADT): 40 and 41% overall (n=1381) and 88 and 78% in the ADT group (n=33). Urinary leakage (most prevalent after radical prostatectomy (n=839, mild 41%, severe 18%)) needed 4.2 (4.1, 4.3) and 27.7 (26.9, 28.5) months survival benefit, respectively. Mild bowel problems (most prevalent (30%) after external beam radiotherapy (n=106)) needed 6.2 (6.1, 6.4) months survival benefit. CONCLUSION: Emerging evidence about survival benefits can be assessed against these patient-based benchmarks. Considerable variation in trade-offs among individuals underlines the need to inform patients of long-term consequences and incorporate patient preferences into treatment decisions. © 2012 Cancer Research UK. All rights reserved

Development of a Model System to Identify Differences in Spring and Winter Oat

Our long-term goal is to develop a Swedish winter oat (Avena sativa). To identify molecular differences that correlate with winter hardiness, a winter oat model comprising of both non-hardy spring lines and winter hardy lines is needed. To achieve this, we selected 294 oat breeding lines, originating from various Russian, German, and American winter oat breeding programs and tested them in the field in south- and western Sweden. By assaying for winter survival and agricultural properties during four consecutive seasons, we identified 14 breeding lines of different origins that not only survived the winter but also were agronomically better than the rest. Laboratory tests including electrolytic leakage, controlled crown freezing assay, expression analysis of the AsVrn1 gene and monitoring of flowering time suggested that the American lines had the highest freezing tolerance, although the German lines performed better in the field. Finally, six lines constituting the two most freezing tolerant lines, two intermediate lines and two spring cultivars were chosen to build a winter oat model system. Metabolic profiling of non-acclimated and cold acclimated leaf tissue samples isolated from the six selected lines revealed differential expression patterns of 245 metabolites including several sugars, amino acids, organic acids and 181 hitherto unknown metabolites. The expression patterns of 107 metabolites showed significant interactions with either a cultivar or a time-point. Further identification, characterisation and validation of these metabolites will lead to an increased understanding of the cold acclimation process in oats. Furthermore, by using the winter oat model system, differential sequencing of crown mRNA populations would lead to identification of various biomarkers to facilitate winter oat breeding

An addressable quantum dot qubit with fault-tolerant control fidelity

Exciting progress towards spin-based quantum computing has recently been made with qubits realized using nitrogen-vacancy (N-V) centers in diamond and phosphorus atoms in silicon, including the demonstration of long coherence times made possible by the presence of spin-free isotopes of carbon and silicon. However, despite promising single-atom nanotechnologies, there remain substantial challenges in coupling such qubits and addressing them individually. Conversely, lithographically defined quantum dots have an exchange coupling that can be precisely engineered, but strong coupling to noise has severely limited their dephasing times and control fidelities. Here we combine the best aspects of both spin qubit schemes and demonstrate a gate-addressable quantum dot qubit in isotopically engineered silicon with a control fidelity of 99.6%, obtained via Clifford based randomized benchmarking and consistent with that required for fault-tolerant quantum computing. This qubit has orders of magnitude improved coherence times compared with other quantum dot qubits, with T_2* = 120 mus and T_2 = 28 ms. By gate-voltage tuning of the electron g*-factor, we can Stark shift the electron spin resonance (ESR) frequency by more than 3000 times the 2.4 kHz ESR linewidth, providing a direct path to large-scale arrays of addressable high-fidelity qubits that are compatible with existing manufacturing technologies

Metallo-cryptophane cages from cis-linked and trans-linked strategies

Trigonal bipyramidal metallo-cage species [Pd₃(dppp)₃(L)₂]∙6OTf (where dppp = bis(diphenylphosphino)propane, OTf = triflate and L is tris(iso-nicotinoyl)cyclotriguaiacylene (L1) or tris(fluoro-iso-nicotinoyl)cyclotriguaiacylene (FL1)) have been characterised in solution to exist predominantly as the anti-isomers. The crystal structure of [Pd₃(dppp)₃(FL1)₂]∙6OTf, however, was found to be the achiral syn-isomer. The complex [Pd₃Cl₃(L2)₂] (where L2 = tris(methylbenzimidazolyl)cyclotriguaiacylene) is a trans-linked M₃L₂ cage, observed by mass spectrometry and in the solid state as the anti-isomer. Ligand L2 also forms a 1:1 co-crystal with cyclotriguaiacylene

Towards Quantum Repeaters with Solid-State Qubits: Spin-Photon Entanglement Generation using Self-Assembled Quantum Dots

In this chapter we review the use of spins in optically-active InAs quantum dots as the key physical building block for constructing a quantum repeater, with a particular focus on recent results demonstrating entanglement between a quantum memory (electron spin qubit) and a flying qubit (polarization- or frequency-encoded photonic qubit). This is a first step towards demonstrating entanglement between distant quantum memories (realized with quantum dots), which in turn is a milestone in the roadmap for building a functional quantum repeater. We also place this experimental work in context by providing an overview of quantum repeaters, their potential uses, and the challenges in implementing them.Comment: 51 pages. Expanded version of a chapter to appear in "Engineering the Atom-Photon Interaction" (Springer-Verlag, 2015; eds. A. Predojevic and M. W. Mitchell

A systematic review of online resources to support patient decision-making for full-thickness rectal prolapse surgery

BACKGROUND: The internet is becoming an increasingly popular resource to support patient decision-making outside of the clinical encounter. The quality of online health information is variable and largely unregulated. The aim of this study was to assess the quality of online resources to support patient decision-making for full-thickness rectal prolapse surgery. METHODS: This systematic review was registered on the PROSPERO database (CRD42017058319). Searches were performed on Google and specialist decision aid repositories using a pre-defined search strategy. Sources were analysed according to three measures: (1) their readability using the Flesch-Kincaid Reading Ease score, (2) DISCERN score and (3) International Patient Decision Aids Standards (IPDAS) minimum standards criteria score (IPDASi, v4.0). RESULTS: Overall, 95 sources were from Google and the specialist decision aid repositories. There were 53 duplicates removed, and 18 sources did not meet the pre-defined eligibility criteria, leaving 24 sources included in the full-text analysis. The mean Flesch-Kincaid Reading Ease score was higher than recommended for patient education materials (48.8 ± 15.6, range 25.2-85.3). Overall quality of sources supporting patient decision-making for full-thickness rectal prolapse surgery was poor (median DISCERN score 1/5 ± 1.18, range 1-5). No sources met minimum decision-making standards (median IPDASi score 5/12 ± 2.01, range 1-8). CONCLUSIONS: Currently, easily accessible online health information to support patient decision-making for rectal surgery is of poor quality, difficult to read and does not support shared decision-making. It is recommended that professional bodies and medical professionals seek to develop decision aids to support decision-making for full-thickness rectal prolapse surgery

Clinical manifestations and outcome in Staphylococcus aureus endocarditis among injection drug users and nonaddicts: a prospective study of 74 patients

BACKGROUND: Endocarditis is a common complication in Staphylococcus aureus bacteremia (SAB). We compared risk factors, clinical manifestations, and outcome in a large, prospective cohort of patients with S. aureus endocarditis in injection drug users (IDUs) and in nonaddicts. METHODS: Four hundred and thirty consecutive adult patients with SAB were prospectively followed up for 3 months. Definite or possible endocarditis by modified Duke criteria was found in 74 patients: 20 patients were IDUs and 54 nonaddicts. RESULTS: Endocarditis was more common in SAB among drug abusers (46%) than in nonaddicts (14%) (odds ratio [OR], 5.12; 95% confidence interval [CI], 2.65–9.91; P < 0.001). IDUs were significantly younger (27 ± 15 vs 65 ± 15 years, P < 0.001), had less ultimately or rapidly fatal underlying diseases (0% vs 37%, P < 0.001) or predisposing heart diseases (20% vs 50%, P = 0.03), and their SAB was more often community-acquired (95% vs 39%, P < 0.001). Right-sided endocarditis was observed in 60% of IDUs whereas 93% of nonaddicts had left-sided involvement (P < 0.001). An extracardiac deep infection was found in 85% of IDUs and in 89% of nonaddicts (P = 0.70). Arterial thromboembolic events and severe sepsis were also equally common in both groups. There was no difference in mortality between the groups at 7 days, but at 3 months it was lower among IDUs (10%) compared with nonaddicts (39%) (OR, 5.73; 95% CI, 1.20–27.25; P = 0.02). CONCLUSION: S. aureus endocarditis in IDUs was associated with as high complication rates including extracardiac deep infections, thromboembolic events, or severe sepsis as in nonaddicts. Injection drug abuse in accordance with younger age and lack of underlying diseases were associated with lower mortality, but after adjusting by age and underlying diseases injection drug abuse was not significantly associated with mortality