The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in biogeographical studies, to study the evolution of gene families, and also within approaches to construct phylogenetic networks. A multilabelled tree in which no leaf-labels are repeated is called a phylogenetic tree, and one in which every label is the same is also known as a tree-shape. In this paper, we consider the complexity of computing metrics on MUL-trees that are obtained by extending metrics on phylogenetic trees. In particular, by restricting our attention to tree shapes, we show that computing the metric extension on MUL-trees is NP-complete for two well-known metrics on phylogenetic trees, namely, the path-difference and Robinson Foulds distances. We also show that the extension of the Robinson Foulds distance is fixed parameter tractable with respect to the distance parameter. The path distance complexity result allows us to also answer an open problem concerning the complexity of solving the quadratic assignment problem for two matrices that are a Robinson similarity and a Robinson dissimilarity, which we show to be NP-complete. We conclude by considering the maximum agreement subtree (MAST) distance on phylogenetic trees to MUL-trees. Although its extension to MUL-trees can be computed in polynomial time, we show that computing its natural generalization to more than two MUL-trees is NP-complete, although fixed-parameter tractable in the maximum degree when the number of given trees is bounded

Non Destructive Determination Of Elastic Moduli By Two Dimensional Fourier Transformation And Laser Ultrasonic Technique

Broadband laser ultrasonics and two dimensional Fourier transformation are used to characterize the properties of varieties of foils and plates. Laser ultrasonics generation is achieved by use of a pulsed laser which deposits pulsed laser energy on the surface of the specimen. The displacement amplitude of the resulting broadband ultrasonic modes are monitored using a two wave mixing photo-refractive interferometer. By applying a two dimensional Fourier transformation to the detected spatial and temporal displacement waveforms, the images of density of state (DOS) for the excited ultrasounds are obtained. Results are presented for a 150 um thick paper sample, a 52.8 um stainless steel foil and a 1.27 mm thick aluminum plate. The DOS image demonstrates the ability to measure the properties of each generated ultrasonic modes and provides a direct, non destructive, measure of elastic moduli of the tested specimensComment: Laser ultrasonics, Fourier transformation, NDT&E, Lamb waves, plate mode

Experimental evaluation of the relationship between lethal or non-lethal virulence and transmission success in malaria parasite infections

BACKGROUND: Evolutionary theory suggests that the selection pressure on parasites to maximize their transmission determines their optimal host exploitation strategies and thus their virulence. Establishing the adaptive basis to parasite life history traits has important consequences for predicting parasite responses to public health interventions. In this study we examine the extent to which malaria parasites conform to the predicted adaptive trade-off between transmission and virulence, as defined by mortality. The majority of natural infections, however, result in sub-lethal virulent effects (e.g. anaemia) and are often composed of many strains. Both sub-lethal effects and pathogen population structure have been theoretically shown to have important consequences for virulence evolution. Thus, we additionally examine the relationship between anaemia and transmission in single and mixed clone infections. RESULTS: Whereas there was a trade-off between transmission success and virulence as defined by host mortality, contradictory clone-specific patterns occurred when defining virulence by anaemia. A negative relationship between anaemia and transmission success was found for one of the parasite clones, whereas there was no relationship for the other. Notably the two parasite clones also differed in a transmission phenotype (gametocyte sex ratio) that has previously been shown to respond adaptively to a changing blood environment. In addition, as predicted by evolutionary theory, mixed infections resulted in increased anaemia. The increased anaemia was, however, not correlated with any discernable parasite trait (e.g. parasite density) or with increased transmission. CONCLUSIONS: We found some evidence supporting the hypothesis that there is an adaptive basis correlating virulence (as defined by host mortality) and transmission success in malaria parasites. This confirms the validity of applying evolutionary virulence theory to biomedical research and adds support to the prediction that partially effective vaccines may select for increasingly virulent malaria parasite strains. By contrast, there was no consistent correlation between transmission and sub-lethal anaemia, a more common outcome of malaria infection. However, overall, the data are not inconsistent with the recent proposal that sub-lethal effects may impose an upper limit on virulence. Moreover, clone specific differences in transmission phenotypes linked to anaemia do suggest that there is considerable adaptive potential relating anaemia and transmission that may lead to uncertain consequences following intervention strategies

“Angular resolution expected from iCHORD orientation maps through a revisited ion channeling model”

International audienceCrystalline orientation maps are obtained in a Focused Ion Beam (FIB) microscope using the ion CHanneling ORientation Determination (iCHORD) method, which relies on the channeling phenomenon observed in ion-induced secondary electron images. The current paper focuses on the angular resolution that can be expected from such orientation maps, obtained using a revisited ion channeling model. A specific procedure was developed to evaluate the angular resolution, based on the distribution of orientation errors when evaluating controlled sample disorientation. The main advantage is that no external reference is required. An angular resolution of 1° is obtained on a nickel based sample using standard acquisition conditions. This value fulfills most of the needs in terms of microstructural characterization usually carried out by Electron Back Scattered Diffraction

On strongly chordal graphs that are not leaf powers

A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a threshold k such that uv is an edge if and only if the distance between u and v in T is at most k. Characterizing leaf powers is a challenging open problem, along with determining the complexity of their recognition. This is in part due to the fact that few graphs are known to not be leaf powers, as such graphs are difficult to construct. Recently, Nevries and Rosenke asked if leaf powers could be characterized by strong chordality and a finite set of forbidden subgraphs. In this paper, we provide a negative answer to this question, by exhibiting an infinite family \G of (minimal) strongly chordal graphs that are not leaf powers. During the process, we establish a connection between leaf powers, alternating cycles and quartet compatibility. We also show that deciding if a chordal graph is \G-free is NP-complete, which may provide insight on the complexity of the leaf power recognition problem

Tillage and phosphorus availability

Non-Peer Reviewe

Strain mapping at the nanoscale using precession electron diffraction in transmission electron microscope with off axis camera

International audiencePrecession electron diffraction is an efficient technique to measure strain in nanostructures by precessing the electron beam, while maintaining a few nanometre probe size. Here, we show that an advanced diffraction pattern treatment allows reproducible and precise strain measurements to be obtained using a default 512 x 512 DigiSTAR off-axis camera both in advanced or non-corrected transmission electron microscopes. This treatment consists in both projective geometry correction of diffraction pattern distortions and strain Delaunay triangulation based analysis. Precision in the strain measurement is improved and reached 2.7 x 10(-4) with a probe size approaching 4.2 nm in diameter. This method is applied to the study of the strain state in InGaAs quantum-well (QW) devices elaborated on Si substrate. Results show that the GaAs/Si mismatch does not induce in-plane strain fluctuations in the InGaAs QW region. (C) 2014 AIP Publishing LLC

AtPME17 is a functional arabidopsis thaliana pectin methylesterase regulated by its PRO region that triggers PME activity in the resistance to botrytis cinerea

Pectin is synthesized in a highly methylesterified form in the Golgi cisternae and partially de-methylesterified in muro by pectin methylesterases (PMEs). Arabidopsis thaliana produces a local and strong induction of PME activity during the infection of the necrotrophic fungus Botrytis cinerea. AtPME17 is a putative A. thaliana PME highly induced in response to B. cinerea. Here, a fine tuning of AtPME17 expression by different defence hormones was identified. Our genetic evidence demonstrates that AtPME17 strongly contributes to the pathogen-induced PME activity and resistance against B. cinerea by triggering jasmonic acid–ethylene-dependent PDF1.2 expression. AtPME17 belongs to group 2 isoforms of PMEs characterized by a PME domain preceded by an N-terminal PRO region. However, the biochemical evidence for AtPME17 as a functional PME is still lacking and the role played by its PRO region is not known. Using the Pichia pastoris expression system, we demonstrate that AtPME17 is a functional PME with activity favoured by an increase in pH. AtPME17 performs a blockwise pattern of pectin de-methylesterification that favours the formation of egg-box structures between homogalacturonans. Recombinant AtPME17 expression in Escherichia coli reveals that the PRO region acts as an intramolecular inhibitor of AtPME17 activity

A critical review of plant protection tools for reducing pesticide use on grapevine and new perspectives for the implementation of IPM in viticulture

Several pests and diseases have grapevine as their favourite host and the vineyard as preferred environment, so an intensive pesticide schedule is usually required to meet qualitative and quantitative production standards. The need to prevent the negative impact of synthetic chemical pesticides on human health and the environment and the consumer expectations in term of chemical residues in food stimulated the research of innovative tools and methods for sustainable pest management. The research project PURE (www.pure-ipm.eu) was a Europe-wide framework, which demonstrated that several solutions are now available for the growers and evaluated several new alternatives that are under development or almost ready for being applied in practice. Although the use of resistant/tolerant varieties is not yet feasible in several traditional grape growing areas, at least part of the synthetic chemical pesticides can be substituted with biocontrol agents to control pests and pathogens and/or pheromone mating disruption, or the number of treatments can be reduced by the use of decision support systems, which identify the optimal timing for the applications. This review presents the state of the art and the perspectives in the field of grapevine protection tools and strategies

Effect of oral prednisolone on symptom duration and severity in nonasthmatic adults with acute lower respiratory tract infection: a randomized clinical trial

Importance: Acute lower respiratory tract infection is common and often treated inappropriately in primary care with antibiotics. Corticosteroids are increasingly used but without sufficient evidence. Objective: To assess the effects of oral corticosteroids for acute lower respiratory tract infection in adults without asthma. Design, Setting, and Participants: Multicenter, placebo-controlled, randomized trial (July 2013 to final follow-up October 2014) conducted in 54 family practices in England among 401 adults with acute cough and at least 1 lower respiratory tract symptom not requiring immediate antibiotic treatment and with no history of chronic pulmonary disease or use of asthma medication in the past 5 years. Interventions: Two 20-mg prednisolone tablets (n = 199) or matched placebo (n = 202) once daily for 5 days. Main Outcomes and Measures: The primary outcomes were duration of moderately bad or worse cough (0 to 28 days; minimal clinically important difference, 3.79 days) and mean severity of symptoms on days 2 to 4 (scored from 0 [not affected] to 6 [as bad as it could be]; minimal clinically important difference, 1.66 units). Secondary outcomes were duration and severity of acute lower respiratory tract infection symptoms, duration of abnormal peak flow, antibiotic use, and adverse events. Results: Among 401 randomized patients, 2 withdrew immediately after randomization, and 1 duplicate patient was identified. Among the 398 patients with baseline data (mean age, 47 [SD, 16.0] years; 63% women; 17% smokers; 77% phlegm; 70% shortness of breath; 47% wheezing; 46% chest pain; 42% abnormal peak flow), 334 (84%) provided cough duration and 369 (93%) symptom severity data. Median cough duration was 5 days (interquartile range [IQR], 3-8 days) in the prednisolone group and 5 days (IQR, 3-10 days) in the placebo group (adjusted hazard ratio, 1.11; 95% CI, 0.89-1.39; P = .36 at an α = .05). Mean symptom severity was 1.99 points in the prednisolone group and 2.16 points in the placebo group (adjusted difference, −0.20; 95% CI, −0.40 to 0.00; P = .05 at an α = .001). No significant treatment effects were observed for duration or severity of other acute lower respiratory tract infection symptoms, duration of abnormal peak flow, antibiotic use, or nonserious adverse events. There were no serious adverse events. Conclusions and Relevance: Oral corticosteroids should not be used for acute lower respiratory tract infection symptoms in adults without asthma because they do not reduce symptom duration or severity