Detecting vapour bubbles in simulations of metastable water

International audienceThe investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguish between liquid- and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure

The phase diagram of water from quantum simulations

The phase diagram of water has been calculated for the TIP4PQ/2005 model, an empirical rigid non-polarisable model. The path integral Monte Carlo technique was used, permitting the incorporation of nuclear quantum effects. The coexistence lines were traced out using the Gibbs-Duhem integration method, once having calculated the free energies of the liquid and solid phases in the quantum limit, which were obtained via thermodynamic integration from the classical value by scaling the mass of the water molecule. The resulting phase diagram is qualitatively correct, being displaced to lower temperatures by 15-20K. It is found that the influence of nuclear quantum effects are correlated to the tetrahedral order parameter.Comment: 10 pages, 6 figures, 1 tabl

Public perceptions of forests across Italy: An exploratory national survey

In a context of progressive expansion of the Italian forest area, we present the results of a national survey exploring public perception of forests across different geographical scales in Italy. Perceptions of forests are assessed in rela-tion to popular beliefs on relevant environmental issues such as countering climate change, protecting biodiversity, and promoting social cohesion and environmental education. Participants (N = 1059) living in five different regions of Northern (Trentino-Alto Adige/Südtirol, Piemonte), Central (Lazio, Molise) and Southern Italy (Puglia), were recruited in the survey and completed a paper-and-pencil questionnaire. Survey questions regarded the estimated percentage of forest cover, the perceived importance of different environmental issues and of different material and non-material forest products, as well as partici-pants’ perceptions regarding connectedness to nature. Results revealed a gen-eralized tendency to overestimate the extension of forest surface area in the participants’ region, in Italy, and in the European Union. Results also showed high scores for participants’ perceived importance of environmental issues, such as climate change and biodiversity protection, and in their belief that forests could play a positive role in addressing these issues and providing im-portant outcomes and benefits for the quality of human life, such as health and well-being or social cohesion

Region proposals for saliency map refinement for weakly-supervised disease localisation and classification

First Online: 29 September 2020The deployment of automated systems to diagnose diseases from medical images is challenged by the requirement to localise the diagnosed diseases to justify or explain the classification decision. This requirement is hard to fulfil because most of the training sets available to develop these systems only contain global annotations, making the localisation of diseases a weakly supervised approach. The main methods designed for weakly supervised disease classification and localisation rely on saliency or attention maps that are not specifically trained for localisation, or on region proposals that can not be refined to produce accurate detections. In this paper, we introduce a new model that combines region proposal and saliency detection to overcome both limitations for weakly supervised disease classification and localisation. Using the ChestX-ray14 data set, we show that our proposed model establishes the new state-of-the-art for weakly-supervised disease diagnosis and localisation. We make our code available at https://github.com/renato145/RpSalWeaklyDet.Renato Hermoza, Gabriel Maicas, Jacinto C. Nascimento, Gustavo Carneir

A saturated consensus linkage map of Picea abies including AFLP, SSR, STS, 5S rDNA and morphological markers

International audienc

Impairment of Sexual Life in 3,485 Dermatological Outpatients From a Multicentre Study in 13 European Countries

Skin conditions may have a strong impact on patients' sexual life, and thus influence personal relationships. Sexual issues are difficult to discuss directly in clinical practice, and a mediated instrument may be useful to capture such information. In this study item 9 of the Dermatology Life Quality Index was used to collect information on sexual impact of several skin conditions in 13 European countries. Among 3,485 patients, 23.1% reported sexual problems. The impairment was particularly high in patients with hidradenitis suppurativa, prurigo, blistering disorders, psoriasis, urticaria, eczema, infections of the skin, or pruritus. Sexual impact was strongly associated with depression, anxiety, and suicidal ideation. It was generally more frequent in younger patients and was positively correlated with clinical severity and itch. It is important to address the issue of sexual well-being in the evaluation of patients with skin conditions, since it is often linked to anxiety, depression, and even suicidal ideation.Peer reviewedFinal Published versio

Anomalies in water as obtained from computer simulations of the TIP4P/2005 model: density maxima, and density, isothermal compressibility and heat capacity minima

The so-called thermodynamic anomalies of water form an integral part of the peculiar behaviour of this both important and ubiquitous molecule. In this paper our aim is to establish whether the recently proposed TIP4P/2005 model is capable of reproducing a number of these anomalies. Using molecular dynamics simulations we investigate both the maximum in density and the minimum in the isothermal compressibility along a number of isobars. It is shown that the model correctly describes the decrease in the temperature of the density maximum with increasing pressure. At atmospheric pressure the model exhibits an additional minimum in density at a temperature of about 200K, in good agreement with recent experimental work on super-cooled confined water. The model also presents a minimum in the isothermal compressibility close to 310K. We have also investigated the atmospheric pressure isobar for three other water models; the SPC/E and TIP4P models also present a minimum in the isothermal compressibility, although at a considerably lower temperature than the experimental one. For the temperature range considered no such minimum is found for the TIP5P model.Comment: 23 pages, 8 figure