Reduced variance analysis of molecular dynamics simulations by linear combination of estimators

Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions, or local transport properties from molecular simulations, we show that the variance can be further reduced by considering optimal linear combinations of such estimators. This control variates approach, well known in statistics and already used in other branches of computational physics, has been comparatively much less exploited in molecular simulations. We illustrate this idea on the radial distribution function and the one-dimensional density of a bulk and confined Lennard-Jones fluid, where the optimal combination of estimators is determined for each distance or position, respectively. In addition to reducing the variance everywhere at virtually no additional cost, this approach cures an artifact of the initial force-based estimators, namely, small but non-zero values of the quantities in regions where they should vanish. Beyond the examples considered here, the present work highlights, more generally, the underexplored potential of control variates to estimate observables from molecular simulations.

Canadian Rhinology Working Group consensus statement: biologic therapies for chronic rhinosinusitis

BACKGROUND

Recent evidence suggests that biologic therapy with targeted activity within the Type 2 inflammatory pathway can improve the clinical signs and symptoms of chronic rhinosinusitis with nasal polyposis (CRSwNP). There remains a population in CRSwNP that despite medical therapy and endoscopic sinus surgery have persistent signs and symptoms of disease. Therefore, biologics, monoclonal antibody agents, could be beneficial therapeutic treatments for these patients. There have been eight randomized, double-blind, placebo-controlled trails performed for CRSwNP targeted components of the Type 2 inflammatory pathway, notably interleukin (IL)-4, IL-5 and IL-13, IL-5R, IL-33, and immunoglobulin (Ig)E. However, there are no formal recommendations for the optimal use of biologics in managing Chronic Rhinosinusitis (CRS) within the Canadian health care environment.

METHODS

A Delphi Method process was utilized involving three rounds of questionnaires in which the first two were completed individually online and the third was discussed on a virtual platform with all the panelists. 17 fellowship trained rhinologists across Canada evaluated the 28 original statements on a scale of 1-10 and provided comments. A rating within 1-3 indicated disagreement, 8-10 demonstrated agreement and 4-7 represented being neutral towards a statement. All ratings were quantitively reviewed by mean, median, mode, range and standard deviation. Consensus was defined by removing the highest and lowest of the scores and using the "3 point relaxed system".

RESULTS

After three rounds, a total of 11 statements achieved consensus. This white paper only contains the final agreed upon statements and clear rationale and support for the statements regarding the use of biologics in patients with CRS.

CONCLUSION

This white paper provides guidance to Canadian physicians on the use of biologic therapy for the management of patients with CRS, but the medical and surgical regimen should ultimately be individualized to the patient. As more biologics become available and additional trials are published we will provide updated versions of this white paper every few years.

Mass-zero constrained molecular dynamics for electrode charges in simulations of electrochemical systems

Classical molecular dynamics simulations have recently become a standard tool for the study of electrochemical systems. State-of-the-art approaches represent the electrodes as perfect conductors, modeling their responses to the charge distribution of electrolytes via the so-called fluctuating charge model. These fluctuating charges are additional degrees of freedom that, in a Born-Oppenheimer spirit, adapt instantaneously to changes in the environment to keep each electrode at a constant potential. Here, we show that this model can be treated in the framework of constrained molecular dynamics, leading to a symplectic and time-reversible algorithm for the evolution of all the degrees of freedom of the system. The computational cost and the accuracy of the new method are similar to current alternative implementations of the model. The advantage lies in the accuracy and long term stability guaranteed by the formal properties of the algorithm and in the possibility to systematically introduce additional kinematic conditions of arbitrary number and form. We illustrate the performance of the constrained dynamics approach by enforcing the electroneutrality of the electrodes in a simple capacitor consisting of two graphite electrodes separated by a slab of liquid water.

SLEEP-GOAL: A multicenter success criteria outcome study on 302 obstructive sleep apnoea (OSA) patients

OBJECTIVE

To demonstrate SLEEP-GOAL as a more holistic and comprehensive success criterion for Obstructive Sleep Apnoea (OSA) treatment.

METHODS

A prospective 7-country clinical trial of 302 OSA patients, who met the selection criteria, and underwent nose, palate and/or tongue surgery. Pre- and post-operative data were recorded and analysed based on both the Sher criteria (apnoea hypopnea index, AHI reduction 50% and <20) and the SLEEP-GOAL.

RESULTS

There were 229 males and 73 females, mean age of 42.4±17.3 years, mean BMI 27.9±4.2. The mean VAS score improved from 7.7±1.4 to 2.5±1.7 (p<0.05), mean Epworth score (ESS) improved from 12.2±4.6 to 4.9±2.8 (p<0.05), mean body mass index (BMI) decreased from 27.9±4.2 to 26.1±3.7 (p>0.05), gross weight decreased from 81.9±14.3kg to 76.6±13.3kg. The mean AHI decreased 33.4±18.9 to 14.6±11.0 (p<0.05), mean lowest oxygen saturation (LSAT) improved 79.4±9.2% to 86.9±5.9% (p<0.05), and mean duration of oxygen <90% decreased from 32.6±8.9 minutes to 7.3±2.1 minutes (p<0.05). The overall success rate (302 patients) based on the Sher criteria was 66.2%. Crosstabulation of respective major/minor criteria fulfilment, based on fulfilment of two major and two minor or better, the success rate (based on SLEEP-GOAL) was 69.8%. Based solely on the Sher criteria, 63 patients who had significant blood pressure reduction, 29 patients who had BMI reduction and 66 patients who had clinically significant decrease in duration of oxygen <90% would have been misclassified as "failures".

CONCLUSION

AHI as a single parameter is unreliable. Assessing true success outcomes of OSA treatment, requires comprehensive and holistic parameters, reflecting true end-organ injury/function; the SLEEP-GOAL meets these requirements.

Transport Properties of Li-TFSI Water-in-Salt Electrolytes

Water-in-salts are a new family of electrolytes that may allow the development of aqueous Li-ion batteries. They have a structure that is reminiscent of ionic liquids, and they are characterized by a high concentration of ionic species. In this work, we study their transport properties and how they evolve with concentration by using molecular dynamic simulations. We first focus on the choice of the force field. By comparing the simulated viscosities and self-diffusion coefficients with experimental measurements, we select a set of parameters that reproduces well the transport properties. We then use the selected force field to study in detail the variations of the self and collective diffusivities of all the species as well as the transport number of the lithium ion. We show that correlations between ions and water play an important role over the whole concentration range. In the water-in-salt regime, the anions form a percolating network that reduces the cation-anion correlations and leads to rather large values for the transport number compared to other standard electrolytes.

International consensus (ICON) on the ENT role in diagnosis of obstructive sleep apnea syndrome

During the 2017 IFOS ENT World Congress, an international expert panel was asked to clarify the role of ENT in the diagnosis process of the obstructive sleep apnea syndrome (OSA) in adults around the world. OSA is a major public health issue throughout the world. OSA is a highly prevalent disease with heavy clinical, social and economical outcomes. This high prevalence raises serious difficulties of diagnosis accessibility if only somnologists are able to confirm OSA diagnosis. First of all, the panellists reviewed the impact of OSA. Secondly, they defined the ENT role stressing ENT legitimacy, professional expertise and academic and institutional tasks. They also defined when somnologists were necessary. For the international panel, the ENT is a major player in the OSA diagnosis process.

Anterior palatoplasty in the treatment of obstructive sleep apnoea - a systemic review

This study seeks to determine the objective and subjective success rates of anterior palatoplasty and its variants for the treatment of obstructive sleep apnoea (OSA). A systematic review with two independent searches of Medline, PubMed, Cochrane Library and Evidence Based Medicine Reviews was performed to identify publications relevant to OSA and anterior palatoplasty. All relevant studies published before 30 June 2015 were included. Six studies were included in the systematic review. The numbers of patients in each paper ranged from 13 to 77 (total = 240), and mean age ranged from 21 to 51 years. Substantial and consistent improvement in polysomnography (PSG) outcomes were observed in patients after the anterior palatoplasty, with or without multilevel surgery. The results showed that the anterior palatoplasty technique provides significantly improvement in the post-operative Apnoea-Hypopnea Index. The mean pre-operative AHI (in the 6 papers) improved from 16.3 to 7.1, the snore visual analogue scale improved from 7.5 to 3.1 and the Epworth score reduced from 11.3 to 7.3 post-operatively. The overall pro-rated pooled success rate for all the patients was 72.5%, with a mean follow-up of 17.3 months. Anterior palatoplasty is an effective option in the management of patients with mild to moderate OSA.

Numerical study of density functional theory with mean spherical approximation for ionic condensation in highly charged confined electrolytes

We investigate numerically a density functional theory (DFT) for strongly confined ionic solutions in the canonical ensemble by comparing predictions of ionic concentration profiles and pressure for the double-layer configuration to those obtained with Monte Carlo (MC) simulations and the simpler Poisson-Boltzmann (PB) approach. The DFT consists of a bulk (ion-ion) and an ion-solid part. The bulk part includes nonideal terms accounting for long-range electrostatic and short-range steric correlations between ions and is evaluated with the mean spherical approximation and the local density approximation. The ion-solid part treats the ion-solid interactions at the mean-field level through the solution of a Poisson problem. The main findings are that ionic concentration profiles are generally better described by PB than by DFT, although DFT captures the nonmonotone co-ion profile missed by PB. Instead, DFT yields more accurate pressure predictions than PB, showing in particular that nonideal effects are important to describe highly confined ionic solutions. Finally, we present a numerical methodology capable of handling nonconvex minimization problems so as to explore DFT predictions when the reduced temperature falls below the critical temperature.

Molecular simulation of aqueous solutions at clay surfaces

We report a molecular simulation study of aqueous solutions at montmorillonite clay surfaces. Unlike most previous studies, ours does not focus on the interlayer nanopores, but looks at both kinds of external surfaces of clay particles: basal surfaces along the clay layers, and lateral surfaces through which interlayer and larger interparticle pores are linked. We present results on structural, dynamic and thermodynamic properties and phenomena, including hydration complexes of ions, H bonding networks, modification of the water dynamics with respect to the bulk, and the role of water in the cation exchange between interlayer and interparticle pores.

Ion dynamics in compacted clays: Derivation of a two-state diffusion-reaction scheme from the lattice Fokker-Planck equation

We show how a two-state diffusion-reaction description of the mobility of ions confined within compacted clays can be constructed from the microscopic dynamics of ions in an external field. The diffusion-reaction picture provides the usual interpretation of the reduced ionic mobility in clays, but the required partitioning coefficient K(d) between trapped and mobile ions is generally an empirical parameter. We demonstrate that it is possible to obtain K(d) from the microscopic dynamics of ions interacting with the clay surfaces by evaluating the ionic mobility using a novel lattice implementation of the Fokker-Planck equation. The resulting K(d) allows a clear-cut characterization of the trapping sites on the clay surfaces and determines the adsorption/desorption rates. The results highlight the limitations of standard approximation schemes and pinpoint the crossover from jump to Brownian diffusion regimes.

Frequency-dependent dielectric permittivity of salt-free charged lamellar systems

We present a new model to analyze dielectric spectroscopy measurements on charged lamellar systems, with the following improvements with respect to the hitherto available models: (i) it does not rely on the hypothesis of local electro-neutrality, and allows to treat the salt-free case; (ii) the chemical exchange governing the partition between free and bound ions is properly taken into account; (iii) a fully analytical solution is provided. The variation of the frequency-dependent dielectric permittivity with both thermodynamic and kinetic characteristics of the free-bound ion equilibrium is presented. In particular, the relative weights of both relaxation modes (exchange and transport), and their characteristic frequencies are discussed. This study opens the way to the analysis of systems for which the usual models are irrelevant, such as salt-free clay gels or membranes.

An Analytical Model for Probing Ion Dynamics in Clays with Broadband Dielectric Spectroscopy

A simple two-state model is proposed to explicitly derive the ionic contribution to the frequency-dependent dielectric permittivity of clay. This model is based on a separation of time scales and accounts for two possible solvation modes (inner/outer-sphere complexes) for ions in the interlayer spacing and a possible chemical exchange between both forms. The influence on the permittivity of thermodynamic (distribution constant K(d)) and dynamic (diffusion coefficient, chemical relaxation rate) parameters is discussed. In turn, this model is used to analyze experimental data obtained with Na-montmorillonite for two relative humidities. The values of the parameters extracted from these measurements, and their variation with water content, show that the proposed model is at least reasonable.

Tamoxifen attenuates glucocorticoid actions on bone formation in vitro

Tamoxifen is a synthetic estrogen analog which may regulate osteogenesis in vivo by virtue of its antiglucocorticoid properties. We have examined tamoxifen regulation of glucocorticoid-induced osteogenesis in two different in vitro bone systems: the chicken periosteal osteogenesis model (CPO) and rat bone marrow stromal cells (RBMC). Hormone uptake studies were conducted with the osteosarcoma cell line, ROS 17/2.8. In the CPO model, alkaline phosphatase (AP) activity and collagen synthesis were stimulated by the glucocorticoid dexamethasone (Dex; 0.1 microM). These Dex-mediated effects were inhibited by increasing concentrations of tamoxifen (10-100 microM). Similarly, in the RBMC model, Dex-dependent (0.01 microM Dex) mineralized tissue formation and AP activity were blocked by tamoxifen (0.1 microM). Although tamoxifen inhibited Dex-mediated increases of AP activity in ROS 17/2.8 cells, it did not inhibit uptake of 3H-Dex or of 3H-estrogen. Northern analyses showed that tamoxifen did not affect messenger RNAs (mRNAs) for AP. Tamoxifen did seem to reduce mRNA for collagen type I, but not bone sialoprotein, osteopontin, and osteocalcin. Dex-induced increases for all proteins mRNAs in the RBMC model were not reduced by tamoxifen. Similarly, tamoxifen had no effects on cellular proliferation. We conclude that tamoxifen has no direct effect on gene expression of bone-related proteins of osteoblastic cells. Further, in the ROS 17/2.8 cell line, the antiglucocorticoid properties of tamoxifen do not appear to be mediated through either Dex or estrogen receptors.