Overcoming timescale and finite-size limitations to compute nucleation rates from small scale Well Tempered Metadynamics simulations

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated, approaching realistic supersaturation conditions, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.Comment: 9 pages, 7 figures, additional figures and data provided as supplementary information. Submitted to the Journal of Chemical Physisc

Crystal nucleation from solution: design and modelling of detection time experiments

Crystal nucleation is the process responsible for the appearance of a thermodynamically stable phase from a metastable parent solution. Given its activated nature, nucleation is affected by stochasticity which, despite originating at the molecular level, affects heavily also the macroscopic behaviour of the system. Being far too small to be observed directly, nuclei are detected by indirect methods, which correlate the formation of the new phase with a measurable change in a property of the system, hence a model linking nuclei formation and crystals detection is always needed. We have previously presented a model describing nucleation in macroscopic systems as a stochastic Poisson process. The model, despite its general character, can describe industrially relevant processes, e.g. batch cooling at different operating conditions. The different scales influenced by the stochastic nature of nucleation demand appropriate theoretical and experimental investigations, particularly for applying the model to industrial scale-up, optimisation, and control. Using statistical tools, we have looked into the issue of estimating stochastic processes by collecting a representative, but limited number of data, produced from a homogeneous set. Moreover, using our model, we analysed the sensitivity of crystallising systems on initial and boundary conditions, with particular emphasis on the effect of supersaturation, temperature and detection conditions. Finally, in light of the stochastic nature of nucleation, we also applied statistical meta-analysis to assess the agreement between the fitting and its parameters and experiments, to gain further insight into the quality of the model. Experimentally, we have first investigated the conditions to perform homogeneous and reproducible measurements, necessary to understand the fundamental physical features and ultimately to estimate reliable kinetic parameters. A second aspect we have explored concerned the size of the crystallising systems. Since in macroscopic reactors various phenomena occur simultaneously (nucleation, growth, breakage, agglomeration) we chose to work with two main system sizes, 1-3 mL reactors (mesoscale) and 1-60 nL reactors (microscale, i.e. microscopic droplets), where at least some of such phenomena could be decoupled. In the mesoscale crystallisers, one can perform experiments where temperature and transmissivity could be measured online, hence monitoring the appearance and disappearance of crystals. Additionally, the influence of fluid-dynamics, typically turbulent in these reactors, was investigated. In the microfluidic chips, on the other hand, a very high through-put (thousands of replicas of the same reactor) can be potentially achieved and, thanks to their very small size, high supersaturations, outside of usual experimental reach, could be explored. Additionally, within the microscopic droplets the fluid motion is generally diffusive or laminar convective, hence hindering breakage and agglomeration. One could thus observe systems where nucleation and growth of single crystals (or of few crystals) occur unperturbed. Nevertheless, some main challenges, which we have been addressing, must be tackled before performing reliable crystallisation experiments: the characterisation and the reproducibility of shape and size of the droplets and their stability (i.e. the loss of mass due to evaporation and perspiration through the chip). In conclusion, we demonstrate that, even if the data are reproducible and reliable, robust probability estimations can be obtained only with a sufficiently large number of experiments, which require careful design to avoid sensitivity regions and data processing to reject the non-homogeneous data. The different sizes investigated have permitted to gain a better insight into the fundamental phenomena occurring in a crystallising system between the first formation of nuclei until crystal detection, which is of utmost importance for understanding the design of the experiments at an industrially relevant scale. Moreover, appropriate mathematical tools allowed to assess the reliability of the fitting obtained from independent measurements of the same system at different conditions

Operations Research in the Red Zone

The EURO Working Group on Operational Research Applied to Health Services (ORAHS) provides a network for researchers involved in the application of systematic and quantitative analysis in the planning and management of the health services sector.</p

Correlation between B7-H4 and Survival of Non-Small-Cell Lung Cancer Patients Treated with Nivolumab

Reliable predictors of benefit from immune checkpoint inhibitors in non-small-cell lung cancer (NSCLC) are still limited. We aimed to evaluate the association between the expression of selected molecules involved in immune response and clinical outcomes in NSCLC patients receiving nivolumab. In our study, the outcomes of 46 NSCLC patients treated with nivolumab in second or subsequent lines (Nivolumab Cohort) were compared with the expression of PD-L1, PD-L2, PD-1, B7-H3, and B7-H4 assessed by immunohistochemistry (IHC). Samples from 17 patients (37.0%) in the Nivolumab Cohort were positive for B7-H4 expression. At univariate analyses, only B7-H4 expression was associated with significantly decreased progression-free survival (PFS; 1.7 vs. 2.0 months; p = 0.026) and with a disadvantage in terms of overall survival (OS) close to statistical significance (4.4 vs. 9.8 months; p = 0.064). At multivariate analyses, B7-H4 expression was significantly associated with decreased PFS (hazard ratio (HR) = 2.28; p = 0.021) and OS (HR = 2.38; p = 0.022). Subsequently, B7-H4 expression was compared with clinical outcomes of 27 NSCLC patients receiving platinum-based chemotherapy (Chemotherapy Cohort), but no significant association was observed. Our results suggest a negative predictive role of B7-H4 in a population of NSCLC treated with immune checkpoint inhibitors, which deserves further research

Harnessing the reverse cholesterol transport pathway to favor differentiation of monocyte-derived APCs and antitumor responses

Lipid and cholesterol metabolism play a crucial role in tumor cell behavior and in shaping the tumor microenvironment. In particular, enzymatic and non-enzymatic cholesterol metabolism, and derived metabolites control dendritic cell (DC) functions, ultimately impacting tumor antigen presentation within and outside the tumor mass, dampening tumor immunity and immunotherapeutic attempts. The mechanisms accounting for such events remain largely to be defined. Here we perturbed (oxy)sterol metabolism genetically and pharmacologically and analyzed the tumor lipidome landscape in relation to the tumor-infiltrating immune cells. We report that perturbing the lipidome of tumor microenvironment by the expression of sulfotransferase 2B1b crucial in cholesterol and oxysterol sulfate synthesis, favored intratumoral representation of monocyte-derived antigen-presenting cells, including monocyte-DCs. We also found that treating mice with a newly developed antagonist of the oxysterol receptors Liver X Receptors (LXRs), promoted intratumoral monocyte-DC differentiation, delayed tumor growth and synergized with anti-PD-1 immunotherapy and adoptive T cell therapy. Of note, looking at LXR/cholesterol gene signature in melanoma patients treated with anti-PD-1-based immunotherapy predicted diverse clinical outcomes. Indeed, patients whose tumors were poorly infiltrated by monocytes/macrophages expressing LXR target genes showed improved survival over the course of therapy. Thus, our data support a role for (oxy)sterol metabolism in shaping monocyte-to-DC differentiation, and in tumor antigen presentation critical for responsiveness to immunotherapy. The identification of a new LXR antagonist opens new treatment avenues for cancer patients

A sex-informed approach to improve the personalised decision making process in myelodysplastic syndromes: a multicentre, observational cohort study

Background Sex is a major source of diversity among patients and a sex-informed approach is becoming a new paradigm in precision medicine. We aimed to describe sex diversity in myelodysplastic syndromes in terms of disease genotype, phenotype, and clinical outcome. Moreover, we sought to incorporate sex information into the clinical decision-making process as a fundamental component of patient individuality. Methods In this multicentre, observational cohort study, we retrospectively analysed 13 284 patients aged 18 years or older with a diagnosis of myelodysplastic syndrome according to 2016 WHO criteria included in the EuroMDS network (n=2025), International Working Group for Prognosis in MDS (IWG-PM; n=2387), the Spanish Group of Myelodysplastic Syndromes registry (GESMD; n=7687), or the Dusseldorf MDS registry (n=1185). Recruitment periods for these cohorts were between 1990 and 2016. The correlation between sex and genomic features was analysed in the EuroMDS cohort and validated in the IWG-PM cohort. The effect of sex on clinical outcome, with overall survival as the main endpoint, was analysed in the EuroMDS population and validated in the other three cohorts. Finally, novel prognostic models incorporating sex and genomic information were built and validated, and compared to the widely used revised International Prognostic Scoring System (IPSS-R). This study is registered with ClinicalTrials.gov, NCT04889729. Findings The study included 7792 (58middot7%) men and 5492 (41middot3%) women. 10 906 (82middot1%) patients were White, and race was not reported for 2378 (17middot9%) patients. Sex biases were observed at the single-gene level with mutations in seven genes enriched in men (ASXL1, SRSF2, and ZRSR2 p<0middot0001 in both cohorts; DDX41 not available in the EuroMDS cohort vs p=0middot0062 in the IWG-PM cohort; IDH2 p<0middot0001 in EuroMDS vs p=0middot042 in IWG-PM; TET2 p=0middot031 vs p=0middot035; U2AF1 p=0middot033 vs p<0middot0001) and mutations in two genes were enriched in women (DNMT3A p<0middot0001 in EuroMDS vs p=0middot011 in IWG-PM; TP53 p=0middot030 vs p=0middot037). Additionally, sex biases were observed in co-mutational pathways of founding genomic lesions (splicing-related genes, predominantly in men, p<0middot0001 in both the EuroMDS and IWG-PM cohorts), in DNA methylation (predominantly in men, p=0middot046 in EuroMDS vs p<0middot0001 in IWG-PM), and TP53 mutational pathways (predominantly in women, p=0middot0073 in EuroMDS vs p<0middot0001 in IWG-PM). In the retrospective EuroMDS cohort, men had worse median overall survival (81middot3 months, 95% CI 70middot4-95middot0 in men vs 123middot5 months, 104middot5-127middot5 in women; hazard ratio [HR] 1middot40, 95% CI 1middot26-1middot52; p<0middot0001). This result was confirmed in the prospective validation cohorts (median overall survival was 54middot7 months, 95% CI 52middot4-59middot1 in men vs 74middot4 months, 69middot3-81middot2 in women; HR 1middot30, 95% CI 1middot23-1middot35; p<0middot0001 in the GEMSD MDS registry; 40middot0 months, 95% CI 33middot4-43middot7 in men vs 54middot2 months, 38middot6-63middot8 in women; HR 1middot23, 95% CI 1middot08-1middot36; p<0middot0001 in the Dusseldorf MDS registry). We developed new personalised prognostic tools that included sex information (the sex-informed prognostic scoring system and the sex-informed genomic scoring system). Sex maintained independent prognostic power in all prognostic systems; the highest performance was observed in the model that included both sex and genomic information. A five-to-five mapping between the IPSS-R and new score categories resulted in the re-stratification of 871 (43middot0%) of 2025 patients from the EuroMDS cohort and 1003 (42middot0%) of 2387 patients from the IWG-PM cohort by using the sex-informed prognostic scoring system, and of 1134 (56middot0%) patients from the EuroMDS cohort and 1265 (53middot0%) patients from the IWG-PM cohort by using the sex-informed genomic scoring system. We created a web portal that enables outcome predictions based on a sex-informed personalised approach. Interpretation Our results suggest that a sex-informed approach can improve the personalised decision making process in patients with myelodysplastic syndromes and should be considered in the design of clinical trials including low-risk patients. Copyright (c) 2022 Published by Elsevier Ltd. All rights reserved

Effect of aliskiren on post-discharge outcomes among diabetic and non-diabetic patients hospitalized for heart failure: insights from the ASTRONAUT trial

Aims The objective of the Aliskiren Trial on Acute Heart Failure Outcomes (ASTRONAUT) was to determine whether aliskiren, a direct renin inhibitor, would improve post-discharge outcomes in patients with hospitalization for heart failure (HHF) with reduced ejection fraction. Pre-specified subgroup analyses suggested potential heterogeneity in post-discharge outcomes with aliskiren in patients with and without baseline diabetes mellitus (DM). Methods and results ASTRONAUT included 953 patients without DM (aliskiren 489; placebo 464) and 662 patients with DM (aliskiren 319; placebo 343) (as reported by study investigators). Study endpoints included the first occurrence of cardiovascular death or HHF within 6 and 12 months, all-cause death within 6 and 12 months, and change from baseline in N-terminal pro-B-type natriuretic peptide (NT-proBNP) at 1, 6, and 12 months. Data regarding risk of hyperkalaemia, renal impairment, and hypotension, and changes in additional serum biomarkers were collected. The effect of aliskiren on cardiovascular death or HHF within 6 months (primary endpoint) did not significantly differ by baseline DM status (P = 0.08 for interaction), but reached statistical significance at 12 months (non-DM: HR: 0.80, 95% CI: 0.64-0.99; DM: HR: 1.16, 95% CI: 0.91-1.47; P = 0.03 for interaction). Risk of 12-month all-cause death with aliskiren significantly differed by the presence of baseline DM (non-DM: HR: 0.69, 95% CI: 0.50-0.94; DM: HR: 1.64, 95% CI: 1.15-2.33; P < 0.01 for interaction). Among non-diabetics, aliskiren significantly reduced NT-proBNP through 6 months and plasma troponin I and aldosterone through 12 months, as compared to placebo. Among diabetic patients, aliskiren reduced plasma troponin I and aldosterone relative to placebo through 1 month only. There was a trend towards differing risk of post-baseline potassium ≥6 mmol/L with aliskiren by underlying DM status (non-DM: HR: 1.17, 95% CI: 0.71-1.93; DM: HR: 2.39, 95% CI: 1.30-4.42; P = 0.07 for interaction). Conclusion This pre-specified subgroup analysis from the ASTRONAUT trial generates the hypothesis that the addition of aliskiren to standard HHF therapy in non-diabetic patients is generally well-tolerated and improves post-discharge outcomes and biomarker profiles. In contrast, diabetic patients receiving aliskiren appear to have worse post-discharge outcomes. Future prospective investigations are needed to confirm potential benefits of renin inhibition in a large cohort of HHF patients without D

Data for "Analysis of Multicomponent Ionic Mixtures using Blind Source Separation - a Processing Case Study"

This file contains the relevant data to run the Python script attached to the publication: Maggioni, G., Kocevska, S., Gover, M., Rousseau, R. Analysis of Multicomponent Ionic Mixtures using Blind Source Separation: A Processing Case Study, Industrial & Engineering Chemistry Research 2019, 58, 50, 22640–22651 DOI:https://pubs.acs.org/doi/10.1021/acs.iecr.9b03214Python script is available at https://github.com/john88gm/BSS_Analysis-SpectroscopyManagement and remediation of complex nuclear waste solutions require identification and quantification of multiple species. Some of the species forming the solution are unknown and they can be different from vessel to vessel, thus limiting the utility of standard calibration approaches. To cope with such limited information, we propose a procedure based on blind source separation (BSS) techniques, in particular independent component analysis and multivariate curve resolution, with a one-point calibration library. Here we show the applicability and reliability of our procedure for on-line measurements of aqueous ionic solutions by proposing an automatic procedure to identify the number of species in the mixture, estimate the spectra of the pure species, and label the spectra with respect to a library of reference components. We test our procedure against simulated and experimental data for mixtures with six species (water plus five sodium salts) for the case of Raman and ATR-FTIR spectroscopy.Department of Energy. Consortium for Risk Evaluation with Stakeholder Participatio