Entropic and gradient flow formulations for nonlinear diffusion

Nonlinear diffusion $\partial_t \rho = \Delta(\Phi(\rho))$ is considered for a class of nonlinearities $\Phi$. It is shown that for suitable choices of $\Phi$, an associated Lyapunov functional can be interpreted as thermodynamics entropy. This information is used to derive an associated metric, here called thermodynamic metric. The analysis is confined to nonlinear diffusion obtainable as hydrodynamic limit of a zero range process. The thermodynamic setting is linked to a large deviation principle for the underlying zero range process and the corresponding equation of fluctuating hydrodynamics. For the latter connections, the thermodynamic metric plays a central role

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as lowlevel customizability, and are computationally efficient, well-tested and field-proven

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements

Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny‐aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp‐derived metrics can classify samples by their diversity‐correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp

Assessing the Impact of Adlayer Description Fidelity on Theoretical Predictions of Coking on Ni(111) at Steam Reforming Conditions

Methane steam reforming is an important industrial process for hydrogen production, employing Ni as a low-cost, highly active catalyst, which, however, suffers from coking due to methane cracking. Coking is the accumulation of a stable poison over time, occurring at high temperatures; thus, to a first approximation, it can be treated as a thermodynamic problem. In this work, we developed an Ab initio kinetic Monte Carlo (KMC) model for methane cracking on Ni(111) at steam reforming conditions. The model captures C−H activation kinetics in detail, while graphene sheet formation is described at the level of thermodynamics, to obtain insights into the “terminal (poisoned) state” of graphene/coke within reasonable computational times. We used cluster expansions (CEs) of progressively higher fidelity to systematically assess the influence of effective cluster interactions between adsorbed or covalently bonded C and CH species on the “terminal state” morphology. Moreover, we compared the predictions of KMC models incorporating these CEs into mean-field microkinetic models in a consistent manner. The models show that the “terminal state” changes significantly with the level of fidelity of the CEs. Furthermore, high-fidelity simulations predict C−CH island/rings that are largely disconnected at low temperatures but completely encapsulate the Ni(111) surface at high temperatures

Intensity-Weighted Physical Activity Volume and Risk of All-Cause and Cardiovascular Mortality: Does the Use of Absolute or Corrected Intensity Matter?

Background: Previous epidemiological studies examining the association between physical activity (PA) and mortality risk have measured absolute PA intensity using standard resting metabolic rate reference values that fail to consider individual differences. This study compared the risk of all-cause and cardiovascular mortality between absolute and corrected estimates of PA volume. Methods: 49,982 adults aged ≥40 years who participated in the Health Survey for England and Scottish Health Survey in 1994–2008 were included in our study. PA was classified as absolute or corrected metabolic equivalent (MET)-hours per week, taking participant’s weight, height, age, and sex into account. Cox regression models were used to examine the association between absolute and corrected PA volumes and all-cause and cardiovascular mortality. Results: The authors found no difference in the association between levels of PA and risk of all-cause and cardiovascular mortality for absolute and corrected MET-hours per week, although there was a consistent decrease in mortality risk with increasing PA. There was no difference in mortality when analyses were stratified by sex, age, and body mass index. Conclusions: The association between PA volume and risk of mortality was similar regardless of whether PA volume was estimated using absolute or corrected METs. There is no empirical justification against the use of absolute METs to estimate PA volume from questionnaires

Does a physically active lifestyle attenuate the association between alcohol consumption and mortality risk? Findings from the UK biobank

Alcohol consumption is common across Western culture, despite its associations with adverse health outcomes, including cancer and cardiovascular disease (CVD). Physical activity (PA) has beneficial effects on many alcohol related outcomes, with data suggesting PA may offset the association between alcohol consumption and mortality. This study examined the joint associations of PA and alcohol on all-cause, CVD and cancer mortality. Participants were recruited between 2006 and 2010 in the United Kingdom. Alcohol consumption was categorised based on current UK guidelines (14 units/week). PA was categorised based on the Metabolic Task Equivalent of PA as low, moderate and high. Data were analysed using Cox proportional-hazard models. The final analysis, conducted in 2019, included 297,988 adults aged ≥40. Over an average follow-up of 6.9 years, 6079 deaths were recorded, including 1219 CVD deaths and 3112 cancer deaths. We observed greater point estimates for risk of all-cause mortality among low PA individuals who consumed alcohol at the same level as active individuals. For example, low PA participants who reported alcohol consumption ≥double guidelines had a greater HR (1.55, 95% CI 1.25, 1.93) than active individuals (moderate PA HR 1.21, 95% CI 0.95, 1.54; high PA HR 1.21, 95% CI 1.00, 1.46). Considering CVD, we observed a similar trend with lower point estimates of risk of mortality among active individuals. We found some evidence that PA modified the associations of alcohol and all-cause and CVD mortality in this large population sample of British adults

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples

Background: The exponential decrease in molecular sequencing cost generates unprecedented amounts of data. Hence, scalable methods to analyze these data are required. Phylogenetic (or Evolutionary) Placement methods identify the evolutionary provenance of anonymous sequences with respect to a given reference phylogeny. This increasingly popular method is deployed for scrutinizing metagenomic samples from environments such as water, soil, or the human gut. Novel methods: Here, we present novel and, more importantly, highly scalable methods for analyzing phylogenetic placements of metagenomic samples. More specifically, we introduce methods for (a) visualizing differences between samples and their correlation with associated meta-data on the reference phylogeny, (b) clustering similar samples using a variant of the k-means method, and (c) finding phylogenetic factors using an adaptation of the Phylofactorization method. These methods enable to interpret metagenomic data in a phylogenetic context, to find patterns in the data, and to identify branches of the phylogeny that are driving these patterns. Results: To demonstrate the scalability and utility of our methods, as well as to provide exemplary interpretations of our methods, we applied them to 3 publicly available datasets comprising 9782 samples with a total of approximately 168 million sequences. The results indicate that new biological insights can be attained via our methods

Can physical activity eliminate the mortality risk associated with poor sleep? A 15-year follow-up of 341,248 MJ Cohort participant

Background: This study examined the joint associations of sleep patterns and physical activity (PA) with all-cause, cardiovascular disease (CVD), and cancer mortality. Methods: A total of 341,248 adults (mean age = 39.7 years; men: 48.3%) were included in the study, with a 15-year follow-up. Participants reported sleep duration and disturbances (difficulty falling asleep, easily awakened, or use of sleeping medication). PA was classified into 4 levels: <7.5, 7.5–14.9, 15–29.9, and ≥30 metabolic equivalent hours per week (MET-h/week). To understand the joint associations of sleep patterns and PA with mortality, Cox proportional hazard models were conducted, with exposure variables combining sleep duration/disturbances and PA. Results: Compared with the reference group (sleeping 6–8 h/day), individuals who slept >8 h/day had higher risk for all-cause mortality (hazard ratios (HR) = 1.31, 95% confidence interval (95%CI): 1.25–1.37), CVD mortality (HR = 1.30, 95%CI: 1.17–1.45), and cancer mortality (HR = 1.13, 95%CI: 1.04–1.22). Short sleep duration was not associated with mortality risk. Increased risk of all-cause and CVD mortality was found in participants who had difficulty falling asleep (HR = 1.12, 95%CI: 1.07–1.18; HR = 1.16, 95%CI: 1.04–1.30, respectively), and used sleeping medication (HR = 1.26, 95%CI: 1.16–1.37; HR = 1.34, 95%CI: 1.10–1.62, respectively) compared with those who slept well. Long sleep duration and sleep disturbances were not associated with risk of all-cause and CVD mortality among individuals achieving a PA level of ≥15 MET-h/week, and in particular among those achieving ≥30 MET-h/week. Conclusions: Long sleep duration, difficulty falling asleep, and use of sleeping medication were related to a higher risk of death. Being physically active at a moderate intensity for 25–65 min/day eliminated these detrimental associations