Energy landscape of the finite-size mean-field 2-spin spherical model and topology trivialization

Motivated by the recently observed phenomenon of topology trivialization of potential energy landscapes (PELs) for several statistical mechanics models, we perform a numerical study of the finite-size 2-spin spherical model using both numerical polynomial homotopy continuation and a reformulation via non-Hermitian matrices. The continuation approach computes all of the complex stationary points of this model while the matrix approach computes the real stationary points. Using these methods, we compute the average number of stationary points while changing the topology of the PEL as well as the variance. Histograms of these stationary points are presented along with an analysis regarding the complex stationary points. This work connects topology trivialization to two different branches of mathematics: algebraic geometry and catastrophe theory, which is fertile ground for further interdisciplinary research

Coastal natural and nature-based features: international guidelines for flood risk management

Natural and nature-based features (NNBF) have been used for more than 100 years as coastal protection infrastructure (e.g., beach nourishment projects). The application of NNBF has grown steadily in recent years with the goal of realizing both coastal engineering and environment and social co-benefits through projects that have the potential to adapt to the changing climate. Technical advancements in support of NNBF are increasingly the subject of peer-reviewed literature, and guidance has been published by numerous organizations to inform technical practice for specific types of nature-based solutions. The International Guidelines on Natural and Nature-Based Features for Flood Risk Management was recently published to provide a comprehensive guide that draws directly on the growing body of knowledge and practitioner experience from around the world to inform the process of conceptualizing, planning, designing, engineering, and operating NNBF. These Guidelines focus on the role of nature-based solutions and natural infrastructure (beaches, dunes, wetlands and plant systems, islands, reefs) as a part of coastal and riverine flood risk management. In addition to describing each of the NNBF types, their use, design, implementation, and maintenance, the guidelines describe general principles for employing NNBF, stakeholder engagement, monitoring, costs and benefits, and adaptive management. An overall systems approach is taken to planning and implementation of NNBF. The guidelines were developed to support decision-makers, project managers, and practitioners in conceptualizing, planning, designing, engineering, implementing, and maintaining sustainable systems for nature-based flood risk management. This paper summarizes key concepts and highlights challenges and areas of future research

The Sloan Digital Sky Survey Reverberation Mapping Project : accretion and broad emission line physics from a hypervariable quasar

Funding: UK STFC grant ST/R000824/1 (K.H.).We analyze extensive spectroscopic and photometric data of the hypervariable quasar SDSS J141324+530527 (RMID 017) at z = 0.456, an optical "changing-look" quasar from the Sloan Digital Sky Survey Reverberation Mapping project that increased in optical luminosity by a factor ≅10 between 2014 and 2017. The observed broad emission lines all respond in luminosity and width to the changing optical continuum, as expected for photoionization in a stratified, virialized broad emission line region. The luminosity changes therefore result from intrinsic changes in accretion power rather than variable obscuration. The variability is continuous and apparently stochastic, disfavoring an origin as a discrete event such as a tidal disruption flare or microlensing event. It is coordinated on day timescales with blue leading red, consistent with reprocessing powering the entire optical spectral energy distribution. We show that this process cannot work in a standard thin disk geometry on energetic grounds, and would instead require a large covering factor reprocessor. Disk instability models could potentially also explain the data, provided that the instability sets in near the inner radius of a geometrically thick accretion disk.Publisher PDFPeer reviewe

The Sloan Digital Sky Survey Reverberation Mapping Project : sample characterization

Y.S. acknowledges support from an Alfred P. Sloan Research Fellowship and NSF grant AST-1715579. P.H. acknowledges support from the Natural Sciences and Engineering Research Council of Canada (NSERC), funding reference number 2017-05983. W.N.B. acknowledges support from NSF grant AST-1516784. C.J.G., W.N.B., and D.P.S. acknowledge support from NSF grant AST-1517113. Funding for SDSS-III has been provided by the Alfred P. Sloan Foundation, the Participating Institutions, the National Science Foundation, and the U.S. Department of Energy Office of Science.We present a detailed characterization of the 849 broad-line quasars from the Sloan Digital Sky Survey Reverberation Mapping (SDSS-RM) project. Our quasar sample covers a redshift range of 0.1 < z < 4.5 and is flux-limited to i PSF < 21.7 without any other cuts on quasar properties. The main sample characterization includes: (1) spectral measurements of the continuum and broad emission lines for individual objects from the coadded first-season spectroscopy in 2014, (2) identification of broad and narrow absorption lines in the spectra, and (3) optical variability properties for continuum and broad lines from multi-epoch spectroscopy. We provide improved systemic redshift estimates for all quasars and demonstrate the effects of the signal-to-noise ratio on the spectral measurements. We compile measured properties for all 849 quasars along with supplemental multi-wavelength data for subsets of our sample from other surveys. The SDSS-RM sample probes a diverse range in quasar properties and shows well-detected continuum and broad-line variability for many objects from first-season monitoring data. The compiled properties serve as the benchmark for follow-up work based on SDSS-RM data. The spectral fitting tools are made public along with this work.Publisher PDFPeer reviewe

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

Age-related changes in DNA methylation have been implicated in cellular senescence and longevity, yet the causes and functional consequences of these variants remain unclear. To elucidate the role of age-related epigenetic changes in healthy ageing and potential longevity, we tested for association between whole-blood DNA methylation patterns in 172 female twins aged 32 to 80 with age and age-related phenotypes. Twin-based DNA methylation levels at 26,690 CpG-sites showed evidence for mean genome-wide heritability of 18%, which was supported by the identification of 1,537 CpG-sites with methylation QTLs in cis at FDR 5%. We performed genome-wide analyses to discover differentially methylated regions (DMRs) for sixteen age-related phenotypes (ap-DMRs) and chronological age (a-DMRs). Epigenome-wide association scans (EWAS) identified age-related phenotype DMRs (ap-DMRs) associated with LDL (STAT5A), lung function (WT1), and maternal longevity (ARL4A, TBX20). In contrast, EWAS for chronological age identified hundreds of predominantly hyper-methylated age DMRs (490 a-DMRs at FDR 5%), of which only one (TBX20) was also associated with an age-related phenotype. Therefore, the majority of age-related changes in DNA methylation are not associated with phenotypic measures of healthy ageing in later life. We replicated a large proportion of a-DMRs in a sample of 44 younger adult MZ twins aged 20 to 61, suggesting that a-DMRs may initiate at an earlier age. We next explored potential genetic and environmental mechanisms underlying a-DMRs and ap-DMRs. Genome-wide overlap across cis-meQTLs, genotype-phenotype associations, and EWAS ap-DMRs identified CpG-sites that had cis-meQTLs with evidence for genotype-phenotype association, where the CpG-site was also an ap-DMR for the same phenotype. Monozygotic twin methylation difference analyses identified one potential environmentally-mediated ap-DMR associated with total cholesterol and LDL (CSMD1). Our results suggest that in a small set of genes DNA methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes

Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response

The Escherichia coli K-12 yfgF gene encodes a protein with domains associated with cyclic di-GMP signalling: GGDEF (associated with diguanylate cyclase activity) and EAL (associated with cyclic di-GMP phosphodiesterase activity). Here, it is shown that yfgF is expressed under anaerobic conditions from a class II FNR (regulator of fumarate and nitrate reduction)-dependent promoter. Anaerobic expression of yfgF is greatest in stationary phase, and in cultures grown at 28 degrees C, suggesting that low growth rates promote yfgF expression. Mutation of yfgF resulted in altered cell surface properties and enhanced sensitivity when anaerobic cultures were exposed to peroxides. The purified YfgF GGDEF-EAL (YfgF(GE)) and EAL (YfgF(E)) domains possessed cyclic di-GMP-specific phosphodiesterase activity, but lacked diguanylate cyclase activity. However, the catalytically inactive GGDEF domain was required for YfgF(GE) dimerization and enhanced cyclic di-GMP phosphodiesterase activity in the presence of physiological concentrations of Mg(2+). The cyclic di-GMP phosphodiesterase activity of YfgF(GE) and YfgF(E) was inhibited by the product of the reaction, 5'-phosphoguanylyl-(3'-5')-guanosine (pGpG). Thus, it is shown that the yfgF gene encodes an anaerobic cyclic di-GMP phosphodiesterase that is involved in remodelling the cell surface of E. coli K-12 and in the response to peroxide shock, with implications for integrating three global regulatory networks, i.e. oxygen regulation, cyclic di-GMP signalling and the oxidative stress response