Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover. We use our predictions to parameterize two mechanistic genome-scale modelling frameworks for proteome-limited metabolism, leading to significantly higher accuracy in the prediction of quantitative proteome data than previous approaches. The presented machine learning models thus provide a valuable tool for understanding metabolism and the proteome at the genome scale, and elucidate structural, biochemical, and network properties that underlie enzyme kinetics

Proof-Pattern Recognition and Lemma Discovery in ACL2

We present a novel technique for combining statistical machine learning for proof-pattern recognition with symbolic methods for lemma discovery. The resulting tool, ACL2(ml), gathers proof statistics and uses statistical pattern-recognition to pre-processes data from libraries, and then suggests auxiliary lemmas in new proofs by analogy with already seen examples. This paper presents the implementation of ACL2(ml) alongside theoretical descriptions of the proof-pattern recognition and lemma discovery methods involved in it

A Preliminary Model of the Hydrologic-Sociologic Flow System of an Urban Area

This report describes the first phase of a larger study which is directed toward the development of a general technique for analyzing and solving urban metropolitan hydrologic problems through a joint consideration of both the physical and social dimensions. This report is limited to the preliminary work of identification of social variables, the first steps in assigning mathematical values to them, and developing a mathematical format for these variables. In addition, the physical-hydrologic system is identified for purposes of clarifying the elements in that system. The ultimate objective of the entire study is directed toward discovering a theoretical and generally applicable mathematical model of both the physical and social dimensions involved in metropolitan flooding problems

Aqueous vanadate removal by iron(II)-bearing phases under anoxic conditions

Copyright © 2020 American Chemical SocietyFunding was provided by the Natural Sciences and Engineering Council of Canada (NSERC) through the Discovery Grants program (Grant No. RGPIN-2014-06589). Additional support awarded to CJV through NSERC – Canada Graduate Scholarship – Masters (NSERC CGS-M) Program. A portion of the research described was performed at the Canadian Light Source, which is supported by the Canada Foundation for Innovation, NSERC, the University of Saskatchewan, the Government of Saskatchewan, Western Economic Diversification Canada, the National Research Council, and the Canadian Institutes of Health Research.Peer ReviewedVanadium contamination is a growing environmental hazard worldwide. Aqueous vanadate (HxVVO4(3−x)− (aq)) concentrations are often controlled by surface complexation with metal (oxyhydr)oxides in oxic environments. However, the geochemical behaviour of this toxic redox sensitive oxyanion in anoxic environments is poorly constrained. Here we describe results of batch experiments to determine kinetics and mechanisms of aqueous H2VVO4− (100 μM) removal under anoxic conditions in suspensions (2.0 g L−1) of magnetite, siderite, pyrite, and mackinawite. We present results of parallel experiments using ferrihydrite (2.0 g L−1) and Fe2+(aq) (200 μM) for comparison. Siderite and mackinawite reached near complete removal (46 µmol g−1) of aqueous vanadate after 3 h and kinetic rates were generally consistent with ferrihydrite. Whereas magnetite removed 18 µmol g−1 of aqueous vanadate after 48 h and uptake by pyrite was limited. Uptake by Fe2+(aq) was observed after 8 h, concomitant with precipitation of secondary Fe phases. X ray absorption spectroscopy revealed V(V) reduction to V(IV) and formation of bidentate corner-sharing surface complexes on magnetite and siderite, and with Fe2+(aq) reaction products. These data also suggest that V(IV) is incorporated into the mackinawite structure. Overall, we demonstrate that Fe(II)-bearing phases can promote aqueous vanadate attenuation and, therefore, limit dissolved V concentrations in anoxic environments

Determining the shape of defects in non-absorbing inhomogeneous media from far-field measurements

International audienceWe consider non-absorbing inhomogeneous media represented by some refraction index. We have developed a method to reconstruct, from far-field measurements, the shape of the areas where the actual index differs from a reference index. Following the principle of the Factorization Method, we present a fast reconstruction algorithm relying on far field measurements and near field values, easily computed from the reference index. Our reconstruction result is illustrated by several numerical test cases

On the Convergence of the Born Series in Optical Tomography with Diffuse Light

We provide a simple sufficient condition for convergence of Born series in the forward problem of optical diffusion tomography. The condition does not depend on the shape or spatial extent of the inhomogeneity but only on its amplitude.Comment: 23 pages, 7 figures, submitted to Inverse Problem

Fourier Method for Approximating Eigenvalues of Indefinite Stekloff Operator

We introduce an efficient method for computing the Stekloff eigenvalues associated with the Helmholtz equation. In general, this eigenvalue problem requires solving the Helmholtz equation with Dirichlet and/or Neumann boundary condition repeatedly. We propose solving the related constant coefficient Helmholtz equation with Fast Fourier Transform (FFT) based on carefully designed extensions and restrictions of the equation. The proposed Fourier method, combined with proper eigensolver, results in an efficient and clear approach for computing the Stekloff eigenvalues.Comment: 12 pages, 4 figure

Mineralogy and geochemistry of oil sands froth treatment tailings: Implications for acid generation and metal(loid) release

Copyright © 2019 Elsevier Ltd. All rights reserved.This research was supported by the Natural Sciences and Engineering Council of Canada (NSERC) and Syncrude Canada Ltd. through the Industrial Research Chairs Grants program (Grant No. IRCPJ 450684−13). Additional support for CJV was provided by the NSERC Canadian Graduate Scholarships – Master’s (NSERC CGS-M) Program.Peer ReviewedFroth treatment tailings (FTT) are one of three principal tailings streams generated during bitumen extraction at oil sands mines in northern Alberta, Canada. Unlike the coarse tailings and fluid fine tailings, FTT are enriched in sulfide-minerals content and exhibit the potential for acid generation and metal(loid) leaching. However, the mineralogical and geochemical characteristics of this sulfide-bearing tailings stream remain poorly constrained. We examined samples of fresh FTT (n = 3) and partially-weathered FTT collected from a sub-aerial beach deposit (n = 15). X-ray diffraction revealed that weathering-resistant silicates, phyllosilicates, and oxides dominated (85 ± 7.3 wt. %) the FTT mineral assemblage, while sulfides (6.2 ± 3.6 wt. %) and carbonates (8.9 ± 4.3 wt. %) were relatively minor phases. Pyrite [FeS2] was the principal sulfide in all samples, while minor amounts of marcasite [FeS2] occurred only in beach samples. Sulfide mineral textures were highly variable and included euhedral to subhedral pyrite crystals, discrete and clustered pyrite framboids, and marcasite replacements of pyrite framboids. Siderite [FeCO3] accounted for 55 to 90 % of all carbonates, while dolomite [CaMg(CO3)2], calcite [CaCO3] and ankerite [Ca(Fe,Mg,Mn)(CO3)2] accounted for the remainder. Statistical analysis of bulk geochemical compositions suggested that environmentally-relevant metal(loid)s, including As, Cu, Co, Fe, Mn, Ni, Pb and Zn, were likely associated with sulfides, carbonates and, to a lesser extent, phyllosilicates. Electron probe microanalyses revealed a wide range of As, Cu, Co, Mn, Ni and Zn concentrations in pyrite, with As and Cu concentrations elevated in framboids. Rare earth elements (REEs), Th and U also occurred at elevated concentrations and statistical analyses suggest they are associated with zircon and, potentially, monazite and xenotime. Static acid-base accounting (ABA) tests indicated that all FTT samples are potentially acid generating. Our study describes the mineralogical and geochemical characteristics of oil sands FTT, and indicates that oxidative weathering has the potential to generate acidic drainage containing elevated dissolved concentrations of several metal(loid)s

Confidentiality and public protection: ethical dilemmas in qualitative research with adult male sex offenders

This paper considers the ethical tensions present when engaging in in-depth interviews with convicted sex offenders. Many of the issues described below are similar to those found in other sensitive areas of research. However, confidentiality and public protection are matters that require detailed consideration when the desire to know more about men who have committed serious and harmful offences is set against the possibility of a researcher not disclosing previously unknown sensitive information that relates to the risk of someone being harmed.</p