OpenGraphGym: A Parallel Reinforcement Learning Framework for Graph Optimization Problems

This paper presents an open-source, parallel AI environment (named OpenGraphGym) to facilitate the application of reinforcement learning (RL) algorithms to address combinatorial graph optimization problems. This environment incorporates a basic deep reinforcement learning method, and several graph embeddings to capture graph features, it also allows users to rapidly plug in and test new RL algorithms and graph embeddings for graph optimization problems. This new open-source RL framework is targeted at achieving both high performance and high quality of the computed graph solutions. This RL framework forms the foundation of several ongoing research directions, including 1) benchmark works on different RL algorithms and embedding methods for classic graph problems; 2) advanced parallel strategies for extreme-scale graph computations, as well as 3) performance evaluation on real-world graph solutions

Characterization of an Alkali- and Halide-Resistant Laccase Expressed in E. coli: CotA from <i>Bacillus clausii</i>

The limitations of fungal laccases at higher pH and salt concentrations have intensified the search for new extremophilic bacterial laccases. We report the cloning, expression, and characterization of the bacterial cotA from Bacillus clausii, a supposed alkalophilic ortholog of cotA from B. subtilis. Both laccases were expressed in E. coli strain BL21(DE3) and characterized fully in parallel for strict benchmarking. We report activity on ABTS, SGZ, DMP, caffeic acid, promazine, phenyl hydrazine, tannic acid, and bilirubin at variable pH. Whereas ABTS, promazine, and phenyl hydrazine activities vs. pH were similar, the activity of B. clausii cotA was shifted upwards by ~0.5-2 pH units for the simple phenolic substrates DMP, SGZ, and caffeic acid. This shift is not due to substrate affinity (K(M)) but to pH dependence of catalytic turnover: The k(cat) of B. clausii cotA was 1 s⁻¹ at pH 6 and 5 s⁻¹ at pH 8 in contrast to 6 s⁻¹ at pH 6 and 2 s⁻¹ at pH 8 for of B. subtilis cotA. Overall, k(cat)/K(M) was 10-fold higher for B. subtilis cotA at pH(opt). While both proteins were heat activated, activation increased with pH and was larger in cotA from B. clausii. NaCl inhibited activity at acidic pH, but not up to 500-700 mM NaCl in alkaline pH, a further advantage of the alkali regime in laccase applications. The B. clausii cotA had ~20 minutes half-life at 80°C, less than the ~50 minutes at 80°C for cotA from B. subtilis. While cotA from B. subtilis had optimal stability at pH~8, the cotA from B. clausii displayed higher combined salt- and alkali-resistance. This resistance is possibly caused by two substitutions (S427Q and V110E) that could repel anions to reduce anion-copper interactions at the expense of catalytic proficiency, a trade-off of potential relevance to laccase optimization

Outcome prediction with a social cognitive battery: a multicenter longitudinal study

The interest in social cognition in schizophrenia is justified by the relationship between deficits in these skills and negative functional outcomes. Although assessment batteries have already been described, there is no consensus about which measures are useful in predicting patient functioning or quality of life (QoL). We investigated a set of five measures of recognition of facial emotions, theory of mind (ToM), and empathy in a cohort of 143 patients with schizophrenia or schizoaffective disorder at inclusion and, amongst whom 79 were reassessed 1 year later. The distribution was satisfactory for the TREF (Facial Emotion Recognition Task), V-SIR (Versailles-Situational Intention Reading), and QCAE (Questionnaire of Cognitive and Affective Empathy). Internal consistency was satisfactory for the TREF, V-SIR, V-Comics (Versailles Intention Attribution Task), and QCAE. Sensitivity to change was acceptable for the TREF. The TREF and V-SIR showed a cross-sectional relationship with functioning beyond the clinical symptoms of schizophrenia but not beyond neurocognition. Moreover, the TREF and V-SIR at inclusion could not predict functioning one year later, whereas most neurocognitive and clinical dimensions at inclusion could. Finally, only affective QCAE showed a significant cross-sectional, but not longitudinal, association with QoL. In conclusion, the TREF had satisfactory psychometric properties and showed a cross-sectional, but not longitudinal, association with objective outcome measures, thus appearing to be reliable in clinical practice and research. The V-SIR also showed promising psychometric properties, despite a possible weakness to detect change. However, these measures should be interpreted within the context of the good predictive power of the neurocognitive and clinical status on the outcome.Sorbonne Universités à Paris pour l'Enseignement et la RechercheFondaMental-Cohorte

Decolorization and detoxification of textile dyes using a versatile Streptomyces laccase-natural mediator system

Currently, there is increasing interest in assessing the potential of bacterial laccases for industrial and environmental applications especially in harsh conditions. The environmental impact of the textile industry requires novel and effective technologies to mitigate the presence of dyes in wastewaters before discharging into the environment. Dyes usually remain stable in the presence of a variety of chemicals, light and are recalcitrant to microbial degradation. Among available technologies the biological treatments offer environmentally friendly strategies for decolorizing and detoxifying these compounds. The recent discovery of versatile laccases in streptomycetes opens up new opportunities for their commercial application. The aim of this study is to assess the potential of a novel bacterial laccase SilA produced by Streptomyces ipomoeae CECT 3341 active over wide temperature and pH ranges for use as an eco-friendly, biological treatment for the degradation of textile dyes. Insights into the enhancement of the oxidative action of this enzyme through the use of natural redox mediators are presented together with an assessment of the potential toxicity of the degradation products. Our results confirm that the combination of the laccase and natural mediators such as acetosyringone and methyl syringate enhanced the decolorization and detoxification of a variety of textile dyes up to sixfold and 20-fold, respectively. Mediator concentration was found to have a significant effect (p &lt; 0.05) on dye decolorization at 60 °C; thus, the decolorization of Acid Orange 63 increased from 6 to 70-fold when the mediator concentration was increased from 0.1 to 0.5 mM. Further, the toxicity of tartrazine decreased 36-fold when the SilA-MeS system was used to decolorize the dye. The thermal properties of the SilA coupled with the stability of SilA at high pH suggest a potential commercial application for use in the decolorization of textile wastewaters which g

Rationally Guided Improvement of NOV1 Dioxygenase for the Conversion of Lignin-Derived Isoeugenol to Vanillin

Biocatalysis is a key tool in both green chemistry and biorefinery fields. NOV1 is a dioxygenase that catalyzes the one-step, coenzyme-free oxidation of isoeugenol into vanillin and holds enormous biotechnological potential for the complete valorization of lignin as a sustainable starting material for biobased chemicals, polymers, and materials. This study integrates computational, kinetic, structural, and biophysical approaches to characterize a new NOV1 variant featuring improved activity and stability compared to those of the wild type. The S283F replacement results in a 2-fold increased turnover rate (kcat) for isoeugenol and a 4-fold higher catalytic efficiency (kcat/Km) for molecular oxygen compared to those of the wild type. Furthermore, the variant exhibits a half-life that is 20-fold higher than that of the wild type, which most likely relates to the enhanced stabilization of the iron cofactor in the active site. Molecular dynamics supports this view, revealing that the S283F replacement decreases the optimal pKa and favors conformations of the iron-coordinating histidines compatible with an increased level of binding to iron. Importantly, whole cells containing the S283F variant catalyze the conversion of &lt;= 100 mM isoeugenol to vanillin, yielding &gt;99% molar conversion yields within 24 h. This integrative strategy provided a new enzyme for biotechnological applications and mechanistic insights that will facilitate the future design of robust and efficient biocatalysts

Intrusive polynomial chaos for CFD using OpenFOAM

We present the formulation and implementation of a stochas- tic Computational Fluid Dynamics (CFD) solver based on the widely used finite volume library - OpenFOAM. The solver employs General- ized Polynomial Chaos (gPC) expansion to (a) quantify the uncertainties associated with the fluid flow simulations, and (b) study the non-linear propagation of these uncertainties. The aim is to accurately estimate the uncertainty in the result of a CFD simulation at a lower computational cost than the standard Monte Carlo (MC) method. The gPC approach is based on the spectral decomposition of the random variables in terms of basis polynomials containing randomness and the unknown determin- istic expansion coefficients. As opposed to the mostly used non-intrusive approach, in this work, we use the intrusive variant of the gPC method in the sense that the deterministic equations are modified to directly solve for the (coupled) expansion coefficients. To this end, we have tested the intrusive gPC implementation for both the laminar and the turbulent flow problems in CFD. The results are in accordance with the analytical and the non-intrusive approaches. The stochastic solver thus developed, can serve as an alternative to perform uncertainty quantification, espe- cially when the non-intrusive methods are significantly expensive, which is mostly true for a lot of stochastic CFD problems