jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sayyed Hossein Hashemi | Massoud Kaykhaii | Ahmad Jamali Keikha | Leila Raisi
Source: ACS Omega (article, 2023-06-23)
Field: Chemistry — Analytical Chemistry

Deep Eutectic Solvent Stir Bar Sorptive Extraction: A Rapid Microextraction Technique for the Determination of Vitamin D<sub>3</sub> by Spectrophotometry In this paper, a new microextraction method, named deep eutectic solvent stir bar sorptive extraction (DES-SBSE), is described that utilizes a hydrophobic DES (hDES) as a coating for SBSE. As a model, vitamin D<sub>3</sub> was extracted efficiently by this technique from different real samples before its spectrophotometric determination. A conventional magnet was encapsulated inside a glass bar (1.0 cm × 2 mm) and coated by the hDES consisting of tetrabutylammonium chloride and heptadecanoic acid (mole ratio 1:2). Parameters affecting microextraction were studied and optimized by one-variable-at-a-time, central composite design, and Box-Behnken design methods. Under the optimum conditions, the detection limit of 0.08 μg L<sup>-1</sup> could be reached. The linear range of the method was between 0.5 and 1000.0 μg L<sup>-1</sup> for the analyte. Precision for intraday repeatability and interday reproducibility of the method was better than 3.1 and 4.2, respectively. A single stir bar could be used for at least 50 successive extractions and the batch-to-batch reproducibility of SB coated with hDES was 4.5%. Chromatography ; Reproducibility ; Repeatability ; Deep eutectic solvent ; Extraction (chemistry) ; Detection limit ; Central composite design ; Bar (unit) ; Materials science ; Analyte ; Solvent ; Spectrophotometry ; Eutectic system ; Analytical Chemistry (journal) ; Chemistry ; Response surface methodology ; Composite material Analytical chemistry methods development ; Ionic liquids properties and applications ; Electrochemical Analysis and Applications
Authors: Bastien Cochereau | Yoran Le Strat | Qiaolin Ji | Audrey Pawtowski | Ludovic Delage | Amélie Weill | Lisa Mazéas | Cécile Hervé | Gaëtan Burgaud | Nina Gunde‐Cimerman | Yves François Pouchus | Nathalie Demont-Caulet | Catherine Roullier | Laurence Meslet‐Cladière
Source: Marine Biotechnology (article, 2023-06-24)
Field: Chemistry — Inorganic Chemistry

Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029 The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (K<sub>m</sub> = 26 µM) than chloride (K<sub>m</sub> = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality. Biology ; Hydrothermal vent ; Heterologous expression ; Hypha ; Microbiology ; Biochemistry ; Botany ; Gene ; Hydrothermal circulation ; Recombinant DNA Vanadium and Halogenation Chemistry ; Metal-Catalyzed Oxygenation Mechanisms ; Cassava research and cyanide
Authors: Yash Pachaury | G. F. Warren | Janelle P. Wharry | Giacomo Po | Anter El‐Azab
Source: International Journal of Plasticity (article, 2023-06-15)
Field: Materials Science — Materials Chemistry

Plasticity in irradiated FeCrAl nanopillars investigated using discrete dislocation dynamics Materials science ; Irradiation ; Nanopillar ; Hardening (computing) ; Alloy ; Ultimate tensile strength ; Dislocation ; Composite material ; Plasticity ; Nanotechnology ; Nuclear physics ; Nanostructure ; Physics Fusion materials and technologies ; Nuclear Materials and Properties ; Microstructure and mechanical properties
Authors: Elena Xerxa | Oliver Laufkötter | Jürgen Bajorath
Source: Molecules (review, 2023-08-01)
Field: Chemistry — Organic Chemistry

Systematic Analysis of Covalent and Allosteric Protein Kinase Inhibitors In drug discovery, protein kinase inhibitors (PKIs) are intensely investigated as drug candidates in different therapeutic areas. While ATP site-directed, non-covalent PKIs have long been a focal point in protein kinase (PK) drug discovery, in recent years, there has been increasing interest in allosteric PKIs (APKIs), which are expected to have high kinase selectivity. In addition, as compounds acting by covalent mechanisms experience a renaissance in drug discovery, there is also increasing interest in covalent PKIs (CPKIs). There are various reasons for this increasing interest such as the anticipated high potency, prolonged residence times compared to non-competitive PKIs, and other favorable pharmacokinetic properties. Due to the popularity of PKIs for therapeutic intervention, large numbers of PKIs and large volumes of activity data have accumulated in the public domain, providing a basis for large-scale computational analysis. We have systematically searched for CPKIs containing different reactive groups (warheads) and investigated their potency and promiscuity (multi-PK activity) on the basis of carefully curated activity data. For seven different warheads, sufficiently large numbers of CPKIs were available for detailed follow-up analysis. For only three warheads, the median potency of corresponding CPKIs was significantly higher than of non-covalent PKIs. However, for CKPIs with five of seven warheads, there was a significant increase in the median potency of at least 100-fold compared to PKI analogues without warheads. However, in the analysis of multi-PK activity, there was no general increase in the promiscuity of CPKIs compared to non-covalent PKIs. In addition, we have identified 29 new APKIs in X-ray structures of PK-PKI complexes. Among structurally characterized APKIs, 13 covalent APKIs in complexes with five PKs are currently available, enabling structure-based investigation of PK inhibition by covalent-allosteric mechanisms. Kinome ; Allosteric regulation ; Potency ; Chemistry ; Drug discovery ; Druggability ; Pharmacology ; Biochemistry ; Kinase ; Enzyme ; Biology ; In vitro Click Chemistry and Applications ; Chemical Synthesis and Analysis ; HER2/EGFR in Cancer Research
Authors: E. I. Abdel Aziz | Fatiha Aouabed | Hossam Abdellah | Adrienn Dineva
Source: Energies (article, 2023-07-07)
Field: Materials Science — Materials Chemistry

Case Study: Optimizing Grading Ring Design for High Voltage Polymeric Insulators in Power Transmission Systems for Enhanced Electric Field and Voltage Distribution by Using a Finite Element Method This research paper aims to investigate the optimal design of grading rings for high-voltage polymeric insulators in an actual power transmission system, with a focus on improving the electrical representation of the insulator strings. One such subsidiary accessory commonly used with porcelain and polymer insulator strings is the grading ring, which is employed to improve the electric field and voltage distribution surrounding the insulator string. The efficiency of insulator strings can be enhanced by grading rings, as they facilitate a more linear potential division along the strings. The design parameters of grading rings significantly influence their performance on insulator strings. In this study, we examine the optimal design of the grading rings of high-voltage polymer insulators, since no uniform design methodology has been developed for high-voltage polymer insulators, and their optimization is currently the subject of many research studies. The electric field on an outdoor polymeric insulator is examined using finite element method (FEM) software and COMSOL Multi-Physics program. A 2D model is utilized to simulate a 220 kV polymeric insulator. The effectiveness of high-voltage polymeric insulators greatly depends on the dimensions and locations of the grading rings. Therefore, the impacts of the radius of the grading ring and that of its tube and the tube’s vertical position are thoroughly investigated, under dry and humid conditions. To achieve this objective, a search algorithm is employed to adjust the dimensions and locations of the grading ring. The optimization approach in this study is based on determining the maximum electric field across the insulator surface, while ensuring that it remains below the corona initiation level. Insulator (electricity) ; Finite element method ; Voltage ; Electric field ; High voltage ; Materials science ; Computer science ; Electrical engineering ; Mechanical engineering ; Optoelectronics ; Engineering ; Physics ; Structural engineering High voltage insulation and dielectric phenomena ; Thermal Analysis in Power Transmission ; Power Transformer Diagnostics and Insulation
Authors: Florent Abdelghafour | Radha Sivarajan Sajeevan | Ingi Abdelmeguid | Maxime Ryckewaert | Jean‐Michel Roger | Ryad Bendoula | Erik Alexandersson
Source: Computers and Electronics in Agriculture (article, 2023-06-15)
Field: Chemistry — Analytical Chemistry

Including measurement effects and temporal variations in VIS-NIRS models to improve early detection of plant disease: Application to Alternaria solani in potatoes Early detection of plant diseases with automated, non destructive and high-throughput techniques is a major objective in plant breeding and crop protection. Near infrared spectroscopy and hyperspectral imaging are proven to be particularly relevant technologies. However, robust discriminant models remains a challenge because of the many uncontrolled sources of variability during the experiment. Indeed, at early stages of most diseases, the temporal variations due to environment and measurement effects can induce signal shifts of greater magnitude than the infection itself, masking the information of interest. Excluding the variations of the measurement environment and the temporal fluctuation of the plant-pathogen interaction can depreciate the model robustness. Here, the problem is addressed in a study of the seven potato cultivars monitored for the presence of early blight disease at 0, 18, 36, and 96 h after inoculation. Three practical corrections are proposed regarding the effect of temporal fluctuations. (i) subclass effect, (ii) kinetic effect of the disease, and (iii) measurement effect. Eventually, the application of EPO-PLSDA to orthogonalise the model regarding temporal variation to produce invariant models proved to be the only suitable and well-performing of the tested solutions. With this approach the disease can be detected from 36 h after inoculation for 6 of the 7 tested cultivars. Classification errors differ among the cultivars but on average are below 25% of errors. Hyperspectral imaging ; Blight ; Robustness (evolution) ; Biological system ; Cultivar ; Alternaria solani ; Plant disease ; Mathematics ; Biology ; Statistics ; Computer science ; Artificial intelligence ; Biotechnology ; Agronomy Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Mycotoxins in Agriculture and Food
Authors: Mauro Mancini | Costanza Mariani | Carmine Mattia Manfredi
Source: Progress in Nuclear Energy (article, 2023-02-06)
Field: Materials Science — Materials Chemistry

Nuclear decommissioning risk management adopting a comprehensive artificial intelligence framework: An applied case in an Italian site The increase of nuclear sites entering the decommissioning phase has drawn the attention of governments, regulatory bodies, and industries to decommissioning projects. However, despite the high number of uncertainties and risks of these projects, there is a lack of dedicated risk management frameworks beyond the guidelines established by the International Atomic Energy Agency (IAEA) and the Project Management Institute (PMI). This study aims to propose an integrated framework for managing risks in Nuclear Decommissioning Projects. For the development of the framework artificial intelligence algorithms were employed, integrating models derived from the manufacturing sector capable of assessing risks, identifying an optimal set of risk mitigation actions, and predicting the additional project delay or cost based on a quantitative risk analysis. To demonstrate its validity, the model was applied to a nuclear decommissioning project currently underway in Italy, generating a forecast of the final project delay. The results showed to be promising, as the delay prediction for the analysed phase of the project differs from the current one only by an error of 4.7%. The proposed model can help project managers in managing risks and predicting delays or additional project costs during the preliminary phase. In addition, the framework is equally useful for controlling risks in the progress stages of the project by dynamically updating forecasts. Nuclear decommissioning ; Risk analysis (engineering) ; Risk management ; Agency (philosophy) ; Atomic energy ; Project management ; Computer science ; Risk assessment ; Systems engineering ; Business ; Engineering Graphite, nuclear technology, radiation studies ; Marine and Offshore Engineering Studies ; Nuclear and radioactivity studies
Authors: Robin Debuysschère | Bart Rimez | Alessio Zaccone | Benoît Scheid
Source: Crystal Growth & Design (article, 2023-06-22)
Field: Materials Science — Materials Chemistry

Experimental and Theoretical Investigation of Nonclassical Shear-Induced Nucleation Mechanism for Small Molecule Crystallization is one of the major steps in industrial production and environmental settings. According to thermodynamics and nucleation theories, the crystallization kinetics can be controlled by adjusting the temperature and concentration. The supersaturated liquid is almost always flown into a crystallization device due to stirring, injection, or other reasons. The role of shear flow on the crystallization kinetics therefore plays a crucial role, but the precise shear-induced nucleation mechanism has so far remained elusive. Here we present a detailed mechanism for the example of glycine, and we validate it by comparing experimental data to theory. A major result is the confirmation that nucleation has a maximum as a function of shear, which can lead to a dramatic enhancement of industrial production. Nucleation ; Crystallization ; Supersaturation ; Thermodynamics ; Kinetics ; Mechanism (biology) ; Shear (geology) ; Chemical physics ; Shear flow ; Materials science ; Classical nucleation theory ; Molecule ; Chemistry ; Physics ; Organic chemistry ; Classical mechanics ; Composite material Crystallization and Solubility Studies ; nanoparticles nucleation surface interactions ; Calcium Carbonate Crystallization and Inhibition
Authors: Rémi Denise | Jill Babor | J.A. Gerlt | Valérie de Crécy‐Lagard
Source: Microbial Genomics (article, 2023-02-02)
Field: Materials Science — Materials Chemistry

Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes Pyridoxal 5’-phosphate or PLP is a cofactor derived from B 6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B 6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B 6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come. Archaea ; Bacillus subtilis ; Biology ; Pyridoxal ; Bacteria ; Cofactor ; Biosynthesis ; Gene ; Genome ; Biochemistry ; Computational biology ; Model organism ; Enzyme ; Nucleotide salvage ; Pyridoxal phosphate ; Genetics ; Nucleotide Enzyme Structure and Function ; Genomics and Phylogenetic Studies ; Bacterial Genetics and Biotechnology
Authors: Hongwei Zhu | Minjie Li | Cuilin Cheng | Ying Han | Shiyao Fu | Ruiling Li | Gaofeng Cao | Miaomiao Liu | Can Cui | Jia Liu | Xin Yang
Source: Foods (article, 2023-11-27)
Field: Materials Science — Materials Chemistry

Recent Advances in and Applications of Electrochemical Sensors Based on Covalent Organic Frameworks for Food Safety Analysis The international community has been paying close attention to the issue of food safety as a matter of public health. The presence of a wide range of contaminants in food poses a significant threat to human health, making it vital to develop detection methods for monitoring these chemical contaminants. Electrochemical sensors using emerging materials have been widely employed to detect food-derived contaminants. Covalent organic frameworks (COFs) have the potential for extensive applications due to their unique structure, high surface area, and tunable pore sizes. The review summarizes and explores recent advances in electrochemical sensors modified with COFs for detecting pesticides, antibiotics, heavy metal ions, and other food contaminants. Furthermore, future challenges and possible solutions will be discussed regarding food safety analysis using COFs. Food safety ; Nanotechnology ; Environmental science ; Contamination ; Human health ; Biochemical engineering ; Computer science ; Materials science ; Chemistry ; Engineering ; Environmental health ; Ecology Covalent Organic Framework Applications ; Electrochemical Analysis and Applications ; Electrochemical sensors and biosensors
Authors: Sławomir Rubinsztajn | Julian Chojnowski | Urszula Mizerska
Source: Molecules (review, 2023-08-08)
Field: Chemistry — Organic Chemistry

Tris(pentafluorophenyl)borane-catalyzed Hydride Transfer Reactions in Polysiloxane Chemistry—Piers–Rubinsztajn Reaction and Related Processes Tris(pentafluorophenyl)borane (TPFPB) is a unique Lewis acid that catalyzes the condensation between hydrosilanes (Si-H) and alkoxysilanes (Si-OR), leading to the formation of siloxane bonds (Si-OSi) with the release of hydrocarbon (R-H) as a byproduct-the so-called Piers-Rubinsztajn reaction. The analogous reactions of hydrosilanes with silanols (Si-OH), alcohols (R-OH), ethers (R-OR') or water in the presence of TPFPB leads to the formation of a siloxane bond, alkoxysilane (Si-OR or Si-OR') or silanol (Si-OH), respectively. The above processes, often referred to as Piers-Rubinsztajn reactions, provide new synthetic tools for the controlled synthesis of siloxane materials under mild conditions with high yields. The common feature of these reactions is the TPFPB-mediated hydride transfer from silicon to carbon or hydrogen. This review presents a summary of 20 years of research efforts related to this field, with a focus on new synthetic methodologies leading to numerous previously difficult to synthesize well-defined siloxane oligomers, polymers and copolymers of a complex structure and potential applications of these new materials. In addition, the mechanistic aspects of the recently discovered reactions involving hydride transfer from silicon to silicon are discussed in more detail. Siloxane ; Chemistry ; Hydride ; Silanol ; Borane ; Lewis acids and bases ; Catalysis ; Polymer chemistry ; Ammonia borane ; Organic chemistry ; Condensation reaction ; Polymer ; Hydrogen ; Hydrogen production Organoboron and organosilicon chemistry ; Catalytic Cross-Coupling Reactions ; Synthesis and characterization of novel inorganic/organometallic compounds
Authors: Sarah Löffelsender | Pierre Beaujean | Marc de Wergifosse
Source: Wiley Interdisciplinary Reviews Computational Molecular Science (article, 2023-11-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Simplified quantum chemistry methods to evaluate non‐linear optical properties of large systems Abstract This review presents the theoretical background concerning simplified quantum chemistry (sQC) methods to compute non‐linear optical (NLO) properties and their applications to large systems. To evaluate any NLO responses such as hyperpolarizabilities or two‐photon absorption (2PA), one should evidently perform first a ground state calculation and compute its response. Because of this, methods used to compute ground states of large systems are outlined, especially the xTB (extended tight‐binding) scheme. An overview on approaches to compute excited state and response properties is given, emphasizing the simplified time‐dependent density functional theory (sTD‐DFT). The formalism of the eXact integral sTD‐DFT (XsTD‐DFT) method is also introduced. For the first hyperpolarizability, 2PA, excited state absorption, and second hyperpolarizability, a brief historical review is given on early‐stage semi‐empirical method applications to systems that were considered large at the time. Then, we showcase recent applications with sQC methods, especially the sTD‐DFT scheme to large challenging systems such as fluorescent proteins or fluorescent organic nanoparticles as well as dynamic structural effects on flexible tryptophan‐rich peptides and gramicidin A. Thanks to the sTD‐DFT‐xTB scheme, all‐atom quantum chemistry methodologies are now possible for the computation of the first hyperpolarizability and 2PA of systems up to 5000 atoms. This review concludes by summing‐up current and future method developments in the sQC framework as well as forthcoming applications on large systems. This article is categorized under: Electronic Structure Theory &gt; Ab Initio Electronic Structure Methods Structure and Mechanism &gt; Molecular Structures Electronic Structure Theory &gt; Density Functional Theory Electronic Structure Theory &gt; Semiempirical Electronic Structure Methods Hyperpolarizability ; Density functional theory ; Electronic structure ; Excited state ; Computational chemistry ; Quantum chemistry ; Computer science ; Ab initio ; Chemistry ; Statistical physics ; Quantum mechanics ; Physics ; Nonlinear system ; Molecule ; Nonlinear optical Nonlinear Optical Materials Research ; Organic Chemistry Cycloaddition Reactions ; Bioactive Compounds and Antitumor Agents