jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Laila Rahmawati | Slamet Widodo | Deni Permana KURNIADI | Pamungkas DAUD | Agus Triyono | Sri Harti | N D Susanti | Nur Kartika Indah Mayasti | Ashri Indriati | Lista Eka YULIANTI | Devry Pramesti PUTRI | Seri Intan KUALA | Cahya Edi Wahyu Anggara | Eko Joni PRISTIANTO | Erry Dwi Kurniawan | Ignatius Fajar APRIYANTO | Dayat KURNIAWAN
Source: Food Science and Technology (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Determination of colorant type in yellow tofu using Vis-NIR and SW-NIR spectroscopy A method that can detect colorant type in food is requisite against illegal practices that used non-food-grade colorants in food. In this study colorant types of yellow tofu were identified using visible near-infrared (Vis-NIR) and shortwave near-infrared spectra (SW-NIR) spectroscopy. Chemometrics analysis using partial least square-discriminant analysis (PLS-DA) and principal component analysis-linear discriminant analysis (PCA-LDA) were used to classify natural colorants, non-food-grade colorants, and food-grade colorants in yellow tofu. The best model obtained using Vis-NIR had calibration accuracy and reliability of 100% for both PCA-LDA and PLS-DA. The best model yielded by SW-NIR had calibration accuracy of 76% and 28% reliability for PLS-DA, and accuracy of 92% and 76% reliability for PCA-LDA. The result showed that Vis-NIR spectroscopy was superior to SW-NIR spectroscopy to distinguish the colorant type used in yellow tofu. Moreover, PCA-LDA yielded better accuracy and reliability compared to PLS-DA. Chemometrics ; Near-infrared spectroscopy ; Linear discriminant analysis ; Principal component analysis ; Partial least squares regression ; Spectroscopy ; Calibration ; Reliability (semiconductor) ; Chemistry ; Analytical Chemistry (journal) ; Mathematics ; Pattern recognition (psychology) ; Chromatography ; Artificial intelligence ; Statistics ; Computer science ; Optics ; Physics Dye analysis and toxicity ; Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis
Authors: Ziwen Zhao | Arunava Naha | Sagar Ganguli | Alina Sekretareva
Source: ChemRxiv (preprint, 2023-06-22)
Field: Chemistry — Electrochemistry

Automated Analysis of Nano-Impact Single-Entity Electrochemistry Signals using Unsupervised Machine Learning and Template Matching Nano-impact single-entity electrochemistry (NIE) is an emerging technique that enables electrochemical investigation of individual entities, ranging from metal nanoparticles to single cells and biomolecules. To extract meaningful information from NIE experiments, statistical analysis of large datasets is necessary. In this study, we developed a method for the automated analysis of NIE data based on unsupervised machine learning and template matching approaches. Template matching not only facilitates downstream processing of the NIE data but also provides a more accurate analysis of the NIE signal characteristics and variations that are difficult to discern with conventional data analysis techniques, such as the height threshold method. The developed algorithm enables fast automated processing of large experimental datasets recorded with different systems, requiring minimal human intervention and thereby eliminating human bias in data analysis. As a result, it improves the standardization of data processing and NIE signal interpretation across various experiments and applications. Computer science ; Matching (statistics) ; Template matching ; Signal processing ; Artificial intelligence ; Pattern recognition (psychology) ; Standardization ; SIGNAL (programming language) ; Data mining ; Unsupervised learning ; Data processing ; Machine learning ; Digital signal processing ; Image (mathematics) Electrochemical Analysis and Applications ; Conducting polymers and applications ; Electrochemical sensors and biosensors
Authors: 李武耀 Li Wuyao | 买买提·沙吾提 Sawut Mamat | 买合木提·巴拉提 Balati Maihemuti
Source: Laser & Optoelectronics Progress (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

基于分数阶微分的土壤有机质含量高光谱反演研究 土壤有机质（SOM）对改善干旱区土地盐碱化、沙漠化和草场退化等环境问题发挥着重要作用。为了探索分数阶微分方法在SOM高光谱反演的可行性，以渭干河-库车河绿洲73个土壤样本为研究对象，通过测定其SOM含量与光谱反射率，利用0.2阶微分为步长，进行0~2阶分数阶微分的数学变换，分析分数阶处理光谱与SOM含量间的相关性，运用支持向量机回归、偏最小二乘回归和随机森林（RF）等方法对SOM含量进行定量反演。结果表明：采用RF的1.2阶微分建立的SOM含量反演模型预测精度最高，决定系数为0.93，均方根误差为1.62，相对分析误差为3.65。研究结果为精准反演该地区的SOM提供了依据，也为其他地区的SOM反演提供一定的参考。 Medicine Spectroscopy and Chemometric Analyses ; Soil Geostatistics and Mapping ; Water Quality Monitoring and Analysis
Authors: Max Walton-Raaby | Tyler Floen | Guillermo García-Díez | Nelaine Mora‐Diez
Source: Antioxidants (article, 2023-07-13)
Field: Chemistry — Organic Chemistry

Calculating the Aqueous pKa of Phenols: Predictions for Antioxidants and Cannabinoids We aim to develop a theoretical methodology for the accurate aqueous pK<sub>a</sub> prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pK<sub>a</sub> values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pK<sub>a</sub> values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pK<sub>a</sub> values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pK<sub>a</sub> units and R<sup>2</sup> values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pK<sub>a</sub> units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pK<sub>a</sub> predictions for other phenols in water and potentially in other solvents where they might be more soluble. Phenols ; Chemistry ; Aqueous solution ; Solvent ; Computational chemistry ; Molecule ; Test set ; Organic chemistry ; Mathematics Free Radicals and Antioxidants ; Computational Drug Discovery Methods ; Chemistry and Chemical Engineering
Authors: Muluh Emmanuel Khan | Chijioke Ezekiel Elum | A. O. Ijeomah | Hilip John Ameji | Izuagbe Gilbert Osigbemhe | Emmanuel E. Etim | John Veshima Anyam | Alexander Abel | Cyprian T. Agber
Source: Journal of the Nigerian Society of Physical Sciences (article, 2023-08-01)
Field: Materials Science — Biomaterials

Isolation, Characterization, Antimicrobial and Theoretical Investigation of Some Bioactive Compounds Obtained from the Bulbs of Calotropisprocera This study characterizes the bioactive molecules from the bulb of Calotropisprocera and investigates the antimicrobial activities of the crude extracts. Theoretical studies on the two isolated compounds in the crude extract were also accomplished.The bulbs were air dried, pulverized, and subjected to extraction procedures by maceration using 500 mL each of normal-hexane, ethyl acetate and methanol. The crude extracts were further tested onmicroorganisms and phytochemical screening using standard procedures. In addition, the bioactive compounds in the extract were screened against DNA gyrase of two Gram negative bacterial species; Escherichia coli and Salmonella typhiusing Molecular Docking simulation techniques and further subjected to ADMET profiling,using the Swiss ADME online server. The Crude ethyl acetate extract has the highest effective activity against Escherichia coli (MIC 2.5mg / mL and MBC/MFC 5mg / mL), Staphylococcus aureus (MIC 2.5mg/mL), Candida albicans, Salmonella typhiand Candida stellafoidea (MIC 5mg/mL). beta-Amyrin acetate and Taraxasterol are the two phytochemicals in the purified white crystalline fractions and were found to fasten to the active sites of DNA gyrase of the Gram negative bacterial species via hydrophobic and hydrogen bond interactions, with binding activity value of -9.6 kcal/mol and -9.5 kcal/mol, respectively. Also, ADMET investigations of the compounds revealed their sound oral bioavailability and excellent pharmacokinetic and toxicity profiles. The findings of this study could provide a platform for discovering safe and potent antibiotics against pathogenic microbes ravaging our society. Ethyl acetate ; Antimicrobial ; Chemistry ; Phytochemical ; DNA gyrase ; Escherichia coli ; Candida albicans ; Antibacterial activity ; Traditional medicine ; Food science ; Chromatography ; Biochemistry ; Bacteria ; Microbiology ; Biology ; Organic chemistry Phytochemistry and Bioactive Compounds ; Phytochemistry and Biological Activities ; Morinda citrifolia extract uses
Authors: Giuseppe Silvestri | Federica Arrigoni | Francesca Persico | Luca Bertini | Giuseppe Zampella | Luca De Gioia | Jacopo Vertemara
Source: Molecules (article, 2023-08-11)
Field: Chemistry — Electrochemistry

Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from <i>Clostridium Beijerinckii</i> and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes. Flavodoxin ; Flavin mononucleotide ; Redox ; Flavoprotein ; Chemistry ; Flavin group ; Cofactor ; Flavin adenine dinucleotide ; Electron transfer ; Rubredoxin ; Computational chemistry ; Ferredoxin ; Photochemistry ; Biochemistry ; Enzyme ; Organic chemistry Electrochemical Analysis and Applications ; CO2 Reduction Techniques and Catalysts ; Free Radicals and Antioxidants
Authors: Haoran Sun | Liguo Zhang | Lijun Ni | Zijun Zhu | Shaorong Luan | Ping Hu
Source: Sensors (article, 2023-01-14)
Field: Chemistry — Analytical Chemistry

Study on Rapid Detection of Pesticide Residues in Shanghaiqing Based on Analyzing Near-Infrared Microscopic Images Aiming at guiding agricultural producers to harvest crops at an appropriate time and ensuring the pesticide residue does not exceed the maximum limit, the present work proposed a method of detecting pesticide residue rapidly by analyzing near-infrared microscopic images of the leaves of Shanghaiqing (Brassica rapa), a type of Chinese cabbage with computer vision technology. After image pre-processing and feature extraction, the pattern recognition methods of K nearest neighbors (KNN), naïve Bayes, support vector machine (SVM), and back propagation artificial neural network (BP-ANN) were applied to assess whether Shanghaiqing is sprayed with pesticides. The SVM method with linear or RBF kernel provides the highest recognition accuracy of 96.96% for the samples sprayed with trichlorfon at a concentration of 1 g/L. The SVM method with RBF kernel has the highest recognition accuracy of 79.16~84.37% for the samples sprayed with cypermethrin at a concentration of 0.1 g/L. The investigation on the SVM classification models built on the samples sprayed with cypermethrin at different concentrations shows that the accuracy of the models increases with the pesticide concentrations. In addition, the relationship between the concentration of the cypermethrin sprayed and the image features was established by multiple regression to estimate the initial pesticide concentration on the Shanghaiqing leaves. A pesticide degradation equation was established on the basis of the first-order kinetic equation. The time for pesticides concentration to decrease to an acceptable level can be calculated on the basis of the degradation equation and the initial pesticide concentration. The present work provides a feasible way to rapidly detect pesticide residue on Shanghaiqing by means of NIR microscopic image technique. The methodology laid out in this research can be used as a reference for the pesticide detection of other types of vegetables. Support vector machine ; Pesticide ; Pesticide residue ; Cypermethrin ; Artificial intelligence ; Pattern recognition (psychology) ; Biological system ; Kernel (algebra) ; Mathematics ; Computer science ; Agronomy ; Biology Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Pavel Valencia-Acuña | Stephanie Amos | Hartwin Peelaers | Hui Zhao
Source: Physical review. B./Physical review. B (article, 2023-08-07)
Field: Materials Science — Materials Chemistry

Energy-valley-dependent charge transfer in few-layer transition metal dichalcogenide heterostructures The effect of the energy valley on interlayer charge transfer in transition metal dichalcogenide (TMD) heterostructures is studied by transient absorption spectroscopy and density functional theory. First-principles calculations confirm that the ${\mathrm{\ensuremath{\Lambda}}}_{\text{min}}$ valley in the conduction band of few-layer ${\mathrm{WSe}}_{2}$ evolves from above its K valley in the monolayer (1L) to below it in 4L. Heterostructure samples of $n\mathrm{L}\text{\ensuremath{-}}{\mathrm{WSe}}_{2}/1\mathrm{L}\text{\ensuremath{-}}{\mathrm{MoS}}_{2}$, where $n=1,2,3$, and 4, are obtained by mechanical exfoliation and dry transfer. Photoluminescence spectroscopy reveals a thickness-dependent ${\mathrm{WSe}}_{2}$ band structure and efficient interlayer charge transfer. Transient absorption measurements show that the electron transfer time from the ${\mathrm{\ensuremath{\Lambda}}}_{\text{min}}$ valley of 4L ${\mathrm{WSe}}_{2}$ to the K valley of ${\mathrm{MoS}}_{2}$ is on the order of 30 ps. This process is much slower than the K-K charge transfer in 1L/1L TMD heterostructures. The momentum-indirect interlayer excitons formed after charge transfer have lifetimes &gt;1 ns. Heterojunction ; Charge (physics) ; Condensed matter physics ; Materials science ; Absorption (acoustics) ; Transition metal ; Exciton ; Physics ; Spectroscopy ; Atomic physics ; Chemistry ; Optics 2D Materials and Applications ; Perovskite Materials and Applications ; Advanced Photocatalysis Techniques
Authors: Cristian Sandoval | Francisco Torrens | Karina Godoy | Camila Reyes | Jorge G. Farías
Source: International Journal of Molecular Sciences (article, 2023-07-31)
Field: Chemistry — Organic Chemistry

Application of Quantitative Structure-Activity Relationships in the Prediction of New Compounds with Anti-Leukemic Activity Leukemia invades the bone marrow progressively and, through unknown mechanisms, outcompetes healthy hematopoiesis. Protein arginine methyltransferases 1 (PRMT1) are found in prokaryotes and eukaryotes cells. They are necessary for a number of biological processes and have been linked to several human diseases, including cancer. Small compounds that target PRMT1 have a significant impact on both functional research and clinical disease treatment. In fact, numerous PRMT1 inhibitors targeting the S-adenosyl-L-methionine binding region have been studied. Through topographical descriptors, quantitative structure-activity relationships (QSAR) were developed in order to identify the most effective PRMT1 inhibitors among 17 compounds. The model built using linear discriminant analysis allows us to accurately classify over 90% of the investigated active substances. Antileukemic activity is predicted using a multilinear regression analysis, and it can account for more than 56% of the variation. Both analyses are validated using an internal "leave some out" test. The developed model could be utilized in future preclinical experiments with novel drugs. Computational biology ; Quantitative structure–activity relationship ; Chemistry ; Biology ; Stereochemistry Click Chemistry and Applications ; Cancer-related gene regulation ; Protein Degradation and Inhibitors
Authors: Lucas Etourneau | Laura Fancello | Samuel Wieczorek | Nelle Varoquaux | Thomas Bürger
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-11-13)
Field: Chemistry — Spectroscopy

Penalized likelihood optimization for censored missing value imputation in proteomics Abstract Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hindered by complex and heterogeneous missing values, which imputation has long remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge using an original likelihood maximization strategy. Notably, it models the instrument limit by learning a global censoring mechanism from the data available. Moreover, it estimates the covariance matrix between enzymatic cleavage products ( i . e ., peptides or precursor ions), while offering a natural way to integrate complementary transcriptomic information when multi-omic assays are available. Our benchmarking on several datasets covering a variety of experimental designs (number of samples, acquisition mode, missingness patterns, etc.) and using a variety of metrics (differential analysis ground truth or imputation errors) shows that Pirat outperforms all pre-existing imputation methods. Beyond the interest of Pirat as an imputation tool, these results pinpoint the need for a paradigm change in proteomics imputation, as most pre-existing strategies could be boosted by incorporating similar models to account for the instrument censorship or for the correlation structures, either grounded to the analytical pipeline or arising from a multi-omic approach. Imputation (statistics) ; Missing data ; Computer science ; Data mining ; Workflow ; Benchmarking ; Proteomics ; Proteome ; Computational biology ; Machine learning ; Bioinformatics ; Biology ; Database Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Biosensing Techniques and Applications
Authors: Fangning Ren | Fang Liu
Source: Chemical Physics Reviews (article, 2023-12-01)
Field: Chemistry — Analytical Chemistry

Data-driven insights into the fluorescence of asphaltene aggregates using extended Frenkel exciton model The origin of the fluorescence redshift during asphaltene aggregation remains debated due to the great diversity of asphaltene molecules, while the extended Frenkel exciton model provided a theoretical framework for studying multi-chromophore systems, such as asphaltene aggregates. We investigated the fluorescence energy of hundreds of asphaltene dimers based on 133 experimental revealed asphaltene monomer structures. Our result shows that the dimer's fluorescence energy is always lower than both of its monomers regardless of its intermolecular conformation, with its redshift dominated by superexchange. The dimer oscillator strength predominantly depends on the monomer with the lower fluorescence energy, and the involvement of charge-transfer states and the cancellation between monomer transition dipole moments suppressed the fluorescence especially when two monomers have similar fluorescence energy. The above-mentioned findings hold for all asphaltene dimers despite their diversity, which offers a theoretical interpretation for comprehending the relationship between asphaltene aggregation and its fluorescence variation. Furthermore, this work provides theoretical guidance to other research areas related to organic planar conjugated systems with multiple chromophores. Chromophore ; Asphaltene ; Monomer ; Intermolecular force ; Fluorescence ; Chemical physics ; Dimer ; Exciton ; Excited state ; Chemistry ; Photochemistry ; Materials science ; Molecule ; Polymer ; Physics ; Atomic physics ; Organic chemistry Petroleum Processing and Analysis ; Enhanced Oil Recovery Techniques ; Hydrocarbon exploration and reservoir analysis
Authors: Rayara Silva dos Santos | Pedro Henrique Poubel Mendonça da Silveira | Beatriz Cruz Bastos | Marceli do Nascimento da Conceição | Roberto Carlos da Conceição Ribeiro | Daniele Cruz Bastos
Source: Recent Progress in Materials (article, 2023-07-18)
Field: Materials Science — Polymers and Plastics

Development of Environmentally Ecofriendly Composites Based on Polypropylene/Bahia Beige Waste: Effect of Reinforcement Content on Physical, Mechanical, Chemical, and Microstructural Properties This article presents the development and characterization of environmentally friendly composites comprising polypropylene (PP) reinforced with Bahia Beige (BB) marble waste. The composites were prepared using different PP/BB weight ratios and analyzed for their chemical, physical, mechanical, microstructural, and thermal properties. X-ray fluorescence (XRF) analysis revealed the composition of BB, which exhibited a significant concentration of CaO, indicating the presence of calcite and other oxides. X-ray diffraction (XRD) analysis confirmed the presence of PP and identified calcite, dolomite, and quartz phases in the composites. Due to enhanced ceramic reinforcement, the composites displayed increased crystallinity with higher BB content. Fourier-transform infrared (FTIR) analysis demonstrated the interaction between PP and BB, with the bands corresponding to PP being replaced by bands related to BB as filler content increased. The density tests indicated a slight increase in composite density without deviating significantly from pure PP, which is advantageous for low-density applications. The hardness of the composites increased with filler content, while the impact resistance decreased notably. Scanning electron microscopy (SEM) images showed the good distribution of BB within the composites and the presence of ductile characteristics on the composite surface. The heat deflection temperature (HDT) results revealed that adding BB up to 40% by weight increased HDT, whereas a significant reduction occurred at a 50% BB content. These composites demonstrated favorable properties for engineering applications, offering a sustainable solution through utilizing natural waste resources and contributing to Brazilian sustainability efforts. Crystallinity ; Polypropylene ; Materials science ; Composite material ; Composite number ; Scanning electron microscope ; Fourier transform infrared spectroscopy ; Chemical engineering Natural Fiber Reinforced Composites ; Polymer Nanocomposites and Properties ; Innovative concrete reinforcement materials