jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Elisabetta De Vito-Francesco | Alessandro Farinelli | Qiuyue Yang | Bhawna Nagar | Ruslán Álvarez-Diduk | Arben Merkoçi | Thorsten Knutz | Alexander Haider | W. Stach | Falko Ziegenbalg | Roza Allabashi
Source: Environmental Monitoring and Assessment (article, 2022-01-24)
Field: Chemistry — Electrochemistry

An innovative autonomous robotic system for on-site detection of heavy metal pollution plumes in surface water Smart monitoring has been studied and developed in recent years to create faster, cheaper, and more user-friendly on-site methods. The present study describes an innovative technology for investigative monitoring of heavy metal pollution (Cu and Pb) in surface water. It is composed of an autonomous surface vehicle capable of semiautonomous driving and equipped with a microfluidic device for detection of heavy metals. Detection is based on the method of square wave anodic stripping voltammetry using carbon-based screen-printed electrodes (SPEs). The focus of this work was to validate the ability of the integrated system to perform on-site detection of heavy metal pollution plumes in river catchments. This scenario was simulated in laboratory experiments. The main performance characteristics of the system, which was evaluated based on ISO 15839 were measurement bias (Pb 75%, Cu 65%), reproducibility (in terms of relative standard deviation: Pb 11-18%, Cu 6-10%) and the limit of detection (4 µg/L for Pb and 7 µg/L for Cu). The lowest detectable change (LDC), which is an important performance characteristic for this application, was estimated to be 4-5 µg/L for Pb and 6-7 µg/L for Cu. The life span of an SPE averaged 39 measurements per day, which is considered sufficient for intended monitoring campaigns. This work demonstrated the suitability of the integrated system for on-site detection of Pb and Cu emissions from large and medium urban areas discharging into small water bodies. Detection limit ; Pollution ; Environmental science ; Pollutant ; Relative standard deviation ; Environmental monitoring ; Anodic stripping voltammetry ; Environmental engineering ; Environmental chemistry ; Chemistry ; Electrode ; Electrochemistry Electrochemical Analysis and Applications ; Analytical Chemistry and Sensors ; Advanced Chemical Sensor Technologies
Authors: Muhammad Hilal Kabir | Mahamed Lamine Guindo | Rongqin Chen | Fei Liu | Xinmeng Luo | Wenwen Kong
Source: Molecules (article, 2022-09-16)
Field: Chemistry — Analytical Chemistry

Deep Learning Combined with Hyperspectral Imaging Technology for Variety Discrimination of Fritillaria thunbergii Traditional Chinese herbal medicine (TCHM) plays an essential role in the international pharmaceutical industry due to its rich resources and unique curative properties. The flowers, stems, and leaves of Fritillaria contain a wide range of phytochemical compounds, including flavonoids, essential oils, saponins, and alkaloids, which may be useful for medicinal purposes. <i>Fritillaria thunbergii</i> Miq. Bulbs are commonly used in traditional Chinese medicine as expectorants and antitussives. In this paper, a feasibility study is presented that examines the use of hyperspectral imaging integrated with convolutional neural networks (CNN) to distinguish twelve (12) Fritillaria varieties (n = 360). The performance of support vector machines (SVM) and partial least squares-discriminant analysis (PLS-DA) was compared with that of convolutional neural network (CNN). Principal component analysis (PCA) was used to assess the presence of cluster trends in the spectral data. To optimize the performance of the models, cross-validation was used. Among all the discriminant models, CNN was the most accurate with 98.88%, 88.89% in training and test sets, followed by PLS-DA and SVM with 92.59%, 81.94% and 99.65%, 79.17%, respectively. The results obtained in the present study revealed that application of HSI in conjunction with the deep learning technique can be used for classification of <i>Fritillaria thunbergii</i> varieties rapidly and non-destructively. Linear discriminant analysis ; Convolutional neural network ; Hyperspectral imaging ; Artificial intelligence ; Principal component analysis ; Pattern recognition (psychology) ; Support vector machine ; Phytochemical ; Deep learning ; Mathematics ; Computer science ; Traditional medicine ; Medicine Spectroscopy and Chemometric Analyses ; Remote Sensing and Land Use ; Remote-Sensing Image Classification
Authors: Andrés Manuel González‐Ramírez | Ana Sofia Grosso | Zhang Yang | Ismael Compañón | Helena Coelho | Yoshiki Narimatsu | Henrik Clausen | Filipa Marcelo | Francisco Corzana | Ramón Hurtado‐Guerrero
Source: Nature Communications (article, 2022-05-03)
Field: Materials Science — Materials Chemistry

Structural basis for the synthesis of the core 1 structure by C1GalT1 C1GalT1 is an essential inverting glycosyltransferase responsible for synthesizing the core 1 structure, a common precursor for mucin-type O-glycans found in many glycoproteins. To date, the structure of C1GalT1 and the details of substrate recognition and catalysis remain unknown. Through biophysical and cellular studies, including X-ray crystallography of C1GalT1 complexed to a glycopeptide, we report that C1GalT1 is an obligate GT-A fold dimer that follows a S<sub>N</sub>2 mechanism. The binding of the glycopeptides to the enzyme is mainly driven by the GalNAc moiety while the peptide sequence provides optimal kinetic and binding parameters. Interestingly, to achieve glycosylation, C1GalT1 recognizes a high-energy conformation of the α-GalNAc-Thr linkage, negligibly populated in solution. By imposing this 3D-arrangement on that fragment, characteristic of α-GalNAc-Ser peptides, C1GalT1 ensures broad glycosylation of both acceptor substrates. These findings illustrate a structural and mechanistic blueprint to explain glycosylation of multiple acceptor substrates, extending the repertoire of mechanisms adopted by glycosyltransferases. Core (optical fiber) ; Basis (linear algebra) ; Computer science ; Computational biology ; Biology ; Mathematics Enzyme Structure and Function ; ATP Synthase and ATPases Research ; Biochemical and Molecular Research
Authors: Andrew M. Teale | Trygve Helgaker | Andreas Savin | Carlo Adamo | Bálint Aradi | Alexei V. Arbuznikov | Paul W. Ayers | Evert Jan Baerends | Vincenzo Barone | Patrizia Calaminici | Éric Cancès | Emily A. Carter | Pratim Kumar Chattaraj | Henry Chermette | Ilaria Ciofini | Daniel A. Crawford | Frank De Proft | John F. Dobson | Caludia Draxl | Thomas Frauenheim | Emmanuel Fromager | Patricio Fuentealba | Laura Gagliardi | Giulia Galli | Jiali Gao | Paul Geerlings | Nikitas Gidopoulous | Peter M. W. Gill | Paola Gori‐Giorgi | Andreas Görling | Tim Gould | Stefan Grimme | O. V. Gritsenko | Hans Jørgen Aa. Jensen | Erin R. Johnson | R. Jones | Martin Kaupp | Andreas M. Köster | Leeor Kronik | Anna I. Krylov | Simen Kvaal | Andre Laestadius | Mel Levy | Mathieu Lewin | Shubin Liu | Pierre‐François Loos | Neepa T. Maitra | Frank Neese | John P. Perdew | Katarzyna Pernal | Pascal Pernot | Piotr Piecuch | Elisa Rebolini | Lucia Reining | Pina Romaniello | Adrienn Ruzsinszky | Dennis R. Salahub | Matthias Scheffler | Peter Schwerdtfeger | Vicktor Staroverov | Jianwei Sun | Erik I. Tellgren | David J. Tozer | Sam Trickey | Carsten A. Ullrich | Alberto Vela | Giovanni Vignale | Tomasz A. Wesołowski | Xin Xu | Weitao Yang
Source: ChemRxiv (preprint, 2022-06-17)
Field: Materials Science — Materials Chemistry

DFT Exchange: Sharing Perspectives on the Workhorse of Quantum Chemistry and Materials Science In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 300 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 776 entries, the paper represents a broad snapshot of DFT, anno 2022. Snapshot (computer storage) ; Density functional theory ; Computer science ; Field (mathematics) ; Chemistry ; Nanotechnology ; Computational chemistry ; Materials science ; Mathematics ; Database ; Pure mathematics Machine Learning in Materials Science ; History and advancements in chemistry ; Computational Drug Discovery Methods
Authors: Igor D. Zlotnikov | Maksim A. Vigovskiy | Maria P. Davydova | Milan R. Danilov | Uliana Dyachkova | Olga Grigorieva | Еlena V. Kudryashova
Source: International Journal of Molecular Sciences (article, 2022-12-18)
Field: Materials Science — Biomaterials

Mannosylated Systems for Targeted Delivery of Antibacterial Drugs to Activated Macrophages Macrophages are a promising target for drug delivery to influence macrophage-associated processes in the body, namely due to the presence of resistant microorganisms in macrophages. In this work, a series of mannosylated carriers based on mannan, polyethylenimine (PEI) and cyclodextrin (CD) was synthesized. The molecular architecture was studied using FTIR and <sup>1</sup>H NMR spectroscopy. The particle size, from small 10-50 nm to large 500 nm, depending on the type of carrier, is potentially applicable for the creation of various medicinal forms: intravenous, oral and inhalation. Non-specific capture by cells with a simultaneous increase in selectivity to CD206+ macrophages was achieved. ConA was used as a model mannose receptor, binding galactosylated (CD206 non-specific) carriers with constants of the order of 10<sup>4</sup> M<sup>-1</sup> and mannosylated conjugates of 10<sup>6</sup>-10<sup>7</sup> M<sup>-1</sup>. The results of such primary "ConA-screening" of ligands are in a good agreement in terms of the comparative effectiveness of the interaction of ligands with the CD206+ macrophages: non-specific (up to 10%) absorption of highly charged and small particles; weakly specific uptake of galactosylated polymers (up to 50%); and high affine capture (more than 70-80%) of the ligands with grafted trimannoside was demonstrated using the cytometry method. Double and multi-complexes of antibacterials (moxifloxacin with its adjuvants from the class of terpenoids) were proposed as enhanced forms against resistant pathogens. In vivo pharmacokinetic experiments have shown that polymeric carriers significantly improve the efficiency of the antibiotic: the half-life of moxifloxacin is increased by 2-3 times in conjugate-loaded forms, bio-distribution to the lungs in the first hours after administration of the drug is noticeably greater, and, after 4 h of observation, free moxifloxacin was practically removed from the lungs of rats. Although, in polymer systems, its content is significant-1.2 µg/g. Moreover, the importance of the covalent crosslinking carrier with mannose label was demonstrated. Thus, this paper describes experimental, scientifically based methods of targeted drug delivery to macrophages to create enhanced medicinal forms. Chemistry ; Drug delivery ; Pharmacology ; Medicine Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; RNA Interference and Gene Delivery
Authors: Swati Gupta | Nilimamayee Samal
Source: Egyptian Journal of Forensic Sciences (review, 2022-03-17)
Field: Chemistry — Spectroscopy

Application of direct analysis in real-time mass spectrometry (DART-MS) in forensic science: a comprehensive review Abstract Background As the rate of crime is constantly increasing, the workload on the forensic analyst also piles up. The availability of a limited number of seized samples makes it crucial to directly analyze the sample, thereby preventing wastage in the prior steps of sample preparation. Due to such needs, the forensic community is consistently working on broadening the usage of direct analysis in real-time mass spectrometry (DART-MS). DART-MS is a relatively new technique for rapid mass spectral analysis. Its use for chemical analysis credits its ability to analyze the sample at atmospheric pressure. Main body This article gives insight into the ionization mechanisms, data analysis tools, and the use of hyphenated techniques like thermal-desorption-DART-MS, infrared-thermal-desorption-DART-MS, Joule-heating thermal-desorption-DART-MS, etc. This review summarizes the applications of DART-MS in the field of Forensic Science reported from 2005 to 2021. The applications include analysis of drugs, warfare agents, gun-shot residues, ink differentiation, and other forensically relevant samples. The paper also presents the relation between the type of DART-MS technique and the ionization mode used for a particular class of compounds. Conclusion The review follows that the high-resolution mass-spectrometers or low-resolution mass-spectrometers systems in the positive or negative mode were highly dependent on the type of analyte under investigation. Drugs, inks, dyes, and paints were mainly analyzed using the positive ionization mode in the HRMS technique. The examinations of fire accelerants predominantly used the positive ionization mode in the LRMS technique. Moreover, the limit of detection values obtained from the qualitative screening of street drugs were of ppb level, indicating high sensitivity of DART-MS. Considering the work done in the past years, there are potential future research needs of this technology, especially in forensic science. Graphical Abstract DART ion source ; Dart ; Mass spectrometry ; Thermal desorption ; Analytical Chemistry (journal) ; Ambient ionization ; Chemistry ; Ionization ; Computer science ; Chemical ionization ; Desorption ; Chromatography ; Electron ionization Mass Spectrometry Techniques and Applications ; Pesticide Residue Analysis and Safety ; Isotope Analysis in Ecology
Authors: Alastair Skeffington | Marc Gentzel | André Ohara | Alexander Milentyev | Christoph Heintze | Lorenz Böttcher | Stefan Görlich | Andrej Shevchenko | Nicole Poulsen | Nils Kröger
Source: The Plant Journal (article, 2022-04-11)
Field: Materials Science — Biomaterials

Shedding light on silica biomineralization by comparative analysis of the silica‐associated proteomes from three diatom species Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species-specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis of the extracts identified 92 proteins that we name 'soluble silicome proteins' (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In-depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall. Diatom ; Thalassiosira pseudonana ; Frustule ; Biomineralization ; Proteome ; Biology ; Cell wall ; Morphogenesis ; Sequence (biology) ; Biochemistry ; Botany ; Gene ; Ecology Diatoms and Algae Research ; Protist diversity and phylogeny ; Paleontology and Stratigraphy of Fossils
Authors: Jersson X. Leon‐Medina | Diego Alexander Tibaduiza Burgos | Martha Cuenca | Dreidy Vásquez
Source: IEEE Access (article, 2022-01-01)
Field: Chemistry — Electrochemistry

Classification of As, Pb and Cd Heavy Metal Ions Using Square Wave Voltammetry, Dimensionality Reduction and Machine Learning The detection and classification of heavy metals is a growing need to guarantee the quality of process water in different industries. However, the official methodologies to evaluate the presence of these contaminants require samples pre-processing, making them time-consuming and expensive; these elements do not allow online monitoring. For this reason, new technologies are required for online monitoring and evaluation. In this work, a new methodology is presented for the detection and classification of different heavy metal ions such as: As, Pb and Cd. Commercial graphite sensors modified with 2D molybdenite were used applying an electroanalytical technique of square wave voltammetry. Subsequently, signal processing based on pattern recognition and machine learning methods was carried out. This classification methodology includes the following steps: data display and arrangement, dimensionality reduction through the t-distributed stochastic neighbor embedding (t-SNE) method, which serves as feature extraction, and the support vector machines (SVM) method as a classifier. The validation is carried out with a data set of 118 aqueous samples. Leave one out cross-validation (LOOCV) was used to obtain classification accuracy. The results showed a classification accuracy of 98.31% with only two errors of the experimental validation with this data set. It is concluded that this methodology is a useful tool for detecting the presence of these ions in aqueous samples with MoS2-2D. Support vector machine ; Dimensionality reduction ; Computer science ; Artificial intelligence ; Pattern recognition (psychology) ; Feature extraction ; Voltammetry ; Machine learning ; Data mining ; Chemistry ; Electrochemistry Electrochemical Analysis and Applications ; Advanced Chemical Sensor Technologies ; Water Quality Monitoring and Analysis
Authors: Lucero Azusena Castillejos-Mijangos | Aracely Acosta-Caudillo | Tzayhrí Gallardo‐Velázquez | Guillermo Osorio‐Revilla | Cristian Jiménez‐Martínez
Source: Foods (review, 2022-02-17)
Field: Chemistry — Analytical Chemistry

Uses of FT-MIR Spectroscopy and Multivariate Analysis in Quality Control of Coffee, Cocoa, and Commercially Important Spices Nowadays, coffee, cocoa, and spices have broad applications in the food and pharmaceutical industries due to their organoleptic and nutraceutical properties, which have turned them into products of great commercial demand. Consequently, these products are susceptible to fraud and adulteration, especially those sold at high prices, such as saffron, vanilla, and turmeric. This situation represents a major problem for industries and consumers' health. Implementing analytical techniques, i.e., Fourier transform mid-infrared (FT-MIR) spectroscopy coupled with multivariate analysis, can ensure the authenticity and quality of these products since these provide unique information on food matrices. The present review addresses FT-MIR spectroscopy and multivariate analysis application on coffee, cocoa, and spices authentication and quality control, revealing their potential use and elucidating areas of opportunity for future research. Nutraceutical ; Multivariate analysis ; Organoleptic ; Food products ; Quality (philosophy) ; Food quality ; Biotechnology ; Business ; Food science ; Agricultural science ; Mathematics ; Environmental science ; Chemistry ; Statistics ; Biology Spectroscopy and Chemometric Analyses ; Phytochemicals and Antioxidant Activities ; Dye analysis and toxicity
Authors: Violina T. Angelova | Tania Pencheva | Nikolay Vassilev | Elena Kalcheva-Yovkova | Rositsa Mihaylova | B. N. Petrov | Violeta Valcheva
Source: Antibiotics (article, 2022-04-22)
Field: Chemistry — Organic Chemistry

Development of New Antimycobacterial Sulfonyl Hydrazones and 4-Methyl-1,2,3-thiadiazole-Based Hydrazone Derivatives Fifteen 4-methyl-1,2,3-thiadiazole-based hydrazone derivatives <b>3a</b>-<b>d</b> and sulfonyl hydrazones <b>5a</b>-<b>k</b> were synthesized. They were characterized by <sup>1</sup>H-NMR, <sup>13</sup>C NMR, and HRMS. <i>Mycobacterium tuberculosis</i> strain H37Rv was used to assess their antimycobacterial activity. All compounds demonstrated significant minimum inhibitory concentrations (MIC) from 0.07 to 0.32 µM, comparable to those of isoniazid. The cytotoxicity was evaluated using the standard MTT-dye reduction test against human embryonic kidney cells HEK-293T and mouse fibroblast cell line CCL-1. 4-Hydroxy-3-methoxyphenyl substituted 1,2,3-thiadiazole-based hydrazone derivative <b>3d</b> demonstrated the highest antimycobacterial activity (MIC = 0.0730 µM) and minimal associated cytotoxicity against two normal cell lines (selectivity index SI = 3516, HEK-293, and SI = 2979, CCL-1). The next in order were sulfonyl hydrazones <b>5g</b> and <b>5k</b> with MIC 0.0763 and 0.0716 µM, respectively, which demonstrated comparable minimal cytotoxicity. All compounds were subjected to ADME/Tox computational predictions, which showed that all compounds corresponded to Lipinski's Ro5, and none were at risk of toxicity. The suitable scores of molecular docking performed on two crystallographic structures of enoyl-ACP reductase (InhA) provide promising insight into possible interaction with the InhA receptor. The 4-methyl-1,2,3-thiadiazole-based hydrazone derivatives and sulfonyl hydrazones proved to be new classes of lead compounds having the potential of novel candidate antituberculosis drugs. Antimycobacterial ; Hydrazone ; Sulfonyl ; Chemistry ; Combinatorial chemistry ; Medicinal chemistry ; Organic chemistry ; Medicine ; Tuberculosis ; Mycobacterium tuberculosis Synthesis and biological activity ; Synthesis and Biological Evaluation ; Phenothiazines and Benzothiazines Synthesis and Activities
Authors: Xavier Le Guével | K. David Wegner | Christian Würth | Vladimir A. Baulin | Benjamin Musnier | Véronique Josserand | Ute Resch‐Genger | Jean‐Luc Coll
Source: Chemical Communications (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Tailoring the SWIR emission of gold nanoclusters by surface ligand rigidification and their application in 3D bioimaging A detailed description of photophysical properties of SWIR emitting probes and their use for pseudo-3D views of vascular blood vessels. Nanoclusters ; Nanotechnology ; Ligand (biochemistry) ; Materials science ; Aggregation-induced emission ; Adsorption ; Chemistry ; Fluorescence ; Organic chemistry ; Optics ; Physics Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications ; Advanced Nanomaterials in Catalysis