jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Elena Abbotto | Beatrice Casini | Francesco Piacente | Naomi Scarano | Elena Cerri | Michele Tonelli | Cecilia Astigiano | Enrico Millo | Laura Sturla | Santina Bruzzone | Elena Cichero
Source: Pharmaceuticals (article, 2023-09-18)
Field: Chemistry — Organic Chemistry

Novel Thiazole-Based SIRT2 Inhibitors Discovered via Molecular Modelling Studies and Enzymatic Assays Recently, the development of sirtuin small molecule inhibitors (SIRTIs) has been gaining attention for the treatment of different cancer types, but also to contrast neurodegenerative disease, diabetes, and autoimmune syndromes. In the search for SIRT2 modulators, the availability of several X-crystallographic data regarding SIRT2-ligand complexes has allowed for setting up a structure-based study, which is herein presented. A set of 116 SIRT2 inhibitors featuring different chemical structures has been collected from the literature and used for molecular docking studies involving 4RMG and 5MAT PDB codes. The information found highlights key contacts with the SIRT2 binding pocket such as Van der Waals and π-π stacking with Tyr104, Phe119, Phe234, and Phe235 in order to achieve high inhibitory ability values. Following the preliminary virtual screening studies, a small in-house library of compounds (<b>1a</b>-<b>7a</b>), previously investigated as putative HSP70 inhibitors, was described to guide the search for dual-acting HSP70/SIRT2 inhibitors. Biological and enzymatic assays validated the whole procedure. Compounds <b>2a</b> and <b>7a</b> were found to be the most promising derivatives herein proposed. SIRT2 ; Virtual screening ; Protein Data Bank (RCSB PDB) ; Computational biology ; Small molecule ; Chemistry ; Sirtuin ; Docking (animal) ; Enzyme ; Cheminformatics ; Combinatorial chemistry ; Drug discovery ; Biochemistry ; Biology ; Medicine ; Computational chemistry ; NAD+ kinase Synthesis and biological activity ; Sirtuins and Resveratrol in Medicine ; Computational Drug Discovery Methods
Authors: Cong Hu | Meng Cheng | Wenqi Jin | Jian Han | Zhihua Yang | Shilie Pan
Source: Research (article, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A Cation-Driven Approach toward Deep-Ultraviolet Nonlinear Optical Materials The design of new materials with special performances is still a great challenge, especially for the deep-ultraviolet nonlinear optical materials in which it is difficult to balance large bandgaps and strong second harmonic generation responses due to their inverse relationship. Cation variation not only influences the whole structure frameworks but also directly participates in the formation of electronic structures, both of which could lead to the uncontrollability of the properties of the designed materials. Here, a novel approach, aiming at purposeful and foreseeable material designs, is proposed to characterize the role of cations. By the verification of several series of borates, the influences of cation variation on property changes are explored systematically. Accordingly, a feasible strategy of designing deep-ultraviolet nonlinear optical materials by substituting barium for lead has been concluded, which could obviously blue-shift the ultraviolet cutoff edge and maintain the relatively strong second harmonic generation response (more than 2 times of KH<sub>2</sub>PO<sub>4</sub>), achieving the property optimization, and especially works efficiently in fluorooxoborates. The property optimization design strategy and the cation characterization method are not only helpful in exploring nonlinear optical materials but also enlightening in material design and selection. Ultraviolet ; Nonlinear system ; Nonlinear optical ; Property (philosophy) ; Characterization (materials science) ; Materials science ; Second-harmonic generation ; Material Design ; Computer science ; Optoelectronics ; Nanotechnology ; Optics ; Physics ; Composite material ; Laser Crystal Structures and Properties ; Perovskite Materials and Applications ; Nonlinear Optical Materials Research
Authors: M. Akiful Haque | Akash Marathakam | Ritesh Rana | Samar J. Almehmadi | Vishal Tambe | Manoj S. Charde | Fahadul Islam | Falak A. Siddiqui | Giulia Culletta | Anna Maria Almerico | Marco Tutone | Sharuk L. Khan
Source: Molecules (article, 2023-01-04)
Field: Chemistry — Organic Chemistry

Fighting Antibiotic Resistance: New Pyrimidine-Clubbed Benzimidazole Derivatives as Potential DHFR Inhibitors The present work describes the design and development of seventeen pyrimidine-clubbed benzimidazole derivatives as potential dihydrofolate reductase (DHFR) inhibitors. These compounds were filtered by using ADMET, drug-likeness characteristics calculations, and molecular docking experiments. Compounds <b>27</b>, <b>29</b>, <b>30</b>, <b>33</b>, <b>37</b>, <b>38</b>, and <b>41</b> were chosen for the synthesis based on the results of the in silico screening. Each of the synthesized compounds was tested for its in vitro antibacterial and antifungal activities using a variety of strains. All the compounds showed antibacterial properties against Gram-positive bacteria (<i>Staphylococcus aureus</i> and <i>Staphylococcus pyogenes</i>) as well as Gram-negative bacteria (<i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i>). Most of the compounds either had a higher potency than chloramphenicol or an equivalent potency to ciprofloxacin. Compounds <b>29</b> and <b>33</b> were effective against all the bacterial and fungal strains. Finally, the 1,2,3,4-tetrahydropyrimidine-2-thiol derivatives with a 6-chloro-2-(chloromethyl)-1<i>H</i>-benzo[<i>d</i>]imidazole moiety are potent enough to be considered a promising lead for the discovery of an effective antibacterial agent. Benzimidazole ; Chemistry ; Staphylococcus aureus ; Dihydrofolate reductase ; Antibacterial activity ; Pseudomonas aeruginosa ; Escherichia coli ; Ciprofloxacin ; Bacteria ; Microbiology ; Antibiotics ; Combinatorial chemistry ; Biochemistry ; Biology ; Enzyme ; Organic chemistry Synthesis and biological activity ; Synthesis and Biological Evaluation ; Quinazolinone synthesis and applications
Authors: Junhang Tian | Jihuan Xie | Weidong Zhuang
Source: Materials (review, 2023-03-08)
Field: Materials Science — Materials Chemistry

Recent Advances in Multi-Site Luminescent Materials: Design, Identification and Regulation The development of novel phosphor materials with excellent performance and modification of their photoluminescence to meet the higher requirements for applications are the essential research subjects for luminescent materials. Multi-site luminescent materials with crystallographic sites for the activator ions that broaden the tunable range of luminescent spectra and even enhance the luminescent performance have attracted significant attention in the pursuit of high-quality luminescence for white light-emitting diodes. Here, we summarize multi-site luminescence characteristics based on the different kinds of host and activator ions, introduce the identifications of multi-site activator ions via optical analysis, provide a structural analysis and theoretical calculation methods, and introduce the regulation strategies and advance applications of multi-site phosphors. The review reveals the relationship between crystal structure and luminescent properties and discusses future opportunities for multi-site phosphors. This will provide guidance for the design and development of luminescent materials or other materials science. Luminescence ; Phosphor ; Activator (genetics) ; Materials science ; Photoluminescence ; Nanotechnology ; Ion ; Crystal structure ; Optoelectronics ; Chemistry ; Crystallography Luminescence Properties of Advanced Materials ; Perovskite Materials and Applications ; Advanced Photocatalysis Techniques
Authors: Xuan Chu | Kun Zhang | Hongyu Wei | Zhiyu Ma | Fu Han | Pu Miao | Hongzhe Jiang | Hongli Liu
Source: Frontiers in Plant Science (article, 2023-06-02)
Field: Chemistry — Analytical Chemistry

A Vis/NIR spectra-based approach for identifying bananas infected with Colletotrichum musae Introduction Anthracnose of banana caused by Colletotrichum species is one of the most serious post-harvest diseases, which can cause significant yield losses. Clarifying the infection mechanism of the fungi using non-destructive methods is crucial for timely discriminating infected bananas and taking preventive and control measures. Methods This study presented an approach for tracking growth and identifying different infection stages of the C. musae in bananas using Vis/NIR spectroscopy. A total of 330 banana reflectance spectra were collected over ten consecutive days after inoculation, with a sampling rate of 24 h. The four-class and five-class discriminant patterns were designed to examine the capability of NIR spectra in discriminating bananas infected at different levels (control, acceptable, moldy, and highly moldy), and different time at early stage (control and days 1-4). Three traditional feature extraction methods, i.e. PC loading coefficient (PCA), competitive adaptive reweighted sampling (CARS) and successive projections algorithm (SPA), combining with two machine learning methods, i.e. partial least squares discriminant analysis (PLSDA) and support vector machine (SVM), were employed to build discriminant models. One-dimensional convolutional neural network (1D-CNN) without manually extracted feature parameters was also introduced for comparison. Results The PCA-SVM and·SPA-SVM models had good performance with identification accuracies of 93.98% and 91.57%, 94.47% and 89.47% in validation sets for the four- and five-class patterns, respectively. While the 1D-CNN models performed the best, achieving an accuracy of 95.18% and 97.37% for identifying infected bananas at different levels and time, respectively. Discussion These results indicate the feasibility of identifying banana fruit infected with C. musae using Vis/NIR spectra, and the resolution can be accurate to one day. Biology ; Colletotrichum ; Botany ; Computational biology Spectroscopy and Chemometric Analyses ; Banana Cultivation and Research ; Plant Pathogens and Fungal Diseases
Authors: Trevor David Rhone | Romakanta Bhattarai | Haralambos Gavras | Bethany Lusch | Misha Salim | Marios Mattheakis | Daniel T. Larson | Yoshiharu Krockenberger | Efthimios Kaxiras
Source: Advanced Theory and Simulations (article, 2023-04-16)
Field: Materials Science — Materials Chemistry

Artificial Intelligence Guided Studies of van der Waals Magnets Abstract A materials informatics framework to explore a large number of candidate van der Waals (vdW) materials is developed. In particular, in this study a large space of monolayer transition metal halides is investigated by combining high‐throughput density functional theory calculations and artificial intelligence (AI) to accelerate the discovery of stable materials and the prediction of their magnetic properties. The formation energy is used as a proxy for chemical stability. Semi‐supervised learning is harnessed to mitigate the challenges of sparsely labeled materials data in order to improve the performance of AI models. This approach creates avenues for the rapid discovery of chemically stable vdW magnets by leveraging the ability of AI to recognize patterns in data, to learn mathematical representations of materials from data and to predict materials properties. Using this approach, previously unexplored vdW magnetic materials with potential applications in data storage and spintronics are identified. van der Waals force ; Spintronics ; Chemical space ; Magnet ; Density functional theory ; Nanotechnology ; Materials science ; Computer science ; Materials informatics ; Stability (learning theory) ; Artificial intelligence ; Ferromagnetism ; Machine learning ; Physics ; Chemistry ; Health informatics ; Computational chemistry ; Condensed matter physics ; Molecule ; Quantum mechanics Machine Learning in Materials Science ; 2D Materials and Applications ; Ferroelectric and Negative Capacitance Devices
Authors: Razan Ibrahim | Violet Kasabri | Suhair Sunoqrot | Dana Shalabi | Rema Alkhateeb | Yusuf Al‐Hiari
Source: Asian Pacific Journal of Cancer Prevention (article, 2023-03-01)
Field: Materials Science — Biomaterials

Preparation and Characterization of Rutin-Encapsulated Polymeric Micelles and Studies of Synergism with Bioactive Benzoic Acids and Triazolofluoroquinolones as Anticancer Nanomedicines Rutin loading in micelles was achieved with a loading efficiency of 59.5 ± 2.9%. The particle size of the micelles was found to be 18 ± 2 nm. Though Rutin loaded nanomicelles were of minimal DPPH radical scavenging activity; they had nitrogen oxide (NO) radical scavenging activity in lipopolysaccharide-induced RAW264.7 macrophages with equipotency to indomethacin (IC50 values (µM) 73.03 vs. 60.88; p=0.057). Remarkably nano-micelle formulation of rutin was proved of significantly more potent antineoplastic bioactivity with submicro-nanomolar affinities in the 6 cancer cell lines vs. both free rutin's and cisplatin's (except A549 lung cancer cell line). Rrutin nanomicelles chemo-sensitized all selected 8 cotreatments with BA derivatives and TFQs and, thus reducing the dose used against breast cancer MCF7 cells to submicro-nanomolar affinities of greater potencies than cisplatin's. Except for Triazolo-4-anisidine cipro butyl acid in PANC1, 2-Amino-3,5-Di iodo BA in A375 and 4-Nitrophenol in A549 incubations; rutin loaded nanomicelles chemosensitized 7/8 cotreating selected benzoic acid (BAs) derivatives and TFQs and chemosensitized pancreatic PANC1, skin A375 and lung A549 cancer cell lines, thus reducing the dose to submicro-nanomolar affinities of greater potencies than cisplatin's. Rutin loaded nanomicelles chemosensitize 6/8 cotreating selected benzoic acid (BA) derivatives and TFQs (except for 2-Amino-5-Bromo Benzoic Acid and Triazolo-4-anisidine cipro butyl acid), thus reducing the dose used against resistant CACO2 colorectal cancer cells. Rutin ; Micelle ; Chemistry ; Nuclear chemistry ; Antioxidant ; DPPH ; Amphiphile ; Cytotoxicity ; Combinatorial chemistry ; Organic chemistry ; Biochemistry ; Aqueous solution ; Copolymer ; In vitro ; Polymer Nanoparticle-Based Drug Delivery ; Ginkgo biloba and Cashew Applications ; Chemotherapy-induced cardiotoxicity and mitigation
Authors: Mahsa Alishiri | Maryam Gonbadi | Mehdi Narimani | Seyyed Amirreza Abdollahi | Negin Shahsavaripour
Source: Scientific Reports (article, 2023-09-02)
Field: Chemistry — Organic Chemistry

Optimization of process parameters for trimethoprim and sulfamethoxazole removal by magnetite-chitosan nanoparticles using Box–Behnken design The contamination of the aquatic environment with antibiotics is among the major and developing problems worldwide. The present study investigates the potential of adsorbent magnetite-chitosan nanoparticles (Fe<sub>3</sub>O<sub>4</sub>/CS NPs) for removing trimethoprim (TMP) and sulfamethoxazole (SMX). For this purpose, Fe<sub>3</sub>O<sub>4</sub>/CS NPs were synthesized by the co-precipitation method, and the adsorbent characteristics were investigated using XRD, SEM, TEM, pH<sub>zpc</sub>, FTIR, and VSM. The effect of independent variables (pH, sonication time, adsorbent amount, and analyte concentration) on removal performance was modeled and evaluated by Box-Behnken design (BBD). The SEM image of the Fe<sub>3</sub>O<sub>4</sub>/CS adsorbent showed that the adsorbent had a rough and irregular surface. The size of Fe<sub>3</sub>O<sub>4</sub>/CS crystals was about 70 nm. XRD analysis confirmed the purity and absence of impurities in the adsorbent. TEM image analysis showed that the adsorbent had a porous structure, and the particle size was in the range of nanometers. In VSM, the saturation magnetization of Fe<sub>3</sub>O<sub>4</sub>/CS adsorbent was 25 emu g<sup>-1</sup> and the magnet could easily separate the adsorbent from the solution. The results revealed that the optimum condition was achieved at a concentration of 22 mg L<sup>-1</sup>, a sonication time of 15 min, an adsorbent amount of 0.13 g/100 mL, and a pH of 6. Among different solvents (i.e., ethanol, acetone, nitric acid, and acetonitrile), significant desorption of TMP and SMX was achieved using ethanol. Also, results confirmed that Fe<sub>3</sub>O<sub>4</sub>/CS NPs can be used for up to six adsorption/desorption cycles. In addition, applying the Fe<sub>3</sub>O<sub>4</sub>/CS NPs on real water samples revealed that Fe<sub>3</sub>O<sub>4</sub>/CS NPs could remove TMP and SMX in the 91.23-95.95% range with RSD (n = 3) < 4. Overall, the Fe<sub>3</sub>O<sub>4</sub>/CS NPs exhibit great potential for removing TMP and SMX antibiotics from real water samples. Adsorption ; Box–Behnken design ; Sonication ; Desorption ; Nuclear chemistry ; Chitosan ; Magnetite ; Materials science ; Response surface methodology ; Particle size ; Chromatography ; Methanol ; Chemistry ; Organic chemistry ; Metallurgy Nanomaterials for catalytic reactions ; Pharmaceutical and Antibiotic Environmental Impacts ; Advanced Photocatalysis Techniques
Authors: Donald R. Baer | John F. Watts | Alberto Herrera‐Gómez | Karen J. Gaskell
Source: Surface and Interface Analysis (article, 2023-01-19)
Field: Materials Science — Surfaces, Coatings and Films

Evolving efforts to maintain and improve XPS analysis quality in an era of increasingly diverse uses and users Based on literature analysis, X‐ray photoelectron spectroscopy (XPS) use continues to increase exponentially. This increased use is accompanied by anecdotal reports and systematic analyses indicating a growing presence of significantly flawed data analyses. Recognition of this problem within the surface analysis community has increased with an understanding that both inexperienced users and increased use of XPS outside the surface analysis community contribute to the problem. The XPS community has initiated several efforts to help address the problem, which is not unique to XPS. This paper describes some of the specific problems identified and some of the community efforts intended to address them. Here, we describe activities focused on three specific issues: (i) requests for detailed guides and protocols and bite‐sized versions of information for non‐experts, (ii) incomplete data and analysis reporting, and (iii) the high rate of peak fitting problems. A 2019 survey identified the need for guides, protocols, and standards to assist XPS users. One set of such guides has been published, and another is being assembled. Providing incremental bites of useful information is the goal of a series of papers on specific challenges to surface analysis with example solutions has been initiated as Notes and Insights papers in Surface and Interface Analysis . Examination of XPS‐containing papers finds that information to establish the credibility and reproducibility of XPS results is often very incomplete. Unfortunately, ISO and ASTM standards require an amount of parameter reporting that seems excessive and unrealistic for many research publications. Initial approaches to develop and distribute a graded approach to parameter reporting are briefly described. Multiple efforts are underway to address the high rate of problems associated with photoelectron peak fitting. These include guides to peak fitting, guides to peak identification and fitting for specific elements, and the development of a peak fitting social network. The fitting social network is designed to facilitate interactions between new and experienced XPS users; analysts trying to fit XPS data (for publication or other reasons) can ask questions and establish dynamic conversations. Encouraging and enabling high‐quality XPS analysis and reporting requires several different types of effort from all members of the surface and interface analysis community. X-ray photoelectron spectroscopy ; Credibility ; Set (abstract data type) ; Computer science ; Quality (philosophy) ; Data science ; Political science ; Engineering ; Law ; Chemical engineering Electron and X-Ray Spectroscopy Techniques ; Advanced Photocatalysis Techniques ; Recycling and Waste Management Techniques
Authors: Jiangui Zhao | Ning Chen | Tingyu Zhu | Xuerong Zhao | Ming Yuan | Zhiqiang Wang | Guo‐Liang Wang | Zhiwei Li | Huiling Du
Source: Plants (article, 2023-08-16)
Field: Chemistry — Analytical Chemistry

Simultaneous Quantification and Visualization of Photosynthetic Pigments in Lycopersicon esculentum Mill. under Different Levels of Nitrogen Application with Visible-Near Infrared Hyperspectral Imaging Technology Leaf photosynthetic pigments play a crucial role in evaluating nutritional elements and physiological states. In facility agriculture, it is vital to rapidly and accurately obtain the pigment content and distribution of leaves to ensure precise water and fertilizer management. In our research, we utilized chlorophyll a (Chla), chlorophyll b (Chlb), total chlorophylls (Chls) and total carotenoids (Cars) as indicators to study the variations in the leaf positions of <i>Lycopersicon esculentum</i> Mill. Under 10 nitrogen concentration applications, a total of 2610 leaves (435 samples) were collected using visible-near infrared hyperspectral imaging (VNIR-HSI). In this study, a "coarse-fine" screening strategy was proposed using competitive adaptive reweighted sampling (CARS) and the iteratively retained informative variable (IRIV) algorithm to extract the characteristic wavelengths. Finally, simultaneous and quantitative models were established using partial least squares regression (PLSR). The CARS-IRIV-PLSR was used to create models to achieve a better prediction effect. The coefficient determination (R<sup>2</sup>), root mean square error (RMSE) and ratio performance deviation (RPD) were predicted to be 0.8240, 1.43 and 2.38 for Chla; 0.8391, 0.53 and 2.49 for Chlb; 0.7899, 2.24 and 2.18 for Chls; and 0.7577, 0.27 and 2.03 for Cars, respectively. The combination of these models with the pseudo-color image allowed for a visual inversion of the content and distribution of the pigment. These findings have important implications for guiding pigment distribution, nutrient diagnosis and fertilization decisions in plant growth management. Hyperspectral imaging ; Partial least squares regression ; Lycopersicon ; VNIR ; Chlorophyll ; Chlorophyll a ; Carotenoid ; Mean squared error ; Photosynthesis ; Photosynthetic pigment ; Multispectral image ; Mathematics ; Biological system ; Horticulture ; Botany ; Artificial intelligence ; Computer science ; Biology ; Statistics Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Remote Sensing in Agriculture