jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hang Yang | Yao Zheng | Keli Yang | Chuanhao Wang | Mochenxuan Li | Yanming Zhang | Jianyu Yan | Rongxue Lv | Yongchuang Wang | Anhua Huang | Daozuan Zhang | Wei Li | Yuelin Wu | Zhenyuan Miao
Source: Chemistry & Biodiversity (article, 2024-01-24)
Field: Chemistry — Organic Chemistry

Synthesis and Antibacterial Evaluation of Novel Psoralen Derivatives against Methicillin‐Resistant <i>Staphylococcus aureus</i> (MRSA) Today, the bacterial infections caused by multidrug-resistant pathogens seriously threaten human health. Thereby, there is an urgent need to discover antibacterial drugs with novel mechanism. Here, novel psoralen derivatives had been designed and synthesized by a scaffold hopping strategy. Among these targeted twenty-five compounds, compound ZM631 showed the best antibacterial activity against methicillin-resistant S. aureus (MRSA) with the low MIC of 1 μg/mL which is 2-fold more active than that of the positive drug gepotidacin. Molecular docking study revealed that compound ZM631 fitted well in the active pockets of bacterial S. aureus DNA gyrase and formed a key hydrogen bond binding with the residue ASP-1083. These findings demonstrated that the psoralen scaffold could serve as an antibacterial lead compound for further drug development against multidrug-resistant bacterial infections. DNA gyrase ; Staphylococcus aureus ; Chemistry ; Antibacterial activity ; Psoralen ; Microbiology ; Multiple drug resistance ; Methicillin-resistant Staphylococcus aureus ; Ciprofloxacin ; Antibiotics ; Drug ; Docking (animal) ; Combinatorial chemistry ; Bacteria ; Pharmacology ; Escherichia coli ; DNA ; Biochemistry ; Biology ; Medicine Synthesis and biological activity ; Multicomponent Synthesis of Heterocycles ; Cancer therapeutics and mechanisms
Authors: Zhixin Liu | Kai Wang | Yongqiang Wu | Hanxiao Zhang | Tianyi Hao | Hongyang Qi | Bosong Liu
Source: Polymers (article, 2024-05-21)
Field: Materials Science — Polymers and Plastics

A Novel Method to Characterize the Damping Capacity of EPDM/CIIR Blends Using Vibrating Rubber Balls An experimental device fixed with a laser displacement sensor was assembled to investigate the rebound behaviors and damping mechanism of rubber balls prepared with ethylene-propylene-diene monomer (EPDM)/chlorinated butyl rubber (CIIR) blends. The result showed that a prediction model was proposed to characterize the damping capacity by using the rebound height of the rubber balls. The lower rebound height corresponded to better damping capacity. A modified equation relating to the rebound height has been obtained from the theoretical derivation on the basis of the dynamic mechanical analysis, showing that the rebound height was affected by the deformation frequency, the external excitation, and the nature of rubber blends. Furthermore, the energy dissipation rate (EDR), defined by the ratio of the height loss to the rebound time, was proposed to further characterize the damping capacity. The EDR value was shown to be highest for the pure CIIR and lowest for the pure EPDM, exhibiting a decreasing trend with the increase in EPDM content in the rubber blends. It can be expected that the damping capacity of the EPDM/CIIR blends decreases with the decrease in external excitation, the conclusion of which plays a key role in the formulation design of viscoelastic damping rubber materials. Materials science ; Natural rubber ; Composite material ; Dissipation ; Viscoelasticity ; Butyl rubber ; Damping capacity ; EPDM rubber ; Loss factor ; Deformation (meteorology) ; Displacement (psychology) ; Ethylene propylene rubber ; Polymer ; Thermodynamics ; Copolymer Polymer Nanocomposites and Properties ; Rheology and Fluid Dynamics Studies ; Polymer crystallization and properties
Authors: Hailey G. Lynch | Aaron Bjarnason | Daniel J. Laky | Cameron J. Brown | Alexander W. Dowling
Source: Systems and Control Transactions (article, 2024-07-09)
Field: Materials Science — Materials Chemistry

Optimizing Batch Crystallization with Model-based Design of Experiments Adaptive and self-optimizing intelligent systems such as digital twins are increasingly important in science and engineering. Digital twins utilize mathematical models to provide added precision to decision-making. However, physics-informed models are challenging to build, calibrate, and validate with existing data science methods. Model-based design of experiments (MBDoE) is a popular framework for optimizing data collection to maximize parameter precision in mathematical models and digital twins. In this work, we apply MBDoE, facilitated by the open-source package Pyomo.DoE, to train and validate mathematical models for batch crystallization. We quantitatively examined the estimability of the model parameters for experiments with different cooling rates. This analysis provides a quantitative explanation for the heuristic of using multiple experiments at different cooling rates. Computer science ; Heuristic ; Design of experiments ; Experimental data ; Artificial intelligence ; Mathematics Crystallization and Solubility Studies ; Machine Learning in Materials Science ; Process Optimization and Integration
Authors: Tanja Holstein | Pieter Verschaffelt | Tim Van Den Bossche | Simon Van de Vyver | Lennart Martens | Bart Mesuere | Thilo Muth
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-05-21)
Field: Chemistry — Spectroscopy

The Peptonizer2000: bringing confidence to metaproteomics Abstract Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available datasets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities. Graphical model ; Computer science ; Artificial intelligence Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Metabolomics and Mass Spectrometry Studies
Authors: Guillaume Helbert | Jessy Simon
Source: International Journal of Non-Linear Mechanics (article, 2024-06-18)
Field: Materials Science — Materials Chemistry

Numerical modeling of systems based on SMA wires and pulleys: A finite element formulation within the Arbitrary Lagrangian–Eulerian framework Pulley ; Finite element method ; SMA* ; Eulerian path ; Lagrangian ; Mathematics ; Structural engineering ; Computer science ; Mathematical analysis ; Engineering ; Algorithm Shape Memory Alloy Transformations ; MXene and MAX Phase Materials ; Titanium Alloys Microstructure and Properties
Authors: Binting Ni | Hao Ma | Shunuo Zhang | Hanghang Chengliu | Yong Xu | Wufei Dai | Peiru Min | Liqun Li
Source: Nanotechnology Reviews (article, 2024-01-01)
Field: Materials Science — Biomaterials

Shell-core-structured electrospinning film with sequential anti-inflammatory and pro-neurogenic effects for peripheral nerve repairment Abstract Inducing an anti-inflammatory response before neurogenesis is crucial in effectively addressing peripheral nerve damage. Herein, we developed shell-core-structured nanofilms (Cur/PLCL@BDNF/CNT) using poly-( l -Lactide)-Caprolactone (PLCL) and curcumin (Cur, an anti-inflammatory agent) as the shell layer, and carbon nanotubes (CNT) and brain-derived neurotrophic factor (BDNF, a neurogenic factor) as the core via coaxial electrospinning technology. The resulting Cur/PLCL@BDNF/CNT film exhibited a characteristic fibrous structure with remarkable shell-core architecture, demonstrating unweakened mechanical properties. Notably, it displayed sustained release kinetics with distinct stages: prioritized Cur release within the initial 12 days and delayed BDNF release between 10 to 30 days. Additionally, the Cur/PLCL@BDNF/CNT film demonstrated high biocompatibility with Schwann cells. Subsequent in vitro analysis revealed the potent anti-inflammatory capabilities of the released Cur from the shell layer, while the BDNF released from the core layer effectively induced neurogenic differentiation of Schwann cells. The Cur/PLCL@BDNF/CNT film was rolled into a nerve conduit and then utilized for nerve regeneration in a 10 mm rat sciatic nerve defect model. The staged release of Cur and BDNF facilitated by the Cur/PLCL@BDNF/CNT film established an anti-inflammatory microenvironment before initiating nerve regeneration, resulting in better nerve restoration. This study emphasizes the significance of shell-core-structured nanofilms in temporally regulating anti-inflammation and neurogenesis. Electrospinning ; Peripheral ; Peripheral nerve ; Core (optical fiber) ; Shell (structure) ; Medicine ; Materials science ; Internal medicine ; Anatomy ; Composite material Electrospun Nanofibers in Biomedical Applications ; Nerve injury and regeneration ; Conducting polymers and applications
Authors: Neamat T. Barakat | Amina M. El-Brashy | Mona E. Fathy
Source: Royal Society Open Science (article, 2024-07-01)
Field: Chemistry — Analytical Chemistry

Green analytical quality by design RP-HPLC technique with fluorimetric detection for simultaneous assay of cinnarizine and dompridone A green and sensitive factorial design-assisted reversed-phase high-performance liquid chromatography (RP-HPLC) approach with fluorimetric detection has been developed for simultaneous determination of cinnarizine and domperidone in pure materials, commercial single and combined tablets. Both drugs are co-formulated in one dosage form and are commonly used for the effective treatment of motion sickness in the ratio of 4 : 3 for cinnarizine and domperidone, respectively. To achieve the developed method's best performance and reliability, a 2<sup>3</sup> full factorial design was applied during the optimization of chromatographic conditions. Subsequently, isocratic elution on a C18 column with a mobile phase mixture of methanol and 0.02 M potassium dihydrogen phosphate buffer (85 : 15 v/v, pH 3.0) was performed to achieve the best separation. Moreover, the flow rate of 0.8 ml min<sup>-1</sup> was applied during the analysis with fluorescence detection at λ<sub>ex</sub> 283 nm/λ<sub>em</sub> 324 nm. The elution process was time effective; it consumed less than 6 min for a complete run as retention time for cinnarizine and domperidone, was 4.5 and 3.5, respectively. Good linearity of the proposed method was achieved within the concentration ranges of 0.2-4.5 and 0.4-5.0 µg ml<sup>-1</sup> for domperidone and cinnarizine, respectively. The suggested approach was carefully validated according to the International Council for Harmonization (ICH) guidelines. Moreover, green analytical procedure index (GAPI), national environmental methods index (NEMI), analytical greenness (AGREE) and analytical eco-scale methods were applied to assess and confirm method greenness. Cinnarizine ; Domperidone ; Chromatography ; High-performance liquid chromatography ; Factorial experiment ; Chemistry ; Mathematics ; Medicine ; Statistics ; Dopamine Analytical Methods in Pharmaceuticals ; Plant-based Medicinal Research ; Cancer Treatment and Pharmacology
Authors: Shreya Talreja | Shashank Tiwari
Source: International Journal of Pharmacy and Pharmaceutical Science (article, 2024-01-01)
Field: Chemistry — Spectroscopy

Harnessing bioactive compounds: Review of emerging extraction technologies Extraction technologies for the recovery of bioactive compounds from natural sources are also important and represent a significant share in different industries such as pharmaceuticals, food or cosmetics. The present review have discussed about various extraction techniques, their principle and merits in noble compounds extractions. The following methodologies are explained in detail including their ability to selectively extract the bioactive compounds with lesser quantity of solvent and environmental friendly viz., Liquid-liquid extraction, Solid Liquid Extraction (SLE) as well as Super Critical Fluid Extraction, SFE), Ultrasound Assisted Extractions. The use of these processes for selective extraction of bioactive compounds such as polyphenols, alkaloids and essential oils is also discussed with special focus on improving the quality and activity of final products. Finally, prospective trends and challenges of such extraction technologies are discussed to provide some future directions for improvements in this field. Extraction (chemistry) ; Biochemical engineering ; Computer science ; Nanotechnology ; Chemistry ; Data science ; Engineering ; Chromatography ; Materials science Analytical Chemistry and Chromatography
Authors: G. Speranza
Source: Materials (article, 2024-02-05)
Field: Materials Science — Surfaces, Coatings and Films

Application of the Van Cittert Algorithm for Deconvolving Loss Features in X-ray Photoelectron Spectroscopy Spectra The convolution of two physical entities, denoted as <i>f</i> and <i>g</i>, delineates the manner in which one entity undergoes modification in response to the other. This transformative process is mathematically represented by the expression <i>f</i> ⨂ <i>g</i>, symbolizing the convolution of the two entities in a resultant function <i>h</i>. Frequently, it becomes imperative to comprehend the magnitude of the induced modifications. From the derived function <i>h</i>, a crucial step involves the separation of the two original signals, a process commonly referred to as deconvolution. Various techniques have been proposed to facilitate the calculation of the deconvolution, with one notable approach originating in 1931 by van Cittert. The algorithm, based on an iterative method, has been scrutinized over time, notably by Bracewell and, more recently, by Jansson. This work represents the current state-of-the-art, focusing specifically on the analysis of Auger spectra obtained through XPS. Emphasis is placed on delineating the procedural aspects of the analysis, and the algorithm utilized in the open-source software <i>RxpsG</i> is comprehensively described. Deconvolution ; Convolution (computer science) ; Algorithm ; Computer science ; Function (biology) ; Spectral line ; Transformative learning ; Physics ; Artificial intelligence Electron and X-Ray Spectroscopy Techniques ; X-ray Spectroscopy and Fluorescence Analysis ; Nuclear Physics and Applications
Authors: Anouk Chevallier | Wajih Akleh | Jason Govilas | Florian Boutenel | Violaine Guicheret-Retel | Johnny Beaugrand | Cédric Clévy | Vincent Placet
Source: Composites Part A Applied Science and Manufacturing (article, 2024-10-18)
Field: Materials Science — Polymers and Plastics

Moisture effects on the transverse compressive behaviour of single flax fibres Studying the effects of moisture on the mechanical behaviour of single flax fibres, particularly in the transverse direction, is of key importance for the reliable use of biobased composites exposed to varying humidity levels. In this study, the apparent transverse Young’s modulus evolution of single flax fibres is recorded through repeated compressive load/unload cycles conducted at three Relative Humidity (RH) levels— 40 %, 60 %, and 80 %. No significant changes in the apparent Young’s modulus, determined from the unloading, were observed during transverse compression cycling or under increasing humidity conditions. The absence of apparent softening with the rise in RH is attributed to the expression of two antagonistic mechanisms: wall softening due to plasticization and structural stiffening linked to fibre compaction. Intriguingly, a noteworthy transverse stiffening is recorded at 40 % RH following the humidification and drying of the fibre. This outcome is ascribed to a hornification phenomenon. Materials science ; Composite material ; Moisture ; Transverse plane ; Compressive strength ; Structural engineering Natural Fiber Reinforced Composites ; Textile materials and evaluations ; Cellular and Composite Structures
Authors: H. Askar | Mona E. Fathy | Manar M. Tolba | Fatma A. Aly | Mohamed Metwally
Source: Royal Society Open Science (article, 2024-07-01)
Field: Chemistry — Analytical Chemistry

Simultaneous determination of diosmin and hesperidin in combined pharmaceutical preparation by synchronous fluorescence spectrofluorimetric method A sensitive, rapid and green synchronous spectrofluorimetric method was developed to simultaneously analyze a binary mixture of diosmin (DSM) and hesperidin (HSP). The RSFI of both medications was measured in methanol at Δ<i>λ</i> of 100 nm. The results indicated that specific experimental factors had an impact on these intensities. The optimization and thorough examination of these parameters were conducted. The plots of synchronous fluorescence intensity-concentration for DSM and HSP were found to be linear within the concentration ranges of 0.5-5.0 µg ml<sup>-1</sup> and 0.2-3.0 µg ml<sup>-1</sup>, respectively. The detection limits for DSM and HSP were 0.107 µg ml<sup>-1</sup> and 0.048 µg ml<sup>-1</sup>, respectively. The limits of quantification were 0.323 µg ml<sup>-1</sup> and 0.144 µg ml<sup>-1</sup> for DSM and HSP, respectively. The method outlined in this study was successfully used to determine the quantities of both drugs present in commercially available mixed tablets. The results obtained using this method were subsequently compared to those of a comparison method. Greenness assessment of the suggested procedure was accomplished by applying the GAPI method. Consequently, the recommended method can be used in the routine quality control analysis of the two cited drugs with minimum harmful effect on the environment as well as the individuals. Diosmin ; Hesperidin ; Fluorescence ; Chemistry ; Chromatography ; Flavonoid ; Biochemistry ; Medicine ; Optics Analytical Methods in Pharmaceuticals ; Analytical Chemistry and Chromatography ; Pharmacological Effects and Assays
Authors: Jiahui Zhang | Guangchao Zhang | De Hou | Jiachang Bi | Ruyi Zhang | Shaoqin Peng | Pengfei Yu | Fangyuan Zhu | Haigang Liu | Liang Wu | Zhigao Sheng | Juan Du | Yanwei Cao
Source: Journal of Applied Physics (article, 2024-04-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Ferroelectric and magnetic properties of Dy-doped BaTiO3 films Element substitution of BaTiO3-based compounds has been demonstrated as a powerful way for designing novel electronic materials (such as polar metals and multiferroics). To trigger magnetism into ferroelectric BaTiO3, general substituted elements are magnetic transition metals (such as Mn, Fe, and Co). The doping effect of rare-earth elements (such as Dy) in BaTiO3-based compounds was barely investigated. Here, we report the coexistence of magnetism and electric polarization in epitaxial Dy0.5Ba0.5TiO3 films. The single-crystalline films were synthesized by high-pressure magnetron sputtering. The crystal and electronic structures were characterized by high-resolution x-ray diffraction, x-ray photoemission spectroscopy, and resonant soft x-ray absorption spectroscopy. Room-temperature electric polarization was demonstrated by optical second-harmonic generation. Temperature-dependent magnetic hysteresis loops were measured to reveal the revolution of magnetism on temperature. Surprisingly, it is uncovered that the Curie temperature of electric-polarized Dy0.5Ba0.5TiO3 films is around 100 K, far above the critical temperature of non-polarized DyTiO3 (near 60 K). Our work provides another view to understand the magnetoelectric materials. Ferroelectricity ; Materials science ; Doping ; Condensed matter physics ; Optoelectronics ; Dielectric ; Physics Multiferroics and related materials ; Ferroelectric and Piezoelectric Materials ; Magnetic and transport properties of perovskites and related materials
Authors: Simone König | Karin Schork | Martin Eisenacher
Source: Proteomes (article, 2024-02-06)
Field: Chemistry — Spectroscopy

Observations from the Proteomics Bench Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data-set-wise quality control is still necessary, and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations. Standardization ; Computer science ; Data science ; Orbitrap ; Software ; Set (abstract data type) ; Proteomics ; Quality (philosophy) ; Risk analysis (engineering) ; Mass spectrometry ; Medicine ; Chemistry Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Maria V. Faustino | Tiago Lourenço | Simon Strobbe | Da Cao | André Salvador Kazantzi Fonseca | Isabel Rocha | Dominique Van Der Straeten | M. Margarida Oliveira
Source: BMC Plant Biology (article, 2024-03-26)
Field: Materials Science — Materials Chemistry

Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway Our study elucidates the critical role of RibA in rice riboflavin biosynthesis pathway, establishing it as the rate-limiting step in the pathway. By identifying and characterizing OsRibA1 and OsRibA2, showcasing their GTPCHII and DHBPS activities, we have advanced the understanding of riboflavin biosynthesis in this staple crop. We further demonstrated that OsRibA1 overexpression in rice callus increases its riboflavin content, providing supporting information for bioengineering efforts. Biology ; Arabidopsis ; Biochemistry ; Heterologous expression ; Heterologous ; Mutant ; Enzyme ; Cofactor ; Biofortification ; Phosphofructokinase 2 ; Gene ; Recombinant DNA ; Chemistry Enzyme Structure and Function ; Photosynthetic Processes and Mechanisms ; Microbial Metabolic Engineering and Bioproduction