jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Samuel P. Loke | Zhengli Wu | Emmanuel Lassalle | Ramón Paniagua‐Domínguez
Source: Scientific Reports (article, 2024-10-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Using optical absorption to reduce cross-talk in spatially multiplexed waveguiding metasurfaces Dual-wavelength metasurfaces often employ spatial multiplexing design concepts where two interleaved lattices of meta-atoms, each designed for a specific wavelength, occupy the same layer. However, this arrangement incurs efficiency losses as each wavelength inevitably "sees" unintended meta-atoms designed for the other wavelength, causing spurious interference (crosstalk) effects, which are especially affecting the shorter wavelength. In this paper, we numerically demonstrate that the crosstalk can be reduced by introducing some optical absorption at the shorter wavelength, unveiling the near-field mechanisms at play. Then, through designing and simulating a dual-wavelength beam-steering metasurface, we demonstrate the benefits of certain level of absorption in terms of wavefront purity (characterized by the diffraction efficiency into a desired blazed order) and beam-steering efficiency. This method also presents some advantages in its simplicity as it allows to use the traditional phase-mapping approach based on the simulations of two independent meta-atom libraries, compared to more complex methods that require accounting for the crosstalk between meta-atoms. Absorption (acoustics) ; Multiplexing ; Computer science ; Optics ; Optoelectronics ; Telecommunications ; Materials science ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Photonic Crystals and Applications
Authors: A.N. Semenov | J. Baschnagel
Source: Polymers (article, 2024-08-18)
Field: Materials Science — Materials Chemistry

General Relations between Stress Fluctuations and Viscoelasticity in Amorphous Polymer and Glass-Forming Systems Mechanical stress governs the dynamics of viscoelastic polymer systems and supercooled glass-forming fluids. It was recently established that liquids with long terminal relaxation times are characterized by transiently frozen stress fields, which, moreover, exhibit long-range correlations contributing to the dynamically heterogeneous nature of such systems. Recent studies show that stress correlations and relaxation elastic moduli are intimately related in isotropic viscoelastic systems. However, the origin of these relations (involving spatially resolved material relaxation functions) is non-trivial: some relations are based on the fluctuation-dissipation theorem (FDT), while others involve approximations. Generalizing our recent results on 2D systems, we here rigorously derive three exact FDT relations (already established in our recent investigations and, partially, in classical studies) between spatio-temporal stress correlations and generalized relaxation moduli, and a couple of new exact relations. We also derive several new approximate relations valid in the hydrodynamic regime, taking into account the effects of thermal conductivity and composition fluctuations for arbitrary space dimension. One approximate relation was heuristically obtained in our previous studies and verified using our extended simulation data on two-dimensional (2D) glass-forming systems. As a result, we provide the means to obtain, in any spatial dimension, all stress-correlation functions in terms of relaxation moduli and vice versa. The new approximate relations are tested using simulation data on 2D systems of polydisperse Lennard-Jones particles. Viscoelasticity ; Relaxation (psychology) ; Isotropy ; Statistical physics ; Stress relaxation ; Stress (linguistics) ; Moduli ; Thermal fluctuations ; Dimension (graph theory) ; Supercooling ; Materials science ; Physics ; Thermodynamics ; Classical mechanics ; Mathematics ; Optics ; Pure mathematics Material Dynamics and Properties ; Rheology and Fluid Dynamics Studies ; Polymer crystallization and properties
Authors: Zheng Ser | Nicholas R. J. Gascoigne | Paul A. MacAry | Radoslaw M. Sobota
Source: STAR Protocols (article, 2024-03-01)
Field: Chemistry — Spectroscopy

Protocol for structural modeling of antibody to human leukocyte antigen interaction using discovery and targeted cross-linking mass spectrometry Cross-linking mass spectrometry (XL-MS) provides low-resolution structural information to model protein structures. Here, we present a protocol to identify cross-links of purified antibody binding to purified human leukocyte antigen (HLA). We describe steps for using a discovery-based XL-MS approach followed by a targeted XL-MS approach. We then detail procedures for using the identified cross-links with other structural data for molecular docking of the antibody to HLA. This protocol has applications for modeling the interacting structure of purified antibody to antigen. For complete details on the use and execution of this protocol, please refer to Ser et al.<sup>1</sup>. Human leukocyte antigen ; Computational biology ; Antibody ; Mass spectrometry ; Antigen ; Protocol (science) ; Chemistry ; Docking (animal) ; High resolution ; Biology ; Immunology ; Chromatography ; Medicine Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Monoclonal and Polyclonal Antibodies Research
Authors: Karuna Baraskar | Archana Tiwari | P. K. Dubey
Source: International Journal of Pharmaceutical Sciences and Medicine (article, 2024-09-24)
Field: Chemistry — Organic Chemistry

In-Silico ADMET Prediction, Structure-Based Drug Design and Molecular Docking Studies of Quinazoline Derivatives as Novel EGFR Inhibitors This Present research provides valuable insights and implications for the development of quinazoline derivatives as novel EGFR inhibitors. The in-silico ADMET predictions indicate that the quinazoline derivatives possess promising drug-like properties, suggesting their potential for further development as oral drugs. The low risk of toxicity and favorable metabolic and excretion profiles enhance their suitability for therapeutic applications Molecular docking studies revealed strong binding interactions between the quinazoline derivatives and the EGFR kinase domain. These interactions suggest that these compound shave the potential to effectively inhibit EGFR activity, making them promising candidates for anti- cancer drug development to progress from in-silico findings to clinical applications, further research is essential. Future work should encompass in vitro and in vivo experiments to validate the inhibitory potential of these compounds against EGFR. Additionally, pharmacokinetic studies are warranted to confirm their ADMET properties. Structural optimization through medicinal chemistry approaches may further enhance their binding affinities and specificity for EGFR. It represents a pivotal step in the exploration of quinazoline derivatives as novel EGFR inhibitors. The combined efforts in ADMET prediction, structure-based drug design, and molecular docking have provided a strong foundation for the development of innovative anti-cancer therapies. The potential of these compounds to target EGFR, a crucial player in various cancers, holds great promise for improving the treatment options available to patients and advancing the field of oncology. In silico ; Docking (animal) ; Quinazoline ; Computational biology ; Drug ; EGFR inhibitors ; Chemistry ; Quantitative structure–activity relationship ; Pharmacology ; Combinatorial chemistry ; Stereochemistry ; Epidermal growth factor receptor ; Biology ; Medicine ; Biochemistry ; Receptor Synthesis of Tetrazole Derivatives ; Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity
Authors: Ying Zhou | Han Zhang | Xiaohui Sheng | Rong Wang | Yao Yao | Qinglan Zhu | Ze Yi | Zhe Xu | Yì Wáng | Chenghang Zheng | Yu Tang
Source: Molecules (article, 2024-08-23)
Field: Chemistry — Analytical Chemistry

Evaluation of Saffron Quality Using Rapid Quantitative Inspection Technology with Near-Infrared Spectroscopy A predictive model utilizing near-infrared spectroscopy was developed to estimate the loss on drying, total contents of crocin I and crocin II, and picrocrocin content of saffron. Initially, the LD values were determined using a moisture-ash analyzer, while HPLC was employed for measuring the total contents of crocin I, crocin II, and picrocrocin. The near-infrared spectra of 928 saffron samples were collected and preprocessed using first derivative, standard normal variable transformation, detrended correction, multivariate scattering correction, Savitzky-Golay smoothing, and mean centering methods. Leveraging the partial least squares method, regression models were constructed, with parameters optimized through a selective combination of the above six preprocessing methods. Subsequently, prediction models for loss on drying, total contents of crocin I and crocin II, and picrocrocin content were established, and the prediction accuracy of the models was verified. The correlation coefficients and root mean square error of loss on drying, total contents of crocin I and crocin II, and picrocrocin content demonstrated high accuracy, with <i>R</i><sup>2</sup> values of 0.8627, 0.8851, and 0.8592 and root mean square error values of 0.0260, 0.0682, and 0.0465. This near-infrared prediction model established in the present study offers a precise and efficient means of assessing loss on drying, total contents of crocin I and crocin II, and picrocrocin content in saffron and is useful for the development of a rapid quality evaluation system. Crocin ; Safranal ; Partial least squares regression ; Chemistry ; Near-infrared spectroscopy ; Mean squared error ; Analytical Chemistry (journal) ; Chromatography ; Mathematics ; Statistics ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Saffron Plant Research Studies ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: James Urban | Roman Joeres | Luc Thomès | Kristina A. Thomsson | Daniel Bojar
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-07-02)
Field: Chemistry — Spectroscopy

Navigating the Maze of Mass Spectra: A Machine-Learning Guide to Identifying Diagnostic Ions in O-Glycan Analysis Abstract Structural details of oligosaccharides, or glycans, often carry biological relevance, which is why they are typically elucidated using tandem mass spectrometry. Common approaches to distinguish isomers rely on diagnostic glycan fragments for annotating topologies or linkages. Diagnostic fragments are often only known informally among practitioners or stem from individual studies, with unclear validity or generalizability, causing annotation heterogeneity and hampering new analysts. Drawing on a curated set of 237,000 O -glycomics spectra, we here present a rule-based machine learning workflow to uncover quantifiably valid and generalizable diagnostic fragments. This results in fragmentation rules to robustly distinguish common O -glycan isomers. We envision this resource to improve glycan annotation accuracy and concomitantly make annotations more transparent and homogeneous across analysts. Glycan ; Ion ; Mass spectrum ; Computer science ; Artificial intelligence ; Machine learning ; Psychology ; Computational biology ; Mass spectrometry ; Chemistry ; Chromatography ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Tiancheng Zhou | Zhangzhang Xie | Xinyu Jiang | Xiangbo Zou | Jiong Cheng | Chuangting Chen | Cao Kuang | Ji Ye | Ying Wang | Fanghua Liu
Source: Water (article, 2024-11-18)
Field: Materials Science — Biomaterials

Efficient Solar-Powered Bioremediation of Hexavalent Chromium in Contaminated Waters by Chlorella sp. MQ-1 Microalgae are known for their efficient removal of hexavalent chromium (Cr(VI)) through biosorption and bioaccumulation, yet the subsequent release of Cr(VI) upon cell death remains a challenge. The reduction of Cr(VI) to the less toxic trivalent chromium [Cr(III)] is another critical remediation strategy that mitigates the risk of Cr(VI) re-release, but research on microalgal reduction of Cr(VI) is scarce. In this study, a microalgal strain designated as MQ-1 was isolated from chromium-contaminated mine effluent, demonstrating the capability to tolerate and remove Cr(VI). Phylogenetic analysis revealed that MQ-1 is closely related to the genus Chlorella; hence, it is classified as Chlorella sp. MQ-1. This strain exhibited robust growth at Cr(VI) concentrations below 2 mg/L, achieving a removal rate higher than 82% for initial Cr(VI) concentrations between 0.5 and 1 mg/L after a 5-day incubation period. Mechanistic studies revealed that MQ-1 promoted the removal of Cr(VI) mainly through intracellular bioreduction and bioaccumulation processes, in which more than 60% of Cr(VI) was reduced to the less toxic Cr(III) and stocked in the cells. A two-stage cultivation strategy, involving initial biomass accumulation followed by Cr(VI) treatment, significantly enhanced the removal efficiency, which was further accelerated under illuminated conditions. Notably, MQ-1 cultures with initial OD680 values of 4 and 6 accomplished 84.28% and 91.31% Cr(VI) removal from 2 mg/L solutions, respectively, within 30 hours under light exposure. These findings highlight the potential of MQ-1 to utilize renewable solar energy to reduce Cr(VI) and to mitigate the risk of its re-release into the environment. This characteristic positions MQ-1 as a potentially sustainable and cost-effective solution for Cr(VI) remediation and suggests its significant potential for large-scale implementation in bioremediation strategies aimed at Cr(VI)-contaminated waters. Hexavalent chromium ; Bioremediation ; Contamination ; Chromium ; Environmental science ; Environmental chemistry ; Contaminated water ; Waste management ; Chemistry ; Materials science ; Biology ; Metallurgy ; Ecology ; Engineering Diatoms and Algae Research
Authors: N. Shalom | Stanly Jones Retnam B | M. Dev Anand | J. Edwin Raja Dhas
Source: Natural and Engineering Sciences (article, 2024-10-30)
Field: Materials Science — Polymers and Plastics

Comparative Analysis of Flexural Properties of Bamboo-Glass Hybrid FRP Composites: Influence of Water Absorption Hybrid fibers are crucial in the self-propelled vehicle industry, with bamboo-glass fiber composites playing a significant role. Bamboo fibers, in particular, feature numerous tiny gaps that enhance their properties and performance. Hence there is a possibility for the absorption of moisture content from the atmosphere when compared to the relevant fibers. These setbacks can be rectified in various ways. Apart from that these fibers are very friendly to echo systems, can degrade quickly, and are flexible in their property. The major drawbacks of most of the fibers are, that they get easily affected by bacteria and fungus when they get soaked and wetted. But as far as the bamboo fibers are concerned they have a high resistance to these attacks. Therefore these materials can be preferred for external use such as engine guards of vehicles. The bamboo fiber in the glass hybridized polyethylene composite is alkali-treated to enhance the adherence of these materials. The high interpenetration of the resin into the fiber surface reduces the contact of this fiber especially the bamboo’s direct reach to the atmosphere. In this work, this hybrid material is preferred for doing a two-wheeler engine safety guard or a protective cover to protect the engine from the external natural compressive or the tensional forces acting on the engine when moves forward along with the vehicle. So, there is a necessity for measuring the flexural strength of the material, whether it will be suitable for this assigned work and also the stiffness of the material is obtained through the flexural modulus curve. Apart from this though these materials are placed in the outdoor sector, these materials can get in contact with external climatic conditions such as rain, dust, and moisture due to cold climatic conditions. This leads to the need for conducting the water absorption test. The test was conducted separately to obtain the water absorption coefficient as well as flexural test before and after water absorption to obtain any deviation if any after water absorption. The test was conducted in the open atmosphere at room temperature for both water absorption and flexural test. The results were tabulated and compared. The comparative study shows that only negligible deviation in property due to water absorption of the hybrid composite is observed. Composite material ; Materials science ; Bamboo ; Flexural strength ; Glass fiber ; Fibre-reinforced plastic ; Fiber ; Composite number Natural Fiber Reinforced Composites ; Bamboo properties and applications ; Mechanical Engineering and Vibrations Research
Authors: Yuqian Gao | Hyeyoon Kim | Reta Birhanu Kitata | Tai‐Tu Lin | Adam Swensen | Tujin Shi | Tao Liu
Source: Advances in cancer research (review, 2024-01-01)
Field: Chemistry — Spectroscopy

Multiplexed quantitative proteomics in prostate cancer biomarker development Biomarker ; Prostate cancer ; Biomarker discovery ; Proteomics ; Proteome ; Cancer biomarkers ; Quantitative proteomics ; Prostate-specific antigen ; Cancer ; Medicine ; Computational biology ; Bioinformatics ; Biology ; Internal medicine ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Prostate Cancer Treatment and Research
Authors: Finan T. Hindam | Amal M. Abou Al Alamein | Reham M. Arafa | Neven Ahmed | Basma M. Eltanany
Source: BMC Chemistry (article, 2024-10-21)
Field: Chemistry — Analytical Chemistry

Greenness and whiteness appraisal for bioanalysis of quetiapine, levodopa and carbidopa in spiked human plasma by high performance thin layer chromatography A sustainable HPTLC-densitometric method was developed for quantitative determination of Quetiapine (QUET), Levodopa (LD) and Carbidopa (CD) in presence of Dopamine (DOP) as an internal standard. This applicable technique was achieved by spiking human plasma and extraction was performed using the protein precipitation approach. The mobile phase used was acetone, dichloromethane, n-butanol, glacial acetic acid and water (3: 2.5: 2: 2: 1.75, by volume). Method validation was done according to US-FDA guidelines and was able to quantify Quetiapine, Levodopa and Carbidopa in the ranges of 100-4000, 200-8000 and 30-1300 ng/mL, respectively. Bioanalytical method validation parameters were assessed for the studied drugs. Finally, the analytical suggested methodology was evaluated using various green and white analytical chemistry metrics and other tools, such as the green solvent selection tool, analytical eco-scale, green analytical procedure index, analytical greenness metric approach and the red-green-blue algorithm tool. The results revealed that the applied analytical method had a minor impact on the environment and is a relatively greener option than other previously reported chromatographic methods. Bioanalysis ; Chromatography ; Carbidopa ; Chemistry ; Protein precipitation ; Levodopa ; Extraction (chemistry) Analytical Methods in Pharmaceuticals ; Electrochemical sensors and biosensors ; Analytical Chemistry and Chromatography
Authors: Aneesh Chauhan | Hendrik de Villiers | Lydia Meesters | M.J.M. Paillart | Željana Grbović | Marko Panić | Sanja Brdar
Source: Acta Horticulturae (article, 2024-06-01)
Field: Chemistry — Analytical Chemistry

Avocado stem-end rot detection using hyperspectral imaging One of the most common postharvest diseases impacting avocado is stem-end rot, a fungal disease whose damage is usually not externally visible. Only after extensive damage do symptoms become visible to the naked eye. Currently infections are primarily detected using the destructive approach (cutting the fruit open). There is significant interest in identifying non-destructive approaches testing entire avocado batches for stem-end rot. We explore visible-near infrared, VIS/NIR (wavelengths 470-1000 nm), hyperspectral imaging and machine learning to non-destructively detect stem-end rot in ‘Hass’ avocados. The data set consisted of 480 avocados, 240 of which were untreated and 240 inoculated (with stem-end rot). An independent test set of 80 avocados was also collected. After pre-processing, spectra from avocado stem pixels (and neighbouring regions) is averaged to obtain mean spectral features. These features are then used for training the Random Forest, XGBoost and a semi-supervised deep autoencoder classifiers at the task of distinguishing between healthy and infected samples. Overall, all classifiers led to similar performance, obtaining between 75 and 83% accuracy over the validation set. However, testing on the independent test set yielded a significant drop in performance with accuracy in the range of 56-65%, as well as elevated levels of false positives, while false negatives remained low. The results suggest that VIS/NIR based models may not be directly applicable for predicting stem-end rot in avocados. We hypothesize that spectral data of independent samples is not sufficient to capture stem-end rot because maturity/age and linked physiological changes might play an important factor, which was not considered in the current study. Hyperspectral imaging ; Remote sensing ; Environmental science ; Horticulture ; Biology ; Geology Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Remote Sensing in Agriculture
Authors: Qiang-mao Wan | Guogang Shu | Jiaxuan Tang | Jianjun Pang | Lisha Chen | Duan Wang | Hui Lin | Hui Ding
Source: Frontiers in Energy Research (article, 2024-07-22)
Field: Materials Science — Materials Chemistry

Cluster dynamics study on nano damage of RPV steels under proton irradiation at 290°C Irradiation-induced defects such as dislocation loops, cavities or solute clusters and chemical composition segregation of reactor pressure vessel (RPV) steel are the root causes of irradiation embrittlement. Combining two nucleation mechanisms, namely, the uniform nucleation and non-uniform nucleation of solute clusters (such as Cu-rich phase), a cluster kinetic simulation was established based on the reaction rate theory, and the co-evolution of matrix damage and Cu-rich phase in low-copper RPV steel was simulated under irradiation. And the average size and number density of defective clusters and solute clusters were established with irradiation dose. Compared with the average size and number density of dislocation loops observed by transmission electron microscopy (TEM) of proton irradiated RPV steel at 290°C, the verification results show that the cluster dynamics model considering both the nucleation mechanism of interstitial dislocation loops and vacancy clusters can well simulate the irradiation damage behavior of materials. Nucleation ; Materials science ; Dislocation ; Irradiation ; Cluster (spacecraft) ; Embrittlement ; Number density ; Transmission electron microscopy ; Phase (matter) ; Reactor pressure vessel ; Molecular dynamics ; Vacancy defect ; Proton ; Crystallography ; Chemical physics ; Composite material ; Thermodynamics ; Nanotechnology ; Chemistry ; Nuclear physics ; Computational chemistry ; Physics Fusion materials and technologies ; Microstructure and mechanical properties ; Nuclear Materials and Properties