jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yuming Shi | Huan Zhong | Jason C. Rogalski | Leonard J. Foster
Source: Computational and Structural Biotechnology Journal (article, 2025-01-01)
Field: Chemistry — Spectroscopy

Optimizing imputation strategies for mass spectrometry-based proteomics considering intensity and missing value rates Missing values (MVs) in omic datasets affect the power, accuracy, and consistency of statistical and functional analyses. In mass spectrometry (MS)-based proteomics, MVs can arise due to several reasons: peptides could be below instrumental detection limits, peptides or proteins might be absent or depleted from the sample for biological or technical reasons, or data processing could fail to detect a real signal. Several statistical and machine-learning methods have been described for imputing MVs in proteomics, such as Bayesian PCA estimation, random forest, and collaborative filtering. However, these approaches typically do not account for the underlying causes of MVs and treat all missing data uniformly, potentially introducing biases that affect the biological validity of the conclusions drawn from the imputed datasets. We found a strong negative correlation between the proportion of MVs and the average intensity for the individual protein, with more abundant proteins having fewer, but rarely zero, MVs. We divided the peptides from all proteins into nine bins based on their intensities and proportion of MV. Assuming the causes of MVs could be different in different regions, we then investigated the optimal imputation method in each bin, using normalized root mean square error (NRMSE), and found that the optimal imputation method varies across bins. A mix-imputed dataset was assembled using the optimal imputation method from each bin, and it was confirmed to exhibit low deviation from the original unimputed dataset, demonstrating mixing the optimal imputation method from each bin is a reliable strategy. Imputation (statistics) ; Missing data ; Mass spectrometry ; Proteomics ; Computer science ; Data mining ; Environmental science ; Statistics ; Chemistry ; Mathematics ; Chromatography Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Hassan Amini | Çığır Biray Avci | Sajed Nazif Kerdar | Ayla Hassani | Meysam Amini | Narges Mardi | Sepideh Saghati | Maryam Taghavi Narmi | Leila Sabour Takanlou | Maryam Sabour Takanlou | Ali Baradar Khoshfetrat | Mohammad Nori | Shahriar Hashemzadeh | Reza Rahbarghazi‬
Source: Cell Communication and Signaling (article, 2025-06-12)
Field: Materials Science — Biomaterials

Intramyocardial injection of pre-cultured endothelial progenitor cells and mesenchymal stem cells inside alginate/gelatin microspheres induced angiogenesis in infarcted rabbits Using several strategies, the stimulation of angiogenesis can alleviate the pathological complications of post-myocardial ischemia. Here, endothelial progenitor cells (EPCs) and mesenchymal stem cells (MSCs) were pre-cultured inside the alginate/gelatin (Alg/Gel) microspheres in the presence of SDF-1α for 7 days, and their angiogenesis potential was monitored in infarcted rabbits. The decapsulated cells were monitored in terms of cell dynamic growth and angiogenesis potential in vitro and after injection into ischemic myocardium in rabbits. Based on the data, 7-day incubation inside the Alg/Gel microspheres led to the stimulation of angiogenesis profile (Ang-1↑, -2↑, Tie-2↑), migration (MMP-2↑, and − 9↑), and autophagic response (Beclin-1↑, LC3↑, and p-62↓) in EPCs containing groups in the presence of SDF-1α. PCR array analysis revealed the expression of angiogenesis-related genes in the presence of SDF-1α. These features coincided with the stimulation of in vitro tubulogenesis properties in EPCs and EPCs + SDF-1α groups. The injection of cells from different groups into the infarcted rabbits led to the reduction of fibrotic area in ischemic myocardium in MSCs-bearing groups, and these effects were intensified in the presence of SDF-1α. Pre-treatment of EPCs and MSCs increased the recruited immune cells into the ischemic area within the myocardium. It was suggested that SDF-1α stimulated the local vascular density (CD31 capillaries, and α-SMA arterioles) in EPCs-bearing groups compared to MSCs and MSCs + SDF-1α groups. These data indicate that pre-culture of EPCs and MSCs inside the Alg-based hydrogels can increase the regenerative potential of these cells, especially when exposed to stimulatory cytokines such as SDF-1α for the alleviation of ischemic changes. Mesenchymal stem cell ; Angiogenesis ; Progenitor cell ; Microsphere ; Stem cell ; Gelatin ; Endothelial stem cell ; Cell biology ; Chemistry ; Biomedical engineering ; Medicine ; Cancer research ; Biology ; In vitro ; Biochemistry ; Engineering Electrospun Nanofibers in Biomedical Applications ; Mesenchymal stem cell research ; Angiogenesis and VEGF in Cancer
Authors: Nixe Adriana Hernández-López | Maribel Plascencia‐Jatomea | Carmen Lizette Del‐Toro‐Sánchez | Carmen María López‐Saiz | Simón Morales-Rodríguez | Miguel Ángel Martínez‐Téllez | Eber Addí Quintana-Obregón
Source: Polysaccharides (article, 2025-01-07)
Field: Materials Science — Biomaterials

Antifungal Activity of Nanochitosan in Colletotrichum musae and Colletotrichum chrysophillum The search for developing materials of natural origin has become imperative due to the resistance shown by phytopathogenic microorganisms to traditional antimicrobial agents. Natural polymers such as chitosan offer a new alternative to fungal infections because, in most cases, these polymers are biocompatible, nontoxic, and natural. This study aimed to synthesize nanochitosan using ultrasonication and evaluate its antifungal activity on Colletotrichum chrysophillum and Colletotrichum musae. Nanochitosan of 302.4 ± 92.3 nm and a zeta potential of +35.9 ± 2.3 Mv, amorphous in shape, and a rough surface, was obtained. Nanochitosan reduced the radial growth 21%, for C. chrysophillum while C. musae showed a maximum inhibition of 26% at a concentration of 1.5 mg mL−1 of nanochitosan. C. musae was the species most affected, with a 38% increase in hyphal diameter to 12 h. Also, nanochitosan affected the integrity of the fungi cell walls, plasma membrane, and generated low oxidative stress level. Our findings indicate that nanochitosan induces notable changes in the intracellular structures of the tested phytopathogens. Nevertheless, additional investigations are required to clarify the mechanisms underlying adaptability or resistance in fungal strains that exhibit reduced sensitivity to this biopolymer. Chemistry ; Antimicrobial ; Hypha ; Microbiology ; Biology Nanocomposite Films for Food Packaging ; Plant Pathogens and Fungal Diseases ; Essential Oils and Antimicrobial Activity
Authors: Kovida Kovida | Juraj Malinčík | Tomáš Šolomek
Source: Helvetica Chimica Acta (article, 2025-01-10)
Field: Chemistry — Organic Chemistry

Effect of π‐Electron Conjugation on the Chiroptical Properties of Helicene Carbon Nanohoops Abstract We designed, synthesized, and investigated a new chiral carbon nanohoop that formally incorporates a benzothiadiazole and [5]helicene units into the structure of [6]cycloparaphenylene. The connection of these units in the chiral nanohoop is designed to allow for π‐electron conjugation between the benzothiadiazole chromophore and the chirality‐inducing [5]helicene. We resolved the enantiomers of the highly fluorescent, near‐IR light emitting benzothiadiazole helicene nanohoop. Electronic circular dichroism spectroscopy then allowed us to investigate whether the selected molecular design leads to an increase in the lowest singlet excited state delocalization to improve the compound's electronic dissymmetry factor in comparison to the previously studied benzothiadiazole carbon nanohoop with planar chiral [2.2]paracyclophane unit with pseudo‐meta connection. Helicene ; Chemistry ; Chromophore ; Circular dichroism ; Chirality (physics) ; Delocalized electron ; Enantiomer ; Photochemistry ; Crystallography ; Stereochemistry ; Molecule ; Organic chemistry ; Symmetry breaking Synthesis and Properties of Aromatic Compounds ; Molecular spectroscopy and chirality ; Liquid Crystal Research Advancements
Authors: Jitao Ji | Zhilin Ye | Zhizhang Wang | Jiacheng Sun | Xueyun Li | Jian Li | Junyi Wang | Bin Fang | Zihan Gao | Shanshan Hu | Shining Zhu | Tao Li
Source: Light Science & Applications (article, 2025-09-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Dynamic holographic display with addressable on-chip metasurface network based on lithium niobate photonics On-chip metasurfaces have been exploited to manipulate guided waves into free space with desired wavefronts and bridge the gap between guided modes and free-space optical fields. However, existing on-chip metasurfaces for guided wave radiation typically lack dynamic tunability and high-capacity multiplexing for their practical applications. Here, we present a dynamic waveguide-based holographic display enabled by on-chip metasurface network on lithium niobate on insulator platform. Based on geometric phase and detour phase, an on-chip multiplexed metasurface network implemented on a 2 × 2 waveguide crossing array is incorporated with a two-stage lithium niobate (LN) switch to construct an addressable framework. Benefiting from the multiplexing capability of on-chip metasurface and the fast electro-optical response of LN modulators, guided wave radiation in the form of eight holographic images is tunable and addressable at high speeds. This work exemplifies a scalable approach for dynamic manipulation of guided signals and paves the way towards holographic displays, high-capacity optical communications and integrated photonic information processing. Holography ; Lithium niobate ; Multiplexing ; Photonics ; Holographic display ; Wavefront ; Scalability ; Spatial light modulator Metamaterials and Metasurfaces Applications ; Photonic and Optical Devices ; Advanced Optical Imaging Technologies
Authors: Erika Kristensen | Jonas Dornonville de la Cour | Tobias Warburg | René Lynge Eriksen | Bjarke Jørgensen | James Emil Avery | Mogens Hinge
Source: Chemometrics and Intelligent Laboratory Systems (article, 2025-09-10)
Field: Chemistry — Analytical Chemistry

High-speed processing of hyperspectral images for enabling demanding industrial applications Inline industrial application of high-speed hyperspectral imaging for real-time chemometric analysis presents a computationally difficult problem due to the complexity of the analysis and the large amount of spectral data that needs to be processed in real-time. The image resolution and acquisition rate of modern sensors, as well as increased ambition for detail and accuracy, makes it a challenge to design computational methods and to implement them sufficiently efficient to complete within the few milliseconds available between frames. Real-time chemometrics, including intensity calibration, Savitzky-Golay filtering, principal component analysis, and support vector machine classification for plastic identification was performed directly on a hyperspectral camera. Three processing scenarios were evaluated: a Python-based CPU implementation, a C++ CPU implementation, and a GPU implementation using OpenCL. The performance was assessed in terms of total processing time per image. The results demonstrate that GPU-based processing increased frame rate to 160 fps compared to 35 fps and 94 fps achieved with CPU-based processing. Analysis shows that the speed of the GPU based processing is limited by the image acquisition rate of the sensor. The GPU processing has excess computational capacity which enables integration of more complex classification models or parallel execution of multiple models with different purposes. Removing the data processing as the limiting factor of performance, increases the industrial relevance of hyperspectral imaging systems. • Plastic identification using hyperspectral imaging • Real-time image processing with intensity calibration, SG-filtering, PCA, and SVM • Python, C++, and OpenCL implementations evaluated for performance • GPU-based processing increased frame rate to 160 fps, limited by image acquisition • Excess GPU capacity enables more complex models and parallel analysis Hyperspectral imaging ; Frame rate ; Image processing ; Data processing ; Support vector machine ; Frame (networking) ; Principal component analysis ; Pattern recognition (psychology) ; Signal processing Spectroscopy and Chemometric Analyses ; Remote-Sensing Image Classification ; Remote Sensing and Land Use
Authors: Vishal Sorathiya | Zen Sbeah | Ahmad M. Alghamdi | Amar Y. Jaffar | Abdullah G. Alharbi
Source: Scientific Reports (article, 2025-08-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Wideband metamaterial perfect absorber using topological insulator material for infrared and visible light spectrum: a numerical approach This study utilises simulations to investigate the potential of a novel multi-layered topological insulator-based wideband absorber design. The proposed design is constructed with a multilayer structure that incorporates meticulously chosen materials to enhance light absorption. The top layer is composed of a metal (Fe/Ti/Cu/Zn/Ag/Au), which is followed by an insulating layer (Si/SiO₂/InP) and a topological insulator (Bi₁.₅Sb₀.₅Te₁.₈Se₁.₂). These layers are sandwiched between two metal layers (Fe/Ti/Cu/Zn/Ag/Au). The proposed structure is analysed for two different resonator-based designs, considering both the L-shaped metal resonator and the complementary L-shaped resonator for the overall computational analysis. The overall structure is computed for the broad range of the wavelength spectrum (0.2-1.6 μm). The proposed metamaterial design achieves an absorption rate of ~ 99% across multiple wavelength bands. This structure also investigated the different parametric values, such as physical dimensions and oblique angle of incident, to identify the optimised values of the different parameters. The metamaterial parameters, such as permittivity, permeability, refractive index, and impedance values, are also investigated over the entire wavelength spectrum, which suggests that the overall structure behaves as a double negative material. The wideband metamaterial structure with topological insulator material can also be compared with the interference mode theory. Metamaterial ; Materials science ; Wideband ; Resonator ; Optoelectronics ; Topological insulator ; Wavelength ; Topology (electrical circuits) ; Microwave ; Metamaterial absorber ; Permittivity ; Optics ; Dielectric ; Physics ; Condensed matter physics Metamaterials and Metasurfaces Applications ; Electromagnetic Scattering and Analysis ; Advanced Antenna and Metasurface Technologies
Authors: Ayaulym Amankeldiyeva | Samal Kaumbekova | Aigerim Khalidulliyeva | Zhanat Salimova | Anel Ibrayeva | Maxime Cochennec | Stéfan Colombano | Yerlan Amanbek | Yanwei Wang | Sagyn Omirbekov
Source: Scientific Reports (article, 2025-07-02)
Field: Chemistry — Organic Chemistry

Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights Colloidal gas aphrons (CGAs) are promising fluids for environmental remediation due to their stability, high viscosity, and effective gas transport. However, previous studies have been limited by narrow concentration ranges, leaving key mechanisms behind bubble stability insufficiently understood. This study systematically explores bubble stability across a wide range of xanthan gum (XG) and sodium dodecyl sulfate (SDS) concentrations (1-10× CMC and 1000-10,000 ppm) using advanced AI-assisted image analysis and molecular dynamics (MD) simulations. AI-enhanced microscopy enabled precise quantification of bubble size and morphology, while MD provided molecular-level insights into surfactant-polymer interactions at bubble interfaces. Results showed optimal CGA stability at specific surfactant-polymer ratios, significantly reducing gas diffusion and bubble coalescence. These integrated experimental and computational methods offer valuable guidelines for designing robust CGA-based remediation fluids. Pulmonary surfactant ; Polymer ; Molecular dynamics ; Colloid ; Stability (learning theory) ; Chemical engineering ; Dynamics (music) ; Materials science ; Chemistry ; Nanotechnology ; Polymer science ; Computer science ; Physics ; Organic chemistry ; Computational chemistry ; Engineering Surfactants and Colloidal Systems ; Phase Equilibria and Thermodynamics ; Indoor Air Quality and Microbial Exposure
Authors: Wenfeng Li | Kun Pan | Yue Huang | Guodong Fu | Wenrong Liu | Jiyu He | Weihua Xiao | Yi Fu | Jin Yu Guo
Source: Agronomy (article, 2025-01-16)
Field: Chemistry — Analytical Chemistry

Monitoring the Maize Canopy Chlorophyll Content Using Discrete Wavelet Transform Combined with RGB Feature Fusion To evaluate the accuracy of Discrete Wavelet Transform (DWT) in monitoring the chlorophyll (CHL) content of maize canopies based on RGB images, a field experiment was conducted in 2023. Images of maize canopies during the jointing, tasseling, and grouting stages were captured using unmanned aerial vehicle (UAV) remote sensing to extract color, texture, and wavelet features and to construct a color and texture feature dataset and a fusion of wavelet, color, and texture feature datasets. Backpropagation neural network (BP), Stacked Ensemble Learning (SEL), and Gradient Boosting Decision Tree (GBDT) models were employed to develop CHL monitoring models for the maize canopy. The performance of these models was evaluated by comparing their predictions with measured CHL data. The results indicate that the dataset integrating wavelet features achieved higher monitoring accuracy compared to the color and texture feature dataset. Specifically, for the integrated dataset, the BP model achieved an R2 value of 0.728, an RMSE of 3.911, and an NRMSE of 15.24%; the SEL model achieved an R2 value of 0.792, an RMSE of 3.319, and an NRMSE of 15.34%; and the GBDT model achieved an R2 value of 0.756, an RMSE of 3.730, and an NRMSE of 15.45%. Among these, the SEL model exhibited the highest monitoring accuracy. This study provides a fast and reliable method for monitoring maize growth in field conditions. Future research could incorporate cross-validation with hyperspectral and thermal infrared sensors to further enhance model reliability and expand its applicability. Canopy ; Feature (linguistics) ; RGB color model ; Wavelet transform ; Wavelet ; Artificial intelligence ; Environmental science ; Remote sensing ; Discrete wavelet transform ; Pattern recognition (psychology) ; Content (measure theory) ; Computer science ; Mathematics ; Botany ; Geology ; Biology Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Smart Agriculture and AI
Authors: Jokin Ezenarro
Source: Analytica Chimica Acta (article, 2025-05-21)
Field: Chemistry — Analytical Chemistry

XYOnion: a layer-based method for splitting datasets into calibration and validation subsets In conclusion, XYOnion offers a practical and reliable approach for dataset splitting in situations where independent test sets are unavailable. By integrating distance information from both predictor and response variables with a layered sampling strategy, the method ensures balanced and representative calibration and validation subsets. This leads to more realistic, reproducible, and trustworthy model evaluations. Chemistry ; Calibration ; Layer (electronics) ; Chromatography ; Statistics ; Organic chemistry Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Smart Agriculture and AI
Authors: Lifang Yin | Yi Zhao | Qiang Gao | Yajun Yin | Tengfei He | Yufei Yang | Ai-Min Ren | Tongshun Wu | Hui Li | Luyi Zou
Source: Chemical Science (article, 2025-12-02)
Field: Materials Science — Materials Chemistry

Regulation of heteroatom positioning in multiple resonance thermally activated delayed fluorescence materials: performance optimization for blue/red emission Strategically incorporating Se into B/N-heteropolycyclic frameworks is key to modulating multiple resonance (MR) systems and developing high-performance TADF materials. Combining density functional theory and spin-component scaled coupled cluster calculations, this study reveals the TADF mechanism regulated by the heavy-atom effect in model molecule BNSSe, and designs two types of high-performance MR-TADF materials based on BNSSe. (1) The blue-emission molecule 1 (469 nm) achieves complementary short-range charge transfer/long-range charge transfer advantages <i>via</i> three <i>para</i>-B-π-N units. Its reverse intersystem crossing rate (<i>k</i> <sub>RISC</sub>) reaches 10<sup>8</sup> s<sup>-1</sup> (three orders of magnitude higher than BNSSe), benefiting from the synergy of a reduced singlet-triplet energy gap, moderately enhanced spin-orbit coupling (SOC), and suppressed structural relaxation. (2) The red-emission molecules 2-7 (≈630 nm) were further developed <i>via</i> a delicately designed π-bonding/non-bonding molecular orbital hybridization strategy. This series of molecules not only maintain a high radiative decay rate but also effectively inhibit the non-radiative decay process, and their design concept is expected to break through the constraints of the traditional energy gap law. Theoretical studies reveal that the spatial position of heteroatoms can modulate molecular geometry and induce axial redistribution of frontier molecular orbital electron density, thereby selectively enhancing the contribution of Se atoms to the excited-state transition orbitals and enabling precise regulation of SOC strength. This work not only deepens the theoretical understanding of the heavy-atom effect mechanism but also provides a new strategy for developing high-performance MR-TADF materials through the targeted regulation of SOC and <i>k</i> <sub>RISC</sub> <i>via</i> atomic site engineering. Heteroatom ; Intersystem crossing ; Density functional theory ; Molecule ; Molecular orbital ; Atomic orbital ; Resonance (particle physics) ; Orbital overlap ; Coupling (piping) Luminescence and Fluorescent Materials ; Organic Light-Emitting Diodes Research ; Magnetism in coordination complexes