jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Rahma SR. Mahrous | Basem Abdel Fattah | Yousef Abdel Rahman | Shaimaa M. Sallam | Eman Shawky
Source: Food and Bioprocess Technology (article, 2025-09-15)
Field: Chemistry — Spectroscopy

Green and Efficient Extraction of Soybean (Glycine max (L.) Merr.) Isoflavones Using Natural Deep Eutectic Solvents-Based Ultrasound-Assisted Extraction Abstract Soybean ( Glycine max (L.) Merr.) is considered a key global food source, valued for their bioactive isoflavones, which exhibit antioxidant, anti-inflammatory, and phytoestrogenic properties. However, conventional solvent-based extractions face challenges such as low selectivity, inefficient recovery of glycosylated isoflavones, and environmental concerns. This study developed a green, efficient extraction method using Natural Deep Eutectic Solvent (NADES)-based ultrasound-assisted extraction (UAE). A choline chloride-ascorbic acid (1:1) NADES system yielded 795.8 µg/g DW isoflavones, outperforming conventional 50% ethanol extraction (723.5 µg/g DW). Optimization using Box-Behnken Design identified 39% water content, 55 °C, and 64 min as ideal conditions, with water content and temperature being key factors. These optimized NADES conditions resulted in isoflavone extraction yield of (1076.78 µg/g DW). COSMO-RS computational modeling revealed NADES-isoflavone interactions, emphasizing hydrogen bonding and polarity. This eco-friendly method enhances efficiency, reduces environmental impact, and supports NADES as a sustainable alternative for bioactive phytochemical extraction. Extraction (chemistry) ; Isoflavones ; Yield (engineering) ; Deep eutectic solvent ; Phytochemical ; Water extraction Analytical Chemistry and Chromatography ; Phytoestrogen effects and research ; Metabolomics and Mass Spectrometry Studies
Authors: Denise Ziegler | Lukas Buck | Katharina Anne Scherf | Lutz Popper | Alexander Schaum | Bernd Hitzmann
Source: Food Analytical Methods (article, 2025-12-05)
Field: Chemistry — Analytical Chemistry

Improved Prediction of Wheat Quality and Functionality Using Near-Infrared Spectroscopy and Novel Approaches Involving Flour Fractionation and Data Fusion Abstract The accurate and rapid determination of wheat quality is of great importance for the wheat supply chain. Near-infrared (NIR) spectroscopy has become an established method for this purpose. So far, however, predictions for most wheat quality characteristics are not accurate enough to replace reference measurements, with the exception of protein content. This study investigates the potential to improve the prediction of 41 wheat quality parameters (protein- and starch-related parameters, solvent retention capacity, farinograph, extensograph, alveograph) based on a flour fractionation approach (sieve fractionation, dough preparation, gluten washing) and data fusion using the established techniques of NIR spectroscopy and chemometrics. Results show that preprocessing of flour significantly altered the composition of the samples, which reflected in spectral differences of their NIR spectra. This also led to a change in the prediction accuracy for many wheat quality parameters. Compared to the prediction using flour spectra, flour fractionation with or without data fusion improved the RMSECV between 5.6 and 28.6% for 35 out of the 41 quality parameters tested, leading to R 2 CV between 0.80 and 0.96 for many of them. Gluten, dough, and the 50–75 µm and the 75–100 µm fractions were particularly important for the improved predictions. The best predictions were often based on data fusion of spectra from different sample types, demonstrating the importance of using complementary information from different data sources to improve predictions. The results underline the potential of this novel approach to be established in the industry as an extension of conventional NIR spectroscopy to improve wheat quality prediction. Fractionation ; Fusion ; Wheat flour ; Spectroscopy ; Sensor fusion ; Quality (philosophy) ; Gluten ; Chemometrics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Food composition and properties
Authors: Neha Singh | Supriya Das | Kuladip Barman | Balak Das Kurmi | Preeti Patel
Source: International Journal of Medical Pharmaceutical and Health Sciences (IJMPHS). (article, 2025-06-30)
Field: Chemistry — Spectroscopy

Analytical Mass Spectrometry as a Versatile Tool in Omics, Diagnostics, and Environmental Monitoring Mass spectrometry (MS) has become an essential tool across all sciences with unparalleled precision, sensitivity, and structural interpretation. This review covers the fundamentals, instrumentation, and applications of MS and its central role in modern analytical chemistry. New developments such as soft ionisation techniques (ESI, MALDI), high resolution mass analysers (Orbitrap, FT-ICR-MS) and hyphenated methods (LC-MS, GC-MS) have expanded the analytical scope of MS, allowing the identification and quantitation of complex analytes in biological, environmental, clinical and industrial matrices. It also explores the impact of mass spectrometry (MS/MS) in systems biology, particularly in proteomics, where it gives deep molecular insights at cellular, tissue, organismal and ecological levels. Applications in biofluid proteomics show MS role in biomarker discovery, non-invasive diagnostics, and enzyme activity assessment. Combining MS with computational tools from molecular dynamics to AI-driven spectral interpretation enhances structural prediction and data analysis, bridging experimental and theoretical chemistry. Miniaturisation of MS and lab-on-chip platforms are enabling real-time, point-of-care analysis. Overall, these developments put analytical mass spectrometry at the forefront of scientific innovation, allowing high-throughput, multi-dimensional characterisation of matter essential for progress in life sciences, environmental monitoring, forensic science, and pharmaceutical development. &nbsp; &nbsp; Mass spectrometry ; Environmental monitoring ; Omics ; Environmental chemistry ; Environmental science ; Computer science ; Computational biology ; Data science ; Chemistry ; Chromatography ; Bioinformatics ; Biology ; Environmental engineering Mass Spectrometry Techniques and Applications ; Pesticide Residue Analysis and Safety ; Advanced Chemical Sensor Technologies
Authors: James N. Cobley
Source: European Journal of Applied Physiology (review, 2025-12-19)
Field: Chemistry — Spectroscopy

Proteoforms as the true units of physiological function Proteomics has matured into a discipline capable of quantifying nearly every protein encoded by the genome, yet it remains largely blind to the true operational units of physiology: proteoforms. Each proteoform—defined by a specific sequence and post-translationally modified state—represents a unique molecular identity with distinct chemical, functional, and structural properties. This review proposes the proteoform functor: a mathematical map between the abstract proteoform state space and the realised physiological space of biological function—and ultimately complex phenotypes. This mapping is not linear or additive. Rather, it is hierarchical, nonlinear, and context-dependent, reflecting the emergent complexity of life. Without resolving proteoforms, proteomics risks describing shadows of biology rather than its material substance. Deciphering complex phenotypes, demands a shift from bulk protein averages to revealing the precise molecular identities—proteoforms—that give rise to physiology. Proteomics ; Sequence (biology) ; Function (biology) ; State space ; State (computer science) ; Human physiology ; Space (punctuation) Advanced Proteomics Techniques and Applications ; Biotin and Related Studies ; Origins and Evolution of Life
Authors: Nabeel Khalid | Mohammadmahdi Koochali | Khola Naseem | Maria Caroprese | Gillian Lovell | Daniel A. Porto | Johan Trygg | Andreas Dengel | Sheraz Ahmed
Source:  (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

SAT: Segment and Track Anything for Microscopy Integrating cell segmentation with tracking is critical for achieving a detailed and dynamic understanding of cellular behavior. This integration facilitates the study and quantification of cell morphology, movement, and interactions, offering valuable insights into a wide range of biological processes and diseases. However, traditional methods rely on labor-intensive and costly annotations, such as full segmentation masks or bounding boxes for each cell. To address this limitation, we present SAT: Segment and Track Anything for Microscopy, a novel pipeline that leverages point annotations in the first frame to automate cell segmentation and tracking across all subsequent frames. By significantly reducing annotation time and effort, SAT enables efficient and scalable analysis, making it well-suited for large-scale studies. The pipeline was evaluated on two diverse datasets, achieving over 80% Multiple Object Tracking Accuracy (MOTA), demonstrating its robustness and effectiveness across various imaging modalities and cell types. These results highlight SAT’s potential to streamline biomedical research and enable deeper exploration of cellular behavior. Track (disk drive) ; Microscopy ; Computer science ; Computer graphics (images) ; Computer vision ; Artificial intelligence ; Optics ; Physics ; Operating system Machine Learning in Materials Science ; Cell Image Analysis Techniques
Authors: Wenjing Zhu | Kaiwen Duan | Xiao Li | Kai Yu | Changfeng Shao
Source: Applied Sciences (article, 2025-05-14)
Field: Chemistry — Analytical Chemistry

Rapid Detection of Key Phenotypic Parameters in Wheat Grains Using Linear Array Camera To address the limitations of traditional manual measurements of phenotypes, a study focused on the rapid acquisition of phenotypic parameters in wheat grains was conducted. This research introduced an index for bud-point determination, which offers valuable insights into breeding selection, optimizing sowing and growth direction for grains, and assessing seed vitality. A grain collection device utilizing a linear array camera was designed and constructed, accompanied by custom software to simplify device operation. Image processing was performed using Halcon image, enabling the development and implementation of a system for extracting key phenotypic parameters. The preprocessing method involves isolating wheat grain regions, combined with S channel extraction, global thresholding, and opening and closing operations to achieve robust segmentation. Based on this preprocessing method, a phenotypic analysis was performed by evaluating the geometric characteristics of wheat grains. The process for extracting phenotypic characteristics and determining the bud point was subjected to experimental analysis. The results demonstrated high correlation and accuracy. The errors estimating the comprehensive grain length of five wheat varieties using the extraction algorithm developed in this study, the determination coefficient and root mean square error indices, were 0.986 and 0.0887, respectively, compared with manual measurements. Similarly, for grain width, the determination coefficient and RMSE were 0.9505 and 0.0541; for grain weight, these values were 0.7635 and 3.8329, respectively. Furthermore, the algorithm achieved a bud point direction determination accuracy rate of 97.5%. The mean error in the positioning accuracy of germination points was within 0.10 mm, and the mean angular error was maintained within ±3 degrees. The phenotype analysis of wheat using the image processing techniques presented in this study shows strong consistency with manual detection methods, providing valuable quantitative data to assist in breeding selection and accelerate genetic improvement practices. Key (lock) ; Computer science ; Computer vision Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Genetic Mapping and Diversity in Plants and Animals
Authors: Kimberly Intonti | Adolfo Mazzotti | Aniello Pelella | Filippo Giubileo | Nadia Martucciello | Stephen O’Sullivan | Vilas Patil | Paul K. Hurley | Lida Ansari | Farzan Gity | Antonio Di Bartolomeo
Source: Materials Horizons (article, 2025-12-12)
Field: Materials Science — Materials Chemistry

Ambipolar to anti-ambipolar light-induced transition in WSe <sub>2</sub> -based FETs The growing need for efficient processing of large amounts of data in compact electronic systems is driving interest in investigating alternative device architectures. 2D material-based devices exhibiting anti-ambipolar behaviour represent a promising option to address this need. In this work, we investigate a WSe<sub>2</sub>-based field-effect transistor that shows ambipolar conduction with dominant n-type behaviour in the dark. Under illumination, using either diffuse white LED light or a collimated red laser, the device exhibits a transition to anti-ambipolar transport, with a prominent current peak in a narrow driving voltage range, which is desirable for fast switching logic applications. This response allows for the identification, under controlled illumination conditions, of three distinct current levels in three different bias regions, which are suitable for implementing a three-state logic device. The peak amplitude varies linearly with light intensity, and the corresponding photodetection performance results in a significant responsivity of 0.13 A W<sup>-1</sup> under red laser illumination. The light-induced transition from ambipolar to anti-ambipolar behaviour is qualitatively described through energy band diagrams, with the photocurrent peak corresponding to the n-p transition point observed in the dark. Ambipolar diffusion ; Responsivity ; Photodetection ; Transistor ; Current (fluid) ; Photocurrent ; Laser ; Band gap ; Chalcogenide 2D Materials and Applications ; Graphene research and applications ; Topological Materials and Phenomena
Authors: Domingo Martínez‐Soto | Erisneida Campos-Jiménez | Alejandro Cabello‐Pasini | Luis Enrique García-Marín | Anaid Meza-Villezcas | Ernestina Castro‐Longoria
Source: Journal of Fungi (article, 2025-10-06)
Field: Materials Science — Biomaterials

Evaluation of Fungal Sensitivity to Biosynthesized Copper-Oxide Nanoparticles (CuONPs) in Grapevine Tissues and Fruits Grape production is one of the most agronomically important activities worldwide. However, it is threatened by diseases caused by phytopathogenic microorganisms, which cause severe economic losses. The primary strategy to control phytopathogenic fungi is the application of fungicides; however, they affect the environment and induce resistance in fungi. Nanomaterials, especially those green-synthesized, emerge as an eco-friendly and sustainable alternative to control fungal pathogens. The objective of this work is to evaluate the sensitivity of fungal phytopathogens to biosynthesized copper-oxide nanoparticles (CuONPs). Nanoparticles were evaluated as preventive and corrective treatments in grapevine green tissues and fruits under field conditions, using in vitro and in vivo experimental approaches. Interestingly, corrective treatment was highly effective and showed little accumulation of Cu on the fruits, even less than a commercial copper-based fungicide. Moreover, we report that <i>Aspergillus niger</i> causes lesions in photosynthetic tissues and severe disease symptoms in grapes. We also describe for the first time the presence of <i>Alternaria alternata</i> causing lesions, mainly on the stems and young leaves of grapevine plants in Mexico. These pathogens were inhibited by the biosynthesized CuONPs. All these findings show the effectiveness of using CuONPs to control phytopathogenic fungi, even under field conditions, shedding light on their potential use in agriculture with a less environmental impact than the commercial fungicides and agrochemicals currently used. Fungicide ; Photosynthesis ; Inoculation ; Agrochemical ; Solanaceae ; Biological pest control ; Fructification ; Vitis vinifera Nanocomposite Films for Food Packaging ; Banana Cultivation and Research ; Pineapple and bromelain studies
Authors: Jan Leppert | Tillman Brehmer | Matthias Wüst
Source: ChemRxiv (preprint, 2025-08-05)
Field: Chemistry — Spectroscopy

Prediction of thermal modulated comprehensive two-dimensional gas chromatographic separation using a modular, graph-based simulation platform Comprehensive two-dimensional gas chromatography (GC×GC) offers exceptional separation performance, but method development remains time-consuming and sensitive to numerous system parameters. In this study, we present a modular simulation framework for GC×GC systems with thermal modulation, implemented in the open-source Julia package GasChromatographySystems.jl. The simulation is based on a graph-based abstraction of the GC system and models solute migration through column and modulator modules using previously established retention models. A simplified but effective model for thermal modulation enables the generation of realistic two-dimensional retention times and peak widths. Simulation results were validated against experimental measurements from a GC×GC–ToF-MS system using different modulation periods and temperature programs. Systematic deviations between simulated and measured retention times could be explained and corrected by adjusting parameters such as actual modulation period, modulator shift, and column film thicknesses. The final model achieved root mean squared error (rmse) of below 20 s (less than 1 %) for first-dimension retention times and 50 ms (5 %) for the second dimension. Peak width predictions were less accurate, with deviations of up to 2 s (40 %) in the first dimension and up to 40 ms (70 %) in the second. This modular and adaptable simulation framework provides a robust foundation for future applications in automated method development and system diagnostics in multidimensional gas chromatography. Modular design ; Separation (statistics) ; Chromatography ; Chromatographic separation ; Graph ; Computer science ; Thermal ; Chemistry ; Process engineering ; Engineering ; Machine learning ; Theoretical computer science ; Physics ; Programming language ; High-performance liquid chromatography ; Thermodynamics Analytical Chemistry and Chromatography ; Chromatography in Natural Products ; Microfluidic and Capillary Electrophoresis Applications
Authors: Li‐Ping Liu | Changsheng Ma | Jinfeng Ji | Rong Gao | Deliang Li
Source: Oncology Letters (review, 2025-04-02)
Field: Chemistry — Organic Chemistry

Role of antidiarrheal agents nifuroxazide in antitumor multi‑target anticancer, multi‑mechanism anticancer drug (Review) Nifuroxazide (NFZ) is an antimicrobial drug, which has been found to be a promising antitumor agent in recent years. In addition to being a classic STAT3 inhibitor, NFZ can also act on IL-6 and exert an anti-tumor role through inflammatory factor pathways. It can also bind to target proteins of aldehyde dehydrogenase 1, one of the families of E-twenty-six transcription factors and ubiquitin-specific protease 21 to play an anti-tumor role in different pathways. NFZ is able to act on the tumor cell microenvironment to inhibit tumor angiogenesis and tumor cell migration, enhance tumor immune cells, increase the cytotoxicity of tumor cells and enhance the anti-tumor effect of other drugs. Furthermore, it has high safety with few toxic side effects. The anti-tumor mechanisms of NFZ were described in the current review, aiming to provide insight and a reference for future studies promoting the implementation of NFZ as an anti-tumor drug in the clinic. Mechanism (biology) ; Oncogene ; Pharmacology ; Anticancer drug ; Molecular medicine ; Drug ; Cell cycle ; Medicine ; Cancer ; Traditional medicine ; Chemistry ; Internal medicine Synthesis and Reactions of Organic Compounds ; Synthesis and biological activity
Authors: Núria Blanco‐Cabra | Joana Admella | Eduard Torrents
Source: Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology (article, 2025-09-01)
Field: Materials Science — Materials Chemistry

<scp> <i>Galleria mellonella</i> </scp> as a Simple Yet Reliable In Vivo Model for Nanotoxicology: Techniques and Applications Nanomaterials are a rapidly advancing tool with applications across various scientific fields. However, their interactions with living organisms have raised numerous safety concerns, making it crucial to develop reliable models to predict and evaluate associated toxicity effects. Traditional in vitro assays fail to mimic the true physiological responses of living organisms to nanomaterials, whereas murine and other in vivo models are time-consuming, costly, and ethically controversial. The greater wax moth, Galleria mellonella, has emerged as a promising in vivo model for nanotoxicology, serving as an effective bridge between in vitro and in vivo mammalian testing. This model combines simplicity and ethical viability with a human-conserved innate immune system, making it ideal for immunotoxicity testing. While it cannot fully replace more complex animal models, G. mellonella represents a valuable alternative for early-stage nanotoxicology screening and deserves greater recognition and integration into toxicological research. In this review, we examine all the methodologies and applications of G. mellonella in nanotoxicological studies, highlighting its potential as a reliable and ethical model for assessing nanomaterial safety. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials. Nanotoxicology ; Simplicity ; Nanomedicine ; In vivo ; Galleria mellonella ; Innate immune system ; In vitro toxicology ; Biodefense Nanoparticles: synthesis and applications ; Nanomaterials for catalytic reactions ; Nanoparticle-Based Drug Delivery
Authors: R.A. Scott | Iain Lyburn | Eleanor Cornford | Pascaline Bouzy | Nicholas Stone | Charlene Greenwood | Sarah Gosling | Emily L. Arnold | Ihsanne Bouybayoune | Sarah E. Pinder | Keith D. Rogers
Source: Scientific Reports (article, 2025-02-14)
Field: Materials Science — Materials Chemistry

Anisotropy visualisation from X-ray diffraction of biological apatite in mixed phase calcified tissue samples X-ray diffraction is widely used to characterise the mineral component of calcified tissue. Broadening of the diffraction peaks yields valuable information on the size of coherently diffracting domains, sometimes loosely described as crystallite size or crystallinity. These domains are markedly anisotropic, hence a single number describing their size is misleading. We present a novel variation on a method for visualising crystallographic anisotropy in X-ray diffraction data. This provides an intuitively interpretable depiction of crystalline domain size and anisotropy. The new method involves creating a polar plot of calculated domain thickness for peaks in a diffractogram versus crystallographic direction. Points with the least error are emphasised. Anisotropic domain dimensions are calculated by refining an ellipsoidal model in a whole pattern fit. These dimensions are then used to overlay an ellipse on the peak broadening plot. This is illustrated by application of the method to calcifications in breast tissue with suspected cancer, which frequently contain whitlockite as well as nanocrystalline apatite. Like most biogenic apatite, this exhibits markedly anisotropic peak broadening. The nature of this anisotropy offers potentially useful information on normal function and pathology of calcified tissue and is a frequently neglected crystallographic feature of these materials. Anisotropy ; Diffraction ; Apatite ; Materials science ; Nanocrystalline material ; Crystallite ; Crystallography ; X-ray crystallography ; Texture (cosmology) ; Mineralogy ; Chemistry ; Optics ; Physics ; Computer science ; Artificial intelligence X-ray Diffraction in Crystallography ; Radiation Shielding Materials Analysis ; Bone health and osteoporosis research