jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Marisa Menezes Leal | Nairiane dos Santos Bilhalva | Rosana Santos de Moraes | Paulo Carteri Coradi
Source: AgriEngineering (article, 2025-06-17)
Field: Chemistry — Analytical Chemistry

Physical Classification of Soybean Grains Based on Physicochemical Characterization Using Near-Infrared Spectroscopy The study aimed to determine the physical and physicochemical properties of soybean grains using NIR spectroscopy coupled with multivariate data analysis. The experiment was carried out in two stages: first, individual characterization of defects and healthy grains; then, analyses of samples classified into different types (type I, type II, basic standard, and out of type). The centesimal composition of the grains (crude protein, lipids, water content, crude fiber, starch, and ash) was determined by NIR spectroscopy, and the data were analyzed by ANOVA, Scott-Knott test, principal component analysis (PCA), k-means clustering, and Pearson correlation. The results showed significant variations between defects and commercial types in all the variables evaluated (p &lt; 0.05), with an emphasis on germinated grains (higher protein content) and broken grains (higher fiber content). The PCA explained 66.6% of the total variance in the defect sets and 52.2% of the types, allowing the formation of groups defined by the clustering algorithms. Pearson correlations indicated important interactions between the chemical variables, such as the negative correlation between protein and crude fiber (r = −0.73) and between lipids and water content (r = −0.66). It is concluded that the NIR method combined with multivariate modeling allows for the rapid assessment of soybean grain quality in real time, optimizing, reducing waste in, and increasing the efficiency of post-harvest processes. Characterization (materials science) ; Spectroscopy ; Infrared spectroscopy ; Infrared ; Materials science ; Near-infrared spectroscopy ; Remote sensing ; Analytical Chemistry (journal) ; Chemistry ; Nanotechnology ; Environmental chemistry ; Geology ; Optics ; Physics ; Organic chemistry ; Astronomy Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Food composition and properties
Authors: Junqing Liu | Jun Kang | Ting Zou | Mingxin Hu | Yuchen Zhang | Shulan Lin | Ye Liang | Jialin Zhong | Yi Zhao | Xi Wei
Source: Journal of Nanobiotechnology (article, 2025-04-09)
Field: Materials Science — Biomaterials

Functional cobalt-doped hydrogel scaffold enhances concurrent vascularization and neurogenesis Achieving functional tissue regeneration hinges on the coordinated growth of intricate blood vessels and nerves within the defect area. However, current strategies do not offer a reliable and effective way to fulfill this critical need. To address this challenge, a three-dimensional (3D) gelatin methacryloyl-multi-walled carbon nanotube/cobalt (GelMA-MWCNTs/Co) hydrogel with controlled release of cobalt (Co) ions was developed for hypoxia-mimicking and dual beneficial effects on promoting vasculogenesis and neurogenesis. GelMA-MWCNTs/Co hydrogel exhibited sustained release of Co ions, promoting laden cell viability and long-term cell survival. GelMA-MWCNTs/Co hydrogel effectively enhanced human umbilical vein endothelial cells (HUVECs) vasculogenesis when cocultured with stem cells from apical papilla (SCAP). Moreover, this hydrogel facilitated the interaction between the pre-formed vascular and neural-like structures generated by electrical stimulation-induced SCAP (iSCAP). Furthermore, our in vivo study revealed that the GelMA-MWCNTs/Co hydrogel remarkably enhanced neovascularization and accelerated anastomosis with the host vasculature. The pre-vascularized scaffolds boosted the presence of neural differentiated SCAP in the regenerated tissue. This study provided proof of integrating functional Co ions release materials and dental-derived stem cells within a hydrogel scaffold as a promising potential for achieving simultaneous vascularization and neurogenesis. Vasculogenesis ; Neurogenesis ; Self-healing hydrogels ; Scaffold ; Chemistry ; Regenerative medicine ; Biomedical engineering ; Umbilical vein ; Neural stem cell ; Regeneration (biology) ; Stem cell ; Biophysics ; Nanotechnology ; Cell biology ; Materials science ; Endothelial stem cell ; Biochemistry ; In vitro ; Biology ; Medicine Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; 3D Printing in Biomedical Research
Authors: Xiaohui Wang | Linqiong Qiu | Hongyu Wang | Wenting Tang | Jiali Leng | John Z. H. Zhang | Piero Procacci | Zhaoxi Sun
Source: Advanced Science (article, 2025-12-14)
Field: Chemistry — Organic Chemistry

Achieving Chemical Accuracy in Cyclodextrin Host–Guest Binding via Integrative Atomistic Modelling Cyclodextrins are amphiphilic macromolecular containers that are particularly valuable in applications ranging from biomedicine to environmental science. Despite years of development of computational techniques for cyclodextrin host-guest coordination, accurate modelling of these supramolecular systems remains challenging. In this work, an integrative computational technique is presented to solve this problem. The protocol integrates a force-field recalibration procedure, equilibrium enhanced sampling, nonequilibrium Hamiltonian switching, a work convolution algorithm, a series of finite-size corrections, and energy decomposition analysis. A large-scale survey of 222 CD host-guest systems is performed to demonstrate that the protocol enables the fast calculation of cyclodextrin host-guest binding strength without compromise in accuracy, an unbiased capture of cyclodextrin dynamics in the free CD, and the multi-modal behavior of the coordination patterns, and further the identification of the physicochemical driving force stabilizing host-guest complexes. Especially, the protocol consistently provides accurate results for various systems while conventional transferable force fields systematically fail for larger and more flexible 𝛾-CD. It thus opens new opportunities for high-throughput screening and rational design across diverse macrocyclic host families. Cyclodextrin ; Supramolecular chemistry ; Molecular dynamics ; Rational design ; Macromolecule ; Protocol (science) ; Ranging ; Amphiphile Supramolecular Chemistry and Complexes ; Drug Solubulity and Delivery Systems ; Crystallography and molecular interactions
Authors: Maria Wahle | Philip M. Remes | Vincent Albrecht | Michal Lorenz | Johannes B. Mueller‐Reif | Sophia Steigerwald | Tim Heymann | Lili Niu | Philip Lössl | Stevan Horning | Cristina C. Jacob | Matthias Mann
Source: Molecular & Cellular Proteomics (article, 2025-08-13)
Field: Chemistry — Spectroscopy

A Novel Hybrid High-Speed Mass Spectrometer Allows Rapid Translation From Biomarker Candidates to Targeted Clinical Tests Using 15N-Labeled Proteins Recent developments in affinity binder or mass spectrometry (MS)-based plasma proteomics are now producing panels of potential biomarker candidates for diagnosis or prognosis. However, clinical validation and implementation of these biomarkers remain limited by the reliance on dated triple quadrupole MS technology. Here, we evaluate a novel hybrid high-speed mass spectrometer, Stellar MS, which integrates the robustness of triple quadrupoles with the enhanced capabilities of an advanced linear ion trap analyzer. This instrument allows for extremely rapid and sensitive parallel reaction monitoring (PRM) and MS3 targeting. The Stellar MS allowed targeting thousands of peptides originally measured on Orbitrap Astral MS, achieving high reproducibility and low coefficients of variation (CV) as well as sensitivity and specificity sufficient for many of the top 1000 plasma proteins. Furthermore, we developed targeted assays for alcohol-related liver disease (ALD) biomarkers, showcasing the potential of Stellar MS in clinical applications. Absolute quantification is typically a requirement for clinical assays, and we explore the use of <sup>15</sup>N-labeled protein standards in a rapid, streamlined, and generic manner. Our results indicate that the Stellar MS can bridge the gap between proteomics discovery and routine clinical testing, enhancing the diagnostic and prognostic utility of protein biomarkers. Mass spectrometry ; Translation (biology) ; Biomarker ; Computational biology ; Proteomics ; Computer science ; Chemistry ; Biology ; Chromatography ; Genetics ; Gene ; Messenger RNA Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ashtar S. Al-Luhybi | Taghreed Khaleefa Mohammed Ali | Diyar N. Qader | Mujahid Ali | Nelson Maureira-Carsalade | Pablo F. Parra | Siva Avudaiappan
Source: Scientific Reports (article, 2025-07-01)
Field: Materials Science — Polymers and Plastics

Evaluating the mechanical performance and durability of cement mortars incorporating sesame shells as partial cement and sand replacement This study examines the mechanical and durability behaviors of cement mortar containing sesame shells (SS) as partial substitutes of cement and sand with regard to sustainable construction using an agricultural by-product. Three types of SS-raw powder, vinegar-treated powder and vinegar-thermal-treated powder (250 °C)-were used as the fine aggregate replacements at 1%, 2%, and 3% by weight. Mechanical performances (compressive strength, dry density) and durability (UPV, water absorption, water porosity, workability) of the composites were investigated in a systematic manner. Results show that substituting sand with SS causes a significant decrease in the compressive strength (up to 54% at 3%of replacement) and the increase in porosity and water absorption that compromised the durability. On the contrary, the use of SS, particularly the treated one, caused strength decrease (up to 42.3%) with improved durability properties specifically lower porosity (8.84%) and lower water absorption (1.7%). UPV of all mixes were above 4.2 km/s representing good internal consistency. Error bars were included in all test figures with replicate specimens to properly demonstrate the variation and to reinforce the reliability of the data. The findings suggest that the optimal use of SS is as a 3% cement replacement in treated form, offering an environmentally friendly alternative with acceptable mechanical performance and significantly improved durability. Durability ; Cement ; Mortar ; Materials science ; Composite material ; Geotechnical engineering ; Geology Natural Fiber Reinforced Composites ; Recycling and utilization of industrial and municipal waste in materials production ; Innovations in Concrete and Construction Materials
Authors: Yongjae Jo | Hyemi Park | Seho Lee | Hyeyoung Yoon | Tae Hoon Lee | Gyusoo Bak | Hanjun Cho | Jong‐Chan Park | Inki Kim
Source: Light Science & Applications (article, 2025-10-13)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Image scanning microscopy based on multifocal metalens for sub-diffraction-limited imaging of brain organoids Image scanning microscopy (ISM) is a promising imaging technique that offers sub-diffraction-limited resolution and optical sectioning. Theoretically, ISM can improve the optical resolution by a factor of two through pixel reassignment and deconvolution. Multifocal array illumination and scanning have been widely adopted to implement ISM because of their simplicity. Conventionally, digital micromirror devices (DMDs)<sup>1</sup> and microlens arrays (MLAs)<sup>2,3</sup> have been used to generate dense and uniform multifocal arrays for ISM, which are critical for achieving fast imaging and high-quality ISM reconstruction. However, these approaches have limitations in terms of cost, numerical aperture (NA), pitch, and uniformity, making it challenging to create dense and high-quality multifocal arrays at high NA. To overcome these limitations, we introduced a novel multifocal metalens design strategy called the hybrid multiplexing method, which combines two conventional multiplexing approaches: phase addition and random multiplexing. Through numerical simulations, we demonstrate that the proposed method generates more uniform and denser multifocal arrays than conventional methods, even at small pitches. As a proof of concept, we fabricated a multifocal metalens generating 40 × 40 array of foci with a 3 μm pitch and NA of 0.7 operating at a wavelength of 488 nm and then constructed the multifocal metalens-based ISM (MMISM). We demonstrated that MMISM successfully resolved sub-diffraction-limited features in imaging of microbead samples and forebrain organoid sections. The results showed that MMISM imaging achieved twice the diffraction-limited resolution and revealed clearer structural features of neurons compared to wide-field images. We anticipate that our novel design strategy can be widely applied to produce multifunctional optical elements and replace conventional optical elements in specialized applications. Microbead (research) ; Microlens ; Digital micromirror device ; Microscopy ; Numerical aperture ; Pixel ; STED microscopy ; Multiplexing ; Resolution (logic) ; Image resolution Metamaterials and Metasurfaces Applications ; Random lasers and scattering media ; Digital Holography and Microscopy
Authors: Nader Javanmard | Mahdi Sovizi | Maryam Aliannezhadi
Source: Scientific Reports (article, 2025-10-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Theoretical and experimental study into laser-induced gold nanoparticles for superior surface-enhanced raman spectroscopy applications This study presents a comprehensive theoretical and experimental investigation into the fabrication of three-dimensional gold nanostructures with tailored optical properties using a laser-induced method, aimed at enhancing applications based on localized surface plasmon resonance (LSPR) and Surface-Enhanced Raman Spectroscopy (SERS). The effects of the second harmonic (without filtering the fundamental harmonic) of Nd:YAG laser pulses, along with key parameters such as laser fluence and pulse count, are analyzed to achieve precise control over nanoparticle size, shape, and arrangement. Theoretical modeling using Fourier heat equations and the novel Generalized Finite Difference Time Domain (G-FDTD) method provides initial insights into the optical fluences necessary for the formation of surface gold nanoparticles. Experimentally, 100 nm gold thin films are irradiated with different fluences (0.48, 0.12, and 0.053 J/cm<sup>2</sup>) and pulse numbers (ranging from 1 to 50 pulses) of Nd:YAG laser with a time width of 60 ns. Results demonstrate that manipulating laser parameters significantly influences the localized surface plasmon resonance, offering a scalable and reproducible platform for designing stable, biocompatible, and high-performance nanostructures for applications based on LSPR, like SERS and enhanced fluorescence. Also, the formed gold elliptical NPs are simulated to understand the obtained results and the efficiency of the samples in SERS applications. Surface-enhanced Raman spectroscopy ; Surface plasmon resonance ; Colloidal gold ; Raman spectroscopy ; Plasmon ; Laser ; Fluence ; Nanostructure Gold and Silver Nanoparticles Synthesis and Applications ; Laser-Ablation Synthesis of Nanoparticles ; Laser-induced spectroscopy and plasma
Authors: Ryan Lee | Montek Singh Boparai | Timothy Q. Duong
Source: Journal of Translational Medicine (review, 2025-01-31)
Field: Materials Science — Materials Chemistry

Detection of breast cancer lesions using APT weighted MRI: a systematic review Amide proton transfer (APT) is a novel magnetic resonance imaging (MRI) technique that has shown promising ability to study cancers. This paper systematically reviewed the literature on the use of APT MRI in the prognosis of breast cancer. A literature search was conducted on Pubmed and Embase and a total of 14 articles comprising 775 patients were included in the review. APT MRI had the ability to distinguish between benign and malignant lesions with an AUC as high as 0.959. There is a positive correlation between APT signal intensity and tumor grade/stage as well as Ki-67, whereas no correlation was found with ER/PR/Her-2 receptor status. There was a greater decrease in APT signal intensity after neoadjuvant chemotherapy (NAC) in responders compared to non-responders, suggesting that APT MRI may serve as a valuable supplemental tool in the early identification of chemotherapy response. APT has the potential to complement with other imaging methods in the diagnosis, prognosis, treatment monitoring, and management of breast cancer. Additional studies and standardization of APT acquisition methods are needed. Medicine ; Breast cancer ; Magnetic resonance imaging ; Cancer ; Radiology ; Chemotherapy ; Stage (stratigraphy) ; Breast MRI ; Oncology ; Internal medicine ; Mammography Lanthanide and Transition Metal Complexes ; Advanced MRI Techniques and Applications ; MRI in cancer diagnosis
Authors: Valentina Di Nisio | Tianyi Li | Zhijie Xiao | Kiriaki Papaikonomou | Anastasios Damdimopoulos | Ákos Végvári | Filipa Lebre | Ernesto Alfaro‐Moreno | Mikael Pedersen | Terje Svingen | Roman A. Zubarev | Ganesh Acharya | Pauliina Damdimopoulou | Andres Salumets
Source: Human Reproduction Open (article, 2025-01-01)
Field: Materials Science — Biomaterials

Silk-Ovarioids: establishment and characterization of a human ovarian primary cell 3D-model system This study was funded by: a research grant from the Center for Innovative Medicine (CIMED) at Karolinska Insitutet; European Union's Horizon 2020 Research and Innovation Programme (project ERIN no. 952516); a Horizon Europe grant (NESTOR, grant no. 101120075) of the European Commission; the Swedish Research Council for Sustainable Development FORMAS (2018-02280, 2020-01621); StratRegen Funding from Karolinska Institute, Swedish Research Council VR (grant no. 2020-02132); Swedish Childhood Cancer Fund (Reference PR2017-0044, PR2020-0096); Estonian Research Council (grant no. PRG1076); Swedish Research Council (grant no. 2024-02530); Novo Nordisk Foundation (grant no. NNF24OC0092384); European Union's H2020 project Sinfonia (no. 857253) (INL research); and SbDToolBox, with reference NORTE-01-0145-FEDER-000047, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (INL research). The authors have no conflicts of interest to declare. Computational biology ; Biology ; Evolutionary biology Silk-based biomaterials and applications
Authors: He Lin | Fuyuan Shen | Zuojun Zhang | Jun Luo | Cheng Huang | Mingbo Pu | Yuetang Wang | Jianping Shi | Xiaoliang Ma | Xiangang Luo
Source: Nanophotonics (article, 2025-07-31)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Trans‐scale hierarchical metasurfaces for multispectral compatible regulation of lasers, infrared light, and microwaves Electromagnetic scattering control of optical windows has significant challenges in improving optical transmission and compatibility, especially for multispectral and large-angle incidences, due to material and structure mismatches. This paper presents trans-scale hierarchical metasurfaces (THM) to achieve wide-angle optical transmission enhancement and electromagnetic scattering-compatible regulation in dual-band lasers, and infrared and microwave ranges. THM comprises an ultrafine hollow metal array (UHMA) and a transmission-enhanced micro-nanocone array (TMCA). The UHMA regulates microwave radar cross-section (RCS) echo diffuse reflection, while the upper-layer TMCA enables wide-angle optical transmission enhancement. A THM sample of 200 × 200 mm<sup>2</sup> was fabricated using multistage nanolithography, demonstrating exceptional multifunctional compatibility and optical performance. Results show that the THM sample achieves 10 dB scattering reduction in the 9.5-17.5 GHz microwave band, with average optical transmittance exceeding 90 % at 0°-60° incidence angles within optical ranges of 1.42, 1.7, and 3-5 μm. Compared to a zinc sulfide (ZnS) window with a UHMA on its surface, the THM improved the average transmission by 34.3 % over wide angles while allowing microwave scattering control. Broadband polarization-independent, low-crosstalk imaging, and hydrophobic characteristics were demonstrated. This study provides a design approach for multifunctional devices with synergistic optical and microwave regulation, particularly for optical transparency in microwave devices. Multispectral image ; Infrared ; Microwave ; Nanomaterials ; Laser ; Optoelectronics ; Materials science ; Optics ; Metamaterial ; Scale (ratio) ; Remote sensing ; Nanotechnology ; Telecommunications ; Physics ; Computer science ; Geology Metamaterials and Metasurfaces Applications ; Optical Wireless Communication Technologies ; Plasmonic and Surface Plasmon Research
Authors: Piya Prajumwongs | Attapol Titapun | Vasin Thanasukarn | Apiwat Jareanrat | Natcha Khuntikeo | Krit Rattanarak | Nisana Namwat | Poramate Klanrit | Arporn Wangwiwatsin | Jarin Chindaprasirt | Supinda Koonmee | Prakasit Sa-Ngiamwibool | Nattha Muangritdech | Sawanya Charoenlappanit | Janthima Jaresitthikunchai | Sittiruk Roytrakul | Watcharin Loilome
Source: Scientific Reports (article, 2025-08-09)
Field: Chemistry — Spectroscopy

Serum peptide biomarkers by MALDI-TOF MS coupled with machine learning for diagnosis and classification of hepato-pancreato-biliary cancers This study aimed to investigate the potential of peptide mass fingerprints (PMFs) of the serum peptidome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), in combination with machine learning algorithms-support vector machine (SVM) and random forest (RF)-for the diagnosis and classification of hepato-pancreato-biliary (HPB) cancers. Serum samples collected from healthy individuals and patients with various HPB cancers were analyzed to generate PMF profiles. The resulting data were randomly split into training and testing sets. Feature selection on the training set identified 71 informative peptide mass fingerprints, which were then used to construct predictive models using SVM and RF algorithms. Visualization using heatmap, PLS-DA, and multiclass RF analysis showed clear separation between healthy individuals and HPB cancer patients, as well as among different HPB cancer subtypes. Both models achieved high classification performance, with accuracy, AUROC, and MCC values exceeding 0.90 in both training and testing datasets. Notably, the models also exhibited strong multiclass discrimination ability. These findings demonstrate that serum PMF profiling using MALDI-TOF MS, combined with SVM and RF models, enables high-performance, non-invasive detection and classification of HPB cancers, with strong potential to support early diagnosis and inform clinical decision-making. Peptide ; Medicine ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Metabolomics and Mass Spectrometry Studies