jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Emily J. Gaizley | Xiuyuan Chen | Amandeep Bhamra | Tariq Enver | Silvia Šurinová
Source: Communications Biology (article, 2025-04-26)
Field: Chemistry — Spectroscopy

Multiplexed phosphoproteomics of low cell numbers using SPARCE Understanding cellular diversity and disease mechanisms requires a global analysis of proteins and their modifications. While next-generation sequencing has advanced our understanding of cellular heterogeneity, it fails to capture downstream signalling networks. Ultrasensitive mass spectrometry-based proteomics enables unbiased protein-level analysis of low cell numbers, down to single cells. However, phosphoproteomics remains limited to high-input samples due to sample losses and poor reaction efficiencies associated with processing low cell numbers. Isobaric stable isotope labelling is a promising approach for reproducible and accurate quantification of low abundant phosphopeptides. Here, we introduce SPARCE (Streamlined Phosphoproteomic Analysis of Rare CElls) for multiplexed phosphoproteomic analysis of low cell numbers. SPARCE integrates cell isolation, water-based lysis, on-tip TMT labelling, and phosphopeptide enrichment. SPARCE outperforms traditional methods by enhancing labelling efficiency and phosphoproteome coverage. To demonstrate the utility of SPARCE, we analysed four patient-derived glioblastoma stem cell lines, reliably quantifying phosphosite changes from 1000 FACS-sorted cells. This workflow expands the possibilities for signalling analysis of rare cell populations. Phosphoproteomics ; Labelling ; Phosphopeptide ; Computational biology ; Isobaric labeling ; Proteomics ; Quantitative proteomics ; Cell ; Tandem mass tag ; Biology ; Lysis ; Cell biology ; Computer science ; Chemistry ; Molecular biology ; Biochemistry ; Phosphorylation ; Protein kinase A ; Protein phosphorylation Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Cancer Genomics and Diagnostics
Authors: Xiaoyan Liu | Cheng-Tang Pan | Ni Sheng | Shuangli Mi | Xuhao Fan | Changlong Liu | Tianning Zhang | Yufeng Shan | Jiaqi Zhu | Shaowen Xu | Wanli Yang | Chixian Liu | T.M. Chen | Huiyong Deng | Ning Dai
Source: Nano Research (article, 2025-04-23)
Field: Materials Science — Materials Chemistry

Controllable polarity photoresponse and imaging based on MoS₂/MLG/MoTe₂ heterostructure The realization of controllable polarity photoresponse within a single device is a crucial advancement for simulating biological bipolar vision cells to drive the development of next-generation optoelectronic technologies. Nevertheless, current polarity photodetectors face significant challenges in fully suppressing symmetric photocurrent cancellation and optimizing carrier transport efficiency. Here, we propose a graphene-intercalated MoS<sub>2</sub>/MoTe<sub>2</sub> heterojunction, featuring a tailorable built-in electric field and a high efficiency transport channel. Spatially resolved photocurrent reveals that the controllable polarity photoresponse originates from the bias-dependent equivalent built-in electric field of MoS<sub>2</sub>/MLG/MoTe<sub>2</sub> heterojunction. The controllable polarity photoresponse realizes a large-area uniform “heart-shaped” photocurrent region. In enhanced polarity photoresponse mode, the photodetector exhibits broadband detection capabilities from visible (638 nm) to infrared (1550 nm) light, achieving a high responsivity of 18.1 A/W and an excellent detectivity of 2.8 × 10<sup>12</sup> Jones, as well as fast response times of 94/119 µs. Furthermore, precise imaging with a resolution better than 0.5 mm was successfully demonstrated, highlighting its polarity photoresponse for practical imaging applications. This work provides a new paradigm for controllable polarity photoresponse programmed by intercalated low-dimensional material structures, paving the way for next-generation intelligent sensing chips. Heterojunction ; Polarity (international relations) ; Materials science ; Optoelectronics ; Nanotechnology ; Chemistry 2D Materials and Applications
Authors: Bregje W. Brinkmann | Lan Dupuis | Sam Houdijk | Pelle Wattel | Cástor Salgado | Andrea Brunelli | J.F. Fernández | Willie J.G.M. Peijnenburg | Martina G. Vijver
Source: Environmental Science & Technology (article, 2025-07-30)
Field: Materials Science — Materials Chemistry

Eugenol-Loaded Nanocarriers Exert Particle-Specific Adverse Effects on <i>Daphnia magna</i> Populations Nanocarriers provide promising prospects for the transition to more sustainable agrochemical practices. However, the unique release dynamics of their loaded chemicals raise concerns about potential adverse effects on nontarget organisms. To address this, we compared the toxicity of bentonite and sepiolite nanocarriers loaded with the anesthetic/antibacterial chemical eugenol to the toxicity of pure eugenol. <i>Daphnia magna</i> was exposed to loaded nanocarriers, pure eugenol, and bare nanocarriers. In acute immobilization tests, a 50% effect concentration (EC<sub>50</sub>) of 0.14 ± 0.01 mg eugenol L<sup>-1</sup> was derived for pure eugenol. Loading eugenol onto bentonite and sepiolite nanocarriers mitigated this acute toxicity, as indicated by respective EC<sub>50</sub> values of 0.48 ± 0.02 and 0.57 ± 0.07 mg eugenol L<sup>-1</sup>. In 12-day toxicity tests, similar concentrations of eugenol were released from both nanocarriers. For the first day of exposure, this temporarily reduced the swimming speed of the daphnids. Moreover, in contrast to sepiolite nanocarriers, bentonite nanocarriers induced marked decreases in population growth. This reveals that nanocarriers exert particle-specific adverse effects on daphnid populations that cannot be predicted based on the toxicity of their individual constituents. We therefore plead to assess nontarget effects of the complete nanocarrier system, including the carrier and its loading, before allowing these products on the market. Nanocarriers ; Daphnia magna ; Microplastics ; Nanotoxicology ; Daphnia ; Eugenol ; Methyl eugenol ; Chemistry ; Toxicology ; Pharmacology ; Environmental chemistry ; Biology ; Toxicity ; Drug ; Zoology Nanoparticles: synthesis and applications ; Heavy metals in environment
Authors: Mughees Shahid | Gediminas Monastyreckis | Daiva Zeleniakienė
Source: Polymers (article, 2025-11-15)
Field: Materials Science — Polymers and Plastics

Numerical Study on Elastic Properties of Natural Fibres in Multi-Hybrid Composites This study investigates the elastic properties of bio-epoxy composites reinforced with natural fibres (flax, hemp) and synthetic fibres (S-glass), with particular focus on the effect of the fibre volume fraction (VF) ranging from 10% to 70%. Three-dimensional representative volume element (RVE) models were developed for single-fibre, hybrid, and multi-fibre systems. The mean-field homogenisation (MF) approach, based on the Mori-Tanaka scheme, and finite element analysis (FEA) with periodic boundary conditions were employed to predict the effective elastic properties, including longitudinal, transverse, and shear moduli, as well as Poisson's ratio. These numerical predictions were validated against analytical models, including the rule of mixtures, Chamis, and composite cylinder assemblage (CCA) methods. The results demonstrate that increasing the VF enhances longitudinal, transverse, and shear moduli while reducing Poisson's ratio in natural fibre composites. The good agreement between numerical, semi-analytical, and analytical methods validates the 3D RVE models as useful tools for predicting the properties of multi-hybrid natural fibre composites, supporting their design for lightweight structural applications. Finite element method ; Volume fraction ; Representative elementary volume ; Composite number ; Elastic modulus ; Shear (geology) ; Boundary value problem ; Numerical analysis ; Cylinder Natural Fiber Reinforced Composites ; Composite Material Mechanics ; Composite Structure Analysis and Optimization
Authors: Michele Cotrufo | Domenico de Ceglia | Hyunseung Jung | Igal Brener | Dragomir N. Neshev | Costantino De Angelis | Andrea Alù
Source: Nanophotonics (article, 2025-06-04)
Field: Materials Science — Materials Chemistry

Nonlinear analog processing with anisotropic nonlinear films Digital signal processing is the cornerstone of several modern-day technologies, yet in multiple applications it faces critical bottlenecks related to memory and speed constraints. Thanks to recent advances in metasurface design and fabrication, light-based analog computing has emerged as a viable option to partially replace or augment digital approaches. Several light-based analog computing functionalities have been demonstrated using patterned flat optical elements, with great opportunities for integration in compact nanophotonic systems. So far, however, the available operations have been restricted to the linear regime, limiting the impact of this technology to a compactification of Fourier optics systems. In this paper, we introduce nonlinear operations to the field of metasurface-based analog optical processing, demonstrating that nonlinear optical phenomena, combined with nonlocality in flat optics, can be leveraged to synthesize kernels beyond linear Fourier optics, paving the way to a broad range of new opportunities. As a practical demonstration, we report the experimental synthesis of a class of nonlinear operations that can be used to realize broadband, polarization-selective analog-domain edge detection. Nonlinear system ; Materials science ; Nanomaterials ; Nonlinear optical ; Anisotropy ; Nanotechnology ; Optics ; Physics ; Quantum mechanics Phase-change materials and chalcogenides ; Advanced Memory and Neural Computing ; Optical and Acousto-Optic Technologies
Authors: Ghania Boukhatem | Said Berdoudi | Messaouda Bencheikh | Mohammed Benzerara | Mehmet Serkan Kırgız | N. Nagaprasad | Krishnaraj Ramaswamy
Source: Scientific Reports (article, 2025-06-06)
Field: Materials Science — Polymers and Plastics

Impact of addition of polyvinyl chloride on the properties of clayey soil using experimental approach and optimization for geotechnical engineering applications In geotechnical engineering, soil stabilization is essential for improving the properties of clayey soils in infrastructure projects. This study explores the use of response surface methodology to optimize the utilization of polyvinyl chloride (PVC) waste as a stabilizing agent in proportions ranging from 2.5 to 30%. The percentages of clay and PVC served as input parameters, while the outputs included the CBR index, compressibility coefficient (Cc), swelling coefficient (Cs), and swelling pressure (Ps). Experimental results showed that replacing up to 30% of clay soil with the PVC improved key properties, such as the methylene blue value which had a relative decrease of 24.9%, consistency limits (LL, LP, and IP) underwent significant reductions of approximately 15.94%, 13.44%, and 17.2%, respectively, compaction parameters OMC and MDD show reductions of 52.38% and 10.32%, and consolidation characteristics Cc, Cs, and Ps show significant reductions of 92.55%, 43.64%, and 77.04%. For mechanical performance, including soaked CBR with a significant increase of 159.69% and penetration pressure, a 10% PVC replacement was identified as optimal. A quadratic predictive model was developed to optimize these responses, achieving a high coefficient of determination (R<sup>2</sup> > 0.97) and statistically significant P-values (< 0.0001) for all outputs. These results underscore the model's reliability and the potential of using PVC waste as a sustainable stabilization material. The approach is cost-effective, scalable, and eco-friendly, utilizing the PVC waste to stabilize soils, reduce environmental impacts, and enable sustainable infrastructure. Clay soil ; Polyvinyl chloride ; Geotechnical engineering ; Geology ; Materials science ; Soil science ; Composite material ; Soil water Polymer Science and PVC ; Polymer Nanocomposites and Properties ; Geotechnical Engineering and Soil Stabilization
Authors: Sakshi Handa | Kristin Isaacs | Jonathan T. Wall | Allison Larger | Scott Burns | Lauren E. Koval | Kenta Baron-Furuyama | Colleen M. Elonen | David Lyons | Kathie L. Dionisio | Matthew Horton | Katherine A. Phillips
Source: Scientific Data (article, 2025-06-06)
Field: Chemistry — Physical and Theoretical Chemistry

The Chemical and Products Database v4.0, an updated resource supporting chemical exposure evaluations Since the initial release of the Chemical and Products Database (CPDat) in 2018, the United States Environmental Protection Agency has added a considerable amount of chemical exposure-related information to the database and has expanded its schema to accommodate new types of data. This data descriptor provides information regarding the structure and types of data contained within CPDat (both existing and new), new controlled vocabularies implemented to harmonize terminology across the different data types, application of a rigorous data curation and quality assurance tracking system, and various methods of accessing CPDat. Computer science ; Database ; Controlled vocabulary ; Terminology ; Schema (genetic algorithms) ; Data curation ; Chemical database ; Resource (disambiguation) ; Data quality ; Information retrieval ; Data science ; Service (business) ; Chemistry ; Business History and advancements in chemistry ; Analytical chemistry methods development ; Pesticide and Herbicide Environmental Studies
Authors: Roman Korol | Andrew C. Turner | Apurba Nandi | Joel M. Bowman | III Goddard | Daniel A. Stolper
Source: Geochimica et Cosmochimica Acta (article, 2025-02-28)
Field: Chemistry — Inorganic Chemistry

Stable isotope equilibria in the dihydrogen-water-methane-ethane-propane system. Part 1: Path-integral calculations with CCSD(T) quality potentials Isotopic compositions of alkanes are typically assumed to be kinetically controlled, but recently it has been proposed that alkanes can isotopically equilibrate for both C and H isotopes during natural gas generation. Evaluation of this requires knowledge of the isotopic equilibrium between alkanes and other common hydrogen and carbon bearing species. Here we calculate isotopic equilibria within and between gaseous dihydrogen (H 2 ), water (H 2 O), methane (CH 4 ), ethane (C 2 H 6 ) and propane (C 3 H 8 ), including isotope fractionation among molecules, clumped isotope effects , as well as among sites of propane (i.e., the site-specific isotope effects) from 0°C to 500°C using a path-integral method paired with high-level descriptions of molecular potentials and the diagonal correction to the Born–Oppenheimer approximation. While path-integral calculations with high-level CCSD(T) potentials are available for the isotopic equilibria involving methane, the path-integral calculations for ethane and propane have only been performed based on lower-level descriptions of the molecular potentials. We analyze the relative importance of various approximations that are commonly employed when isotopic equilibria are evaluated. We find that clumped isotope effects can be calculated to the same accuracy using computationally inexpensive combination of the Bigeleisen-Mayer-Urey model with the molecular potential from density functional theory . In contrast, fractionation and site preferences of both deuterium and carbon-13 benefit from the use of the higher level CCSD(T) potentials and accounting for anharmonic effects. Additionally, for fractionation and site preference of deuterium , corrections to Born–Oppenheimer approximation can also be important. Propane ; Methane ; Path (computing) ; Path integral formulation ; Quality (philosophy) ; Kinetic isotope effect ; Chemistry ; Thermodynamics ; Computational chemistry ; Physics ; Atomic physics ; Deuterium ; Quantum mechanics ; Organic chemistry ; Computer science ; Quantum Radioactive element chemistry and processing ; Chemical Reactions and Isotopes ; Nuclear Physics and Applications
Authors: Junoh Lee | Sun‐Je Kim
Source: Micromachines (review, 2025-09-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Meta-Optics for Optical Engineering of Next-Generation AR/VR Near-Eye Displays Meta-optics, enabled by metasurfaces consisting of two-dimensional arrays of meta-atoms, offers ultrathin and multi-functional control over the vectorial wavefront of light at subwavelength scales. The unprecedented optical element technology is a promising candidate to overcome key limitations in augmented reality (AR) and virtual reality (VR) near-eye displays particularly in achieving compact, eyeglass-type form factors with a wide field-of-view, a large eyebox, high resolution, high brightness, and reduced optical aberrations, at the same time. This review highlights key performance bottlenecks of AR/VR displays in the perspective of optical design, with an emphasis on their practical significance for advancing current technologies. We then examine how meta-optical elements are applied to VR and AR systems by introducing and analyzing the major milestone studies. In case of AR systems, particularly, two different categories, free-space and waveguide-based architectures, are introduced. For each category, we summarize studies using metasurfaces as lenses, combiners, or waveguide couplers. While meta-optics enables unprecedented miniaturization and functionality, it also faces several remaining challenges. The authors suggest potential technological directions to address such issues. By surveying recent progress and design strategies, this review provides a comprehensive perspective on the role of meta-optics in advancing the optical engineering of next-generation AR/VR near-eye displays. Miniaturization ; Key (lock) ; Perspective (graphical) ; Wavefront ; Augmented reality ; Optical engineering Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Advanced Optical Imaging Technologies
Authors: Tianyu Ma | Liming Si | Chenyang Dang | Rong Niu | Genhao Wu | Xiue Bao | Houjun Sun | Weiren Zhu
Source: Nanoscale Advances (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Graphene spatiotemporal reconfigurable intelligent surface (GSRIS) for terahertz polarization-state manipulation and holographic imaging The integration of 2D materials and metamaterials/metasurfaces presents an effective approach for the intelligent, real-time dynamic control of electromagnetic (EM) waves in the terahertz (THz) frequency range. Herein, we demonstrate a graphene spatiotemporal reconfigurable intelligent surface (GSRIS) for THz polarization-state manipulation, multi-beam generation and holographic imaging using EM theory and full-wave EM simulations. The chemical potential of graphene can be changed through time-varying modulation, such as field-programmable gate arrays (FPGAs), of the electric field or voltage. By dynamically controlling the spatiotemporal chemical potential of graphene, both the amplitude and phase of orthogonally polarized reflected waves can be simultaneously adjusted, enabling polarization state manipulation at different harmonics, multi-beam generation, and holographic imaging. As a proof of concept, a multifunctional GSRIS designed for 1.3 THz demonstrates polarization-state manipulation and multi-beam generation at the +1<sup>st</sup> order harmonic, as well as high-quality holographic imaging at the -1<sup>st</sup> order harmonic. The presented GSRIS provides a novel approach for designing THz circuits and systems, which can exhibit various potential applications in imaging, sensing, beam control, and 6G wireless communications. Terahertz radiation ; Graphene ; Holography ; Polarization (electrochemistry) ; Optoelectronics ; Materials science ; Optics ; Physics ; Nanotechnology ; Chemistry Metamaterials and Metasurfaces Applications ; Superconducting and THz Device Technology ; Terahertz technology and applications
Authors: Yixin Wu | Xu Shen | Mengqing Sun | Hui Wei | Muhammad Faheem | Lizhu Liu | G Shi | Yan Gao
Source: Chemical and Biological Technologies in Agriculture (article, 2025-07-14)
Field: Materials Science — Materials Chemistry

Mn-doped cerium dioxide nanozyme mediates ROS homeostasis and hormone metabolic network to promote wheat germination under low-temperature conditions Nanozymes are a class of nanocatalytic materials that mimic the functions of natural enzymes. Their enzyme-like properties enable the catalytic scavenging of excess reactive oxygen species (ROS) generated in plants under abiotic stress, thereby alleviating oxidative stress. Research on nanozymes’ role and related mechanisms in alleviating low-temperature stress in crops is still unclear. Therefore, developing nanozymes that enhance early stage cold tolerance in crops is critical for maintaining agricultural production and global food security. We synthesized a nanozyme with catalase (CAT)-like activity, manganese-doped cerium oxide (MCNPs) nanoparticles. This study demonstrates that priming with MCNPs significantly accelerated wheat germination under cold stress, increasing the germination index by 7.1% and seedling biomass by 6.2–17.2% compared to hydropriming. Through SP–ICP–MS analysis, we confirmed that MCNPs can enter the seed. We also found that the catalase-like activity of MCNPs synergistically enhanced endogenous antioxidant enzymes (CAT and superoxide dismutase) to effectively eliminate excessive ROS in wheat seeds. Further analysis using LC–MS and qPCR showed that this ROS homeostasis influenced hormone metabolism by regulating the expression of genes involved in the hormone metabolic network, elevating growth-promoting hormones (gibberellin and ethylene) by 25.5–27.2% while suppressing stress-responsive hormones (jasmonic acid and abscisic acid). Subsequent activation of the gibberellin-responsive transcription factor TaGAMYB up-regulated amylase genes, boosting β-amylase activity by 17.1–18.5% and accelerating starch hydrolysis into reducing sugars, collectively enhancing low-temperature germination. MCNP priming significantly alleviated the inhibitory effects of low temperature on wheat seed germination by coordinately regulating the processes of “ROS homeostasis,” “hormone metabolism,” and “starch hydrolysis,” offering a promising strategy for enhancing plant cold tolerance and maintaining food security in the face of climate change. Germination ; Homeostasis ; Hormone ; Cerium ; Cell biology ; Chemistry ; Biology ; Biochemistry ; Botany ; Inorganic chemistry Advanced Nanomaterials in Catalysis ; Carbon and Quantum Dots Applications ; Nanoparticles: synthesis and applications