jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhiwei Liu | Pu‐Kun Liu | Yingying Sun | Zan Nie | Xiaofan Zhang | Yuqi Zhang | Yi Chen | Tiannan Guo
Source: Nature Communications (article, 2025-04-14)
Field: Chemistry — Spectroscopy

DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis Data-independent acquisition mass spectrometry (DIA-MS) has become increasingly pivotal in quantitative proteomics. In this study, we present DIA-BERT, a software tool that harnesses a transformer-based pre-trained artificial intelligence (AI) model for analyzing DIA proteomics data. The identification model was trained using over 276 million high-quality peptide precursors extracted from existing DIA-MS files, while the quantification model was trained on 34 million peptide precursors from synthetic DIA-MS files. When compared to DIA-NN, DIA-BERT demonstrated a 51% increase in protein identifications and 22% more peptide precursors on average across five human cancer sample sets (cervical cancer, pancreatic adenocarcinoma, myosarcoma, gallbladder cancer, and gastric carcinoma), achieving high quantitative accuracy. This study underscores the potential of leveraging pre-trained models and synthetic datasets to enhance the analysis of DIA proteomics. End-to-end principle ; Proteomics ; Computer science ; Transformer ; Computational biology ; Biology ; Artificial intelligence ; Engineering ; Electrical engineering ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Bioinformatics and Genomic Networks
Authors: Akrivi Korba | Lucyna Łȩkawska-Andrinopoulou | Kostas Chatziioannou | Georgios Tsimiklis | Angelos Amditis
Source: Open Research Europe (review, 2025-01-10)
Field: Chemistry — Organic Chemistry

Wood Waste Valorization and Classification Approaches: A systematic review This systematic literature review delves into various wood waste valorization and classification approaches, aiming to evaluate their efficacy in fostering sustainable wood resource management while enhancing the economic value of wood waste. By synthesizing findings from a diverse array of research studies, the review highlights the multifaceted nature of wood waste valorization, emphasizing the critical role of sorting and separation technologies in ensuring high-quality recovery of materials. It also identifies the wood classification practices in Europe, which are crucial for creating a harmonized valorization framework that aligns technological advancements with regulatory standards. The analysis reveals that integrating these components-technologies, sorting methods, and classification practices can significantly improve the overall efficiency and effectiveness of wood waste management. Furthermore, the review identifies existing gaps in research and practice, providing actionable recommendations for stakeholders aiming to optimize wood valorization waste systems. These recommendations emphasize the necessity for a holistic approach and a clearly defined, comprehensive framework for wood valorization that considers all elements involved in the process. By addressing these areas, the review not only aims to contribute to the body of knowledge in wood waste valorization but also seeks to promote sustainable practices that benefit both the environment and the economy, paving the way for a more circular approach to wood resource utilization. Systematic review ; Environmental science ; Biochemical engineering ; Waste management ; Engineering ; Computer science ; MEDLINE ; Chemistry Wood and Agarwood Research
Authors: Yang Fu | Yuanxin Ge | Shixiong Yi | Qifeng Peng | Heng Jiang | Jie Zhou
Source: Discover Oncology (review, 2025-07-21)
Field: Materials Science — Biomaterials

A review of synergistic strategies in cancer therapy: resveratrol-loaded hydrogels for targeted and multimodal treatment Resveratrol (RSV), a natural polyphenol with multifaceted anticancer mechanisms, faces significant pharmacokinetic challenges that limit its clinical utility. This review explores the synergistic integration of RSV with hydrogel-based delivery systems to overcome these limitations and enhance therapeutic efficacy in cancer treatment. Hydrogels, renowned for their tunable physicochemical properties and stimuli-responsive behavior, enable precise spatiotemporal control over RSV release, improving stability, bioavailability, and tumor-targeted delivery. Compared to alternative delivery systems (e.g., liposomes, polymeric nanoparticles), RSV-loaded hydrogels offer distinct advantages in sustained local release and microenvironmental modulation. Advanced hydrogel designs, including pH- and temperature-responsive systems, nanocomposites, and self-healing networks, further amplify RSV's bioactivity by sustaining therapeutic concentrations, modulating tumor microenvironments, and synergizing with chemo-photothermal or immunotherapeutic strategies. Preclinical applications in colorectal cancer and glioblastoma demonstrate RSV-hydrogel platforms' ability to suppress metastasis, reverse chemoresistance, and eradicate cancer stem cells through mechanisms such as Wnt/β-catenin inhibition and ROS-triggered drug activation. While these preclinical results are promising, significant translational challenges remain, including scalable manufacturing, biocompatibility, and clinical translation. Future research priorities include developing more sophisticated stimuli-responsive systems and exploring potential synergies with emerging therapeutic modalities to bridge the gap towards clinical application. Resveratrol ; Self-healing hydrogels ; Multimodal therapy ; Cancer therapy ; Cancer ; Medicine ; Pharmacology ; Chemistry ; Surgery ; Internal medicine ; Organic chemistry Electrospun Nanofibers in Biomedical Applications ; Graphene and Nanomaterials Applications ; Pancreatic function and diabetes
Authors: Michele Stofella | Neeleema Seetaloo | Alexander St John | Emanuele Paci | Jonathan J. Phillips | Frank Sobott
Source: Analytical Chemistry (article, 2025-01-29)
Field: Chemistry — Spectroscopy

Recalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to interrogate protein structure and dynamics. With the ability to study almost any protein without a size limit, including intrinsically disordered ones, HDX-MS has shown fast growing importance as a complement to structural elucidation techniques. Current experiments compare two or more related conditions (sequences, interaction partners, excipients, conformational states, etc.) to determine statistically significant differences at a number of fixed time points and highlight areas of changed structural dynamics in the protein. The work presented here builds on the fundamental research performed in the early days of the technique and re-examines exchange rate calculations with the aim of establishing HDX-MS as an <i>absolute</i> and <i>quantitative</i>, rather than <i>relative</i> and <i>qualitative</i>, measurement. We performed millisecond HDX-MS experiments on a mixture of three unstructured peptides (angiotensin, bradykinin, and atrial natriuretic peptide amide rat) and compared experimental deuterium uptake curves with theoretical ones predicted using established exchange rate calculations. With poly-dl-alanine (PDLA) commonly used as a reference,<sup>,</sup> we find that experimental rates are sometimes faster than theoretically possible, while they agree much better, and are never faster, with the fully unstructured trialanine peptide (3-Ala). Molecular dynamics (MD) simulations confirm the high helical propensity of the longer and partially structured PDLA peptides, which need as few as 15 residues to form a stable helix and are therefore not suitable as an unstructured reference. Reanalysis of previously published data by Weis et al. at 100 mM NaCl however still shows a discrepancy with predictions based on 3-Ala in the absence of salt, highlighting the need for a better understanding of salt effects on exchange rates. Such currently unquantifiable salt effects prevent us from proposing a comprehensive, universal calibration framework at the moment. Nevertheless, an accurate recalibration of intrinsic exchange rate calculations is crucial to enable kinetic modeling of the exchange process and to ultimately allow HDX-MS to move toward a direct link with atomistic structural models. Chemistry ; Deuterium ; Mass spectrometry ; Hydrogen–deuterium exchange ; Millisecond ; Hydrogen ; Analytical Chemistry (journal) ; Radiochemistry ; Chromatography ; Nuclear physics ; Organic chemistry Mass Spectrometry Techniques and Applications ; Radioactive element chemistry and processing ; Analytical Chemistry and Chromatography
Authors: Hongyan Zhu | Chengzhi Lin | Zhihao Dong | Jun‐Li Xu | Yong He
Source: Agriculture (article, 2025-05-19)
Field: Chemistry — Analytical Chemistry

Early Yield Prediction of Oilseed Rape Using UAV-Based Hyperspectral Imaging Combined with Machine Learning Algorithms Oilseed rape yield critically reflects varietal superiority. Rapid field-scale estimation enables efficient high-throughput breeding. This study evaluates unmanned aerial vehicle (UAV) hyperspectral imagery’s potential for yield prediction at the pod stage by utilizing wavelength selection and vegetation indices. Meanwhile, optimized feature selection algorithms identified effective wavelengths (EWs) and vegetation indices (VIs) for yield estimation. The optimal yield estimation models based on EWs and VIs were established, respectively, by using multiple linear regression (MLR), partial least squares regression (PLSR), extreme learning machine (ELM), and a least squares support vector machine (LS-SVM). The main results were as follows: (i) The yield prediction of oilseed rape using EWs showed better prediction and robustness compared to the full-spectral model. In particular, the competitive adaptive reweighted sampling–extreme learning machine (CARS-ELM) model (Rpre = 0.8122, RMSEP = 170.4 kg/hm2) achieved the best prediction performance. (ii) The ELM model (Rpre = 0.7674 and RMSEP = 187.6 kg/hm2), using 14 combined VIs, showed excellent performance. These results indicate that the remote sensing image data obtained from the UAV hyperspectral remote sensing system can be used to enable the high-throughput acquisition of oilseed rape yield information in the field. This study provides technical guidance for the crop yield estimation and high-throughput detection of breeding information. Hyperspectral imaging ; Yield (engineering) ; Algorithm ; Machine learning ; Artificial intelligence ; Agronomy ; Computer science ; Environmental science ; Remote sensing ; Biology ; Materials science ; Geology Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Water Quality Monitoring and Analysis
Authors: Chris Hsu | Nicholas Shulman | Hamish Stewart | J. Petzoldt | Anna Pashkova | Deanna L. Plubell | Eduard Denisov | Bernd Hagedorn | Eugen Damoc | Brendan MacLean | Philip M. Remes | Jesse D. Canterbury | Alexander Makarov | Christian Hock | Vlad Zabrouskov | Christine C. Wu | Michael J. MacCoss
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-05-31)
Field: Chemistry — Spectroscopy

Evaluation of a prototype Orbitrap Astral Zoom mass spectrometer for quantitative proteomics – Beyond identification lists Mass spectrometry instrumentation continues to evolve rapidly yet quantifying these advances beyond conventional peptide and protein detections remain challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) prototype and compare its performance to the standard Orbitrap Astral MS. Across a range of acquisition methods and sample inputs, the prototype instrument outperformed the standard Orbitrap Astral MS in precursor and protein identifications, ion beam utilization, and quantitative precision. To enable meaningful cross-platform comparisons, we implemented an ion calibration framework that converts signal intensity from arbitrary units to ion per second. This benchmarking strategy showed that the prototype sampled 30% more ions per peptide than the original Orbitrap Astral MS. This increase in the ion beam utilization resulted in improved sensitivity and quantitative precision. To make these metrics broadly accessible, we added new metrics to the Skyline document grid to report the number of ions measured in a spectrum at the apex of the elution peak or the sum of ions between the peak integration boundaries. Taken together, our results demonstrate the prototype Orbitrap Astral Zoom as a high-performance platform for DIA proteomics and establish a generalizable framework for evaluation of mass spectrometer performance based on the number of ions detected for each analyte. Data are available on Panorama Public and on ProteomeXchange under the identifier PXD064536. Orbitrap ; Mass spectrometry ; Zoom ; Computer science ; Quantitative proteomics ; Chemistry ; Proteomics ; Physics ; Optics ; Chromatography Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ivayla Dincheva | Ilian Badjakov | Vasil Georgiev | İvanka Semerdjıeva | Radka Vrancheva | Ivan Ivanov | Atanas Pavlov
Source: Plants (article, 2025-01-18)
Field: Chemistry — Organic Chemistry

Comprehensive GC-MS Characterization and Histochemical Assessment of Various Parts of Three Colchicum Species from Bulgarian Flora This study presents a comprehensive phyto- and histochemical analysis of three <i>Colchicum</i> species: <i>Colchicum autumnale</i> L., the Balkan endemic <i>Colchicum bivonae</i> Guss., and the Bulgarian endemic <i>Colchicum diampolis</i> Delip. et Česchm. Using gas chromatography-mass spectrometry (GC-MS), 66 metabolites were identified, encompassing free amino, organic, phenolic, and fatty acids, sugars, and alkaloids, which were distributed among various plant parts. Organ-specific metabolic patterns revealed that corms and seeds are particularly rich in alkaloids, supporting their roles in chemical defense and survival during dormancy. Conversely, flowers, leaves, and capsules were enriched with energy-related and phenolic compounds, playing critical roles in reproduction and stress tolerance. Histochemical investigations localized alkaloids predominantly in the endosperm of seeds, parenchyma of corms, and vascular bundles of flowers. Notably, the endemic <i>C. bivonae</i> and <i>C. diampolis</i> displayed unique chemical profiles. Moderate acetylcholinesterase inhibitory activity (AChE) was observed across various plant organs. Statistical analyses demonstrated significant interspecies and organ-specific chemical differentiation, with certain metabolites serving as key markers. These findings enhance our understanding of the chemical composition, organ specialization, and potential as a source of new biomolecules in these <i>Colchicum</i> species. They underscore the ecological and pharmacological importance of endemic taxa and provide a framework for future research into their sustainable utilization and potential bioactivities. Biology ; Botany ; Gas chromatography–mass spectrometry ; Metabolomics ; Corm ; Chemistry ; Mass spectrometry Chemical synthesis and alkaloids ; Phytochemistry and Biological Activities ; Sesquiterpenes and Asteraceae Studies
Authors: Elena Gardey | Johannes C. Brendel | Andreas Stallmach
Source: Advanced Therapeutics (article, 2025-01-19)
Field: Materials Science — Biomaterials

Pathophysiology of IBD as a Key Strategy for Polymeric Nanoparticle Development Abstract Inflammatory bowel disease (IBD) is a complex chronic inflammatory disorder of the gastrointestinal (GI) tract with an uncertain etiology. Currently, IBD therapy relies on the induction of clinical remission followed by maintenance therapy using anti‐inflammatory drugs and immunosuppressants; however, a definite cure of the disease is still out of scope. Established approaches are characterized by adverse drug‐related side effects that can even be potentially life‐threatening. In contrast, increased interest and remarkable scientific progress in targeted drug delivery systems offer a promising approach to reduce systemic adverse events, delivering the therapeutic substances only to inflamed tissue. All alteration in gastrointestinal barrier integrity, especially a disturbed epithelial barrier, a unique pattern of the receptors on cell surface and/or an oxidative stress milieu in inflamed areas can be used as effective approaches for targeted and controlled drug delivery. Hence, this review focuses on the pathophysiology of the inflamed GI tract as a potential strategy for targeted polymeric nanoparticles for IBD treatment. Interdisciplinary efforts between the polymeric chemistry and gastroenterology/immunology promise to create novel synergies that improve the development of effective nanoparticle systems with significant clinical impact. In this regard, the current challenges in the clinical translation of promising nanomedicine are also discussed. Key (lock) ; Nanotechnology ; Pathophysiology ; Medicine ; Materials science ; Computer science ; Pathology ; Computer security Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems ; Inflammatory Bowel Disease
Authors: Hengrui Liang | Runchen Wang | Ran Cheng | Zhiming Ye | Na Zhao | Xiaohong Zhao | Ying Huang | Zhanpeng Jiang | Wang‐Zhong Li | Jianqi Zheng | Hongsheng Deng | Yu Jiang | Yuechun Lin | Yan Yun | Lei Song | Jie Li | Xin Xu | Wenhua Liang | Jun Liu | Jianxing He
Source: Clinical and Translational Medicine (article, 2025-01-01)
Field: Chemistry — Spectroscopy

LcProt: Proteomics‐based identification of plasma biomarkers for lung cancer multievent, a multicentre study Our study developed an innovative nanomaterial, Zeolite NaY, which addressed the masking effect and improved the depth of the proteome. The performance of NaY-based plasma proteomics as a preclinical diagnostic tool was validated through both internal and external cohort. Furthermore, we explored the different patterns of plasma protein changes during the progression of lung cancer and used the explanations method to elucidate the roles of proteins in the multitask predictive model. Medicine ; Biomarker ; Lung cancer ; Lasso (programming language) ; Oncology ; Prospective cohort study ; Stage (stratigraphy) ; Internal medicine ; Cohort ; Receiver operating characteristic ; Computer science ; Biology Advanced Proteomics Techniques and Applications ; Ferroptosis and cancer prognosis ; Machine Learning in Bioinformatics
Authors: Charlotte Wouters | Vikram Kestens | Eveline Verleysen | Jan Mast
Source: Scientific Reports (article, 2025-04-06)
Field: Materials Science — Surfaces, Coatings and Films

Assessing particle count in electron microscopy measurements of nanomaterials to support regulatory guidance In the European Union, nanomaterials are regulated through different pieces of sectoral legislation. This legislation often requires risk assessments and thus reliable characterization data, for which regulatory guidance generally recommend electron microscopy. The guidance provides best practices for measurements but lacks requirements on how many particles to measure. Using transmission electron microscopy data of nanomaterials, a strategy based on repeated subsampling is proposed to establish, for different particle size and shape measurands, mathematical relationships between particle count and precision, and subsequently to determine the minimum particle count. Our results confirm that the minimum particle count generally depends on the width of the size and shape distributions and that the median of the distribution can be determined with the highest precision compared to other percentiles. Upon combining the precision uncertainty related to particle number with uncertainties from other sources, such as sample preparation, calibration and trueness, we reach an optimal particle count above which additional particle measurements only yield negligible improvements to the combined measurement uncertainty. Our findings offer an experimental approach for determining the minimum particle count to measure particle size and shape by electron microscopy. It enables efficient analyses and facilitates compliance with legislation addressing nanomaterials across various application domains. Nanomaterials ; Particle size ; Particle (ecology) ; Calibration ; Percentile ; Measure (data warehouse) ; Microscopy ; Materials science ; Nanotechnology ; European union ; Legislation ; Particle-size distribution ; Biological system ; Statistics ; Computer science ; Mathematics ; Data mining ; Physics ; Optics ; Engineering ; Chemical engineering ; Biology Electron and X-Ray Spectroscopy Techniques ; Surface and Thin Film Phenomena ; Electrostatics and Colloid Interactions
Authors: Zhennan Zhang | Kaiyu Wang | Brett A. Bednarcyk | Louise Le Barbenchon | Yanyu Chen
Source: Composites Part B Engineering (article, 2025-06-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Tailoring the architecture of fractal lattice metamaterials for tunable energy absorption Materials science ; Metamaterial ; Fractal ; Composite material ; Lattice (music) ; Absorption (acoustics) ; Engineering physics ; Optoelectronics ; Acoustics Metamaterials and Metasurfaces Applications ; Polydiacetylene-based materials and applications ; Advanced Materials and Mechanics
Authors: Han Wang | Zhigang Wang | Cheng Gong | Xinyu Li | Tiansheng Cui | Huiqi Jiang | Minghui Deng | Bo Yan | Weiwei Liu
Source: Light Science & Applications (article, 2025-01-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Using light to image millimeter wave based on stacked meta-MEMS chip A stacked metamaterial MEMS (meta-MEMS) chip is proposed, which can perfectly absorb electromagnetic waves, convert them into mechanical energy, drive movement of the optical micro-reflectors array, and detect millimeter waves. It is equivalent to using visible light to image a millimeter wave. The meta-MEMS adopts the design of upper and lower chip separation and then stacking to achieve the "dielectric-resonant-air-ground" structure, reduce the thickness of the metamaterial and MEMS structures, and improve the performance of millimeter wave imaging. For verification, we designed and prepared a 94 GHz meta-MEMS focal plane array chip, in which the sum of the thickness of the metamaterial and MEMS structures is only 1/2500 wavelength, the pixel size is less than 1/3 wavelength, but the absorption rate is as high as 99.8%. Moreover, a light readout module was constructed to test the millimeter wave imaging performance. The results show that the response speed can reach 144 Hz and the lens-less imaging resolution is 1.5 mm. Microelectromechanical systems ; Metamaterial ; Extremely high frequency ; Optics ; Millimeter ; Chip ; Materials science ; Wavelength ; Optoelectronics ; Ground plane ; Physics ; Computer science ; Telecommunications ; Antenna (radio) Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Millimeter-Wave Propagation and Modeling