jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Linyuan Fan | Yi Liu | Haichao Zhou | Yang Feng | Guangyi Jiang | Guixue Hou | Zhihan Cao | Zhiguo Zheng | Lu Sun | Hao Chen | Yuefei Zhang | Weiran Chen | Yun Xi | Benliang Cheng | Qinghai Yang | Yan Ren | Jianqing Zhu | Siqi Liu
Source: Clinical and Translational Medicine (article, 2025-07-01)
Field: Chemistry — Spectroscopy

Spatially resolved proteomics surveys the chemo‐refractory proteins related to high‐grade serous ovarian cancer High-grade serous ovarian carcinoma (HGSC) is a lethal malignancy characterized by high incidence, mortality, and chemoresistance. However, its molecular drivers are unknown. In this study, spatially resolved proteomics was applied to 1144 formalin-fixed paraffin-embedded tissue spots obtained by laser capture microdissection from 10 patients with HGSC and divergent carboplatin-paclitaxel (CP) responses. Specific sampling revealed stroma-driven tumour heterogeneity, identifying 642 tumour-specific and 180 stroma-specific proteins, with 505 CP-responsive therapeutic targets. Most of these protein signatures represented previously unreported associations with chemoresistance in HGSCs. Two clinically significant spatial proteomic maps were generated by introducing tumour (TS) and chemical (CS) scores. TS analysis revealed conserved tissue architecture across CP response groups, whereas CS mapping revealed pretreatment metabolic reprogramming (rather than proliferation) as the defining feature of chemo-resistant tumours, challenging current resistance paradigms. Immunohistochemical validation of HGSC tissue microarrays confirmed the spatial proteomic localization of TFRC and PDLIM3, which are linked to tumour progression, while establishing their novel role as chemotherapy resistance biomarkers through this study, with broader predictive potential observed across additional targets in the discovery cohort. This study developed a spatially resolved proteomic framework to enhance the diagnostic and therapeutic strategies for HGSC. KEY POINTS: HGSC intra-tumour heterogeneity is predominantly driven by stroma, as revealed by spatial proteomic compartmentalization (tumour/stroma). Spatial proteomics expands the therapeutic target database, enabling prediction of platinum-based chemotherapy response. Chemo-resistant patients exhibit pre-treatment metabolic activation rather than proliferative signatures. TFRC (iron transport) and PDLIM3 (cytoskeletal remodelling) are spatially validated as chemo-response biomarkers. Proteomics ; Stroma ; Serous fluid ; Laser capture microdissection ; Ovarian cancer ; Biology ; Cancer ; Cancer research ; Pathology ; Bioinformatics ; Computational biology ; Medicine ; Immunohistochemistry ; Internal medicine ; Gene ; Gene expression Advanced Proteomics Techniques and Applications ; Ferroptosis and cancer prognosis ; Single-cell and spatial transcriptomics
Authors: Patrick Royer | Elias Björnson | Martin Adiels | Anders Gummesson | Göran Bergström
Source: Journal of Cardiovascular Translational Research (article, 2025-10-10)
Field: Chemistry — Spectroscopy

Plasma Proteomics for Predicting Cardiovascular Disease: How Many Proteins are Enough? Proteomics ; Human genetics ; Posttranslational modification ; Blood proteins ; Proteome Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Metabolomics and Mass Spectrometry Studies
Authors: Tyler Blazey | Andrei G. Vlassenko | Manu S. Goyal | Hany Soliman | Charles H. Cunningham | Cornelius von Morze
Source: Imaging Neuroscience (article, 2025-01-01)
Field: Chemistry — Spectroscopy

Spatial distribution of hyperpolarized [1-13C]pyruvate MRI and metabolic PET in the human brain Magnetic resonance imaging (MRI) of hyperpolarized (HP) [1-<sup>13</sup>C]pyruvate is a promising method for measuring cerebral energy metabolism <i>in vivo</i>. The substantial increase in signal provided by HP makes it possible to dynamically monitor the conversion of [1-<sup>13</sup>C]pyruvate to [1-<sup>13</sup>C]lactate and [<sup>13</sup>C]bicarbonate. The HP [1-<sup>13</sup>C]lactate signal is commonly associated with glycolic activity, whereas [<sup>13</sup>C]bicarbonate, a by-product of the reaction that forms acetyl-CoA, is linked to oxidative metabolism. However, there is compelling evidence that other factors, such as the concentration of monocarboxylate transporters, influence the production of HP [1-<sup>13</sup>C]lactate. To clarify the processes responsible for producing the topography of HP [1-<sup>13</sup>C]pyruvate and its metabolites, we spatially correlated group-average HP <sup>13</sup>C MRI images with [<sup>18</sup>F]FDG, [<sup>15</sup>O]H<sub>2</sub>O, [<sup>15</sup>O]O<sub>2</sub>, and [<sup>15</sup>O]CO positron emission topography (PET) images from a separate group of 35 age- and sex-matched adults. We found that [1-<sup>13</sup>C]pyruvate correlated best with cerebral blood volume (CBV), whereas [1-<sup>13</sup>C]lactate and [<sup>13</sup>C]bicarbonate were most strongly associated with cerebral blood flow (CBF), glucose consumption (CMRglc), and oxygen metabolism (CMRO<sub>2</sub>). Neither [1-<sup>13</sup>C]lactate nor [<sup>13</sup>C]bicarbonate was correlated with non-oxidative glucose consumption, also known as aerobic glycolysis. These results are consistent with the view that in the healthy brain, the production of [1-<sup>13</sup>C]lactate reflects overall energy metabolism rather than being specific to glycolysis. Human brain ; Cerebral blood flow ; Magnetic resonance imaging ; Energy metabolism ; SIGNAL (programming language) ; Oxygen ; Positron emission tomography ; Metabolism ; Cerebral blood volume Advanced NMR Techniques and Applications ; Medical Imaging Techniques and Applications ; Enzyme Structure and Function
Authors: Aimeric Eustache | Guillaume Martin | C. Chabert | F. Sudreau | Cécile EVANS | F. Laugier | Guillaume Vaast | B. Carlier | O. Tougait
Source: Progress in Nuclear Science and Technology (article, 2025-09-30)
Field: Materials Science — Materials Chemistry

Simulation of the Performances of a Pressurized Water Reactors Multi-Recycling Nuclear System for Material Valorization Pressurized water reactor ; Water cooling ; Production (economics) ; Water cooled Graphite, nuclear technology, radiation studies ; Nuclear and radioactivity studies ; Nuclear reactor physics and engineering
Authors: Florian Bruckner | Kristýna Davídková | Claas Abert | Andrii V. Chumak | Dieter Suess
Source: Scientific Reports (preprint, 2025-06-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Micromagnetic simulation and optimization of spin-wave transducers The increasing demand for higher data volume and faster transmission in modern wireless telecommunication systems has elevated requirements for 5G high-band RF hardware. Spin-Wave technology offers a promising solution, but its adoption is hindered by significant insertion loss stemming from the low efficiency of magnonic transducers. This work introduces a micromagnetic simulation method for directly computing the spin-wave resistance, the real part of spin-wave impedance, which is crucial for optimizing magnonic transducers. By integrating into finite-difference micromagnetic simulations, this approach extends analytical models to arbitrary transducer geometries. We demonstrate its effectiveness through parameter studies on transducer design and waveguide properties, identifying key strategies to enhance the overall transducer efficiency. Our studies show that by varying single parameters of the transducer geometry or the YIG thickness, the spin-wave efficiency, the parameter describing the efficiency of the transfer of electromagnetic energy to the spin wave, can reach values up to 0.75. The developed numerical model allows further fine-tuning of the transducers to achieve even higher efficiencies. Transducer ; Micromagnetics ; Spin (aerodynamics) ; Acoustics ; Computer science ; Physics ; Magnetization ; Quantum mechanics ; Magnetic field ; Thermodynamics Magnetic Properties of Alloys ; Magnetic properties of thin films ; Magnetic Properties and Applications
Authors: Jiahao Wang | Kai Qu | Junzhe Ni | Weixu Yang | Kui Tang | Shufang Dong | Shaojie Wang | Junming Zhao | Tian Jiang | Ke Chen | Yijun Feng
Source: PhotoniX (article, 2025-12-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Broadband spin-unlocked achromatic meta-devices empowered by hybrid-phase cooperative dispersion engineering Abstract Broadband achromatic meta-devices have emerged as a transformative platform for dispersion-engineered wavefront manipulation, offering significant potential for full-color imaging, multi-band spectral sensing, and integrated photonic systems. However, realizing spin-unlocked achromatic functionality remains fundamentally challenging due to the intrinsic dispersion correlations between orthogonal spin channels in conventional metasurface architectures. Here, we propose a hybrid-phase strategy that synergistically combines the distinct dispersion characteristics of Aharonov-Anandan and Pancharatnam-Berry geometric phases. This mechanism is implemented through a single-layer double-arc meta-structure that enables broadband achromatic wavefront control with complete spin-channel independence. As experimental validation, we demonstrate spin-unlocked achromatic meta-devices including dual-functionality beam deflectors and high-efficiency meta-lenses, both exhibiting broadband chromatic-aberration-free performances. This approach establishes a new paradigm for spin-unlocked achromatic metasurfaces and paves the way for multi-channel optical imaging, on-chip spectral detection, and other emerging spin-photonic applications. Achromatic lens ; Broadband ; Wavefront ; Dispersion (optics) ; Photonics Metamaterials and Metasurfaces Applications ; Random lasers and scattering media ; Plasmonic and Surface Plasmon Research
Authors: Yehuda Baum | Dorit Arad | Rachel Gringols Yarden | Sharon Karepov | Jacob Scheuer
Source: Scientific Reports (article, 2025-11-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Ultra-broadband wide-angle anti-reflection scheme utilizing multi-layer resonant metasurfaces Suppressing reflection at the interface separating media with different optical properties has always been an objective, common to many disciplines involving wave phenomena. This task constitutes an even greater challenge for beams exhibiting complex spatiotemporal profiles as broadband (spectral and spatial) operation is required. Here we present a new approach for obtaining broadband antireflection properties by utilizing nanostructure arrays in a multi-layer metasurface configuration with periodicity in the order of a wavelength. As a concrete example, we show the ability to attain ultra-broadband reflection suppression exceeding -30dB in a Silicon-Air interface, over a bandwidth of ~ 400 nm at telecom wavelengths and an incidence angle of ± 30˚. This method offers several inherent advantages over moth-eye-like approaches as it allows for a more repetitive fabrication process while facilitating a monolithic, single-material antireflection structure. Furthermore, such AR structures can also be realized using additive manufacturing techniques such as 3D printing and Nano-Imprint Lithography. Broadband ; Bandwidth (computing) ; Fabrication ; Reflection (computer programming) ; Wavelength ; Nanostructure ; Process (computing) ; Interface (matter) Metamaterials and Metasurfaces Applications ; Optical Coatings and Gratings ; Plasmonic and Surface Plasmon Research
Authors: Wenwen Lei | Muhamad Azry Khoiry | Azrul A. Mutalib
Source: Journal of the Croatian Association of Civil Engineers (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Systematic review of the identification, assessment, and mitigation of safety risks in high-rise building construction The construction industry accounts for a large proportion of the national GDP; however, it is one of the world’s most dangerous industrial sectors. Existing studies have inadequately reviewed safety risk-related research in high-rise building construction. Therefore, this study conducts a systematic review of safety risks in high-rise building construction from 2004 to 2024. First, the paper presents investigates the causes of accidents and risk factors that endanger occupational safety and health, comprising 8 main factors and 60 sub-factors. Second, the paper explores the assessment methods for evaluating and ranking these safety risk factors, of which nine typical methods are elaborated. Finally, a technical framework for mitigating the eight main safety risk factors is established in paper, providing safety practitioners with access to cutting-edge technologies and methods in the construction industry. Furthermore, this study provides suggestions and future directions for addressing the drawbacks of current mitigation measures to sustainably improve building construction safety. Identification (biology) ; Forensic engineering ; Construction engineering ; Risk assessment ; Risk analysis (engineering) ; Engineering ; Architectural engineering ; Business ; Computer science ; Computer security Structural mechanics and materials ; Construction Management and Sustainability
Authors: Christopher Below | Oliver M. Bernhardt | Stephanie Kaspar-Schönefeld | Sander Willems | E. Coronado‐Barrientos | Ino D. Karemaker | Bettina Streckenbach | Monika Pepelnjak | Luca Raess | Sandra Schär | Dennis Trede | Jonathan R. Krieger | Tejas Gandhi | Roland Bruderer | Lukas Reiter
Source: Molecular & Cellular Proteomics (article, 2025-12-10)
Field: Chemistry — Spectroscopy

Enhanced Identifications and Quantification Through Retention Time Down-Sampling in Fast-Cycling Diagonal-PASEF Methods Data-independent acquisition (DIA) mass spectrometry is essential for comprehensive quantification of proteomes, enabling deeper insights into cellular processes and disease mechanisms. On the timsTOF platform, diagonal-PASEF acquisition methods have recently been introduced to directly and continuously cover the observed diagonal shape of the peptide precursor ion distributions. Diagonal-PASEF has already shown great promise, and its adaptation as a routine workflow can be further pushed with improved method development as well as enhanced algorithmic solutions. Here, we conducted a systematic and comprehensive optimization of diagonal-PASEF for 17-min gradients on the timsTOF HT in conjunction with Spectronaut. We demonstrate that Spectronaut fully supports all tested diagonal-PASEF methods independent of the number of slices or overlaps and with minimal user intervention required. We derive an optimized analysis strategy where we coupled diagonal-PASEF acquisitions to retention time down-sampling by summation (RTsum) and thereby exploit the fast-cycling nature of diagonal-PASEF methods. Through the combination of RTsum with diagonal-PASEF, we demonstrate that this strategy yields higher signal-to-noise ratios while retaining the peak shape for analytes of interest ultimately improving overall number of peptide and protein identifications of diagonal-PASEF. Importantly, combining RTsum with diagonal-PASEF improved overall identifications and quantitative precision when compared to dia-PASEF with variable quadrupole isolation widths and across different input amounts for cell line injections. We also tested the performance of diagonal-PASEF in controlled quantitative experiments where diagonal-PASEF outperformed dia-PASEF in the overall number of retained candidates below 1% or 5% error-rate, quantitative precision, and identifications on peptide level and protein level. These data indicate that RTsum demonstrates a positive use case of the high sampling rate of diagonal-PASEF and might therefore be a valuable addition to existing analysis pipelines. Collectively, our findings imply that diagonal-PASEF is developing into a competitive alternative to dia-PASEF and that the data analysis options are making fast progress. Analyte ; Mass spectrometry ; Workflow ; Retention time ; Quantitative proteomics ; Peptide ; Diagonal ; Quadrupole Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Erkka Järvinen | Xiaonan Liu | Markku Varjosalo | Salla Keskitalo
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-05-11)
Field: Chemistry — Spectroscopy

Automated MagNet Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics Abstract Plasma is an ideal material for proteomics due to its diverse protein content reflecting physiological and pathological states, and its compatibility with minimally invasive sampling. Deep proteomic profiling of plasma is hindered by the dominance of high-abundant proteins that mask the detection of low-abundant proteins. To overcome this, we compared five plasma protein enrichment methods, MagNet, ENRICHplus, ENRICHiST, EasySep, and EXONET, against neat plasma using LC-MS proteomics. All five methods substantially increased protein identifications, with MagNet, ENRICHplus, EasySep, and EXONET yielding up to 4200 proteins per sample, over 7-fold more than neat plasma, using a 44-minute gradient on the Evosep One and data-independent acquisition on the timsTOF Pro 2. These methods enriched extracellular vesicle-associated proteins while effectively depleting high-abundant proteins. We further optimized the cost-effective MagNet protocol by increasing the plasma-to-bead ratio and automated the workflow, including Evotip loading, on the Biomek i5 liquid handler. Automated MagNet demonstrated high reproducibility and a remarkably low total cost of just a few dollars per sample. This streamlined enrichment strategy enables scalable, high-throughput LC-MS plasma proteomics, supporting biomarker discovery across large clinical cohorts. Proteomics ; Plasma ; Chromatography ; Computer science ; Chemistry ; Physics ; Nuclear physics ; Biochemistry Advanced Proteomics Techniques and Applications
Authors: Shyam Panjwani | Alice Almazan | Wei Hao | Konstantinos Spetsieris
Source: Journal of Advanced Manufacturing and Processing (article, 2025-04-17)
Field: Chemistry — Analytical Chemistry

A comparative evaluation of the enhanced <scp>PLS</scp> ‐ <scp>Tree</scp> algorithm with multiple latent score vectors Abstract Multicollinearity and heterogeneity are prevalent challenges in the analysis of process industry datasets, necessitating algorithms capable of addressing both simultaneously. The partial least squares (PLS)‐Tree algorithm, which integrates PLS regression with decision tree methodologies, stands out by concurrently addressing data heterogeneity and improving predictive performance. However, the PLS‐Tree algorithm remains underexplored compared to other machine learning approaches. This study delves into the intricacies of the PLS‐Tree algorithm, utilizing synthetic data that mirrors the complexity of real‐world process industry scenarios characterized by high collinearity and clustering. This paper further enhances the original PLS‐Tree framework by introducing multiple latent score vectors, with the objective of refining the clustering process and boosting predictive accuracy beyond that of standard PLS and regression tree algorithms. Additionally, a comparative analysis is presented, evaluating the performance of the enhanced PLS‐Tree against regular PLS and regression tree, highlighting its potential for sophisticated data analysis in the process industries. Tree (set theory) ; Computer science ; Algorithm ; Mathematics ; Combinatorics Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models ; Water Quality Monitoring and Analysis
Authors: Jinlong Wang | Weizhong Sun | Jun Zhou | Lei Wang | L. Chen | Pengcheng Chen | Qichao Chen | Weichao Zhang
Source: Sensors (article, 2025-01-09)
Field: Materials Science — Materials Chemistry

Partial Discharge Detection from Large Motor Stator Slots Using EFPI Sensors This study addresses the challenges of electromagnetic interference and unstable signal transmission encountered by traditional sensors in detecting partial discharge (PD) within stator slots of large motors. A novel Extrinsic Fabry-Perot Interferometer (EFPI) sensor with a vibration-coupling air gap was designed to enhance the narrowband resonant detection sensitivity for PD ultrasonic signals by optimizing the diaphragm structure and coupling interface. The sensor features a quartz diaphragm with a thickness of 20 μM, an effective constrained radius of 0.9 mm, a vibration-coupling air gap depth of 100 μM, and a first-order natural resonant frequency of 66 kHz. Simulation and experimental analyses revealed the distribution characteristics and propagation paths of ultrasonic signals within stator slots. The results demonstrate that the EFPI sensor effectively detects PD ultrasonic signals at its resonant frequency of 66 kHz with a localization error of less than 5 mm, meeting engineering requirements. This study provides theoretical and practical insights into the efficient detection and precise localization of insulation faults in large motor stators. Partial discharge ; Stator ; Acoustics ; Engineering ; Materials science ; Electrical engineering ; Computer science ; Voltage ; Physics High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Electrostatic Discharge in Electronics
Authors: Zhaotang Liu | Zhenxu Wang | Tiefu Li | Jinxin Gu | Yunzhou Shi | Jie Zhang | Huiting Sun | Jiafu Wang
Source: Electronics (article, 2025-10-30)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Transmission-Reflection-Integrated Bifunctional Metasurface by Hybridizing Geometric Phase and Propagation Phase Multifunctional metasurfaces, capable of flexible electromagnetic wave manipulation, have become a focus of research for their high integration and utility. In particular, those operating simultaneously in transmission and reflection modes have attracted growing interest, as they integrate multiple functions within a single aperture, save physical space, and further expand wave control capabilities across full space. In this work, an inspiring strategy of transmission-reflection-integrated bifunctional metasurface by hybridizing geometric phase and propagation phase is proposed. The transmission and reflection modes can be independently and flexibly controlled in full space: the co-polarized reflection under left-handed circular polarization (LCP) incidence is governed by rotation-induced geometric phase modulation, while the co-polarized transmission under right-handed circular polarization (RCP) incidence is modulated through scaling-induced propagation phase modulation. Moreover, arbitrary amplitude modulation of the co-polarized transmission under RCP incidence can be realized by incorporating lumped resistors. As a proof of concept, a bifunctional meta-device is constructed, which can generate vortex beam carrying arbitrary topological charge for LCP reflected wave and achieve high-quality holographic imaging for RCP transmitted wave. Both the simulated and experimental results validate the feasibility of the proposed strategy, which significantly enhances the integration density of multifunctional metasurfaces while reducing inter-functional crosstalk, expanding its potential applications in electronic engineering. Moreover, it can also serve as a fundamental machine learning platform, facilitating multimodal fusion and cross-modal learning in radar signals and visual imaging. Polarization (electrochemistry) ; Reflection (computer programming) ; Transmission (telecommunications) ; Phase modulation ; Phase (matter) ; Holography ; Optical vortex ; Circular polarization ; Physical optics ; Amplitude Metamaterials and Metasurfaces Applications ; Advanced Wireless Communication Technologies ; Advanced Antenna and Metasurface Technologies