jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Anastasia Kontiza | Johanna von Gerichten | Matt Spick | Emily Fraser | Catia Costa | Kyle D. G. Saunders | Anthony D. Whetton | Carla F. Newman | Melanie J. Bailey
Source: The Analyst (article, 2025-01-01)
Field: Chemistry — Spectroscopy

Single-cell lipidomics: protocol development for reliable cellular profiling using capillary sampling Single-cell lipidomics enables detailed analysis of the lipidomes of cells, but is challenged by small sample volumes, the risk of background interference and a lack of validation data. In this study, we explore the effect of different sampling variables on the lipid profiles of single pancreatic cancer cells, detected using liquid chromatography-mass spectrometry (LC-MS). We use automated and manual capillary sampling methods to isolate living single cells and evaluate different sampling media, capillary tips, aspiration volume, and temperature and humidity control. We demonstrate that automated and manual capillary sampling yield comparable lipid profiles when key parameters are controlled. Our findings highlight that appropriate blank correction, capillary tip type, and the control of aspiration volumes are all critical to preserving detection sensitivity. Conversely, choice of sampling medium does not affect lipidomics results. We also set out suggested best practices for these methodological variables, laying a foundation for robust, adaptable workflows in single-cell lipidomics for applications such as biomarker discovery and metabolic research. Lipidomics ; Profiling (computer programming) ; Protocol (science) ; Computer science ; Computational biology ; Chromatography ; Chemistry ; Bioinformatics ; Biology ; Medicine ; Pathology Advanced Proteomics Techniques and Applications ; Biosensors and Analytical Detection ; Cell Image Analysis Techniques
Authors: Andrew C. Regan | John Wilson | Anthony Peyton
Source: Sensors (article, 2025-02-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Extension to the Jiles–Atherton Hysteresis Model Using Gaussian Distributed Parameters for Quenched and Tempered Engineering Steels The Jiles-Atherton (J-A) model has seen extensive use for modelling the hysteresis behaviour of ferromagnetic materials due to its computational efficiency, simplicity of use, and small number of physically related parameters. However, in this work, the application of the J-A model to hysteresis curves obtained from experimental measurements for as-quenched and quenched-and-tempered engineering steels is considered. It has been demonstrated that the current form of the J-A model is not capable of representing certain observed features in the obtained hysteresis curves of these steels, in particular, the rapid narrowing of the loops seen for as-quenched steels and the sharp corners seen for quenched-and-tempered steels. This work has shown that a superior fit to the major loops for such steels can be obtained by applying Gaussian variations with respect to the applied magnetic field to the model parameters. The findings are supported by experimental results from engineering steels used in the oil and gas industry. Hysteresis ; Materials science ; Work (physics) ; Ferromagnetism ; Magnetic hysteresis ; Gaussian ; Metallurgy ; Mechanics ; Statistical physics ; Thermodynamics ; Condensed matter physics ; Magnetic field ; Physics ; Magnetization Magnetic Properties and Applications ; Microstructure and Mechanical Properties of Steels ; Magnetic properties of thin films
Authors: Thanh Son Pham | Bùi Xuân Khuyến | Vũ Đình Lãm | Liang‐Yao Chen | YoungPak Lee
Source: Photonics (article, 2025-04-02)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Wide-Angle, Polarization-Independent Broadband Metamaterial Absorber by Using Plasmonic Metasurface-Based Split-Circular Structure Absorption of electromagnetic waves in a broadband frequency range with polarization insensitivity and wide incidence angles is greatly needed in modern technological applications. Many methods using metamaterials have been suggested to address this requirement; they can be complex multilayer structures or use external electronic components. In this paper, we present a plasmonic metasurface structure that was simply fabricated using the standard printed circuit board technique but provided a high absorption above 90%, also covering a broadband frequency range from 12.30 to 14.80 GHz. This plasmonic metasurface consisted of structural unit cells composed of multiple split rings connected by a copper bar. Analysis, simulation, and measurement results showed that the metasurface also showed polarization-insensitive properties and maintained an absorption above 90% at incident angles up to 45 degrees. The suggested plasmonic metasurface is a fundamental design that can also be used to design the absorber in different frequency ranges and is able to adapt well to being fabricated at various scales. Metamaterial ; Broadband ; Plasmon ; Polarization (electrochemistry) ; Optics ; Metamaterial absorber ; Optoelectronics ; Circular polarization ; Materials science ; Tunable metamaterials ; Physics Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: M Moskov | Julia Hedlund Lindberg | Maria Lycke | Emma Ivansson | Ulf Gyllensten | Karin Sundfeldt | Karin Stålberg | Stefan Enroth
Source: Communications Medicine (article, 2025-06-12)
Field: Chemistry — Spectroscopy

Deep plasma proteomics identifies and validates an eight-protein biomarker panel that separate benign from malignant tumors in ovarian cancer Our results indicates that up to one third of benign cases can be identified by molecular measures thereby reducing the need for diagnostic surgery. Ovarian cancer ; Biomarker ; Proteomics ; Cancer ; Medicine ; Pathology ; Oncology ; Internal medicine ; Biology ; Gene Advanced Proteomics Techniques and Applications ; Cancer, Lipids, and Metabolism ; Ferroptosis and cancer prognosis
Authors: Xiang Liu | Haidan Sun | Xinhang Hou | Jian Sun | Min Tang | Yong‐Biao Zhang | Yongqian Zhang | Wei Sun | Chao Liu | Urine Test Sample Working Group | Youhe Gao | Shuxuan Tang | Ziyun Shen | Kehui Liu | Lulu Jia | Jing Wei | Jianqiang Wu | Xiaoyue Tang | Yanchang Li | Guibin Wang | Xinying Sui | Lihua Zhang | Huiming Yuan | Xinxin Liu | Dong Liu | Qi Zhang | Xiaoyan Qiu | Guanbo Wang | Mo Hu | Ye Tian | Minjie Tan | Xue Peng | Liman Guo | Qing Zhang | Yongsheng Chen | Jianguo Ji | Weiyi Hu | Wenyuan Zhu | Min Huang | Yingzi Qi | Xianming Liu | Xiaoxian Du | Ji Luo | Lingsheng Chen | Yinghua Zhao
Source: Nature Communications (article, 2025-01-26)
Field: Chemistry — Spectroscopy

Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary proteomics data across diverse liquid chromatography-mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study, we conduct a comprehensive evaluation of urinary proteome across multiple LC-MS platforms. To systematically analyze and assess the quality of large-scale urinary proteomics data, we develop a comprehensive quality control (QC) system named MSCohort, which extracted 81 metrics for individual experiment and the whole cohort quality evaluation. Additionally, we present a standard operating procedure (SOP) for high-throughput urinary proteome analysis based on MSCohort QC system. Our study involves 20 LC-MS platforms and reveals that, when combined with a comprehensive QC system and a unified SOP, the data generated by data-independent acquisition (DIA) workflow in urine QC samples exhibit high robustness, sensitivity, and reproducibility across multiple LC-MS platforms. Furthermore, we apply this SOP to hybrid benchmarking samples and clinical colorectal cancer (CRC) urinary proteome including 527 experiments. Across three different LC-MS platforms, the analyses report high quantitative reproducibility and consistent disease patterns. This work lays the groundwork for large-scale clinical urinary proteomics studies spanning multiple platforms, paving the way for precision medicine research. Proteomics ; Computer science ; Proteome ; Urinary system ; Data mining ; Bioinformatics ; Medicine ; Chemistry ; Biology ; Internal medicine Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Pınar Mert Cuce
Source: Sustainability (article, 2025-06-04)
Field: Chemistry — Spectroscopy

Sustainable Insulation Technologies for Low-Carbon Buildings: From Past to Present Building facade insulation technologies have evolved from primitive thermal barriers to high-performance, multifunctional systems that enhance energy efficiency and indoor comfort. Historical insulation methods, such as thick masonry walls and timber-based construction, have gradually been replaced by advanced materials and innovative facade designs. Studies indicate that a significant proportion of a building’s heat loss occurs through its external walls and windows, highlighting the need for effective insulation strategies. The development of double-skin facades (D-SFSs), adaptive facades (AFs), and green facades has enabled substantial reductions in heating and cooling energy demands. Materials such as vacuum insulation panels (VIPs), aerogels, and phase change materials (PCMs) have demonstrated superior thermal resistance, contributing to improved thermal regulation and reduced carbon emissions. Green facades offer additional benefits by lowering surface temperatures and mitigating urban heat island effects, while D-SF configurations can reduce cooling loads by over 20% in warm climates. Despite these advancements, challenges remain regarding the initial investment costs, durability, and material sustainability. The future of facade insulation technologies is expected to focus on bio-based and recyclable insulation materials, enhanced thermal performance, and climate-responsive facade designs. This study provides a comprehensive review of historical and modern facade insulation technologies, examining their impact on energy efficiency, sustainability, and future trends in architectural design. Architectural engineering ; Engineering ; Carbon fibers ; Environmental science ; Civil engineering ; Business ; Construction engineering ; Materials science ; Composite material Aerogels and thermal insulation ; Building Energy and Comfort Optimization ; Urban Heat Island Mitigation
Authors: Yuchen He | Ka Yang | S. Li | Martin Zeller | Graeme C. McAlister | Hamish Stewart | Christian Hock | Eugen Damoc | Vlad Zabrouskov | Steven P. Gygi | João A. Paulo | Qing Yu
Source: Molecular & Cellular Proteomics (article, 2025-04-09)
Field: Chemistry — Spectroscopy

TMT-Based Multiplexed (Chemo)Proteomics on the Orbitrap Astral Mass Spectrometer Ongoing advancements in instrumentation has established mass spectrometry (MS) as an essential tool in proteomics research and drug discovery. The newly released Asymmetric Track Lossless (Astral) analyzer represents a major step forward in MS instrumentation. Here, we evaluate the Orbitrap Astral mass spectrometer in the context of tandem mass tag (TMT)-based multiplexed proteomics and activity-based proteome profiling, highlighting its sensitivity boost relative to the Orbitrap Tribrid platform-50% at the peptide and 20% at the protein level. We compare TMT data-dependent acquisition and label-free data-independent acquisition on the same instrument, both of which quantify over 10,000 human proteins per sample within 1 h. TMT offers higher quantitative precision and data completeness, while data-independent acquisition is free of ratio compression and is thereby more accurate. Our results suggest that ratio compression is prevalent with the high-resolution MS2-based quantification on the Astral, while real-time search-based MS3 quantification on the Orbitrap Tribrid platform effectively restores accuracy. Additionally, we benchmark TMT-based activity-based proteome profiling by interrogating cysteine ligandability. The Astral measures over 30,000 cysteines in a single-shot experiment, a 54% increase relative to the Orbitrap Eclipse. We further leverage this remarkable sensitivity to profile the target engagement landscape of FDA-approved covalent drugs, including sotorasib and adagrasib. We herein provide a reference for the optimal use of the advanced MS platform. Orbitrap ; Mass spectrometry ; Proteomics ; Multiplexing ; Chemistry ; Computer science ; Chromatography ; Telecommunications Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Microbial Community Ecology and Physiology
Authors: Chuan Hu | Xiaoqi He | Huile Gao | Jinming Zhang
Source: Acta Pharmaceutica Sinica B (article, 2025-01-24)
Field: Materials Science — Biomaterials

DELIVER: The core principles for the clinic translation of nanomedicines Translation (biology) ; Core (optical fiber) ; Medicine ; Computer science ; Chemistry Nanoparticle-Based Drug Delivery ; RNA Interference and Gene Delivery ; Monoclonal and Polyclonal Antibodies Research
Authors: Huoming Zhang | Dalila Bensaddek
Source: Journal of Proteome Research (article, 2025-01-22)
Field: Chemistry — Spectroscopy

Optimized Time-Segmented Acquisition Expands Peptide and Protein Identification in TIMS-TOF Pro Mass Spectrometry We introduce here a novel approach, termed time-segmented acquisition (Seg), to enhance the identification of peptides and proteins in trapped ion mobility spectrometry (TIMS)-time-of-flight (TOF) mass spectrometry. Our method exploits the positive correlation between ion mobility values and reversed-phase liquid chromatography (LC) retention time to improve ion separation and resolution. By dividing the LC retention time into multiple segments and applying a segment-specific narrower ion mobility range within the TIMS tunnel, we achieved better separation and higher resolution of ion mobility. In comparison to conventional TIMS methods, which typically scan a static ion mobility range (either from 0.6 to 1.6 [Wide] or from 0.85 to 1.3 [Narrow], V × s/cm<sup>2</sup>), the Seg method demonstrates marked improvements in identification rates. Compared to Wide scanning, the Seg method increases peptide identifications by 17-27% and protein identifications by 6-16% depending on the gradient length and the sample load. The enhancement in peptide identification is even more pronounced when compared to Narrow scanning, with an increase of 34-86%. These findings highlight the potential of the Seg dda-PASEF method in expanding the capabilities of TIMS-TOF mass spectrometry, especially for peptide-focused analyses, such as post-translational modifications and peptidomics. Mass spectrometry ; Protein mass spectrometry ; Chemistry ; Peptide ; Proteomics ; Isobaric labeling ; Identification (biology) ; Chromatography ; Tandem mass spectrometry ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Hanna Boruczkowska | Tomasz Boruczkowski | Monika Bronkowska | Maja Prajzner | Elżbieta Rytel
Source: Processes (article, 2025-04-22)
Field: Chemistry — Analytical Chemistry

Comparison of Colour Measurement Methods in the Food Industry Colour is a key parameter in the evaluation of food products. Accurate colour measurement enables us to maintain their consistent quality. The aim of this study was to compare three colour measurement methods. The food products used for the study were French fries, the colour of which was checked after defined frying times. Their colour was measured using a professional Minolta C-5 spectrophotometer (Konica Minolta Sensing Europe B.V., Nieuwegein, The Netherlands) as well as a low-cost SparkFun SEN-15050 spectrophotometer (SparkFun Electronics, Niwot, CO, USA) and a readily available HP SkanJet 4850 scanner (Hewlett Packard, Palo Alto, CA, USA). The images obtained were analysed using free ImageJ software ver. 1.54. The results indicate that low-cost spectrophotometers used in the Internet of Things (IoT) systems and colour measurement methods based on vision techniques are suitable for less precise but fast measurements and, in such cases, can successfully replace the expensive and often bulky devices. Food industry ; Food science ; Business ; Computer science ; Environmental science ; Chemistry Spectroscopy and Chemometric Analyses ; Dye analysis and toxicity ; Meat and Animal Product Quality
Authors: Christian M. Beusch | Ken Braesch-Andersen | Ulrika Felldin | Pierre Sabatier | Anna Widgren | Jonas Bergquist | Karl‐Henrik Grinnemo | Sergey Rodin
Source: Communications Biology (article, 2025-01-17)
Field: Chemistry — Spectroscopy

A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research Recent developments in mass spectrometry-based proteomics have established it as a robust tool for system-wide analyses essential for pathophysiological research. While post-mortem samples are a critical source for these studies, our understanding of how body decomposition influences the proteome remains limited. Here, we have revisited published data and conducted a clinically relevant time-course experiment in mice, revealing organ-specific proteome regulation after death, with only a fraction of these changes linked to protein autolysis. The liver and spleen exhibit significant proteomic alterations within hours post-mortem, whereas the heart displays only modest changes. Additionally, subcellular compartmentalization leads to an unexpected surge in proteome alterations at the earliest post-mortem interval (PMI). Additionally, we have conducted a comprehensive analysis of semi-tryptic peptides, revealing distinct consensus motifs for different organs, indicating organ-specific post-mortem protease activity. In conclusion, our findings emphasize the critical importance of considering PMI effects when designing proteomics studies, as these effects may significantly overshadow the impacts of diseases. Preferably, the samples should be taken in the operation room, especially for studies including subcellular compartmentalization or trans-organ comparison. In single-organ studies, the planning should involve careful control of PMI. Proteomics ; Compartmentalization (fire protection) ; Proteome ; Biology ; Autolysis (biology) ; Computational biology ; Quantitative proteomics ; Bioinformatics ; Biochemistry ; Enzyme Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Jian Wang | Jianfeng He | Xiaohan Chen | Tian Tian | Chenguo Yao | Ahmed Abu‐Siada
Source: Energies (article, 2025-07-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Power Transformer Short-Circuit Force Calculation Using Three and Two-Dimensional Finite-Element Analysis In a power transformer short-circuit, transient current and magnetic flux interactions create strong electromagnetic forces that can deform windings and the core, risking failure. Accurate calculation of these forces during design is critical to prevent such outcomes. This paper employs two-dimensional (2D) and three-dimensional (3D) finite-element analysis (FEA) to model a 110 kV, 40 MVA three-phase transformer, calculating magnetic flux density, short-circuit current, and electromagnetic forces. The difference in force values at inner and outer core window positions, reaching up to 40%, is analyzed. The impact of physical winding displacement on axial forces is also studied. Simulation results, validated against analytical calculations, show peak short-circuit currents of 6963 A on the high-voltage (HV) winding and 70,411 A on the low-voltage (LV) winding. Average radial forces were 136 kN on the HV winding and 89 kN on the LV winding, while average axial forces were 8 kN on the HV and 9 kN on the LV. This agreement verifies the FEA models’ reliability. The results provide insights into winding behavior under severe faults and enhance transformer design reliability. Finite element method ; Transformer ; Electrical engineering ; Network analysis ; Short circuit ; Electronic engineering ; Engineering ; Structural engineering ; Voltage Magnetic Properties and Applications ; Power Transformer Diagnostics and Insulation ; Non-Destructive Testing Techniques
Authors: Julien Steffen
Source: The Journal of Physical Chemistry C (article, 2025-07-17)
Field: Materials Science — Materials Chemistry

Simulation of Hydrogen Storage in MOF-5 and Li-MOF-5 by Ring Polymer Molecular Dynamics on Self-Consistently Fine-Tuned Machine-Learned Interatomic Potentials The hydrogen storage in MOF-5 and lithiated MOF-5 (Li-MOF-5) is simulated with ring polymer molecular dynamics (RPMD) on machine-learned interatomic potentials (MLIPs). The MLIPs were parametrized based on the message-passing atomic cluster expansion (MACE) foundation model. It was fine-tuned for H2 storage in MOF-5 and Li-MOF-5, using density-functional theory (DFT) single point calculations of each 100th frame from MD trajectories calculated with it. In order to focus the samplings on the most relevant parts of configuration space and reduce the overhead due to erroneous samplings with the foundation model, the fine-tuning was done self-consistently: MD samplings were performed with the fine-tuned MLIP, DFT single points calculated and the data used for another fine-tuning, until the property of interest (the spatial H2 distribution in this case) has converged. With this, highly accurate MLIPs were obtained that allowed for the simulation of H2 storage, depending on the temperature and the H2 loading. Nuclear quantum effects, important for the description of H2 at the low temperatures relevant for storage, were accounted for with RPMD. In MOF-5, the H2 molecules are loosely associated with the edges of the framework, whereas in Li-MOF-5, each Li atom coordinates 2–3 H2 molecules up to room temperature. Its H2 capacity is therefore increased significantly. Nuclear quantum effects lead to a slight decrease in storage capacity for both MOF-5 and Li-MOF-5, in agreement with previous studies. The outlined fine-tuning strategy facilitates the fast and systematic generation of high-quality MLIPs for hydrogen storage in arbitrary MOFs. Molecular dynamics ; Ring (chemistry) ; Polymer ; Hydrogen storage ; Chemical physics ; Materials science ; Hydrogen ; Hydrogen bond ; Nanotechnology ; Computational chemistry ; Chemistry ; Molecule ; Composite material ; Organic chemistry Machine Learning in Materials Science ; Metal-Organic Frameworks: Synthesis and Applications ; Inorganic Chemistry and Materials