jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tassiani Sarretto | Mika T. Westerhausen | Jayden C. McKinnon | David Bishop | Shane R. Ellis
Source: Analytical and Bioanalytical Chemistry (article, 2025-01-20)
Field: Chemistry — Spectroscopy

Evaluation of combined workflows for multimodal mass spectrometry imaging of elements and lipids from the same tissue section The wide range of mass spectrometry imaging (MSI) technologies enables the spatial distributions of many analyte classes to be investigated. However, as each approach is best suited to certain analytes, combinations of different MSI techniques are increasingly being explored to obtain more chemical information from a sample. In many cases, performing a sequential analysis of the same tissue section is ideal to enable a direct correlation of multimodal data. In this work, we explored different workflows that allow sequential lipid and elemental imaging on the same tissue section using atmospheric pressure laser desorption/ionisation-plasma post-ionisation-MSI (AP-MALDI-PPI-MSI) and laser ablation-inductively coupled plasma-MSI (LA-ICP-MSI), respectively. It is found that performing lipid imaging first using matrix-coated samples, followed by elemental imaging on matrix-coated samples, provides high-quality MSI datasets for both lipids and elements, with the resulting distributions being similar to those obtained when each is performed in isolation. The effect of matrix removal prior to elemental imaging, and of performing elemental imaging first were also investigated but found to generally yield lower quality elemental imaging data but comparable lipid imaging data. Finally, we used the ability to acquire both elemental and lipid imaging data from the same section to investigate the spatial correlations between different lipids (including ceramides, phosphatidylethanolamine, and hexosylceramides) and elements within mouse brain tissue. Mass spectrometry imaging ; Chemistry ; Analyte ; Elemental analysis ; MALDI imaging ; Mass spectrometry ; Chemical imaging ; Sample preparation ; Analytical Chemistry (journal) ; Matrix (chemical analysis) ; Matrix-assisted laser desorption/ionization ; Desorption ; Chromatography ; Hyperspectral imaging ; Computer science ; Artificial intelligence ; Adsorption Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Analytical Chemistry and Chromatography
Authors: Haris Ishaq | Curran Crawford
Source: RSC Sustainability (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

Negative emission technologies: a way forward? The role and potential implications of Negative Emission Technologies (NETs) for atmospheric CO 2 removal and long-term storage, supporting global efforts toward net-zero climate goals. Computer science Catalytic Processes in Materials Science ; Gas Dynamics and Kinetic Theory ; Advanced Aircraft Design and Technologies
Authors: Xiao Zhang | Yingqun Gao | L. Fu | Yiran Zhang | Zeyu Li | Qingtai Shu
Source: Scientific Reports (article, 2025-07-21)
Field: Chemistry — Analytical Chemistry

Early feature study of Yunnan pine pinewood nematode disease based on hyperspectral remote sensing of ground objects Pine Wilt Disease (PWD), caused by the pine wood nematode, is a major global forest pathology characterized by the rapid death of pine trees within a span of three months. Forestry management policy requires the eradication of all infected trees during the initial outbreak phase of a disease to contain its spread. This measure substantially relies on the timely identification of diseased trees. Accurate early diagnosis is a critical core component for effective disease control, preventing the spread of the epidemic, and maintaining the integrity of forest ecosystems. Therefore, this study proposes a new approach for early detection of PWD using hyperspectral data combined with measured physiological parameters to obtain diagnostic spectra and optimal biochemical parameters for early detection. This study investigated early-stage PWD by integrating 350-2500 nm hyperspectral data acquired with an ASD FieldSpec 4 and biochemical analysis. Results revealed significant declines in total sugar, reducing sugar, and moisture content during early infection. Study identified the spectral ranges 455-677 nm and 1974-2340 nm as optimal diagnostic windows. Using Competitive Adaptive Reweighted Sampling (CARS) and Successive Projections Algorithm (SPA), we identified diagnostic spectral bands: CARS selected 20 moisture-sensitive bands in red-edge (680-760 nm) and SWIR regions, while SPA pinpointed 4 critical bands (758, 1074, 1124, 1663 nm) across red-edge, NIR, and SWIR. This leaf-scale methodology establishes a technical foundation for regional-scale airborne and satellite hyperspectral monitoring of PWD. The XGBoost classifier achieved 91% accuracy (CARS) and 83% accuracy (SPA) in distinguishing healthy from early-stage infected trees, with AUC > 0.8 for both feature sets, demonstrating reliable spectral discrimination of infection status. This study proposes a novel method for the early detection of PWD based on spectral characteristics, offering valuable insights for the application of hyperspectral remote sensing at a regional scale. Hyperspectral imaging ; Remote sensing ; Feature (linguistics) ; Computer science ; Artificial intelligence ; Pattern recognition (psychology) ; Geography Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Water Quality Monitoring and Analysis
Authors: Weikang Li | Shengai Cui | Yupeng Li | Ying Zeng | Guang Zeng | Wei Xia
Source: Nanomaterials (article, 2025-08-01)
Field: Materials Science — Materials Chemistry

Mechanistic Insights into the Fracture Toughness Enhancement of Nano-TiO2 and Basalt Fiber Bar Reinforced Magnesium Phosphate Cement Magnesium phosphate cement (MPC) exhibits brittleness when utilized as a repair material for bridge decks. To address this issue, this study employs nano-TiO<sub>2</sub> (NT) and a novel material (basalt fiber bar) as modifiers. A double-K fracture model is developed for the modified MPC to quantitatively evaluate the enhancement of fracture toughness induced by NT and basalt fiber bars. The cracking behavior and toughening mechanisms of the NT and basalt fiber bar reinforced MPC are investigated using extended finite element theory and composite material theory. Additionally, a formula is proposed to calculate the incremental fracture toughness of NT and basalt fiber bar reinforced MPC. The results indicated that NT and basalt fiber bar can effectively enhance the ultimate bending capacity of MPC. The improvement increases with the fiber volume fraction, and noticeable bending hardening occurs when the fiber content exceeds 2%. With the same fiber volume fraction, the peak load can be increased by up to 11.7% with the addition of NT. The crack initiation toughness of the NT group without basalt fiber bars is 58% higher than that of the CC group. The content and diameter of basalt fiber bar are critical parameters affecting the toughness of the NT and basalt fiber bar reinforced MPC. Basalt fiber ; Materials science ; Composite material ; Volume fraction ; Fiber ; Brittleness ; Bending ; Fracture toughness ; Toughness ; Fiber pull-out ; Magnesium phosphate ; Composite number ; Cement ; Composite laminates Magnesium Oxide Properties and Applications ; Numerical methods in engineering ; Innovative concrete reinforcement materials
Authors: Wenqing Wu | Chengzhi Zhang | Tong Bao | Yi Zhao
Source: Expert Systems with Applications (article, 2025-02-11)
Field: Materials Science — Materials Chemistry

SC4ANM: Identifying optimal section combinations for automated novelty prediction in academic papers Novelty ; Section (typography) ; Computer science ; Artificial intelligence ; Machine learning ; Data mining ; Operating system ; Psychology Machine Learning in Materials Science ; Online Learning and Analytics ; Advanced Text Analysis Techniques
Authors: Yuqi Gu | Hong Zhong | Jianhua Wu | Kaixuan Li | Yu Dong Huang | Huimin Fang | Muhammad Hassan | Lijian Yao | Chao Zhao
Source: Foods (article, 2025-05-22)
Field: Chemistry — Analytical Chemistry

Application of Portable Near-Infrared Spectroscopy for Quantitative Prediction of Protein Content in Torreya grandis Kernels Under Different States Protein content is a key quality indicator in nuts, influencing their color, taste, storage, and processing properties. Traditional methods for protein quantification, such as the Kjeldahl nitrogen method, are time-consuming and destructive, highlighting the need for rapid, convenient alternatives. This study explores the feasibility of using portable near-infrared spectroscopy (NIRS) for the quantitative prediction of protein content in <i>Torreya grandis</i> (<i>T. grandis</i>) kernels by comparing different sample states (with shell, without shell, and granules). Spectral data were acquired using a portable NIR spectrometer, and the protein content was determined via the Kjeldahl nitrogen method as a reference. Outlier detection was performed using principal component analysis combined with Mahalanobis distance (PCA-MD) and concentration residual analysis. Various spectral preprocessing techniques and partial least squares regression (PLSR) were applied to develop protein prediction models. The results demonstrated that portable NIRS could effectively predict protein content in <i>T. grandis</i> kernels, with the best performance being achieved using granulated samples. The optimized model (1Der-SNV-PLSR-G) significantly outperformed models based on whole kernels (with or without shell), with determination coefficients for the calibration set (Rc2) and prediction set (Rp2) of 0.92 and 0.86, respectively, indicating that the sample state critically influenced prediction accuracy. This study confirmed the potential of portable NIRS as a rapid and convenient tool for protein quantification in nuts, offering a practical alternative to conventional methods. The findings also suggested its broader applicability for quality assessment in other nuts and food products, contributing to advancements in food science and agricultural technology. Partial least squares regression ; Kjeldahl method ; Principal component analysis ; Biological system ; Near-infrared spectroscopy ; Calibration ; Mahalanobis distance ; Chemometrics ; Computer science ; Artificial intelligence ; Pattern recognition (psychology) ; Mathematics ; Chemistry ; Machine learning ; Statistics ; Nitrogen Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Meat and Animal Product Quality
Authors: Victor G Chrone | Alina Błaszczyk | Derrick H. Zhang | Solveig B. Nielsen | Janne Crawford | Veit Schwämmle | Peter Højrup | Thomas Kofoed | Niomi Peckham | Ejvind Mørtz
Source: Journal of Pharmaceutical and Biomedical Analysis (article, 2025-07-03)
Field: Chemistry — Spectroscopy

Host cell protein quantitation by LC-MS. Experimental demonstration, qualification, and comparison of methods in USP 1132.1 The development of biologics necessitates reliable assays to characterize and control Host Cell Protein (HCP) impurities. Liquid Chromatography-Mass Spectrometry (LC-MS)-based HCP assays have emerged as a powerful orthogonal method to HCP ELISA, providing detailed information on individual HCPs. In response to a growing need, the U.S Pharmacopeia (USP) introduced General Chapter < 1132.1 > , which provides the best practices and outlines three quantitative LC-MS methods. This study explores the practical application and validation readiness of the following strategies: A - Relative to Product Protein, B - Relative to Spiked-in Protein, and C - Relative to Spiked-in Peptide. Two common HCPs-Clusterin and Lipoprotein Lipase-were quantified using LC-MS in a purified mAb drug substance spiked with a CHO cell culture harvest to simulate in-process HCP levels. All three methods were demonstrated in the same samples and dilutions, enabling direct comparison of the three methods from a single dataset. Method performance was assessed according to ICH Q2(R2) guidelines for analytical method validation, focusing on linearity, accuracy, precision, and specificity. Results include a comparative assessment and discussion of the advantages and disadvantages, and application of each aforementioned HCP quantification method. This study provides practical insights into the implementation of USP < 1132.1 > supporting the growing role of LC-MS in HCP analysis for biologics development. Chemistry ; Chromatography ; Host (biology) Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ariana E. Shannon | Rachael Teodorescu | No Joon Song | Lilian R. Heil | Cristina C. Jacob | Philip M. Remes | Zihai Li | Mark P. Rubinstein | Brian C. Searle
Source: Nature Communications (article, 2025-04-22)
Field: Chemistry — Spectroscopy

Rapid assay development for low input targeted proteomics using a versatile linear ion trap Advances in proteomics and mass spectrometry enable the study of limited cell populations, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive low-mass specificity measurements, these instruments are effectively restricted to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. Here, we describe a workflow using a hybrid quadrupole-LIT instrument that rapidly develops targeted proteomics assays from global data-independent acquisition (DIA) measurements without high-mass accuracy. Using an automated software approach for scheduling parallel reaction monitoring assays (PRM), we show consistent quantification across three orders of magnitude in a matched-matrix background. We demonstrate measuring low-level proteins such as transcription factors and cytokines with quantitative linearity below two orders of magnitude in a 1 ng background proteome without requiring stable isotope-labeled standards. From a 1 ng sample, we found clear consistency between proteins in subsets of CD4<sup>+</sup> and CD8<sup>+</sup> T cells measured using high dimensional flow cytometry and LIT-based proteomics. Based on these results, we believe hybrid quadrupole-LIT instruments represent a valuable solution to expanding mass spectrometry in a wide variety of laboratory settings. Proteomics ; Quantitative proteomics ; Quadrupole ion trap ; Mass spectrometry ; Stable isotope labeling by amino acids in cell culture ; Proteome ; Ion trap ; Computer science ; Computational biology ; Chemistry ; Bioinformatics ; Chromatography ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Receptor Mechanisms and Signaling
Authors: Maarten Klaverdijk | Marcel Ottens | Marieke E. Klijn
Source: Analytical and Bioanalytical Chemistry (article, 2025-02-06)
Field: Chemistry — Analytical Chemistry

Single compound data supplementation to enhance transferability of fermentation specific Raman spectroscopy models Raman spectroscopy is a valuable analytical tool for real-time analyte quantification in fermentation processes. Quantification is performed with chemometric models that translate Raman spectra into concentration values, which are typically calibrated with process data from multiple comparable fermentations. However, process-specific models underperform for minor process variation(s) or different operation modes due to the integration of cross-correlations, resulting in low target analyte specificity. Thus, model transferability is poor and labor-intensive (re-)calibration of models is required for related processes. In this work, partial least-squares models for glucose, ethanol, and biomass were calibrated with Saccharomyces cerevisiae batch fermentation data and subsequently transferred to a fed-batch operation. To enhance model transferability without additional process runs, single compound data supplementation was performed. The supplemented models increased overall target analyte specificity and demonstrated sufficient prediction accuracy for the fed-batch process (root-mean-square errors of prediction (RMSEP) of 3.06 mM, 8.65 mM, and 0.99 g/L for glucose, ethanol, and biomass), while maintaining high prediction accuracy for the batch process (RMSEP of 1.71 mM, 4.20 mM, and 0.17 g/L for glucose, ethanol, and biomass). This work showcases that process data in combination with single compound spectra is a fast and efficient strategy to apply Raman spectroscopy for real-time process monitoring across related processes. Analyte ; Partial least squares regression ; Calibration ; Raman spectroscopy ; Chemistry ; Transferability ; Fermentation ; Process (computing) ; Chemometrics ; Process analytical technology ; Biomass (ecology) ; Biological system ; Analytical Chemistry (journal) ; Chromatography ; Computer science ; Machine learning ; Mathematics ; Work in process ; Statistics ; Food science ; Engineering Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Listeria monocytogenes in Food Safety
Authors: Somayyeh Asgari | Tapio Fabritius
Source: Scientific Reports (article, 2025-08-07)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Frequency-multiplexed tunable logic device based on terahertz graphene-integrated metamaterial composed of two circular ring resonator array This paper presents a novel terahertz (THz) graphene-based tunable metamaterial that operates as a frequency-multiplexed logic device. The structure consists of a gold layer, a dielectric substrate, and an array of graphene resonators formed by two circular ring resonators per unit cell. The metamaterial is simulated and designed in CST Software. The equivalent circuit model (ECM) for the metamaterial is obtained using MATLAB code. Logical input values are set by adjusting the Fermi levels of graphene-based circular resonators, while output logic states are determined by analyzing the reflection spectrum. The proposed device operates within the THz range, enabling the realization of OR, XNOR, and NAND logic gates at three distinct frequencies. Additionally, the working frequencies of these gates can be tuned by modifying the graphene's Fermi level. The highest extinction ratios (ERs) achieved for the OR, XNOR, and NAND gates are 36.93, 65.66, and 22.38 dB, respectively. Owing to its simple design and versatility, this metamaterial shows strong potential for use in THz digital systems. Terahertz radiation ; Metamaterial ; XNOR gate ; Resonator ; Optoelectronics ; NAND gate ; Split-ring resonator ; Logic gate ; Graphene ; Materials science ; Physics ; Optics ; Electronic engineering ; Engineering ; Nanotechnology Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Advanced Antenna and Metasurface Technologies
Authors: Ryo Konno | M. Ishikawa | Daisuke Nakajima | Kaori Inukai | Osamu Ohara | Yusuke Kawashima
Source: DNA Research (article, 2025-07-04)
Field: Chemistry — Spectroscopy

Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics Proteomics using mass spectrometry (MS) has significantly advanced, offering deep insights into complex proteomes. The timsTOF MS platform with its parallel accumulation-serial fragmentation (PASEF) technology has achieved high scan speeds and high-quality spectra. Bruker's timsTOF HT, which features TIMS-XR technology, offers an improved dynamic range and analysis depth, supporting high sample loadings. Moreover, various improvements to the data-independent acquisition method based on the PASEF technology (diaPASEF) have been reported. Despite these advancements, most high-level deep proteomic reports are based on the Orbitrap Astral and Orbitrap Exploris 480, and analytical systems using timsTOF MS still require improvement. Here, Bruker's timsTOF HT was used to validate and optimize key diaPASEF parameters, leading to the development of a Thin-diaPASEF method. This method provides a high quantitative accuracy and consistency. In our validation, 9,400 proteins were identified in a single shot from HEK cells (strictly controlled protein false discovery rate <1%), the highest number analysed by the timsTOF MS series using standard human cultured cells. Furthermore, by combining Thin-diaPASEF with an improved Lycopersicon esculentum lectin method, over 5,000 proteins were identified in a 24-sample/d analysis from the plasma, and we succeeded in constructing a system with high proteome coverage that can be used for biomarker discovery. Proteome ; Orbitrap ; Biomarker discovery ; Proteomics ; False discovery rate ; Mass spectrometry ; Computational biology ; Quantitative proteomics ; High resolution ; Computer science ; Chromatography ; Bioinformatics ; Analytical Chemistry (journal) ; Biology ; Chemistry ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Identification and Quantification in Food
Authors: Jie Zhou | Xin Sun | Jun Xu | Shiyue Wu | Kyong Hwan Jin | Yongjian Tang | Zao Yi | Yougen Yi
Source: Molecules (article, 2025-02-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Versatile Tunable Terahertz Absorption Device Based on Bulk Dirac Semimetals and Graphene We employed the CST Microwave Studio software 2020 and the FDID algorithm for simulation. We have designed a terahertz broadband absorber based on Dirac semimetals and graphene, achieving continuous broadband absorption with a rate exceeding 80% over the range from 7.6776 to 9.172 THz. This broadband absorber features two independent tuning modes, utilizing graphene and Dirac semimetals, and exhibits strong electromagnetic adaptability. Furthermore, we conducted an in-depth analysis of the physical mechanisms underlying the high absorption in these absorbers using impedance matching theory and localized surface plasmon resonance (LSPR) theory. Variations in the dielectric constants of different dielectric layers and the relaxation time of graphene can also modulate the absorption rate. In summary, our proposed terahertz broadband absorber, employing two distinct tunable materials, enhances the device's flexibility and environmental adaptability, offering promising prospects for wideband absorption applications. Graphene ; Terahertz radiation ; Materials science ; Absorption (acoustics) ; Dirac (video compression format) ; Optoelectronics ; Microwave ; Impedance matching ; Broadband ; Dielectric ; Wideband ; Electrical impedance ; Optics ; Nanotechnology ; Physics ; Telecommunications ; Computer science Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Plasmonic and Surface Plasmon Research