jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Chuxuan Zhao | Weitian Wang | Ning Zhu | Zihao Song | Xing Chao
Source: Measurement Science and Technology (article, 2024-01-09)
Field: Chemistry — Spectroscopy

Quantitative, multi-species gas sensing using broadband terahertz time-domain spectroscopy Abstract The broadband terahertz wave, with its correspondence to the fingerprint spectra of gas molecules and relatively high transmittance through smoke, aerosol, and combustion environments, bears great potential for gas detection and combustion diagnostics. While access to rotational spectral fingerprints in the terahertz region provides opportunities for species-selective diagnostics with minimized background and cross interference, few studies have been devoted to direct, quantitative, and simultaneous analysis of multiple components exploiting the terahertz region. In this work, we achieve quantitative measurements of CO, NH 3 and H 2 O gas concentrations at standard temperatures and pressures over a bandwidth of 1 THz, using direct absorption spectrum from femtosecond-laser-based terahertz time-domain spectroscopy. Spectral fitting of the fully resolved rotational lines yields good precision and accuracy with validation against calibrated mixtures. The estimated detection limits of the multi-species sensing system are 250 ppm m, 7 ppm m and 4 ppm m for CO, NH 3 and H 2 O, respectively. The demonstration of quantitative, multi-species gas sensing indicates the feasibility and practical value of using broadband terahertz absorption spectroscopy for real-time, quantitative analysis and speciation of multicomponent gases in complicated practical environments such as combustion and multi-phase flows. Terahertz radiation ; Spectroscopy ; Materials science ; Combustion ; Broadband ; Terahertz spectroscopy and technology ; Femtosecond ; Absorption spectroscopy ; Terahertz time-domain spectroscopy ; Optics ; Absorption (acoustics) ; Analytical Chemistry (journal) ; Laser ; Interference (communication) ; Optoelectronics ; Physics ; Chemistry ; Computer science ; Telecommunications Spectroscopy and Laser Applications ; Terahertz technology and applications ; Photonic and Optical Devices
Authors: Anguo Xie | Yù Zhang | Han Wu | Meng Chen
Source: Foods (article, 2024-06-17)
Field: Chemistry — Analytical Chemistry

Monitoring the Aging and Edible Safety of Pork in Postmortem Storage Based on HSI and Wavelet Transform The process of meat postmortem aging is a complex one, in which improved tenderness and aroma coincide with negative effects such as water loss and microbial growth. Determining the optimal postmortem storage time for meat is crucial but also challenging. A new visual monitoring technique based on hyperspectral imaging (HSI) has been proposed to monitor pork aging progress. <i>M. longissimus thoracis</i> from 15 pigs were stored at 4 °C for 12 days while quality indexes and HSI spectra were measured daily. Based on changes in physical and chemical indicators, 100 out of the 180 pieces of meat were selected and classified into rigor mortis, aged, and spoilt meat. Discrete wavelet transform (DWT) technology was used to improve the accuracy of classification. DWT separated approximate and detailed signals from the spectrum, resulting in a significant increase in classification speed and precision. The support vector machine (SVM) model with 70 band spectra achieved remarkable classification accuracy of 97.06%. The study findings revealed that the aging and microbial spoilage process started at the edges of the meat, with varying rates from one pig to another. Using HSI and visualization techniques, it was possible to evaluate and portray the postmortem aging progress and edible safety of pork during storage. This technology has the potential to aid the meat industry in making informed decisions on the optimal storage and cooking times that would preserve the quality of the meat and ensure its safety for consumption. Rigor mortis ; Tenderness ; Artificial intelligence ; Hyperspectral imaging ; Support vector machine ; Pattern recognition (psychology) ; Food spoilage ; Computer science ; Food science ; Mathematics ; Computer vision ; Biology Spectroscopy and Chemometric Analyses ; Meat and Animal Product Quality ; Advanced Chemical Sensor Technologies
Authors: Hao Wang | Yongchu Laram | Hu Li | Yingchun Hu | Muhu Chen
Source: BMC Infectious Diseases (article, 2024-08-31)
Field: Materials Science — Biomaterials

Exploring the potential mechanisms of Rehmannia glutinosa in treating sepsis based on network pharmacology The present study utilized network pharmacology to identify therapeutic targets and mechanisms of Rehmannia glutinosa in sepsis treatment. RNA-sequencing was conducted on peripheral blood samples collected from 23 sepsis patients and 10 healthy individuals. Subsequently, the RNA sequence data were analyzed for differential expression. Identification of active components and their putative targets was achieved through the HERB and SwissTarget Prediction databases, respectively. Functional enrichment analysis was performed using GO and KEGG pathways. Additionally, protein-protein interaction networks were constructed and survival analysis of key targets was conducted. Single-cell RNA sequencing provided cellular localization data, while molecular docking explored interactions with central targets. Results indicated significant involvement of identified targets in inflammation and Th17 cell differentiation. Survival analysis linked several targets with mortality rates, while molecular docking highlighted potential interactions between active components and specific targets, such as rehmaionoside a with ADAM17 and rehmapicrogenin with CD81. Molecular dynamics simulations confirmed the stability of these interactions, suggesting Rehmannia glutinosa's role in modulating immune functions in sepsis. Rehmannia glutinosa ; In silico ; Biology ; Computational biology ; KEGG ; Sepsis ; RNA ; Docking (animal) ; Bioinformatics ; Transcriptome ; Immunology ; Genetics ; Medicine ; Gene ; Traditional Chinese medicine ; Gene expression Phytochemistry and Bioactive Compounds ; Bioinformatics and Genomic Networks ; Phytochemistry and Biological Activities
Authors: Xiaoqing Cao | Jing Huang | Jinjing Chen | Yingjie Niu | Sisi Wei | Haibin Tong | Mingjiang Wu | Yue Yang
Source: Foods (article, 2024-06-05)
Field: Chemistry — Analytical Chemistry

Rapid Measurement of Antioxidant Properties of Dendrobium officinale Using Near-Infrared Spectroscopy and Chemometrics <i>Dendrobium officinale</i> (<i>D. officinale</i>), often used as a dual-use plant with herbal medicine and food applications, has attracted considerable attention for health-benefiting components and wide economic value. The antioxidant ability of <i>D. officinale</i> is of great significance to ensure its health care value and safeguard consumers' interests. However, the common analytical methods for evaluating the antioxidant ability of <i>D. officinale</i> are time-consuming, laborious, and costly. In this study, near-infrared (NIR) spectroscopy and chemometrics were employed to establish a rapid and accurate method for the determination of 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) scavenging capacity, 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging capacity, and ferric reducing antioxidant power (FRAP) in <i>D. officinale</i>. The quantitative models were developed based on the partial least squares (PLS) algorithm. Two wavelength selection methods, namely the genetic algorithm (GA) and competitive adaptive reweighted sampling (CARS) method, were used for model optimization. The CARS-PLS models exhibited superior predictive performance compared to other PLS models. The root mean square errors of cross-validation (<i>RMSECVs</i>) for ABTS, FRAP, and DPPH were 0.44%, 2.64 μmol/L, and 2.06%, respectively. The results demonstrated the potential application of NIR spectroscopy combined with the CARS-PLS model for the rapid prediction of antioxidant activity in <i>D. officinale</i>. This method can serve as an alternative to conventional analytical methods for efficiently quantifying the antioxidant properties in <i>D. officinale</i>. Chemometrics ; ABTS ; DPPH ; Antioxidant ; Partial least squares regression ; Chemistry ; Antioxidant capacity ; Food science ; Chromatography ; Computer science ; Machine learning ; Biochemistry Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Essential Oils and Antimicrobial Activity
Authors: Misaki Ozawa | Jean‐Louis Barrat | Walter Kob | Francesco Zamponi
Source: Journal of Statistical Mechanics Theory and Experiment (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Creating equilibrium glassy states via random particle bonding Abstract Creating amorphous solid states by randomly bonding an ensemble of dense liquid monomers is a common procedure that is used to create a variety of materials, such as epoxy resins, colloidal gels, and vitrimers. However, the properties of the resulting solid do a priori strongly depend on the preparation history. This can lead to substantial aging of the material; for example, properties such as mechanical moduli and transport coefficients rely on the time elapsed since solidification, which can lead to a slow degradation of the material in technological applications. It is therefore important to understand under which conditions random monomer bonding can lead to stable solid states, that is, long-lived metastable states whose properties do not change over time. This work presents a theoretical and computational analysis of this problem and introduces a random bonding procedure that ensures the proper equilibration of the resulting amorphous states. Our procedure also provides a new route to investigate the fundamental properties of glassy energy landscapes by producing translationally invariant ultrastable glassy states in simple particle models. Amorphous solid ; Metastability ; Statistical physics ; Materials science ; Particle (ecology) ; A priori and a posteriori ; Monomer ; Chemical physics ; Nanotechnology ; Polymer ; Composite material ; Physics ; Chemistry ; Crystallography Material Dynamics and Properties ; Liquid Crystal Research Advancements ; Pickering emulsions and particle stabilization
Authors: Amanda M. Figueroa‐Navedo | Alexander R. Ivanov
Source: Cell Reports Methods (review, 2024-02-01)
Field: Chemistry — Spectroscopy

Experimental and data analysis advances in thermal proteome profiling Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures. Proteome ; Computational biology ; Prioritization ; Profiling (computer programming) ; Mass spectrometry ; Drug discovery ; Chemistry ; Small molecule ; Proteomics ; Bioinformatics ; Computer science ; Biology ; Chromatography ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Tim van der Velden | Tim Brepols | Stefanie Reese | Hagen Holthusen
Source: International Journal for Numerical Methods in Engineering (article, 2024-08-11)
Field: Materials Science — Materials Chemistry

A comparative study of micromorphic gradient‐extensions for anisotropic damage at finite strains Abstract Modern inelastic material model formulations rely on the use of tensor‐valued internal variables. When inelastic phenomena include softening, simulations of the former are prone to localization. Thus, an accurate regularization of the tensor‐valued internal variables is essential to obtain physically correct results. Here, we focus on the regularization of anisotropic damage at finite strains. Thus, a flexible anisotropic damage model with isotropic, kinematic, and distortional hardening is equipped with three gradient‐extensions using a full and two reduced regularizations of the damage tensor. Theoretical and numerical comparisons of the three gradient‐extensions yield excellent agreement between the full and the reduced regularization based on a volumetric‐deviatoric regularization using only two nonlocal degrees of freedom. Finite element method ; Anisotropy ; Computer science ; Mathematics ; Structural engineering ; Physics ; Engineering ; Optics Nonlocal and gradient elasticity in micro/nano structures ; Elasticity and Material Modeling ; High-Velocity Impact and Material Behavior
Authors: Fulin Jiang | Jingyu Liu | Yagang Li | Zihan Lu | Qian Liu | Yunhui Xing | Janshon Zhu | Min Huang | Guoping Zhong
Source: Journal of Pharmaceutical Analysis (article, 2024-02-24)
Field: Chemistry — Spectroscopy

Signal interference between drugs and metabolites in LC-ESI-MS quantitative analysis and its evaluation strategy Liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS) is a widely utilized technique for in vivo pharmaceutical analysis. Ionization interference within electrospray ion source, occurring between drugs and metabolites, can lead to signal variations, potentially compromising quantitative accuracy. Currently, method validation often overlooks this type of signal interference, which may result in systematic errors in quantitative results without matrix-matched calibration. In this study, we conducted an investigation using ten different groups of drugs and their corresponding metabolites across three LC-ESI-MS systems to assess the prevalence of signal interference. Such interferences can potentially cause or enhance nonlinearity in the calibration curves of drugs and metabolites, thereby altering the relationship between analyte response and concentration for quantification. Finally, we established an evaluation scheme through a step-by-step dilution assay and employed three resolution methods: chromatographic separation, dilution, and stable labeled isotope internal standards correction. The above strategies were integrated into the method establishment process to improve quantitative accuracy. Chemistry ; Analyte ; Electrospray ionization ; Chromatography ; Ion suppression in liquid chromatography–mass spectrometry ; Isotope dilution ; Interference (communication) ; Quantitative analysis (chemistry) ; Mass spectrometry ; Matrix (chemical analysis) ; Tandem mass spectrometry ; Calibration ; Electrospray ; SIGNAL (programming language) ; Bioanalysis ; Calibration curve ; Detection limit ; Computer science ; Channel (broadcasting) Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Analytical Chemistry and Chromatography
Authors: Zhongzhi Guo | You Huang | Mingcheng Cai | Chunxing Li | M. Shen | Mengqi Wang | Pei Yu | Ya Wang | Fazhan Shi | Pengfei Wang | Jiangfeng Du
Source: npj Quantum Information (article, 2024-02-21)
Field: Materials Science — Materials Chemistry

Wide-field Fourier magnetic imaging with electron spins in diamond Abstract Wide-field magnetic imaging based on nitrogen-vacancy (NV) centers in diamond has been shown the applicability in material and biological science. However, the spatial resolution is limited by the optical diffraction limit (&gt;200 nm) due to the optical real-space localization and readout of NV centers. Here, we report the wide-field Fourier magnetic imaging technique to improve spatial resolution beyond the optical diffraction limit while maintaining the large field of view. Our method relies on wide-field pulsed magnetic field gradient encoding of NV spins and Fourier transform under pixel-dependent spatial filters. We have improved spatial resolution by a factor of 20 compared to the optical resolution and demonstrated the wide-field super-resolution magnetic imaging of a gradient magnetic field. This technique paves a way for efficient magnetic imaging of large-scale fine structures at the nanoscale. Spins ; Diamond ; Fourier transform ; Magnetic field ; Electron ; Physics ; Field (mathematics) ; Nuclear magnetic resonance ; Optics ; Condensed matter physics ; Materials science ; Quantum mechanics ; Mathematics Diamond and Carbon-based Materials Research ; Force Microscopy Techniques and Applications ; High-pressure geophysics and materials
Authors: Daniel Jensen | David R. Thompson | Marc Simard | Elena Solohin | Edward Castañeda‐Moya
Source: Journal of Geophysical Research Biogeosciences (article, 2024-09-01)
Field: Chemistry — Analytical Chemistry

Imaging Spectroscopy‐Based Estimation of Aboveground Biomass in Louisiana's Coastal Wetlands: Toward Consistent Spectroscopic Retrievals Across Atmospheric States Abstract Developing accurate landscape‐scale aboveground biomass (AGB) maps is critical to understanding coastal deltaic wetland resilience, as AGB influences stability and elevation dynamics in herbaceous wetlands. Here we used AVIRIS‐NG imaging spectrometer (or “hyperspectral”) data from NASA's 2021 Delta‐X mission in coastal Louisiana to map seasonal changes in herbaceous AGB across two deltaic basins with contrasting sediment delivery and hydrologic regimes: the Atchafalaya (active) and Terrebonne (inactive). We assessed the impact of atmospheric effects on our retrievals, as high water vapor content in August 2021 caused significant noise in the 880–1,000 and 1,080–1,200 nm near‐infrared (NIR) wavelengths. We hypothesized that correcting these wavelengths with our conditional Gaussian interpolation algorithm would improve AGB estimates due to their association with plant canopy water content. We empirically assessed the performance of the corrected spectra on AGB estimates using Partial Least Squares Regression (PLSR), finding that the corrected NIR bands attained high variable importance and reduced estimation errors. Our Random Forest regression approach based on the corrected spectra attained equivalent error metrics via leave‐one‐out‐cross‐validation as the PLSR models ( R 2 = 0.43, mean absolute error = 257.3 g/m 2 ) while greatly improving the AGB maps' visual quality, having better captured variability while reducing noise and discontinuities in AGB estimates across flightlines. The maps show differing seasonal growth, with the Atchafalaya and Terrebonne Basins' AGB increasing from means of 4.3–9.4 and 4.6–8.9 Mg/ha, respectively. We demonstrated that imaging spectroscopy can be applied to assess herbaceous biomass stocks, growth patterns, and resilience in coastal ecosystems. Wetland ; Environmental science ; Biomass (ecology) ; Spectroscopy ; Biomass burning ; Atmospheric sciences ; Imaging spectroscopy ; Climatology ; Remote sensing ; Oceanography ; Ecology ; Geography ; Meteorology ; Geology ; Physics ; Hyperspectral imaging Spectroscopy and Chemometric Analyses ; Geochemistry and Geologic Mapping ; Water Quality Monitoring and Analysis
Authors: Zhenzhen Zhou | Yiqian Qu | Xin Cheng | Yu‐Ting Cheng | Shuqi Lan | Zhengqi Yang | Liancheng Wei | Wei Sun | Hanning Wu
Source: ACS Omega (article, 2024-10-23)
Field: Chemistry — Analytical Chemistry

Effects of Microheterogeneous Wettability and Pore-Throat Structure on Asphaltene Precipitation in Tight Sandstone: Results from Nuclear Magnetic Resonance The pore throat structure and microheterogeneous wettability of tight sandstone reservoirs are complex, which leads to varying asphaltene precipitation locations, contents, and distributions in different pores during CO<sub>2</sub> flooding. Clarifying the heterogeneous wettability of different pore throat structures and their effects on asphaltene precipitation and adsorption is crucial for improving CO<sub>2</sub> displacement efficiency. A series of experiments were conducted in this study, including X-ray diffraction (XRD), cast thin section (CTS), field emission scanning electron microscopy (FE-SEM), high-pressure mercury intrusion (HPMI), environmental scanning electron microscopy (E-SEM), nuclear magnetic resonance (NMR), and CO<sub>2</sub> flooding experiments, to investigate the pore structure complexity of tight sandstone reservoirs of the Yanchang Formation in the Ordos Basin, China. Furthermore, we investigated the variations in microheterogeneous wettability across diverse pore-throat structures and elucidated the impact of heterogeneous wettability on asphaltene precipitation during CO<sub>2</sub> flooding. The findings indicate that the type and configuration of pore throats are crucial factors influencing microheterogeneous wettability. The intergranular pores are dominated by mixed wetting, and most of the dissolution pores exhibit oil wetting. The surface of Illite shows drop-like water under E-SEM, which is mainly oil wetting, whereas the surface of chlorite shows film-like water, which is water wetting. The configuration of chlorite intercrystalline pores and intergranular pores shows water wetting, whereas the configuration of Illite intergranular pores and dissolution pores shows oil wetting. During the CO<sub>2</sub> flooding process, asphaltene tends to be adsorbed in the intercrystalline Illite with dissolution pores, reducing the dissolution pore volume and blocking small pores, and the displacement efficiency becomes low. In addition, asphaltene precipitation also occurs in the pore configuration of chlorite intercrystalline and intergranular pores, causing a wetting reversal on hydrophilic mineral surfaces. This reversal increases the pore throat structure complexity but has less of an impact on the flooding efficiency. A high Illite content is more likely to lead to asphaltene precipitation, significantly influencing small pore structure and the oil displacement efficiency. Wetting ; Asphaltene ; Nuclear magnetic resonance ; Precipitation ; Throat ; Materials science ; Mineralogy ; Geology ; Composite material ; Physics ; Meteorology Petroleum Processing and Analysis ; Hydrocarbon exploration and reservoir analysis ; Enhanced Oil Recovery Techniques
Authors: Zheng Tang | Fangyuan Ma | Feng Li | Yugui Yao | Di Zhou
Source: Physical Review Letters (article, 2024-09-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Fully Polarized Topological Isostatic Metamaterials in Three Dimensions Topological surface states are unique to topological materials and are immune to disturbances. In isostatic lattices, mechanical topological floppy modes exhibit softness depending on the polarization relative to the terminating surface. However, in three dimensions, the polarization of topological floppy modes is disrupted by the ubiquitous mechanical Weyl lines. Here, we demonstrate, both theoretically and experimentally, the fully polarized topological mechanical phases free of Weyl lines. Floppy modes emerge exclusively on a particular surface of the three-dimensional isostatic structure, leading to the strongly asymmetric stiffness between opposing boundaries. Additionally, uniform soft strains can reversibly shift the lattice configuration to Weyl phases, switching the stiffness contrast to a trivially comparable level. Our work demonstrates the fully polarized topological mechanical phases in three dimensions, and paves the way towards engineering soft and adaptive metamaterials. Metamaterial ; Topology (electrical circuits) ; Physics ; Materials science ; Condensed matter physics ; Optics Metamaterials and Metasurfaces Applications ; Topological Materials and Phenomena ; Photonic Crystals and Applications