jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nathan G. Hendricks | Santosh D. Bhosale | Angel J. Keoseyan | J Ortiz | Aleksandr Stotland | Saeed Seyedmohammad | Chi Nguyen | Jonathan D. Bui | Annie Moradian | Susan M. Mockus | Jennifer E. Van Eyk
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-04-27)
Field: Chemistry — Spectroscopy

An inflection point in high-throughput proteomics with Orbitrap Astral: analysis of biofluids, cells, and tissues This technical note presents a comprehensive proteomics workflow for the new combination of Orbitrap and Astral mass analyzers across biofluids, cells, and tissues. Central to our workflow is the integration of Adaptive Focused Acoustics (AFA) technology for cells and tissue lysis, to ensure robust and reproducible sample preparation in a high-throughput manner. Furthermore, we automated the detergent-compatible single-pot, solid-phase-enhanced sample Preparation (SP3) method for protein digestion, a technique that streamlines the process by combining purification and digestion steps, thereby reducing sample loss and improving efficiency. The synergy of these advanced methodologies facilitates a robust and high-throughput approach for cells and tissue analysis, an important consideration in translational research. This work disseminates our platform workflow, analyzes the effectiveness, demonstrates reproducibility of the results, and highlights the potential of these technologies in biomarker discovery and disease pathology. For cells and tissues (heart, liver, lung, and intestine) proteomics analysis by data-independent acquisition mode, identifications exceeding 10,000 proteins can be achieved with a 24-minute active gradient. In 200ng injections of HeLa digest across multiple gradients, an average of more than 80% of proteins have a CV less than 20%, and a 45-minute run covers ~90% of the expressed proteome. In plasma samples including naive, depleted, perchloric acid precipitated, and Seer nanoparticle captured, all with a 24-minute gradient length, we identified 87, 108, 96 and 137 out of 216 FDA approved circulating protein biomarkers, respectively. This complete workflow allows for large swaths of the proteome to be identified and is compatible across diverse sample types. Orbitrap ; Inflection point ; Throughput ; Computer science ; Point (geometry) ; Proteomics ; Inflection ; Computational biology ; Information retrieval ; Chemistry ; Biology ; Mass spectrometry ; Artificial intelligence ; Mathematics ; Chromatography ; Biochemistry ; Telecommunications ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Cell Image Analysis Techniques
Authors: Liuya Zhang | Debao Yuan | Yuqing Fan | Renxu Yang | Maochen Zhao | Jinbao Jiang | Wenxuan Zhang | Ziyi Huang | G. Ye | Weining Li
Source: Remote Sensing (article, 2024-09-09)
Field: Chemistry — Analytical Chemistry

Hyperspectral Estimation of Chlorophyll Content in Wheat under CO2 Stress Based on Fractional Order Differentiation and Continuous Wavelet Transforms The leaf chlorophyll content (LCC) of winter wheat, an important food crop widely grown worldwide, is a key indicator for assessing its growth and health status in response to CO2 stress. However, the remote sensing quantitative estimation of winter wheat LCC under CO2 stress conditions also faces challenges such as an unclear spectral sensitivity range, baseline drift, overlapping spectral peaks, and complex spectral response due to CO2 stress changes. To address these challenges, this study introduced the fractional order derivative (FOD) and continuous wavelet transform (CWT) techniques into the estimation of winter wheat LCC. Combined with the raw hyperspectral data, we deeply analyzed the spectral response characteristics of winter wheat LCC under CO2 stress. We proposed a stacking model including multiple linear regression (MLR), decision tree regression (DTR), random forest (RF), and adaptive boosting (AdaBoost) to filter the optimal combination from a large number of feature variables. We use a dual-band combination and vegetation index strategy to achieve the accurate estimation of LCC in winter wheat under CO2 stress. The results showed that (1) the FOD and CWT methods significantly improved the correlation between the raw spectral reflectance and LCC of winter wheat under CO2 stress. (2) The 1.2-order derivative dual-band index (RVI (R720, R522)) constructed by combining the sensitive spectral bands of the CO2 response of winter wheat leaves achieved a high-precision estimation of the LCC under CO2 stress conditions (R2 = 0.901). Meanwhile, the red-edged vegetation stress index (RVSI) constructed based on the CWT technique at specific scales also demonstrated good performance in LCC estimation (R2 = 0.880), verifying the effectiveness of the multi-scale analysis in revealing the mechanism of the CO2 impact on winter wheat. (3) By stacking the sensitive spectral features extracted by combining the FOD and CWT methods, we further improved the LCC estimation accuracy (R2 = 0.906). This study not only provides a scientific basis and technical support for the accurate estimation of LCC in winter wheat under CO2 stress but also provides new ideas and methods for coping with climate change, optimizing crop-growing conditions, and improving crop yield and quality in agricultural management. The proposed method is also of great reference value for estimating physiological parameters of other crops under similar environmental stresses. Hyperspectral imaging ; Content (measure theory) ; Wavelet ; Order (exchange) ; Computer science ; Environmental science ; Remote sensing ; Mathematics ; Artificial intelligence ; Geology ; Mathematical analysis Spectroscopy and Chemometric Analyses ; Remote Sensing and Land Use ; Remote Sensing in Agriculture
Authors: Julia A. Bubis | Tabiwang N. Arrey | Eugen Damoc | Bernard Delanghe | Jana Slováková | Theresa Maria Sommer | Harunobu Kagawa | Peter Pichler | Nicolas Rivron | Karl Mechtler | Manuel Matzinger
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-02-01)
Field: Chemistry — Spectroscopy

Challenging the Astral <sup>™</sup> mass analyzer - up to 5300 proteins per single-cell at unseen quantitative accuracy to study cellular heterogeneity ABSTRACT A detailed proteome map is crucial for understanding molecular pathways and protein functions. Despite significant advancements in sample preparation, instrumentation, and data analysis, single-cell proteomics is currently limited by proteomic depth and quantitative performance. We combine a zero dead-end volume chromatographic column running at high throughput with the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer running in DIA mode. We demonstrate unprecedented depth of proteome coverage as well as accuracy and precision for quantification of ultra-low input amounts. Using a tailored library, we identify up to 7400 protein groups from as little as 250 pg HeLa at a throughput of 50 samples per day (SPD). We benchmark multiple data analysis strategies, estimate their influence on FDR and show that FDR on protein level can easily be maintained at 1 %. Using a two-proteome mix, we check for optimal parameters of quantification and show that fold change differences of 2 can still be successfully determined at single-cell level inputs. Eventually, we apply our workflow to A549 cells yielding a proteome coverage of up to 5300 protein groups from a single cell, which allows the observation of heterogeneity in a cellular population and studying dependencies between cell size and cell-cycle phase. Additionally, our work-flow enables us to distinguish between in vitro analogs of two human blastocyst lineages: naïve human pluripotent stem cells (epiblast) and trophectoderm (TE)-like cells. Gene Ontology analysis of enriched proteins in TE-like cells harmoniously aligns with transcriptomic data, indicating that single-cell proteomics possesses the capability to identify biologically relevant differences between these two lineages within the blastocyst. Proteome ; Proteomics ; Computational biology ; Population ; Biology ; Quantitative proteomics ; Chemistry ; Computer science ; Bioinformatics ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications
Authors: Elliot J. Carr | Giuseppe Pontrelli
Source: International Journal of Heat and Mass Transfer (article, 2024-01-03)
Field: Materials Science — Surfaces, Coatings and Films

Modelling functionalized drug release for a spherical capsule Advances in material design have led to the rapid development of novel materials with increasing complexity and functions in bioengineering. In particular, functionally graded materials (FGMs) offer important advantages in various fields of application. In this work, we consider a heterogeneous reaction-diffusion model for an FGM spherical drug release system that generalizes the multi-layer configuration to arbitrary spatially-variable coefficients. Our model proposes a possible form for the drug diffusivity and reaction rate functions exhibiting fixed average material properties and a drug release profile that can be continuously varied between the limiting cases of a homogeneous system (constant coefficients) and two-layer system (stepwise coefficients). A semi-analytical solution is then used to solve the model, which provides closed-form expressions for the drug concentration and drug release profiles in terms of generalized Fourier series. Our results show how the release rate of the proposed FGM drug release system can be controlled and continuously varied between a fast (homogeneous) and slow (two-layer) release while maintaining the same averaged values for the diffusivity and reaction rate. Materials science ; Thermal diffusivity ; Diffusion ; Work (physics) ; Homogeneous ; Biological system ; Thermodynamics ; Physics Polymer Surface Interaction Studies ; Dendrimers and Hyperbranched Polymers ; Rheology and Fluid Dynamics Studies
Authors: Manna Dai | Yang Jiang | Feng Yang | Joyjit Chattoraj | Yingzhi Xia | Xinxing Xu | Weijiang Zhao | My Ha Dao | Yong Liu
Source: Neural Networks (article, 2024-08-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A surrogate-assisted extended generative adversarial network for parameter optimization in free-form metasurface design Metamaterial ; Computer science ; Constraint (computer-aided design) ; Deep learning ; Electronic engineering ; Artificial intelligence ; Optics ; Physics ; Mathematics Metamaterials and Metasurfaces Applications ; Millimeter-Wave Propagation and Modeling ; Animal Vocal Communication and Behavior
Authors: Jae Hyun Nam | Peter Bruggeman
Source: Plasma Processes and Polymers (article, 2024-09-03)
Field: Chemistry — Electrochemistry

Effect of the pH on the Formation of Gold Nanoparticles Enabled by Plasma‐Driven Solution Electrochemistry ABSTRACT Plasma‐driven solution electrochemistry offers alternatives to wet‐chemical methods for synthesizing nanomaterials. This study examines how precursor solution pH affects gold nanoparticle formation, specifically the conversion of precursor ions by solvated electrons and H 2 O 2 , and particle size. Our experiments show that –enabled autocatalytic reduction selectivity is 43%–65%, suggesting a catalytic decomposition of by gold nanoparticles. The solubility of gold monomers, increasing with decreasing pH, influences nucleation and resulting particle size, affecting the particle size distribution significantly at pH between 3 and 5. A 1‐D film reaction‐diffusion model quantitatively reproduces and explains the experimental results, demonstrating the impact of pH on different plasma‐produced species, enabling the gold ion conversion and nucleation rates, which directly impact particle size distributions. Electrochemistry ; Colloidal gold ; Plasma ; Nanoparticle ; Nanotechnology ; Materials science ; Chemical engineering ; Electrode ; Chemistry ; Physical chemistry ; Engineering Electrochemical Analysis and Applications ; Electrocatalysts for Energy Conversion ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Jana Dobrovská | Petra Skalková | Ľubomíra DROZDOVÁ | Ivan Labaj | Simona Zlá | Andrej Dubec | Monika KAWULOKOVÁ
Source: Journal of Thermal Analysis and Calorimetry (article, 2024-02-26)
Field: Materials Science — Materials Chemistry

Pyrolysis of natural rubber–cellulose composites: isoconversional kinetic analysis based on thermogravimetric data Abstract Despite the current growing interest in rubber composites with natural organic fillers, there is a lack of kinetic analyses that describe the decomposition of these materials during pyrolysis. For this reason, the main objective of this study was the kinetic analysis and determination of formal kinetic parameters for the pyrolytic decomposition of NR–CEL composites with different cellulose content (0, 30, 45, and 55 phr). Thermogravimetric measurements were made at heating rates of 2, 4, 6, 8, 10, and 20 °C min –1 in the temperature range of 20–600 °C. First, Friedman and KAS model-free methods were applied. Therefore, model-based methods and the model-fitting procedure were used to find the optimal multi-step kinetic model. The proposed final model consists of two parallel processes, which are kinetically independent: A → B → C and D → E → F. For each step, a kinetic triplet was calculated: the apparent activation energy, the pre-exponential factor, and the kinetic parameters of the extended empirical Prout–Tompkins model. The master plots method was used to determine the kinetic decomposition mechanism of the individual steps. It was found that step A → B has the shape of an nth-order model, step B → C mainly follows the diffusion model, the mechanism of step D → E transfers from a random scission kinetics model to an nth-order model with an increasing amount of CEL, and step E → F obeys the chain scission mechanism. Thermogravimetric analysis ; Activation energy ; Kinetic energy ; Pyrolysis ; Kinetics ; Natural rubber ; Materials science ; Thermodynamics ; Cellulose ; Pyrolytic carbon ; Decomposition ; Order of reaction ; Thermal decomposition ; Reaction mechanism ; Composite material ; Chemistry ; Physical chemistry ; Reaction rate constant ; Organic chemistry ; Physics ; Catalysis Thermal and Kinetic Analysis ; Polymer crystallization and properties ; Polymer Nanocomposites and Properties
Authors: Feride N. Türk | Muhammet Ş. A. Eren | Hasan Arslanoğlu
Source: Inorganic Chemistry Communications (article, 2024-11-21)
Field: Materials Science — Biomaterials

Adsorption of Reactive Black 5 dye from aqueous solutions with a clay halloysite having a nanotubular structure: Interpretation of mechanism, kinetics, isotherm and thermodynamic parameters Halloysite ; Kinetics ; Aqueous solution ; Adsorption ; Interpretation (philosophy) ; Chemical engineering ; Mechanism (biology) ; Materials science ; Clay minerals ; Chemistry ; Physical chemistry ; Mineralogy ; Physics ; Computer science Clay minerals and soil interactions ; Iron oxide chemistry and applications ; Adsorption and biosorption for pollutant removal
Authors: Jie Liu | Jie Jin | Robert Conka | Paul Van Steenberge | Dagmar D’hooge | Zheng‐Hong Luo | Yin‐Ning Zhou
Source: Macromolecules (article, 2024-05-15)
Field: Materials Science — Polymers and Plastics

The Dynamic Interplay of Cross-Linking and Exchange Reaction Probabilities during Vitrimer Synthesis: A Monte Carlo Approach Covalent adaptable networks (CANs) are based on an associative exchange mechanism, and hence, vitrimers have been shown to be an attractive candidate for the synthesis of sustainable cross-linked materials due to synergetic structural stability and reprocessability. Herein, matrix-based kinetic Monte Carlo (kMC) simulations are performed to increase our mechanistic understanding of vitrimer synthesis, selecting step-growth vinylogous carbamothioate (VC)-based CANs as dynamic chemistry. Novelties are (i) the consideration of 8 elementary reaction categories differentiating between cross-linking and exchange reactions as well as inter- and intramolecular reactions (22 in total); and (ii) a dedicated tuning strategy of both intrinsic and diffusion parameters, employing experimental data from Fourier transform infrared spectroscopy and rheological measurements. Upon a model validation at different temperatures (30–60 °C), revealing a key role for mobility constraints due to viscosity increases, emphasis is on the evolution of molecular properties such as the branching density, the reduced mass-average degree of polymerization, the mass-average molar mass, and the mass fraction of the sol, to understand the relationship of kinetics, reaction probabilities, and molecular network properties. The simulation results demonstrate that increasing the temperature to, e.g., 60 °C, sufficiently promotes the exchange rate, leading to a gel point realization at higher conversion enabling the production of more uniform cross-linked structures. They also show that at higher yield, more intramolecular reactions come in to play, complicating the network structural arrangement. It is further shown that the traditional Flory and Macosko–Miller theories are no longer applicable to predicting gel points and molecular properties in dynamic network systems with higher exchange rates. Moreover, the generation of branched and cross-linked structures can be delayed with the increase of the molar ratio of primary amine groups to acetoacetate groups. The current study provides an in-depth understanding of the reaction kinetics for the synthesis of VC-based CANs, and it is an important step toward a generalized elementary reaction step driven kinetic model as well as chemistry design for vitrimer synthesis. Chemistry ; Monte Carlo method ; Rheology ; Reptation ; Intramolecular force ; Kinetic Monte Carlo ; Thermodynamics ; Polymer ; Organic chemistry ; Physics Polymer composites and self-healing ; Advanced Polymer Synthesis and Characterization ; Lignin and Wood Chemistry
Authors: Amin Abid | Saqlain Raza | Ahmad Kaleem Qureshi | Sajjad Ali | Isham Areej | Shahid Nazeer | Bien Tan | Wedad A. Al-onazi | Muhammad Rizwan | Rashid Iqbal
Source: Scientific Reports (article, 2024-05-17)
Field: Materials Science — Materials Chemistry

Facile synthesis of anthranilic acid based dual functionalized novel hyper cross-linked polymer for promising CO2 capture and efficient Cr3+ adsorption A novel hyper cross-linked polymer of 2-Aminobenzoic acid (HCP-AA) is synthesized for the adsorption of Cr<sup>3+</sup> and CO<sub>2</sub>. The Brunauer-Emmett-Teller surface area of HCP-AA is 615 m<sup>2</sup> g<sup>-1</sup>. HCP-AA of particle size 0.5 nm showed maximum adsorption of Cr<sup>3+</sup> for lab prepared wastewater (93%) while it was 88% for real industrial wastewater. It is might be due to electrostatic interactions, cation-π interactions, lone pair interactions and cation exchange at pH 7; contact time of 8 min; adsorbent dose 0.8 g. The adsorption capacity was calculated 52.63 mg g<sup>-1</sup> for chromium metal ions at optimum conditions. Freundlich isotherm studies R<sup>2</sup> = 0.9273 value is the best fit and follows pseudo second order kinetic model (R<sup>2</sup> = 0.979). The adsorption is found non-spontaneous and exothermic through thermodynamic calculations like Gibbs free energy (ΔG), enthalpy change (ΔH) and entropy change (ΔS) were 6.58 kJ mol<sup>-1</sup>, - 60.91 kJ mol<sup>-1</sup> and - 45.79 kJ mol<sup>-1</sup> K<sup>-1</sup>, respectively. The CO<sub>2</sub> adsorption capacity of HCP-AA is 1.39 mmol/g with quantity of 31.1 cm<sup>3</sup>/g (6.1 wt%) at 273Kwhile at 298 K adsorption capacity is 1.12 mmol/g with quantity 25.2 cm<sup>3</sup>/g (5 wt%). Overall, study suggests that carboxyl (-COOH) and amino (-NH<sub>2</sub>) groups may be actively enhancing the adsorption capacity of HCP-AA for Cr<sup>3+</sup> and CO<sub>2</sub>. Anthranilic acid ; Adsorption ; Polymer ; Dual (grammatical number) ; Combinatorial chemistry ; Chemistry ; Organic chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Carbon Dioxide Capture Technologies
Authors: Lars Grunenberg | Christopher Keßler | Tiong Wei Teh | Robin Schuldt | Fabian Heck | Johannes Kästner | Joachim Groß | Niels Hansen | Bettina V. Lotsch
Source: ACS Nano (article, 2024-06-11)
Field: Materials Science — Materials Chemistry

Probing Self-Diffusion of Guest Molecules in a Covalent Organic Framework: Simulation and Experiment Covalent organic frameworks (COFs) are a class of porous materials whose sorption properties have so far been studied primarily by physisorption. Quantifying the self-diffusion of guest molecules inside their nanometer-sized pores allows for a better understanding of confinement effects or transport limitations and is thus essential for various applications ranging from molecular separation to catalysis. Using a combination of pulsed field gradient nuclear magnetic resonance measurements and molecular dynamics simulations, we have studied the self-diffusion of acetonitrile and chloroform in the 1D pore channels of two imine-linked COFs (PI-3-COF) with different levels of crystallinity and porosity. The higher crystallinity and porosity sample exhibited anisotropic diffusion for MeCN parallel to the pore direction, with a diffusion coefficient of <i>D</i><sub>par</sub> = 6.1(3) × 10<sup>-10</sup> m<sup>2</sup> s<sup>-1</sup> at 300 K, indicating 1D transport and a 7.4-fold reduction in self-diffusion compared to the bulk liquid. This finding aligns with molecular dynamics simulations predicting 5.4-fold reduction, assuming an offset-stacked COF layer arrangement. In the low-porosity sample, more frequent diffusion barriers result in isotropic, yet significantly reduced diffusivities (<i>D</i><sub>B</sub> = 1.4(1) × 10<sup>-11</sup> m<sup>2</sup> s<sup>-1</sup>). Diffusion coefficients for chloroform at 300 K in the pores of the high- (<i>D</i><sub>par</sub> = 1.1(2) × 10<sup>-10</sup> m<sup>2</sup> s<sup>-1</sup>) and low-porosity (<i>D</i><sub>B</sub> = 4.5(1) × 10<sup>-12</sup> m<sup>2</sup> s<sup>-1</sup>) samples reproduce these trends. Our multimodal study thus highlights the significant influence of real structure effects such as stacking faults and grain boundaries on the long-range diffusivity of molecular guest species while suggesting efficient intracrystalline transport at short diffusion times. Crystallinity ; Materials science ; Porosity ; Molecular dynamics ; Diffusion ; Chemical physics ; Pulsed field gradient ; Covalent organic framework ; Physisorption ; Molecule ; Analytical Chemistry (journal) ; Physical chemistry ; Computational chemistry ; Chemistry ; Thermodynamics ; Organic chemistry ; Composite material Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Radioactive element chemistry and processing