jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Anna Sophie Welter | Maximilian Gerwien | Robert Kerridge | Keziban Merve | Philipp Mertins | Matthias Selbach
Source: Molecular & Cellular Proteomics (article, 2024-09-11)
Field: Chemistry — Spectroscopy

Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification Data-independent acquisition (DIA) is increasingly preferred over data-dependent acquisition due to its higher throughput and fewer missing values. Whereas data-dependent acquisition often uses stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mass differential tags for relative and absolute quantification and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins in vivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios and certain high-throughput experiments. Spike-in SILAC (SiS) methods use an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA-SiS, leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed DIA-SiS and rigorously assessed its performance with mixed-species benchmark samples on bulk and single cell-like amount level. We demonstrate that DIA-SiS substantially improves proteome coverage and quantification compared to label-free approaches and reduces incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate, and comprehensive proteome profiling. Stable isotope labeling by amino acids in cell culture ; Proteome ; Computational biology ; Computer science ; Quantitative proteomics ; Proteomics ; Chemistry ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Machine Learning in Bioinformatics
Authors: H.C. Li | Zhenning Li | Kaiyu Liu | Kaijiang Xu | Chao Luo | You Lv | Yunkai Deng
Source: Remote Sensing (article, 2024-04-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

A Broadband Information Metasurface-Assisted Target Jamming System for Synthetic Aperture Radar In recent years, jamming strategies for Synthetic Aperture Radar (SAR) pertaining to target detection and identification, such as the creation of false targets, electromagnetic (EM) deception, and signal spoofing, have been increasingly emphasized. Distinct from traditional SAR jamming approaches, the introduction of an innovative artificial material cloak in SAR target jamming presents augmented capabilities. These methods demonstrate a proficient redirection of incident EM waves in specific or arbitrary directions, effectively masking the vital information linked to critical targets. This study introduces a broadband SAR target jamming system employing an information metasurface that incorporates intelligent information processing algorithms in conjunction with a space-time-coding digital metasurface, endowing it with the capacity to adeptly modulate incident EM waves. This integration facilitates a versatile approach to jamming, enabling the deployment of multi-mode protective measures against critical targets. The conducted simulation and experiment results validate the system’s ability to adjustably produce EM deception and generate multiple false targets independently of the SAR system. The outcomes of this research significantly advance the practicality of SAR protection strategies, pushing the boundaries toward more dynamic, broadband, and controllable scenarios, thereby substantially improving the concealment of critical targets in highly sensitive conflict areas. Computer science ; Jamming ; Broadband ; Synthetic aperture radar ; Radar jamming and deception ; Software deployment ; Radar ; Remote sensing ; Artificial intelligence ; Telecommunications ; Radar imaging ; Pulse-Doppler radar Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Wireless Communication Security Techniques
Authors: Valeriy G. Narushin | Н. А. Волкова | А. Н. Ветох | Alan Yu. Dzhagaev | Danila A. Sotnikov | Л. А. Волкова | Stefan T. Orszulik | Darren K. Griffin | Michael N Romanov | N. A. Zinovieva
Source: Food and Bioproducts Processing (article, 2024-07-22)
Field: Chemistry — Analytical Chemistry

Reimagining Archimedes: An innovative and accurate calculation of volumes and asserting another standard method for defining the surface area of quail and any avian eggs Quail ; Surface (topology) ; Engineering ; Biology ; Mathematics ; Ecology ; Geometry Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models ; Leaf Properties and Growth Measurement
Authors: Sriteja Mantha | Alec Glisman | Decai Yu | Eric P. Wasserman | Scott A. Backer | Zhen‐Gang Wang
Source: Langmuir (article, 2024-03-18)
Field: Chemistry — Physical and Theoretical Chemistry

Adsorption Isotherm and Mechanism of Ca<sup>2+</sup> Binding to Polyelectrolyte Polyelectrolytes, such as poly(acrylic acid) (PAA), can effectively mitigate CaCO<sub>3</sub> scale formation. Despite their success as antiscalants, the underlying mechanism of binding of Ca<sup>2+</sup> to polyelectrolyte chains remains unresolved. Through all-atom molecular dynamics simulations, we constructed an adsorption isotherm of Ca<sup>2+</sup> binding to sodium polyacrylate (NaPAA) and investigated the associated binding mechanism. We find that the number of calcium ions adsorbed [Ca<sup>2+</sup>]<sub>ads</sub> to the polymer saturates at moderately high concentrations of free calcium ions [Ca<sup>2+</sup>]<sub>aq</sub> in the solution. This saturation value is intricately connected with the binding modes accessible to Ca<sup>2+</sup> ions when they bind to the polyelectrolyte chain. We identify two dominant binding modes: the first involves binding to at most two carboxylate oxygens on a polyacrylate chain, and the second, termed the high binding mode, involves binding to four or more carboxylate oxygens. As the concentration of free calcium ions [Ca<sup>2+</sup>]<sub>aq</sub> increases from low to moderate levels, the polyelectrolyte chain undergoes a conformational transition from an extended coil to a hairpin-like structure, enhancing the accessibility to the high binding mode. At moderate concentrations of [Ca<sup>2+</sup>]<sub>aq</sub>, the high binding mode accounts for at least one-third of all binding events. The chain's conformational change and its consequent access to the high binding mode are found to increase the overall Ca<sup>2+</sup> ion binding capacity of the polyelectrolyte chain. Polyelectrolyte ; Chemistry ; Carboxylate ; Adsorption ; Conformational change ; Ion ; Crystallography ; Polymer ; Inorganic chemistry ; Stereochemistry ; Physical chemistry ; Organic chemistry Electrostatics and Colloid Interactions ; Calcium Carbonate Crystallization and Inhibition ; Surfactants and Colloidal Systems
Authors: Jiawei Zhang | Jingjing Ma | Chen Liu | Qi Wang | Yiling Xu | Long Fang | Kai Xia | Deshuai Sun
Source: Korean Journal of Chemical Engineering (article, 2024-06-04)
Field: Chemistry — Inorganic Chemistry

Bio-base Metal Organic Frameworks as Potential CO2 Adsorbents Adsorption ; Chemistry ; Metal-organic framework ; Base metal ; Catalysis ; Base (topology) ; Metal ; Chemical engineering ; Organic chemistry ; Materials science ; Metallurgy ; Mathematics ; Engineering Metal-Organic Frameworks: Synthesis and Applications ; Carbon Dioxide Capture Technologies ; Covalent Organic Framework Applications
Authors: Nguyễn Thu Phương | Quang Khánh Nguyễn | Ramasamy Shanmugam | Shuchi Sharma | Thi Thanh Thuy Phan | Hoang Giang Pham | Nguyễn Huy Tiệp | Quang Hoa Nguyen | Thi Xuyen Nguyen | Bach Pham | Thi Ngoc Mai Pham | G. Ranga Rao | Yen‐Hsun Su | Jyh‐Ming Ting | Duc Thang Pham
Source: Materials Chemistry and Physics (article, 2024-07-05)
Field: Chemistry — Organic Chemistry

Adsorptive removal of oxytetracycline antibiotics on magnetic nanoparticles NiFe2O4/Au: Characteristics, mechanism and theoretical calculations Oxytetracycline ; Mechanism (biology) ; Antibiotics ; Nanoparticle ; Magnetic nanoparticles ; Materials science ; Chemical engineering ; Chemistry ; Nanotechnology ; Biochemistry ; Physics Nanomaterials for catalytic reactions ; Gold and Silver Nanoparticles Synthesis and Applications ; Nanocluster Synthesis and Applications
Authors: Ylva K. Hommedal | Marianne Etzelmüller Bathen | Vilde Mari Reinertsen | K. M. Johansen | Lasse Vines | Ymir Kalmann Frodason
Source: Journal of Applied Physics (article, 2024-05-02)
Field: Materials Science — Materials Chemistry

Theoretical modeling of defect diffusion in wide bandgap semiconductors Since the 1940s, it has been known that diffusion in crystalline solids occurs due to lattice defects. The diffusion of defects can have a great impact on the processing and heat treatment of materials as the microstructural changes caused by diffusion can influence the material qualities and properties. It is, therefore, vital to be able to control the diffusion. This implies that we need a deep understanding of the interactions between impurities, matrix atoms, and intrinsic defects. The role of density functional theory (DFT) calculations in solid-state diffusion studies has become considerable. The main parameters to obtain in defect diffusion studies with DFT are formation energies, binding energies, and migration barriers. In particular, the utilization of the nudged elastic band and the dimer methods has improved the accuracy of these parameters. In systematic diffusion studies, the combination of experimentally obtained results and theoretical predictions can reveal information about the atomic diffusion processes. The combination of the theoretical predictions and the experimental results gives a unique opportunity to compare parameters found from the different methods and gain knowledge about atomic migration. In this Perspective paper, we present case studies on defect diffusion in wide bandgap semiconductors. The case studies cover examples from the three diffusion models: free diffusion, trap-limited diffusion, and reaction diffusion. We focus on the role of DFT in these studies combined with results obtained with the experimental techniques secondary ion mass spectrometry and deep-level transient spectroscopy combined with diffusion simulations. Wide-bandgap semiconductor ; Materials science ; Semiconductor ; Band gap ; Diffusion ; Semiconductor materials ; Condensed matter physics ; Optoelectronics ; Physics ; Thermodynamics ZnO doping and properties ; Semiconductor materials and devices ; Ga2O3 and related materials
Authors: Jeremy M. Quintana | Mikyung Kang | Huiyu Hu | Thomas S.C. Ng | Gregory R. Wojtkiewicz | Ella Scott | Sareh Parangi | Jan Schuemann | Ralph Weissleder | Miles A. Miller
Source: ACS Central Science (article, 2024-06-21)
Field: Materials Science — Biomaterials

Extended Pharmacokinetics Improve Site-Specific Prodrug Activation Using Radiation Radiotherapy is commonly used to treat cancer, and localized energy deposited by radiotherapy has the potential to chemically uncage prodrugs; however, it has been challenging to demonstrate prodrug activation that is both sustained <i>in vivo</i> and truly localized to tumors without affecting off-target tissues. To address this, we developed a series of novel phenyl-azide-caged, radiation-activated chemotherapy drug-conjugates alongside a computational framework for understanding corresponding pharmacokinetic and pharmacodynamic (PK/PD) behaviors. We especially focused on an albumin-bound prodrug of monomethyl auristatin E (MMAE) and found it blocked tumor growth in mice, delivered a 130-fold greater amount of activated drug to irradiated tumor versus unirradiated tissue, was 7.5-fold more efficient than a non albumin-bound prodrug, and showed no appreciable toxicity compared to free or cathepsin-activatable drugs. These data guided computational modeling of drug action, which indicated that extended pharmacokinetics can improve localized and cumulative drug activation, especially for payloads with low vascular permeability and diffusivity and particularly in patients receiving daily treatments of conventional radiotherapy for weeks. This work thus offers a quantitative PK/PD framework and proof-of-principle experimental demonstration of how extending prodrug circulation can improve its localized activity <i>in vivo</i>. Prodrug ; Pharmacokinetics ; Pharmacology ; Chemistry ; Medicine Nanoparticle-Based Drug Delivery ; Cancer therapeutics and mechanisms ; Click Chemistry and Applications
Authors: Zaidoon M. Shakor | Ahmed Alasseel | Emad N. Al-Shafei
Source: The Canadian Journal of Chemical Engineering (article, 2024-02-27)
Field: Chemistry — Inorganic Chemistry

The structure of deposited coke on hydrocracking and reforming catalysts: Coke deactivation and kinetics Abstract This comprehensive study investigates the structural deposition of coke, particularly its association with sulphides, in spent hydrocracking and reforming catalysts, leveraging advanced kinetic modelling and characterization techniques. Its objective is to elucidate coke removal kinetics, offering insights into optimizing catalyst regeneration. Utilizing thermogravimetric analysis, spectroscopic methods, and modelling, the research outlines the characteristics and kinetic behaviour of coke during regeneration. The novelty aspect of this study is the use of a reaction‐based model for accurate kinetic analysis and identifying optimal conditions for coke removal. The study recognized both hydrogen‐deficient and hydrogen‐rich amorphous coke, alongside graphitic coke spent catalysts. Thermogravimetric analysis revealed that coke constitutes ~23.8% and 4.6% of the total weight in hydrocracking and reforming catalysts, respectively. The traditional model‐free method for deactivation was found inadequate in predicting coke in the spent reforming catalyst, likely due to the presence of low‐temperature hydrocarbons of soft coke within the catalyst pores. In contrast, a reaction model‐based deactivation approach yielded more consistent evaluations for soft and hard coke of spent catalyst. For the spent hydrocracking catalyst, the estimated activation energies for coke decomposition were 41.56 and 128.97 kJ/mol for soft and hard coke, respectively, during regeneration. Although the coke in the spent reforming catalyst displayed similar temperature trends for decomposition, the average activation energies were 52.61 and 128.62 kJ/mol for soft and hard coke, respectively. The theoretical results from the multi‐reaction model for coke decomposition are consistent with the experimental results for both catalysts. Coke ; Thermogravimetric analysis ; Catalysis ; Cracking ; Chemical engineering ; Decomposition ; Chemistry ; Materials science ; Metallurgy ; Organic chemistry Zeolite Catalysis and Synthesis ; Catalysis and Hydrodesulfurization Studies ; Thermochemical Biomass Conversion Processes
Authors: Jana K. Alwattar | Mohammed M. Mehanna
Source: International Journal of Nanomedicine (article, 2024-11-01)
Field: Materials Science — Biomaterials

Engineered Porous Beta-Cyclodextrin-Loaded Raloxifene Framework with Potential Anticancer Activity: Physicochemical Characterization, Drug Release, and Cytotoxicity Studies The cytotoxic behavior provided evidence that the incorporation of raloxifene within the nanosponges structure enhanced its anticancer activity and represents a potential nanocarrier for anticancer agent delivery. Cytotoxicity ; Raloxifene ; Cyclodextrin ; Drug ; Pharmacology ; Chemistry ; BETA (programming language) ; Materials science ; Nanotechnology ; Chromatography ; Medicine ; In vitro ; Biochemistry ; Cancer ; Breast cancer ; Computer science Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Supramolecular Self-Assembly in Materials
Authors: Qaisar Maqbool | Isabella Cavallini | Niusha Lasemi | Simona Sabbatini | Francesca Tittarelli | Günther Rupprechter
Source: Small Science (article, 2024-02-02)
Field: Materials Science — Biomaterials

Waste‐Valorized Nanowebs for Crystal Violet Removal from Water Lightweight, metal-free, sustainable, and reusable adsorbent materials are of paramount significance in addressing the challenges of wastewater treatment. Accordingly, semi-crystalline nanocellulose (NC) is extracted from tissue paper waste and used to modify polyacrylonitrile (PAN) to produce electrospun nanowebs with strand diameters from ≈180-300 nm. The incorporation of NC into PAN is confirmed by infrared and Raman spectroscopy and X-Ray diffraction. When tested for crystal violet (CV) adsorption, NC-modified PAN (20% NC@PAN) exhibits the highest CV removal capacity, achieving 91-94% removal over three cycles each, demonstrating exceptional recyclability. In contrast, unmodified PAN significantly decreases in CV adsorption capacity (from 59% to 48% in the third cycle), possibly due to an increased (≈36%) nanofiber diameter. The adsorption kinetics, exhibiting pseudo-second order, interparticle (in between nanofibers) diffusion, and Elovich kinetic models emphasize the role of multilayer CV adsorption through reversible chemical interactions. Confocal micro-Raman spectroscopy unveils a multifaceted CV adsorption mechanism, suggesting both surface and multilayer diffusion, with NC-enhancing interactions. These findings demonstrate the potential of NC-modified PAN nanowebs as effective and environmentally sustainable adsorbents for removing CV from aqueous solutions, suggesting promising practical applications. Polyacrylonitrile ; Adsorption ; Crystal violet ; Raman spectroscopy ; Chemical engineering ; Materials science ; Aqueous solution ; Nanocellulose ; Nanofiber ; Nanotechnology ; Chemistry ; Composite material ; Polymer ; Organic chemistry ; Cellulose ; Optics Advanced Cellulose Research Studies ; Electrospun Nanofibers in Biomedical Applications ; Pickering emulsions and particle stabilization
Authors: Ying Lin | Changjiang Wang | Jinxiang Wu | Jian Tang | Guangmao Ye | Xiaobing Zhao | Hua Li | Yi He
Source: Small (article, 2024-03-25)
Field: Materials Science — Materials Chemistry

Imaging the Iodine Sorption‐Induced Synchronous Skeleton–Pore Interactions of Single Covalent Organic Framework Particles Covalent organic frameworks (COFs) are promising iodine adsorbents. For improved performances, it is critical and essential to fundamentally understand the underlying mechanism. Here, using the operando dark-field optical microscopy (DFM) imaging technique, the observation of an extraordinary structure shrinkage of 2D triphenylbenzene (TPB)-dimethoxyterephthaldehyde (DMTP)-COF upon the adsorption of I<sub>2</sub> vapor at the single-particle resolution is reported. Combining single-particle DFM imaging with other experimental and theoretical methods, it is revealed that the shrinkage mechanism of the TPB-DMTP-COF is attributed to the I<sub>2</sub> sorption-induced synchronous skeleton-pore interactions. The redox reaction of I<sub>2</sub> and TPB-DMTP-COF yields some cationic skeletons and I<sub>3</sub> <sup>-</sup> species, which triggers the multi-directional halogen-bonding interactions of I<sub>2</sub> and I<sub>3</sub> <sup>-</sup> as well as strong cation-π interactions between neutral and cationic skeletons, accompanying the synchronous in-plane skeleton shrinking in the xy plane and compact out-of-plane layer packing in the z-direction. This understanding of the synchronous action between the skeleton and pore breaks the perspective on the structure robustness of 2D COFs with excellent stability during the I<sub>2</sub> uptake, which offers pivotal guidance for the rational design and creation of advanced microporous adsorbents. Sorption ; Materials science ; Adsorption ; Chemical engineering ; Covalent bond ; Cationic polymerization ; Chemical physics ; Nanotechnology ; Chemistry ; Organic chemistry ; Polymer chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Luminescence and Fluorescent Materials
Authors: Ludovic Berthier | Federico Ghimenti | Frédéric van Wijland
Source: The Journal of Chemical Physics (article, 2024-09-16)
Field: Materials Science — Materials Chemistry

Monte Carlo simulations of glass-forming liquids beyond Metropolis Monte Carlo simulations are widely employed to measure the physical properties of glass-forming liquids in thermal equilibrium. Combined with local Monte Carlo moves, the Metropolis algorithm can also be used to simulate the relaxation dynamics, thus offering an efficient alternative to molecular dynamics. Monte Carlo simulations are, however, more versatile because carefully designed Monte Carlo algorithms can more efficiently sample the rugged free energy landscape characteristic of glassy systems. After a brief overview of Monte Carlo studies of glass-formers, we define and implement a series of Monte Carlo algorithms in a three-dimensional model of polydisperse hard spheres. We show that the standard local Metropolis algorithm is the slowest and that implementing collective moves or breaking detailed balance enhances the efficiency of the Monte Carlo sampling. We use time correlation functions to provide a microscopic interpretation of these observations. Seventy years after its invention, the Monte Carlo method remains the most efficient and versatile tool to compute low-temperature properties in supercooled liquids. Monte Carlo method ; Statistical physics ; Monte Carlo molecular modeling ; Dynamic Monte Carlo method ; Hybrid Monte Carlo ; Monte Carlo method in statistical physics ; Monte Carlo algorithm ; Relaxation (psychology) ; Kinetic Monte Carlo ; Monte Carlo integration ; Quantum Monte Carlo ; Markov chain Monte Carlo ; Physics ; Mathematics ; Statistics Material Dynamics and Properties ; Phase Equilibria and Thermodynamics ; Theoretical and Computational Physics
Authors: Dmitriy A. Yablonskiy | Alexander L. Sukstanskii
Source: Magnetic Resonance in Medicine (article, 2024-01-19)
Field: Chemistry — Spectroscopy

Quantum dipole interactions and transient hydrogen bond orientation order in cells, cellular membranes and myelin sheath: Implications for <scp>MRI</scp> signal relaxation, anisotropy, and <scp>T<sub>1</sub></scp> magnetic field dependence By incorporating quantum proton interactions involved in brain imaging, the THB approach introduces new insights on the complex relationship between brain tissue cellular structure and MRI measurements, thus offering a promising new tool for better understanding of brain microstructure in health and disease. Dipole ; Relaxation (psychology) ; Anisotropy ; Nuclear magnetic resonance ; Quantum ; Chemistry ; Molecular physics ; Proton ; Physics ; Condensed matter physics ; Quantum mechanics ; Neuroscience Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; Electron Spin Resonance Studies
Authors: Amira I. Abousaty | Fifi M. Reda | Wessam A. Hassanin | Walaa M. Felifel | Walaa H. El‐Shwiniy | Heba Mohammed Refat M. Selim | Mahmoud M. Bendary
Source: BMC Microbiology (article, 2024-07-18)
Field: Materials Science — Materials Chemistry

Sorbate metal complexes as newer antibacterial, antibiofilm, and anticancer compounds Our findings offer potential for pharmaceutical companies to explore the development of novel combinations involving traditional antibiotics or anticancer drugs with sorbate copper complex. Bacillus cereus ; Nuclear chemistry ; Antibacterial activity ; Minimum inhibitory concentration ; Chemistry ; Microbiology ; Bacteria ; In vitro ; Biology ; Biochemistry Nanoparticles: synthesis and applications ; Metal complexes synthesis and properties ; Corrosion Behavior and Inhibition