jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mridula Prasad | Geert Postma | Pietro Franceschi | L.M.C. Buydens | Jeroen J. Jansen
Source: Scientific Reports (article, 2022-09-20)
Field: Chemistry — Analytical Chemistry

Evaluation and comparison of unsupervised methods for the extraction of spatial patterns from mass spectrometry imaging data (MSI) For the extraction of spatially important regions from mass spectrometry imaging (MSI) data, different clustering methods have been proposed. These clustering methods are based on certain assumptions and use different criteria to assign pixels into different classes. For high-dimensional MSI data, the curse of dimensionality also limits the performance of clustering methods which are usually overcome by pre-processing the data using dimension reduction techniques. In summary, the extraction of spatial patterns from MSI data can be done using different unsupervised methods, but the robust evaluation of clustering results is what is still missing. In this study, we have performed multiple simulations on synthetic and real MSI data to validate the performance of unsupervised methods. The synthetic data were simulated mimicking important spatial and statistical properties of real MSI data. Our simulation results confirmed that K-means clustering with correlation distance and Gaussian Mixture Modeling clustering methods give optimal performance in most of the scenarios. The clustering methods give efficient results together with dimension reduction techniques. From all the dimension techniques considered here, the best results were obtained with the minimum noise fraction (MNF) transform. The results were confirmed on both synthetic and real MSI data. However, for successful implementation of MNF transform the MSI data requires to be of limited dimensions. Mass spectrometry imaging ; Computer science ; Mass spectrometry ; Extraction (chemistry) ; Data extraction ; Pattern recognition (psychology) ; Artificial intelligence ; Computational biology ; Data mining ; Chromatography ; MEDLINE ; Chemistry ; Biology Spectroscopy and Chemometric Analyses ; Metabolomics and Mass Spectrometry Studies ; Advanced Chemical Sensor Technologies
Authors: Marc Isaksson | Christofer Karlsson | Thomas Laurell | Agnete Kirkeby | Moritz Heusel
Source: Journal of Proteome Research (article, 2022-01-19)
Field: Chemistry — Spectroscopy

MSLibrarian: Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics Data-independent acquisition-mass spectrometry (DIA-MS) is the method of choice for deep, consistent, and accurate single-shot profiling in bottom-up proteomics. While classic workflows for targeted quantification from DIA-MS data require auxiliary data-dependent acquisition (DDA) MS analysis of subject samples to derive prior-knowledge spectral libraries, library-free approaches based on <i>in silico</i> prediction promise deep DIA-MS profiling with reduced experimental effort and cost. Coverage and sensitivity in such analyses are however limited, in part, by the large library size and persistent deviations from the experimental data. We present MSLibrarian, a new workflow and tool to obtain optimized predicted spectral libraries by the integrated usage of spectrum-centric DIA data interpretation via the DIA-Umpire approach to inform and calibrate the <i>in silico</i> predicted library and analysis approach. Predicted-vs-observed comparisons enabled optimization of intensity prediction parameters, calibration of retention time prediction for deviating chromatographic setups, and optimization of the library scope and sample representativeness. Benchmarking via a dedicated ground-truth-embedded experiment of species-mixed proteins and quantitative ratio-validation confirmed gains of up to 13% on peptide and 8% on protein level at equivalent FDR control and validation criteria. MSLibrarian is made available as an open-source R software package, including step-by-step user instructions, at https://github.com/MarcIsak/MSLibrarian. Computer science ; Workflow ; Profiling (computer programming) ; Data mining ; Software ; Data acquisition ; Database Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Coralie Chuberre | Philippe Chan | Marie-Laure Walet-Balieu | François Thiébert | Carole Burel | Julie Hardouin | Bruno Gügi | Muriel Bardor
Source: Frontiers in Plant Science (article, 2022-03-21)
Field: Materials Science — Biomaterials

Comparative Proteomic Analysis of the Diatom Phaeodactylum tricornutum Reveals New Insights Into Intra- and Extra-Cellular Protein Contents of Its Oval, Fusiform, and Triradiate Morphotypes <i>Phaeodactylum tricornutum</i> is an atypical diatom since it can display three main morphotypes: fusiform, triradiate, and oval. Such pleomorphism is possible thanks to an original metabolism, which is tightly regulated in order to acclimate to environmental conditions. Currently, studies dedicated to the comparison of each morphotype issued from one specific strain are scarce and little information is available regarding the physiological significance of this morphogenesis. In this study, we performed a comparative proteomic analysis of the three morphotypes from <i>P. tricornutum</i>. Cultures highly enriched in one dominant morphotype (fusiform, triradiate, or oval) of <i>P. tricornutum</i> Pt3 strain were used. Pairwise comparisons highlighted biological processes, which are up- and down-regulated in the oval (e.g., purine and cellular amino acid metabolism) and triradiate morphotypes (e.g., oxido-reduction and glycolytic processes) compared to the fusiform one used as a reference. Intersection analysis allowed us to identify the specific features of the oval morphotype. Results from this study confirmed previous transcriptomic RNA sequencing observation showing that the oval cells present a distinct metabolism with specific protein enrichment compared to fusiform and triradiate cells. Finally, the analysis of the secretome of each morphotype was also performed. Phaeodactylum tricornutum ; Biology ; Diatom ; Transcriptome ; Digital image analysis ; Botany ; Cell biology ; Biochemistry ; Gene ; Gene expression Diatoms and Algae Research ; Advanced Proteomics Techniques and Applications ; Algal biology and biofuel production
Authors: Shang Zhang | Ethan Stanifer | Vishwas V. Vasisht | Leyou Zhang | Emanuela Del Gado | Xiaoming Mao
Source: Physical Review Research (article, 2022-12-12)
Field: Materials Science — Materials Chemistry

Prestressed elasticity of amorphous solids Prestress in amorphous solids bears the memory of their formation and plays a profound role in their mechanical properties. Here we develop a set of mathematical tools to investigate mechanical response of prestressed systems, using stress rather than strain as the fundamental variable. This theory allows microscopic prestress to vary for the same bond or contact configuration and is particularly convenient for nonconservative systems, such as granular packings and jammed suspensions, where there is no well-defined reference state, invalidating conventional elasticity. Using prestressed nonconservative triangular lattices and a computational model of amorphous solids, we show that drastically different mechanical responses can show up in amorphous materials at the same density, due to nonconservative interactions which evolve over time, or different preparation protocols. In both cases, the information is encoded in the prestress of the network and not visible at all from the configurations of the network in the case of nonconservative interactions. Amorphous solid ; Elasticity (physics) ; Materials science ; Statistical physics ; Mechanics ; Composite material ; Physics ; Crystallography ; Chemistry Material Dynamics and Properties ; Adhesion, Friction, and Surface Interactions ; Force Microscopy Techniques and Applications
Authors: Shuang Zhang
Source: Light Science & Applications (article, 2022-08-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Intelligent metasurfaces: digitalized, programmable, and intelligent platforms Distinguished from conventional ones, intelligent metasurfaces are endowed with three important characteristics: digitalization, programmability, and intelligence, which can be further integrated with detection, artificial neural networks, and feedback systems into a smart platform. Metasurface-based smart systems are expected to play an important role in wireless communications, advanced sensing technologies and artificial intelligence. Computer science ; Artificial neural network ; Wireless ; Intelligent decision support system ; Computer architecture ; Embedded system ; Systems engineering ; Telecommunications ; Artificial intelligence ; Engineering Metamaterials and Metasurfaces Applications ; Advanced Wireless Communication Technologies ; Opportunistic and Delay-Tolerant Networks
Authors: Haowei Liu | Pengchao Wu | Lumiao Hou | Xiaofan Zhang | He Zheng | Bolin Niu | Shaohua Liu | Jianwei Fu
Source: Colloids and Surfaces A Physicochemical and Engineering Aspects (article, 2022-09-11)
Field: Materials Science — Materials Chemistry

A cyclophosphazene-derived porous organic polymer with P-N linkage for environmental adsorption applications Adsorption ; Chemistry ; Aqueous solution ; Sorption ; Imine ; Polymer ; Chemical engineering ; Hydrogen bond ; Langmuir adsorption model ; Kinetics ; Inorganic chemistry ; Polymer chemistry ; Catalysis ; Organic chemistry ; Molecule Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport
Authors: Peter K. Walhout | Zhe He | Bercem Dutagaci | Grzegorz Nawrocki | Michael Feig
Source: The Journal of Physical Chemistry B (article, 2022-11-28)
Field: Chemistry — Physical and Theoretical Chemistry

Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions Polyelectrolytes continue to find wide interest and application in science and engineering, including areas such as water purification, drug delivery, and multilayer thin films. We have been interested in the dynamics of small molecules in a variety of polyelectrolyte (PE) environments; in this paper, we report simulations and analysis of the small dye molecule rhodamine B (RB) in several very simple polyelectrolyte solutions. Translational diffusion of the RB zwitterion has been measured in fully atomistic, 2 μs long molecular dynamics simulations in four different polyelectrolyte solutions. Two solutions contain the common polyanion sodium poly(styrene sulfonate) (PSS), one with a 30-mer chain and the other with 10 trimers. The other two solutions contain the common polycation poly(allyldimethylammonium) chloride (PDDA), one with two 15-mers and the other with 10 trimers. RB diffusion was also simulated in several polymer-free solutions to verify its known experimental value for the translational diffusion coefficient, <i>D</i><sub>RB</sub>, of 4.7 × 10<sup>-6</sup> cm<sup>2</sup>/s at 300 K. RB diffusion was slowed in all four simulated PE solutions, but to varying degrees. <i>D</i><sub>RB</sub> values of 3.07 × 10<sup>-6</sup> and 3.22 × 10<sup>-6</sup> cm<sup>2</sup>/s were found in PSS 30-mer and PSS trimer solutions, respectively, whereas PDDA 15-mer and trimer solutions yielded values of 2.19 × 10<sup>-6</sup> and 3.34 × 10<sup>-6</sup> cm<sup>2</sup>/s. Significant associations between RB and the PEs were analyzed and interpreted via a two-state diffusion model (bound and free diffusion) that describes the data well. Crowder size effects and anomalous diffusion were also analyzed. Finally, RB translation along the polyelectrolytes during association was characterized. Polyelectrolyte ; Zwitterion ; Trimer ; Diffusion ; Molecular dynamics ; Chemistry ; Polymer ; Chemical physics ; Rhodamine B ; Polymer chemistry ; Molecule ; Chemical engineering ; Computational chemistry ; Thermodynamics ; Dimer ; Organic chemistry ; Physics Electrostatics and Colloid Interactions ; Surfactants and Colloidal Systems ; Spectroscopy and Quantum Chemical Studies
Authors: Yue Liu | Xiaoyi Liu | Chen Lai | Jie Ma | Xianfang Meng | Long Zhang | Guanglong Xu | Yiwen Lu | Hongyi Li | Jinshu Wang | Shuqun Chen
Source: International Journal of Refractory Metals and Hard Materials (article, 2022-11-24)
Field: Materials Science — Materials Chemistry

Boriding of tungsten by the powder-pack process: Phase formation, growth kinetics and enhanced neutron shielding Materials science ; Boriding ; Boride ; Tungsten ; Boron ; Microstructure ; Diffusion ; Coating ; Electromagnetic shielding ; Layer (electronics) ; Phase (matter) ; Metallurgy ; Composite material ; Thermodynamics ; Chemistry Nuclear Materials and Properties ; Fusion materials and technologies ; Advanced materials and composites
Authors: Kenta Sato | Hiroaki Sukegawa | Kentaro Ogata | Gang Xiao | Hideo Kaiju
Source: Scientific Reports (article, 2022-05-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Large magnetocapacitance beyond 420% in epitaxial magnetic tunnel junctions with an MgAl2O4 barrier Magnetocapacitance (MC) effect has been observed in systems where both symmetries of time-reversal and space-inversion are broken, for examples, in multiferroic materials and spintronic devices. The effect has received increasing attention due to its interesting physics and the prospect of applications. Recently, a large tunnel magnetocapacitance (TMC) of 332% at room temperature was reported using MgO-based (001)-textured magnetic tunnel junctions (MTJs). Here, we report further enhancement in TMC beyond 420% at room temperature using epitaxial MTJs with an MgAl<sub>2</sub>O<sub>4</sub>(001) barrier with a cation-disordered spinel structure. This large TMC is partially caused by the high effective tunneling spin polarization, resulted from the excellent lattice matching between the Fe electrodes and the MgAl<sub>2</sub>O<sub>4</sub> barrier. The epitaxial nature of this MTJ system sports an enhanced spin-dependent coherent tunneling effect. Among other factors leading to the large TMC are the appearance of the spin capacitance, the large barrier height, and the suppression of spin flipping through the MgAl<sub>2</sub>O<sub>4</sub> barrier. We explain the observed TMC by the Debye-Fröhlich modelled calculation incorporating Zhang-sigmoid formula, parabolic barrier approximation, and spin-dependent drift diffusion model. Furthermore, we predict a 1000% TMC in MTJs with a spin polarization of 0.8. These experimental and theoretical findings provide a deeper understanding on the intrinsic mechanism of the TMC effect. New applications based on large TMC may become possible in spintronics, such as multi-value memories, spin logic devices, magnetic sensors, and neuromorphic computing. Spintronics ; Condensed matter physics ; Magnetocapacitance ; Quantum tunnelling ; Materials science ; Nanosheet ; Multiferroics ; Neuromorphic engineering ; Spin polarization ; Ferromagnetism ; Nanotechnology ; Physics ; Optoelectronics ; Ferroelectricity ; Computer science ; Quantum mechanics Multiferroics and related materials ; Magnetic and transport properties of perovskites and related materials ; Advanced Condensed Matter Physics
Authors: Liyao Cao | Hongchang Wang | Hua Shen | Ruiliu Wang | Fumei Wang | Guangbiao Xu
Source: Cellulose (article, 2022-03-10)
Field: Materials Science — Biomaterials

Adsorption performance of human-like collagen by alkali-modified Kapok fiber: a kinetic, equilibrium, and mechanistic investigation Adsorption ; Alkali metal ; Fiber ; Chemical engineering ; Materials science ; Physisorption ; Diffusion ; Chemisorption ; Hemicellulose ; Lignin ; Composite material ; Chemistry ; Organic chemistry ; Thermodynamics Collagen: Extraction and Characterization ; Textile materials and evaluations ; Electrospun Nanofibers in Biomedical Applications
Authors: Jianqiao Wu | Ying Pan | Ziyi Ruan | Ziji Zhao | Jing Ai | Jinghai Ban | Xianghai Jing
Source: Frontiers in Materials (article, 2022-11-24)
Field: Materials Science — Polymers and Plastics

Carbon fiber-reinforced epoxy with 100% fiber recycling by transesterification reactions Carbon fiber (CF)-reinforced epoxy is the most commonly used advanced composite with high performance. However, these composites usually face intractable disposal problems in their lifecycles, due to the stable cross-linked network structures of epoxy. To address this dilemma, this work proposes a facile yet efficient strategy for recycling carbon fibers from traditional carbon fiber-reinforced epoxy composites using epoxy–anhydride systems as a matrix. Diglycidyl ester of aliphatic cyclo (DGEAC) and methylhexahydrophthalic anhydride (MHHPA) were used as matrix, while T300 woven carbon fiber was used as reinforcement, to construct the composites CF/DGEAC/MHHPA. The epoxy matrix exhibited a high glass transition temperature ( T g = 126°C), high decomposition temperature ( T d5 = 300°C), and good solvent resistance. By using 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) as a catalyst, the DGEAC/MHHPA networks could be degraded completely in ethylene glycol (EG) at 180°C within 6 h because of transesterification reactions between EG and the networks. Taking advantage of this result, a fiber recycling process was developed for carbon fiber composites, where the cross-linked networks of epoxy could be degraded with 100% carbon fiber recycling. Furthermore, the recycled carbon fiber maintained nearly 100% similarity in surface microscopic morphology and chemical structure compared with virgin carbon fiber. This work proposes a simple and efficient strategy for recycling carbon fiber from traditional high-performance composites, offering a convenient concept for the cyclic utilization of advanced composites. Epoxy ; Materials science ; Composite material ; Fiber ; Composite number ; Transesterification ; Catalysis ; Organic chemistry ; Chemistry Polymer composites and self-healing ; Fiber-reinforced polymer composites ; Carbon dioxide utilization in catalysis
Authors: Luiz Eduardo Nochi Castro | Débora Alessandra Jones Battocchio | Leomara Floriano Ribeiro | Leda Maria Saragiotto Colpini
Source: Brazilian Archives of Biology and Technology (article, 2022-11-11)
Field: Chemistry — Analytical Chemistry

Development of Adsorbent Materials Using Residue from Coffee Industry and Application in Food dye Adsorption Processes HIGHLIGHTS The adsorbent activated with H2PO4 removed around 100% of Ponceau 4R dye. The increase in temperature influenced the increase in maximum adsorptive capacity. Langmuir's isotherm was better suited to the experimental data of the Ponceau 4R dye. Adsorption ; Residue (chemistry) ; Langmuir adsorption model ; Chemical engineering ; Chemistry ; Sorption isotherm ; Chromatography ; Langmuir ; Materials science ; Organic chemistry Spectroscopy and Chemometric Analyses ; Dye analysis and toxicity ; Water Quality Monitoring and Analysis
Authors: Lizhi Gong | Yuzhen Wu | Xiaohan Qiu | Xiujuan Xin | Faliang An | Miaomiao Guo
Source: Marine Drugs (article, 2022-03-28)
Field: Chemistry — Analytical Chemistry

Adsorption Characteristics and Enrichment of Emodin from Marine-Derived Aspergillus flavipes HN4-13 Extract by Macroporous Resin XAD-16 Emodin, a hydroxyanthraquinone derivative, has been used as medicine for more than 2000 years due to its extensive pharmacological activities. Large-scale production of emodin has been achieved by optimizing the fermentation conditions of marine-derived <i>Aspergillus flavus</i> HN4-13 in a previous study. However, the fermentation broth contained complex unknown components, which adversely affected the study of emodin. Herein, the conditions for the enrichment of emodin from <i>A</i>. <i>flavipes</i> HN4-13 extract using XAD-16 resin were optimized, and a separation method with high efficiency, simple operation, a low cost, and a large preparative scale was established. The adsorption process of emodin on the XAD-16 resin conformed to pseudo-second-order kinetics and Langmuir models. The optimal conditions for the adsorption process were as follows: An emodin concentration, flow rate, and loading volume of 0.112 mg/mL, 2 BV/h, and 10 BV, respectively. For desorption, 50% ethanol was used to elute impurities and 80% ethanol was used to desorb emodin. After enrichment with XAD-16 resin, the emodin content increased from 1.16% to 11.48%, and the recovery rate was 75.53% after one-step treatment. These results demonstrate the efficiency of the simple adsorption-desorption strategy, using the XAD-16 resin for emodin enrichment. Emodin ; Adsorption ; Chemistry ; Chromatography ; Organic chemistry Chromatography in Natural Products ; Phytochemistry and biological activity of medicinal plants ; Pharmacological Effects of Natural Compounds
Authors: Irene Bonadies | Roberta Capuano | Roberto Avolio | Rachele Castaldo | Mariacristina Cocca | Gennaro Gentile | Maria Emanuela Errico
Source: Polymers (article, 2022-02-19)
Field: Materials Science — Biomaterials

Sustainable Cellulose-Aluminum-Plastic Composites from Beverage Cartons Scraps and Recycled Polyethylene The sustainable management of multilayer paper/plastic waste is a technological challenge due to its composite nature. In this paper, a mechanical recycling approach for multilayer cartons (MC) is reported, illustrating the realization of thermoplastic composites based on recycled polyethylene and an amount of milled MC ranging from 20 to 90 wt%. The effect of composition of the composites on the morphology and on thermal, mechanical, and water absorption behavior was investigated and rationalized, demonstrating that above 80 wt% of MC, the fibrous nature of the filler dominates the overall properties of the materials. A maleated polyethylene was also used as a coupling agent and its effectiveness in improving mechanical parameters of composites up to 60 wt% of MC was highlighted. Materials science ; Polyethylene ; Composite material ; Carton ; Composite number ; Filler (materials) ; Wood-plastic composite ; Absorption of water ; Thermoplastic ; Cellulose ; Waste management ; Chemical engineering Advanced Cellulose Research Studies ; Natural Fiber Reinforced Composites ; biodegradable polymer synthesis and properties
Authors: Hongyan Mei | Alexander Koch | Chenghao Wan | Jura Rensberg | Zhen Zhang | Jad Salman | Martin Hafermann | Maximilian Schaal | Yuzhe Xiao | Raymond Wambold | Shriram Ramanathan | Carsten Ronning | Mikhail A. Kats
Source: Nanophotonics (article, 2022-06-13)
Field: Materials Science — Polymers and Plastics

Tuning carrier density and phase transitions in oxide semiconductors using focused ion beams We demonstrate spatial modification of the optical properties of thin-film metal oxides, zinc oxide (ZnO) and vanadium dioxide (VO<sub>2</sub>) as representatives, using a commercial focused ion beam (FIB) system. Using a Ga<sup>+</sup> FIB and thermal annealing, we demonstrated variable doping of a wide-bandgap semiconductor, ZnO, achieving carrier concentrations from 10<sup>18</sup> cm<sup>-3</sup> to 10<sup>20</sup> cm<sup>-3</sup>. Using the same FIB without subsequent thermal annealing, we defect-engineered a correlated semiconductor, VO<sub>2</sub>, locally modifying its insulator-to-metal transition (IMT) temperature by up to ∼25 °C. Such area-selective modification of metal oxides by direct writing using a FIB provides a simple, mask-less route to the fabrication of optical structures, especially when multiple or continuous levels of doping or defect density are required. Materials science ; Doping ; Semiconductor ; Annealing (glass) ; Focused ion beam ; Optoelectronics ; Vanadium oxide ; Band gap ; Nanomaterials ; Wide-bandgap semiconductor ; Oxide ; Nanotechnology ; Ion ; Composite material ; Metallurgy ; Chemistry Transition Metal Oxide Nanomaterials ; ZnO doping and properties ; Ga2O3 and related materials