jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Martín | Reiko Watanabe | Kosuke Hashimoto | Kazuma Higashisaka | Yuya Haga | Yasuo Tsutsumi | Kenji Mizuguchi
Source: ACS Nano (article, 2023-05-31)
Field: Materials Science — Materials Chemistry

Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles Developing a generalized model for a robust prediction of nanotoxicity is critical for designing safe nanoparticles. However, complex toxicity mechanisms of nanoparticles in biological environments, such as biomolecular corona formation, prevent a reliable nanotoxicity prediction. This is exacerbated by the potential evaluation bias caused by internal validation, which is not fully appreciated. Herein, we propose an evidence-based prediction method for distinguishing between cytotoxic and noncytotoxic nanoparticles at a given condition by uniting literature data mining and machine learning. We illustrate the proposed method for amorphous silica nanoparticles (SiO<sub>2</sub>-NPs). SiO<sub>2</sub>-NPs are currently considered a safety concern; however, they are still widely produced and used in various consumer products. We generated the most diverse attributes of SiO<sub>2</sub>-NP cellular toxicity to date, using >100 publications, and built predictive models, with algorithms ranging from linear to nonlinear (deep neural network, kernel, and tree-based) classifiers. These models were validated using internal (4124-sample) and external (905-sample) data sets. The resultant categorical boosting (CatBoost) model outperformed other algorithms. We then identified 13 key attributes, including concentration, serum, cell, size, time, surface, and assay type, which can explain SiO<sub>2</sub>-NP toxicity, using the Shapley Additive exPlanation values in the CatBoost model. The serum attribute underscores the importance of nanoparticle-corona complexes for nanotoxicity prediction. We further show that internal validation does not guarantee generalizability. In general, safe SiO<sub>2</sub>-NPs can be obtained by modifying their surfaces and using low concentrations. Our work provides a strategy for predicting and explaining the toxicity of any type of engineered nanoparticles in real-world practice. Nanotoxicology ; Nanoparticle ; Computer science ; Machine learning ; Cheminformatics ; Artificial intelligence ; Artificial neural network ; Biological system ; Materials science ; Nanotechnology ; Chemistry Nanoparticles: synthesis and applications
Authors: Ding Luo | Zihao Wu | Yuying Yan | Dongxu Ji | Ziming Cheng | Ruochen Wang | Ying Li | Xuelin Yang
Source: Applied Thermal Engineering (article, 2023-03-09)
Field: Materials Science — Materials Chemistry

Optimal design of a heat exchanger for automotive thermoelectric generator systems applied to a passenger car Heat exchanger ; Thermoelectric generator ; Multiphysics ; Materials science ; Automotive engineering ; Generator (circuit theory) ; Automotive industry ; Power (physics) ; Mechanical engineering ; Engineering ; Nuclear engineering ; Thermoelectric effect ; Thermodynamics ; Structural engineering ; Finite element method ; Physics Advanced Thermoelectric Materials and Devices ; Thermal Radiation and Cooling Technologies ; Refrigeration and Air Conditioning Technologies
Authors: Isaac J. Gresham | Seamus G. Lilley | Andrew Nelson | Kaloian Koynov | Chiara Neto
Source: Angewandte Chemie International Edition (article, 2023-08-08)
Field: Materials Science — Surfaces, Coatings and Films

Nanostructure Explains the Behavior of Slippery Covalently Attached Liquid Surfaces Slippery covalently-attached liquid surfaces (SCALS) with low contact angle hysteresis (CAH, <5°) and nanoscale thickness display impressive anti-adhesive properties, similar to lubricant-infused surfaces. Their efficacy is generally attributed to the liquid-like mobility of the constituent tethered chains. However, the precise physico-chemical properties that facilitate this mobility are unknown, hindering rational design. This work quantifies the chain length, grafting density, and microviscosity of a range of polydimethylsiloxane (PDMS) SCALS, elucidating the nanostructure responsible for their properties. Three prominent methods are used to produce SCALS, with characterization carried out via single-molecule force measurements, neutron reflectometry, and fluorescence correlation spectroscopy. CO<sub>2</sub> snow-jet cleaning was also shown to reduce the CAH of SCALS via a modification of their grafting density. SCALS behavior can be predicted by reduced grafting density, Σ, with the lowest water CAH achieved at Σ≈2. This study provides the first direct examination of SCALS grafting density, chain length, and microviscosity and supports the hypothesis that SCALS properties stem from a balance of layer uniformity and mobility. Nanostructure ; Covalent bond ; Materials science ; Nanotechnology ; Polymer science ; Chemistry ; Organic chemistry Surface Modification and Superhydrophobicity ; Polymer Surface Interaction Studies ; Surface Chemistry and Catalysis
Authors: Kajsa Ahlgren | Christoffer Olsson | Inna Ermilova | Jan Swenson
Source: Physical Chemistry Chemical Physics (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

New insights into the protein stabilizing effects of trehalose by comparing with sucrose Disaccharides are well known to be efficient stabilizers of proteins, for example in the case of lyophilization or cryopreservation. However, although all disaccharides seem to exhibit bioprotective and stabilizing properties, it is clear that trehalose is generally superior compared to other disaccharides. The aim of this study was to understand this by comparing how the structural and dynamical properties of aqueous trehalose and sucrose solutions influence the protein myoglobin (Mb). The structural studies were based on neutron and X-ray diffraction in combination with empirical potential structure refinement (EPSR) modeling, whereas the dynamical studies were based on quasielastic neutron scattering (QENS) and molecular dynamics (MD) simulations. The results show that the overall differences in the structure and dynamics of the two systems are small, but nevertheless there are some important differences which may explain the superior stabilizing effects of trehalose. It was found that in both systems the protein is preferentially hydrated by water, but that this effect is more pronounced for trehalose, <i>i.e.</i> trehalose forms less hydrogen bonds to the protein surface than sucrose. Furthermore, the rotational motion around dihedrals between the two glucose rings of trehalose is slower than in the case of the dihedrals between the glucose and fructose rings of sucrose. This leads to a less perturbed protein structure in the case of trehalose. The observations indicate that an aqueous environment closest to the protein molecules is beneficial for an efficient bioprotective solution. Trehalose ; Aqueous solution ; Chemistry ; Sucrose ; Crystallography ; Myoglobin ; Neutron scattering ; Molecular dynamics ; Sugar ; Hydrogen bond ; Fructose ; Neutron diffraction ; Molecule ; Protein dynamics ; Biophysics ; Chemical physics ; Neutron ; Biochemistry ; Computational chemistry ; Physical chemistry ; Organic chemistry ; Crystal structure ; Biology Enzyme Structure and Function ; Hemoglobin structure and function ; Protein Structure and Dynamics
Authors: Paulo H. S. Paioti | Katherine E. Lounsbury | Filippo Romiti | Michele Formica | Valentin Bauer | Claudio Zandonella | Meagan Hackey | Juan del Pozo | Amir H. Hoveyda
Source: Nature Chemistry (article, 2023-12-13)
Field: Chemistry — Organic Chemistry

Click processes orthogonal to CuAAC and SuFEx forge selectively modifiable fluorescent linkers Chemistry ; Bioconjugation ; Combinatorial chemistry ; Click chemistry ; Cycloaddition ; Triazole ; Nitrile ; Fluorescence ; Polymer chemistry ; Organic chemistry ; Catalysis Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Advanced biosensing and bioanalysis techniques
Authors: Cristina Rodríguez-Carrillo | Miriam Benítez | Jamal El Haskouri | Pedro Amorós | José V. Ros‐Lis
Source: Molecules (review, 2023-03-30)
Field: Materials Science — Materials Chemistry

Novel Microwave-Assisted Synthesis of COFs: 2020–2022 Covalent organic frameworks (COFs) have emerged as a new type of crystalline porous polymers of great interest. However, their preparation requires long reaction times. Microwave-assisted synthesis (MAS) offers an interesting approach to increasing the reaction rate of chemical processes. Thus, microwaves can be a key tool for the fast and scalable synthesis of COFs. Since our previous review on the topic, the preparation of COFs with microwaves has been evolving. Herein, we present a compilation of COFs studies and experiments published in the last three years on the synthesis of COFs using microwave-assisted synthesis as a source of energy. The articles include imine, triazine, and other 2D COFs synthesized using MAS. The 3D COFs have also been compiled. The chemical structure of the monomers and the COFs and their main parameters of synthesis and application are summarized for each article. Nanotechnology ; Microwave ; Triazine ; Computer science ; Covalent bond ; Materials science ; Chemistry ; Telecommunications ; Polymer chemistry ; Organic chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport
Authors: Shannan P. McClain | Xiang Ma | Desiree A. Johnson | Caroline A. Johnson | Aryanna E. Layden | Jean C. Yung | Susan T. Lubejko | Giulia Livrizzi | Xinyi Jenny He | Jingjing Zhou | Janie Chang-Weinberg | Emilya Ventriglia | Arianna Rizzo | Marjorie R. Levinstein | Juan L. Gomez | Jordi Bonaventura | Michael Michaelides | Matthew R. Banghart
Source: Neuron (article, 2023-10-16)
Field: Materials Science — Materials Chemistry

In vivo photopharmacology with light-activated opioid drugs Traditional methods for site-specific drug delivery in the brain are slow, invasive, and difficult to interface with recordings of neural activity. Here, we demonstrate the feasibility and experimental advantages of in vivo photopharmacology using "caged" opioid drugs that are activated in the brain with light after systemic administration in an inactive form. To enable bidirectional manipulations of endogenous opioid receptors in vivo, we developed photoactivatable oxymorphone (PhOX) and photoactivatable naloxone (PhNX), photoactivatable variants of the mu opioid receptor agonist oxymorphone and the antagonist naloxone. Photoactivation of PhOX in multiple brain areas produced local changes in receptor occupancy, brain metabolic activity, neuronal calcium activity, neurochemical signaling, and multiple pain- and reward-related behaviors. Combining PhOX photoactivation with optical recording of extracellular dopamine revealed adaptations in the opioid sensitivity of mesolimbic dopamine circuitry in response to chronic morphine administration. This work establishes a general experimental framework for using in vivo photopharmacology to study the neural basis of drug action. Opioid ; (+)-Naloxone ; Neuroscience ; Oxymorphone ; In vivo ; Chemistry ; Pharmacology ; Opioid receptor ; Neurochemical ; Microdialysis ; Agonist ; Dopamine ; Opioid antagonist ; Morphine ; Receptor ; Medicine ; Biology ; Biochemistry Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Olfactory and Sensory Function Studies
Authors: Kundo Park | Chihyeon Song | Jinkyoo Park | Seunghwa Ryu
Source: Materials Horizons (article, 2023-01-01)
Field: Materials Science — Biomaterials

Multi-objective Bayesian optimization for the design of nacre-inspired composites: optimizing and understanding biomimetics through AI The hierarchical structures found in biological materials lead to an outstanding balance of multiple material properties, and numerous research studies have been initiated to emulate the key concepts for the designing of engineering materials, the so-called bioinspired composites. However, the optimization of bioinspired composites has long been difficult as it usually falls into the category of 'black-box problem', the objective functions not being available in a functional form. Also, bioinspired composites possess multiple material properties that are in a trade-off relationship, making it impossible to reach a unique optimal design solution. As a breakthrough, we propose a data-driven material design framework which can generate bioinspired composite designs with an optimal balance of material properties. In this study, a nacre-inspired composite is chosen as the subject of study and the optimization framework is applied to determine the designs that have an optimal balance of strength, toughness, and specific volume. Gaussian process regression was adopted for the modeling of a complex input-output relationship, and the model was trained with the data generated from the crack phase-field simulation. Then, multi-objective Bayesian optimization was carried out to determine pareto-optimal composite designs. As a result, the proposed data-driven algorithm could generate a 3D pareto surface of optimal composite design solutions, from which a user can choose a design that suits his/her requirement. To validate the result, several pareto-optimal designs are built using a PolyJet 3D printer, and their tensile test results show that each of the characteristic designs is well optimized for its specific target objective. Optimal design ; Bayesian optimization ; Multi-objective optimization ; Computer science ; Engineering design process ; Composite number ; Design of experiments ; Kriging ; Mathematical optimization ; Materials science ; Mechanical engineering ; Algorithm ; Mathematics ; Engineering ; Artificial intelligence ; Machine learning Calcium Carbonate Crystallization and Inhibition ; Machine Learning in Materials Science ; Cephalopods and Marine Biology
Authors: Yao Zhang | Shan Huang | Xialei Lv | Kuangyu Wang | Huimin Yin | Siyao Qiu | Jinhui Li | Guoping Zhang | Rong Sun
Source: Polymer Chemistry (article, 2023-01-01)
Field: Materials Science — Polymers and Plastics

Polyimides with low dielectric constants and dissipation factors at high frequency derived from novel aromatic diamines with bistrifluoromethyl pendant groups Fan-out wafer-level packaging (FOWLP) urgently demands low dielectric constant and dissipation factor interlayer dielectric materials to mitigate high transmission losses at high frequencies. Dielectric ; Dissipation ; Dissipation factor ; Wafer ; Materials science ; Dielectric loss ; Composite material ; Transmission (telecommunications) ; High-κ dielectric ; Polymer chemistry ; Optoelectronics ; Electrical engineering ; Thermodynamics ; Physics ; Engineering Synthesis and properties of polymers ; 3D IC and TSV technologies ; Epoxy Resin Curing Processes
Authors: Rajeev Shrestha | Anusree Thenissery | Rahul Khupse | Gireesh Rajashekara
Source: Molecules (review, 2023-11-18)
Field: Materials Science — Biomaterials

Strategies for the Preparation of Chitosan Derivatives for Antimicrobial, Drug Delivery, and Agricultural Applications: A Review Chitosan has received much attention for its role in designing and developing novel derivatives as well as its applications across a broad spectrum of biological and physiological activities, owing to its desirable characteristics such as being biodegradable, being a biopolymer, and its overall eco-friendliness. The main objective of this review is to explore the recent chemical modifications of chitosan that have been achieved through various synthetic methods. These chitosan derivatives are categorized based on their synthetic pathways or the presence of common functional groups, which include alkylated, acylated, Schiff base, quaternary ammonia, guanidine, and heterocyclic rings. We have also described the recent applications of chitosan and its derivatives, along with nanomaterials, their mechanisms, and prospective challenges, especially in areas such as antimicrobial activities, targeted drug delivery for various diseases, and plant agricultural domains. The accumulation of these recent findings has the potential to offer insight not only into innovative approaches for the preparation of chitosan derivatives but also into their diverse applications. These insights may spark novel ideas for drug development or drug carriers, particularly in the antimicrobial, medicinal, and plant agricultural fields. Chitosan ; Drug delivery ; Antimicrobial ; Nanotechnology ; Drug ; Combinatorial chemistry ; Biopolymer ; Chemistry ; Biotechnology ; Biochemical engineering ; Organic chemistry ; Materials science ; Pharmacology ; Medicine ; Biology ; Engineering Nanocomposite Films for Food Packaging ; Pineapple and bromelain studies ; Advanced Drug Delivery Systems
Authors: Patryk Szymaszek | Wiktoria Tomal | Tomasz Świergosz | Iwona Kamińska-Borek | Roman Popielarz | Joanna Ortyl
Source: Polymer Chemistry (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Review of quantitative and qualitative methods for monitoring photopolymerization reactions Authomatic in-situ monitoring and characterization of photopolymerization. Photopolymer ; In situ ; Characterization (materials science) ; Chemistry ; Nanotechnology ; Materials science ; Organic chemistry ; Polymerization ; Polymer Photopolymerization techniques and applications ; Advanced Polymer Synthesis and Characterization
Authors: Arina G. Kicheeva | Ekaterina S. Sushko | Lyubov Bondarenko | Kamila Kydralieva | Denis Pankratov | N. S. Tropskaya | Artur Dzeranov | Gulzhian I. Dzhardimalieva | Mauro Zarrelli | Nadezhda S. Kudryasheva
Source: International Journal of Molecular Sciences (article, 2023-01-06)
Field: Materials Science — Biomaterials

Functionalized Magnetite Nanoparticles: Characterization, Bioeffects, and Role of Reactive Oxygen Species in Unicellular and Enzymatic Systems The current study evaluates the role of reactive oxygen species (ROS) in bioeffects of magnetite nanoparticles (MNPs), such as bare (Fe3O4), humic acids (Fe3O4-HA), and 3-aminopropyltriethoxysilane (Fe3O4-APTES) modified MNPs. Mössbauer spectroscopy was used to identify the local surrounding for Fe atom/ions and the depth of modification for MNPs. It was found that the Fe3O4-HA MNPs contain the smallest, whereas the Fe3O4-APTES MNPs contain the largest amount of Fe2+ ions. Bioluminescent cellular and enzymatic assays were applied to monitor the toxicity and anti-(pro-)oxidant activity of MNPs. The contents of ROS were determined by a chemiluminescence luminol assay evaluating the correlations with toxicity/anti-(pro-)oxidant coefficients. Toxic effects of modified MNPs were found at higher concentrations (>10−2 g/L); they were related to ROS storage in bacterial suspensions. MNPs stimulated ROS production by the bacteria in a wide concentration range (10−15−1 g/L). Under the conditions of model oxidative stress and higher concentrations of MNPs (>10−4 g/L), the bacterial bioassay revealed prooxidant activity of all three MNP types, with corresponding decay of ROS content. Bioluminescence enzymatic assay did not show any sensitivity to MNPs, with negligible change in ROS content. The results clearly indicate that cell-membrane processes are responsible for the bioeffects and bacterial ROS generation, confirming the ferroptosis phenomenon based on iron-initiated cell-membrane lipid peroxidation. Reactive oxygen species ; Magnetite ; Nanoparticle ; Enzyme ; Magnetite Nanoparticles ; Characterization (materials science) ; Chemistry ; Nanotechnology ; Oxygen ; Biophysics ; Biochemistry ; Magnetic nanoparticles ; Materials science ; Biology ; Organic chemistry Nanoparticle-Based Drug Delivery ; Nanoparticles: synthesis and applications ; Advanced Nanomaterials in Catalysis
Authors: Yuchen He | Evgenia Shishkova | Trenton M. Peters-Clarke | Dain R. Brademan | Michael S. Westphall | David Bergen | Jingjing Huang | Romain Huguet | Michael W. Senko | Vlad Zabrouskov | Graeme C. McAlister | Joshua J. Coon
Source: Analytical Chemistry (article, 2023-06-30)
Field: Chemistry — Spectroscopy

Evaluation of the Orbitrap Ascend Tribrid Mass Spectrometer for Shotgun Proteomics Mass spectrometry (MS)-based proteomics is a powerful technology to globally profile protein abundances, activities, interactions, and modifications. The extreme complexity of proteomics samples, which often contain hundreds of thousands of analytes, necessitates continuous development of MS techniques and instrumentation to improve speed, sensitivity, precision, and accuracy, among other analytical characteristics. Here, we systematically evaluated the Orbitrap Ascend Tribrid mass spectrometer in the context of shotgun proteomics, and we compared its performance to that of the previous generation of Tribrid instruments─the Orbitrap Eclipse. The updated architecture of the Orbitrap Ascend includes a second ion-routing multipole (IRM) in front of the redesigned C-trap/Orbitrap and a new ion funnel that allows gentler ion introduction, among other changes. These modifications in Ascend hardware configuration enabled an increase in parallelizable ion injection time during higher-energy collisional dissociation (HCD) Orbitrap tandem MS (FTMS<sup>2</sup>) analysis of ∼5 ms. This enhancement was particularly valuable in the analyses of limited sample amounts, where improvements in sensitivity resulted in up to 140% increase in the number of identified tryptic peptides. Further, analysis of phosphorylated peptides enriched from the K562 human cell line yielded up to ∼50% increase in the number of unique phosphopeptides and localized phosphosites. Strikingly, we also observed a ∼2-fold boost in the number of detected N-glycopeptides, likely owing to the improvements in ion transmission and sensitivity. In addition, we performed the multiplexed quantitative proteomics analyses of TMT11-plex labeled HEK293T tryptic peptides and observed 9-14% increase in the number of quantified peptides. In conclusion, the Orbitrap Ascend consistently outperformed its predecessor the Orbitrap Eclipse in various bottom-up proteomic analyses, and we anticipate that it will generate reproducible and in-depth datasets for numerous proteomic applications. Orbitrap ; Chemistry ; Mass spectrometry ; Shotgun proteomics ; Proteomics ; Top-down proteomics ; Tandem mass spectrometry ; Quantitative proteomics ; Context (archaeology) ; Chromatography ; Protein mass spectrometry ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies