jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sandra Sefa | D. C. Florian Wieland | Heike Helmholz | Berit Zeller‐Plumhoff | Ann Wennerberg | Julian Moosmann | Regine Willumeit‐Römer | Silvia Galli
Source: Frontiers in Biomaterials Science (article, 2022-09-20)
Field: Materials Science — Biomaterials

Assessing the long-term in vivo degradation behavior of magnesium alloys - a high resolution synchrotron radiation micro computed tomography study Biodegradable magnesium (Mg) implants are emerging as a potential game changer in implant technology in situations where the implant temporarily supports the bone thereby avoiding secondary surgery for implant removal. However, the consequences of the alteration in the degradation rate to bone healing and the localization of degradation and alloying products in the long term remain unknown. In this study, we present the long-term osseointegration of three different biodegradable Mg alloys, Mg-10Gd, Mg-4Y-3RE and Mg-2Ag, which were implanted into rabbit femur for 6 and 9 months. In addition, we have investigated the effect of blood pre-incubation on the in vivo performance of the aforementioned alloys. Using high-resolution synchrotron radiation based micro computed tomography, the bone implant contact (BIC), bone volume fraction (BV/TV) and implant morphology were studied. The elemental traces have been characterized using micro X-ray fluorescence. Qualitative histological evaluation of the surrounding bone was also performed. Matured bone formed around all three implant types and Ca as well as P which represent parts of the degradation layer were in intimate contact with the bone. Blood pre-incubation prior to implantation significantly improved BIC in Mg-2Ag screws at 9 months. Despite different implant degradation morphologies pointing toward different degradation dynamics, Mg-10Gd, Mg-4Y-3RE and Mg-2Ag induced a similar long-term bone response based on our quantified parameters. Importantly, RE elements Gd and Y used in the alloys remained at the implantation site implying that they might be released later on or might persist in the implantation site forever. As the bone formation was not disturbed by their presence, it might be concluded that Gd and Y are non-deleterious. Consequently, we have shown that short and mid-term in vivo evaluations do not fully represent indicators for long-term osseointegration of Mg-based implants. Osseointegration ; Implant ; Materials science ; Biomedical engineering ; Femur ; Degradation (telecommunications) ; Magnesium ; Metallurgy ; Surgery ; Medicine Magnesium Alloys: Properties and Applications ; Hydrogen Storage and Materials ; Aluminum Alloys Composites Properties
Authors: Yanchun Lin | Michael L. Gross
Source: Biomolecules (review, 2022-01-15)
Field: Chemistry — Spectroscopy

Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), "fast photochemical oxidation of proteins" (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including "protein-ligand interactions by mass spectrometry, titration and HD exchange" (PLIMSTEX) and "ligand titration, fast photochemical oxidation of proteins and mass spectrometry" (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions. Proteomics ; Mass spectrometry ; Chemistry ; Top-down proteomics ; Tandem mass tag ; Metal ; Chromatography ; Protein mass spectrometry ; Quantitative proteomics ; Tandem mass spectrometry ; Biochemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Molecular Biology Techniques and Applications
Authors: Dwight R. Stoll | Gudrun Kainz | Tina A. Dahlseid | Trevor Kempen | Tyler Brau | Bob W.J. Pirok
Source: Journal of Chromatography A (article, 2022-07-17)
Field: Chemistry — Spectroscopy

An approach to high throughput measurement of accurate retention data in liquid chromatography Chemistry ; Column (typography) ; Throughput ; Chromatography ; Inlet ; Analytical Chemistry (journal) ; Retention time ; Overhead (engineering) ; Volume (thermodynamics) ; Computer science ; Thermodynamics Analytical Chemistry and Chromatography ; Microfluidic and Capillary Electrophoresis Applications ; Protein purification and stability
Authors: Rajan Jagpal | Evangelos Evangelou | Richard Butler | Evripides G. Loukaides
Source: Journal of Composite Materials (article, 2022-05-24)
Field: Materials Science — Polymers and Plastics

Preforming of non-crimp fabrics with distributed magnetic clamping and Bayesian optimisation A novel preforming process was developed for non-crimp fabric (NCF) materials that generated in-plane tension through discontinuous blank boundary conditions. The method employed magnetic clamps and was designed to be both flexible and scalable, with clear routes to industrialisation. The capability of the process was explored in physical trials for a hemispherical and a cubic geometry. Characterisation of a biaxial veiled NCF showed the veil had a dominant effect on the bending mechanics. Subsequently a macroscale finite element model was developed to include an efficient bending idealisation and non-orthogonal in-plane material behaviour. Finally, global process optimisation of the preforming process was demonstrated. The optimisation approach used Gaussian process modelling with a periodic kernel to estimate the wrinkle size for untested clamping arrangements and then deployed Bayesian optimisation to find the optimal configuration. Results indicated that distributed magnetic clamping was effective and amenable to surrogate modelling. Crimp ; Clamping ; Materials science ; Finite element method ; Bending ; Structural engineering ; Process (computing) ; Tension (geology) ; Composite material ; Computer science ; Mechanical engineering ; Ultimate tensile strength ; Engineering Textile materials and evaluations ; Structural Analysis and Optimization ; Mechanical Behavior of Composites
Authors: Xiao Li | Marc N. Muñiz | Karlun Chun | Jonathan Tai | Francesca Guerra | Darrin M. York
Source: Journal of Chemical Education (article, 2022-03-15)
Field: Chemistry — Physical and Theoretical Chemistry

Inquiry-Based Activities and Games That Engage Students in Learning Atomic Orbitals Atomic orbitals represent an essential construct used to develop chemical bonding models, upon which other more advanced chemistry topics are built. In this article, we share a series of active-learning activities and a gamified approach to develop students' representational competence about atomic orbitals and to engage students in learning the properties of atomic orbitals. These properties are essential for understanding an array of fundamental concepts such as penetration and shielding, relationships such as periodic trends, and models used to describe chemical bonding. The activities employ an inquiry-based approach to engage students in exploring the relationship between atomic orbitals' spatial properties and quantum numbers. The activities guide students to collect data to verify periodic trends and construct electronic configurations. The activities utilize Orbital Explorer Web site for visualization, comparison and analysis of atomic orbitals. The Orbital Explorer Web site is described in a related Technology Report. The activities and the game are suitable to be conducted in both in-person and remote-teaching settings. Atomic orbital ; Construct (python library) ; Competence (human resources) ; Computer science ; Chemistry ; Psychology ; Physics ; Quantum mechanics Various Chemistry Research Topics ; Educational Strategies and Epistemologies ; Science Education and Pedagogy
Authors: Samahe Sadjadi | Fatemeh Koohestani | Majid M. Heravı
Source: Scientific Reports (article, 2022-01-21)
Field: Chemistry — Organic Chemistry

A novel composite of ionic liquid-containing polymer and metal–organic framework as an efficient catalyst for ultrasonic-assisted Knoevenagel condensation 1-Butyl-3-vinylimidazolium chloride was synthesized and polymerized with acrylamide to furnish an ionic liquid-containing polymer, which was then used for the formation of a composite with iron-based metal-organic framework. The resultant composite was characterized with XRD, TGA, FE-SEM, FTIR, EDS and elemental mapping analyses and its catalytic activity was appraised for ultrasonic-assisted Knoevenagel condensation. The results confirmed that the prepared composite could promote the reaction efficiently to furnish the corresponding products in high yields in very short reaction times. Moreover, the composite exhibited high recyclability up to six runs. It was also established that the activity of the composite was higher compared to pristine metal-organic framework or polymer. Knoevenagel condensation ; Composite number ; Ionic liquid ; Catalysis ; Polymer ; Polymerization ; Materials science ; Acrylamide ; Chemical engineering ; Fourier transform infrared spectroscopy ; Condensation reaction ; Polymer chemistry ; Chemistry ; Organic chemistry ; Composite material ; Monomer Multicomponent Synthesis of Heterocycles ; Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Reactions
Authors: Colby A. Whitcomb | Anna Sviripa | Michael I. Schapowal | Konstantin Mamedov | Raymond R. Unocic | Christopher Paolucci | Robert J. Davis
Source: ACS Catalysis (article, 2022-12-05)
Field: Materials Science — Materials Chemistry

Mechanistic Insights on the Low-Temperature Oxidation of CO Catalyzed by Isolated Co Ions in N-Doped Carbon Isolated cobalt ions on nitrogen-doped carbon (Co–N–C) catalyze CO oxidation at temperatures as low as 196 K, but the active site and mechanism for this reaction remain elusive. In this work, steady-state CO oxidation around 273 K over Co–N–C revealed nearly first-order behavior in both CO and O2 as well as a negative apparent activation energy. Isotopic transient analysis of the reaction confirmed a rapid turnover frequency and low surface coverage of adsorbed intermediates leading to CO2 (<10% of the Co). Results from kinetics experiments combined with quantum chemical calculations and molecular dynamics simulations are consistent with a reaction path involving weak adsorption of CO onto Co ions followed by a low barrier for the CO-assisted activation of weakly adsorbed O2. This proposed mechanism for dioxygen activation does not involve a redox cycle with the transition-metal ion and may be important in other low-temperature catalytic reactions involving O2. Catalysis ; Chemistry ; Adsorption ; Cobalt ; Redox ; Activation energy ; Carbon fibers ; Photochemistry ; Reaction mechanism ; Kinetics ; Inorganic chemistry ; Ion ; Chemical kinetics ; Physical chemistry ; Materials science ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Electrocatalysts for Energy Conversion
Authors: Sarah J. Rayment | Jocelyn Evans | Karen Moss | Mary Coffey | Sandra H. Kirk | Shiva Sivasubramaniam
Source: Journal of Biological Education (article, 2022-01-04)
Field: Chemistry — Physical and Theoretical Chemistry

Using lessons from a comparative study of chemistry &amp; bioscience pre-lab activities to design effective pre-lab interventions : a case study Laboratory classes form an important aspect of bioscience education. However, this environment is challenging for students due to cognitive load and lack of confidence. Familiarising students with aspects of their laboratory classes prior to the session can improve this. This study compares the pre-laboratory scaffolding that bioscience and chemistry students experience across UK HE institutions. Typically, bioscience modules used fewer types of activities than chemistry although reading the protocol was the most common activity for both disciplines. Within bioscience, pre-laboratory activities differed by level: first year undergraduates were more likely to be asked to read the protocol, watch videos or do calculation practice in their modules whereas final year undergraduates were more likely to experience experimental design or contextualised activities. Alongside this, this paper discusses an institutional case study of the development and evaluation of technical laboratory videos as prelaboratory scaffolding for first year students. These were found to benefit both student focus and enhance confidence: implying that using the videos impacted on cognitive load and hence learning. Exploring barriers to the uptake of these resources identified a lack of awareness of them as a major factor, suggesting that greater integration of such resources would enhance engagement and impact. Session (web analytics) ; Protocol (science) ; Psychological intervention ; Science education ; Reading (process) ; Psychology ; Laboratory safety ; Mathematics education ; Medical education ; Computer science ; Chemistry ; Medicine Various Chemistry Research Topics ; Innovative Teaching Methods ; Science Education and Pedagogy
Authors: Tommi Välikangas | Tomi Suomi | Courtney E. Chandler | Alison Scott | Bao Tran | Robert K. Ernst | David R. Goodlett | Laura L. Elo
Source: Nature Communications (article, 2022-12-22)
Field: Chemistry — Spectroscopy

Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach Quantitative proteomics has matured into an established tool and longitudinal proteomics experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, and has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a Robust longitudinal Differential Expression (RolDE) approach. The methods are evaluated using over 3000 semi-simulated spike-in proteomics datasets and three large experimental datasets. In the comparisons, RolDE performs overall best; it is most tolerant to missing values, displays good reproducibility and is the top method in ranking the results in a biologically meaningful way. Furthermore, RolDE is suitable for different types of data with typically unknown patterns in longitudinal expression and can be applied by non-experienced users. Proteomics ; Computer science ; Benchmarking ; Ranking (information retrieval) ; Data mining ; Missing data ; Protein expression ; Differential (mechanical device) ; Expression (computer science) ; Artificial intelligence ; Machine learning ; Biology Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Gene expression and cancer classification
Authors: Michiko Yoshitake | Fumitaka Sato | Hiroyuki Kawano | Hiroshi Teraoka
Source: Science and Technology of Advanced Materials Methods (article, 2022-09-16)
Field: Materials Science — Materials Chemistry

MaterialBERT for natural language processing of materials science texts A BERT (Bidirectional Encoder Representations from Transformers) model, which we named “MaterialBERT”, has been generated using scientific papers in wide area of material science as a corpus. A new vocabulary list for tokenizer was generated using material science corpus. Two BERT models with different vocabulary lists for the tokenizer, one with the original one made by Google and the other newly made by the authors, were generated. Word vectors embedded during the pre-training with the two MaterialBERT models reasonably reflect the meanings of materials names in material-class clustering and in the relationship between base materials and their compounds or derivatives for not only inorganic materials but also organic materials and organometallic compounds. Fine-tuning with CoLA (The Corpus of Linguistic Acceptability) using the pre-trained MaterialBERT showed a higher score than the original BERT. The two MaterialBERTs could be also utilized as a starting point for transfer learning of a narrower domain-specific BERT. Vocabulary ; Computer science ; Transformer ; Natural language processing ; Encoder ; Artificial intelligence ; Point (geometry) ; Class (philosophy) ; Domain (mathematical analysis) ; Cluster analysis ; Information retrieval ; Linguistics Machine Learning in Materials Science ; Topic Modeling ; Computational Drug Discovery Methods
Authors: Alicia Vallet | Jacqueline Martin‐Laffon | Adrien Favier | Benoît Revel | Titouan Bonnot | Claude Vidaud | Jean Armengaud | Jean‐Charles Gaillard | Pascale Delangle | Fabienne Devime | Sylvie Figuet | Nelson BC Serre | Elisabetta Boeri Erba | Bernhard Brutscher | Stéphane Ravanel | Jacques Bourguignon | Claude Alban
Source: Journal of Hazardous Materials (article, 2022-12-24)
Field: Chemistry — Inorganic Chemistry

The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein Arabidopsis ; Uranyl ; Arabidopsis thaliana ; Chemistry ; Biochemistry ; Mutant ; Cytosol ; Binding protein ; Binding site ; Plasma protein binding ; Biophysics ; Biology ; Gene ; Enzyme Radioactive element chemistry and processing ; Radioactive contamination and transfer ; Plant Micronutrient Interactions and Effects
Authors: Lukas Schmidheini | Raphael F. Tiefenauer | Volker Gatterdam | Andreas Frutiger | Takumi Sannomiya | Morteza Aramesh
Source: Biosensors (article, 2022-02-28)
Field: Materials Science — Materials Chemistry

Self-Assembly of Nanodiamonds and Plasmonic Nanoparticles for Nanoscopy Nanodiamonds have emerged as promising agents for sensing and imaging due to their exceptional photostability and sensitivity to the local nanoscale environment. Here, we introduce a hybrid system composed of a nanodiamond containing nitrogen-vacancy center that is paired to a gold nanoparticle via DNA hybridization. Using multiphoton optical studies, we demonstrate that the harmonic mode emission generated in gold nanoparticles induces a coupled fluorescence emission in nanodiamonds. We show that the flickering of harmonic emission in gold nanoparticles directly influences the nanodiamonds' emissions, resulting in stochastic blinking. By utilizing the stochastic emission fluctuations, we present a proof-of-principle experiment to demonstrate the potential application of the hybrid system for super-resolution microscopy. The introduced system may find applications in intracellular biosensing and bioimaging due to the DNA-based coupling mechanism and also the attractive characteristics of harmonic generation, such as low power, low background and tissue transparency. Nanodiamond ; Nanotechnology ; Nanoparticle ; Materials science ; Colloidal gold ; Biosensor ; Plasmon ; Nanoscopic scale ; Second-harmonic generation ; Fluorescence ; Optoelectronics ; Optics ; Diamond ; Physics Diamond and Carbon-based Materials Research ; Nonlinear Optical Materials Studies ; Advanced Fiber Laser Technologies
Authors: Sihai Luo | Andrea Mancini | Enkui Lian | Wenqi Xu | Rodrigo Berté | Yi Li
Source: Nanomaterials (article, 2022-10-31)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Large Area Patterning of Highly Reproducible and Sensitive SERS Sensors Based on 10-nm Annular Gap Arrays Applicable surface-enhanced Raman scattering (SERS) active substrates typically require low-cost patterning methodology, high reproducibility, and a high enhancement factor (EF) over a large area. However, the lack of reproducible, reliable fabrication for large area SERS substrates in a low-cost manner remains a challenge. Here, a patterning method based on nanosphere lithography and adhesion lithography is reported that allows massively parallel fabrication of 10-nm annular gap arrays on large areas. The arrays exhibit excellent reproducibility and high SERS performance, with an EF of up to 10<sup>7</sup>. An effective wearable SERS contact lens for glucose detection is further demonstrated. The technique described here extends the range of SERS-active substrates that can be fabricated over large areas, and holds exciting potential for SERS-based chemical and biomedical detection. Materials science ; Nanotechnology ; Fabrication ; Lithography ; Raman scattering ; Reproducibility ; Nanosphere lithography ; Optoelectronics ; Raman spectroscopy ; Optics ; Chemistry Gold and Silver Nanoparticles Synthesis and Applications ; Biosensors and Analytical Detection ; Quantum Dots Synthesis And Properties
Authors: Hironobu Watanabe | Arihiro Kanazawa | Satoshi Okumoto | Sadahito Aoshima
Source: Macromolecules (article, 2022-06-02)
Field: Chemistry — Organic Chemistry

Role of the Counteranion in the Stereospecific Living Cationic Polymerization of <i>N</i>-Vinylcarbazole and Vinyl Ethers: Mechanistic Investigation and Synthesis of Stereo-Designed Polymers The effects of counteranions in the cationic polymerization of N-vinylcarbazole (NVC) and vinyl ethers were investigated to develop guidelines for stereospecific living cationic polymerization. The counteranion structure, such as the charge number, metal center, and ligand, was systematically examined using the CF3SO3H/onium halide/metal halide initiating system. As a result, the electronic properties rather than the steric bulkiness of the counteranion were demonstrated to be key to stereoregulation during the polymerization of N-vinylcarbazole. Fine-tuning the stereoregularity of the resultant polymers was achieved (mm = 45–95%) while maintaining the living nature of polymerization. Computational analysis indicated that the stereoregulation was attributed to electrostatic interactions between the counteranion and pendant aromatic rings. These findings also allowed stereospecific polymerization of vinyl ethers containing an aromatic ring in the pendant. Moreover, the successful synthesis of “stereo-designed” polymers, such as stereoblock and stereocontrolled block copolymers, was achieved by appropriately designing counteranions for living cationic polymerization. Cationic polymerization ; Living cationic polymerization ; Stereospecificity ; Polymer chemistry ; Polymerization ; Polymer ; Chemistry ; Polymer science ; Organic chemistry ; Ring-opening polymerization ; Catalysis Advanced Polymer Synthesis and Characterization ; Organometallic Complex Synthesis and Catalysis ; biodegradable polymer synthesis and properties