jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Elmira Shajari | David Gagné | Mandy Malick | Patricia Roy | Jean-François Noël | Hugo Gagnon | Marie A. Brunet | Maxime Delisle | François‐Michel Boisvert | Jean‐François Beaulieu
Source: Biomedicines (article, 2024-02-01)
Field: Chemistry — Spectroscopy

Application of SWATH Mass Spectrometry and Machine Learning in the Diagnosis of Inflammatory Bowel Disease Based on the Stool Proteome Inflammatory bowel disease (IBD) flare-ups exhibit symptoms that are similar to other diseases and conditions, making diagnosis and treatment complicated. Currently, the gold standard for diagnosing and monitoring IBD is colonoscopy and biopsy, which are invasive and uncomfortable procedures, and the fecal calprotectin test, which is not sufficiently accurate. Therefore, it is necessary to develop an alternative method. In this study, our aim was to provide proof of concept for the application of Sequential Window Acquisition of All Theoretical Mass Spectra-Mass spectrometry (SWATH-MS) and machine learning to develop a non-invasive and accurate predictive model using the stool proteome to distinguish between active IBD patients and symptomatic non-IBD patients. Proteome profiles of 123 samples were obtained and data processing procedures were optimized to select an appropriate pipeline. The differentially abundant analysis identified 48 proteins. Utilizing correlation-based feature selection (Cfs), 7 proteins were selected for proceeding steps. To identify the most appropriate predictive machine learning model, five of the most popular methods, including support vector machines (SVMs), random forests, logistic regression, naive Bayes, and k-nearest neighbors (KNN), were assessed. The generated model was validated by implementing the algorithm on 45 prospective unseen datasets; the results showed a sensitivity of 96% and a specificity of 76%, indicating its performance. In conclusion, this study illustrates the effectiveness of utilizing the stool proteome obtained through SWATH-MS in accurately diagnosing active IBD via a machine learning model. Support vector machine ; Random forest ; Artificial intelligence ; Naive Bayes classifier ; Machine learning ; Proteome ; Gold standard (test) ; Computer science ; Inflammatory bowel disease ; Calprotectin ; Pipeline (software) ; Feature selection ; Logistic regression ; Disease ; Medicine ; Bioinformatics ; Pathology ; Biology ; Internal medicine Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Gut microbiota and health
Authors: Giuliano Aretusi | Christian Cardillo | Antonello Salvatori | Ewa Bednarczyk | Roberto Fedele
Source: Zeitschrift für angewandte Mathematik und Physik (article, 2024-08-24)
Field: Materials Science — Materials Chemistry

A simple extension of Timoshenko beam model to describe dissipation in cementitious elements Abstract In this paper, an extension of the Timoshenko model for plane beams is outlined, with the aim of describing, under the assumption of small displacements and strains, a class of dissipative mechanisms observed in cementitious materials. In the spirit of micromorphic continua, the modified beam model includes a novel kinematic descriptor, conceived as an average sliding relevant to a density of micro-cracks not varying along time. For the pairs of rough surfaces, in which such a distribution of micro-cracks is articulated, both an elastic deformation and a frictional dissipation are considered, similarly to what occurs for the fingers of the joints having a tooth saw profile. The system of governing differential equations, of the second order, is provided by a variational approach, endowed by standard boundary conditions. To this purpose, a generalized version of the principle of virtual work is used, in the spirit of Hamilton–Rayleigh approach, including as contributions: (i) the variation of the inner elastic energy, generated by the linear elasticity of the sound material and, in a nonlinear way, by the mutual, reversible deformation of the asperities inside the micro-cracks; (ii) the virtual work of the external actions consistent with the beam model, i.e., the distributed transversal forces and the moments per unit lengths; besides these two contributions, constituting the conservative part of the system, (iii) the dissipation due to friction specified through a smooth Rayleigh potential, entering a nonlinear dependence of viscous and Coulomb type on the sliding rate. Through a COMSOL Multiphysics"Equation missing" implementation, 1D finite element analyses are carried out to simulate structural elements subjected to three- and four-point bending tests with alternating loading cycles. The dissipation of energy is investigated at varying the model parameters, and the predictions turn out to be in agreement with preliminary data from an experimental campaign. The present approach is expected to provide a valuable tool for the quantitative and comparative assessment of the hysteresis cycles, favoring the robust design of cementitious materials. Dissipation ; Timoshenko beam theory ; Nonlinear system ; Classical mechanics ; Mechanics ; Physics ; Boundary value problem ; Beam (structure) ; Virtual work ; Mathematical analysis ; Mathematics ; Finite element method Nonlocal and gradient elasticity in micro/nano structures ; Force Microscopy Techniques and Applications ; Vibration and Dynamic Analysis
Authors: Kamel El Omari | Ismay Forsyth | Ramona Duman | Christian M. Orr | Vitaliy Mykhaylyk | Erika J. Mancini | Armin Wagner
Source: Acta Crystallographica Section D Structural Biology (article, 2024-09-18)
Field: Materials Science — Materials Chemistry

Utilizing anomalous signals for element identification in macromolecular crystallography AlphaFold2 has revolutionized structural biology by offering unparalleled accuracy in predicting protein structures. Traditional methods for determining protein structures, such as X-ray crystallography and cryo-electron microscopy, are often time-consuming and resource-intensive. AlphaFold2 provides models that are valuable for molecular replacement, aiding in model building and docking into electron density or potential maps. However, despite its capabilities, models from AlphaFold2 do not consistently match the accuracy of experimentally determined structures, need to be validated experimentally and currently miss some crucial information, such as post-translational modifications, ligands and bound ions. In this paper, the advantages are explored of collecting X-ray anomalous data to identify chemical elements, such as metal ions, which are key to understanding certain structures and functions of proteins. This is achieved through methods such as calculating anomalous difference Fourier maps or refining the imaginary component of the anomalous scattering factor f''. Anomalous data can serve as a valuable complement to the information provided by AlphaFold2 models and this is particularly significant in elucidating the roles of metal ions. Anomalous scattering ; Complement (music) ; Structural biology ; Protein Data Bank ; Identification (biology) ; Computer science ; Cryo-electron microscopy ; Biological system ; Chemistry ; Crystallography ; Computational biology ; Physics ; Protein structure ; Scattering ; Biology ; Biochemistry ; Optics Enzyme Structure and Function ; Mass Spectrometry Techniques and Applications ; X-ray Spectroscopy and Fluorescence Analysis
Authors: Benjamin M. Gyori | Olga Vitek
Source: Nature Methods (article, 2024-08-01)
Field: Chemistry — Spectroscopy

Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge Context (archaeology) ; Computational biology ; Interpretation (philosophy) ; Data science ; Computer science ; Proteomics ; Biology ; Genetics ; Gene ; Programming language Advanced Proteomics Techniques and Applications ; Genetics, Bioinformatics, and Biomedical Research ; Biomedical Text Mining and Ontologies
Authors: Jianghan Bao | Weihan Li | Siqi Huang | Wenming Yu | Che Liu | Tie Jun Cui
Source: iScience (article, 2024-07-26)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Physics-driven unsupervised deep learning network for programmable metasurface-based beamforming Programmable metasurfaces have garnered significant attention for their capacity to dynamically manipulate electromagnetic (EM) waves. In particular, the programmable metasurfaces offer to generate a wide range of EM beams when the appropriate digital coding patterns are designed. Traditionally, optimizing the coding patterns involves time-consuming nonlinear optimization algorithms due to the high computational complexity. In this study, we propose a physics-assisted deep learning (DL) model that can calculate the coding pattern in milliseconds, requiring only a simple depiction of the desired beam. An extended version of the macroscopic model for digital coding metasurface is introduced as the physics-driven component, which can compute the radiation pattern rapidly based on the provided coding pattern. The integration of the macroscopic model ensures to generate the physics-compliant coding designs. We validate the proposed method experimentally by measuring several coding patterns for both single-beam and dual-beam scenarios, which demonstrate good performance of beamforming. Beamforming ; Nanotechnology ; Computer science ; Materials science ; Telecommunications Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Millimeter-Wave Propagation and Modeling
Authors: Eunji Chae | Seong Ryong Yang | Sung‐Seen Choi
Source: Polymers (article, 2024-07-17)
Field: Materials Science — Polymers and Plastics

Abrasion Behaviors of Silica-Reinforced Solution Styrene–Butadiene Rubber Compounds Using Different Abrasion Testers Solution styrene-butadiene rubber (SSBR) is widely used to improve the properties of tire tread compounds. Tire wear particles (TWPs), which are generated on real roads as vehicles traverse, represent one of significant sources of microplastics. In this study, four SSBR compounds were prepared using two SSBRs with high styrene (STY samples) and 1,2-unit (VIN samples) contents, along with dicyclopentadiene resin. The abrasion behaviors were investigated using four different abrasion testers: cut and chip (CC), Lambourn, DIN, and laboratory abrasion tester (LAT100). The abrasion rates observed in the Lambourn and LAT100 abrasion tests were consistent with each other, but the results of CC and DIN abrasion tests differed from them. The addition of the resin improved the abrasion rate and resulted in the generation of large wear particles. The abrasion rates of STY samples in the Lambourn and LAT100 abrasion tests were lower than those of VIN samples, whereas the values in the CC and DIN abrasion tests were higher than those of VIN samples. The wear particles were predominantly larger than 1000 μm, except for the VIN sample in the DIN abrasion test. However, TWPs > 1000 μm are rarely produced on real roads. The size distributions of wear particles > 1000 μm were 74.0-99.5%, 65.9-93.4%, 7.2-95.1%, and 37.5-83.0% in the CC, Lambourn, DIN, and LAT100 abrasion tests, respectively. The size distributions of wear particles in the Lambourn and LAT100 abrasion tests were broader than those in the other tests, whereas the distributions in the CC abrasion test were narrower. The abrasion patterns and the morphologies and size distributions of wear particles generated by the four abrasion tests varied significantly, attributable to differences in the bound rubber contents, crosslink densities, and tensile properties. Abrasion (mechanical) ; Natural rubber ; Styrene-butadiene ; Materials science ; Composite material ; Precipitated silica ; Styrene ; Polymer ; Copolymer Polymer Nanocomposites and Properties ; Tribology and Wear Analysis ; Polymer crystallization and properties
Authors: Chandra Prakash Beura | Jorim Wolters | Stefan Tenbohlen
Source: Sensors (article, 2024-01-21)
Field: Materials Science — Materials Chemistry

Application of Pathfinding Algorithms in Partial Discharge Localization in Power Transformers The introduction of artificial intelligence (AI) to ultra-high-frequency (UHF) partial discharge (PD) monitoring systems in power transformers for the localization of PD sources can help create a robust and reliable system with high usability and precision. However, training the AI with experimental data or data from electromagnetic simulation is costly and time-consuming. Furthermore, electromagnetic simulations often calculate more data than needed, whereas, for localization, the signal time-of-flight information is the most important. A tailored pathfinding algorithm can bypass the time-consuming and computationally expensive process of simulating or collecting data from experiments and be used to create the necessary training data for an AI-based monitoring system of partial discharges in power transformers. In this contribution, Dijkstra's algorithm is used with additional line-of-sight propagation algorithms to determine the paths of the electromagnetic waves generated by PD sources in a three-dimensional (3D) computer-aided design (CAD) model of a 300 MVA power transformer. The time-of-flight information is compared with results from experiments and electromagnetic simulations, and it is found that the algorithm maintains accuracy similar to that of the electromagnetic simulation software, with some under/overestimations in specific scenarios, while being much faster at calculations. Algorithm ; Computer science ; Transformer ; Partial discharge ; Pathfinding ; Ultra high frequency ; Software ; Voltage ; Engineering ; Electrical engineering ; Shortest path problem ; Graph High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Lightning and Electromagnetic Phenomena
Authors: Giuseppina Crescente | Giovanni Cascone | Maria Grazia Volpe | Stefania Moccia
Source: Foods (article, 2024-06-12)
Field: Materials Science — Biomaterials

Application of PLA-Based Films to Preserve Strawberries’ Bioactive Compounds Poly-(Lactic Acid) (PLA) is regarded as one of the most promising bio-based polymers due to its biocompatibility, biodegradability, non-toxicity, and processability. The investigation of the potential of PLA films in preserving the quality of strawberries is fully in line with the current directives on the sustainability of food packaging. The study aims to investigate the effects of PLA films on strawberries' physical and chemical properties, thereby determining whether they can be used as a post-harvest solution to control antioxidant loss, reduce mold growth, and extend the shelf-life of strawberries. Well-designed PLA films with different-sized holes obtained by laser perforation (PLA<b><sub>0</sub></b>, PLA<b><sub>16</sub></b> and PLA<b><sub>23</sub></b>) were tested against a conventional packaging polypropylene (PP) tray for up to 20 days of storage. Weight loss and mold growth were significantly slower in strawberries packed in PLA films. At the same time, PLA-based films effectively preserved the deterioration of vitamin C content, polyphenols and antioxidant activity compared to the control. Furthermore, among all, the micro-perforated PLA film (PLA<b><sub>23</sub></b>) showed better preservation in the different parameters evaluated. These results could effectively inhibit the deterioration of fruit quality, showing promising expectations as an effective strategy to extend the shelf-life of strawberries. Shelf life ; Polypropylene ; Materials science ; Food science ; Polyphenol ; Food packaging ; Antioxidant ; Modified atmosphere ; Biodegradation ; Biocompatibility ; Lactic acid ; Chemistry ; Composite material ; Biology ; Organic chemistry Nanocomposite Films for Food Packaging ; Postharvest Quality and Shelf Life Management ; Phytochemicals and Antioxidant Activities
Authors: Victoria Effiong Effanga | Dana Akilbekova | Fariza Mukasheva | Xiao Ling Zhao | Dilhan M. Kalyon | Cevat Erişken
Source: Gels (article, 2024-11-15)
Field: Materials Science — Biomaterials

In Vitro Investigation of 3D Printed Hydrogel Scaffolds with Electrospun Tidemark Component for Modeling Osteochondral Interface Osteochondral (OC) tissue plays a crucial role due to its ability to connect bone and cartilage tissues. To address the complexity of structure and functionality at the bone-cartilage interface, relevant to the presence of the tidemark as a critical element at the bone-cartilage boundary, we fabricated graded scaffolds through sequential 3D printing. The scaffold's bottom layer was based on a gelatin/oxidized alginate mixture enriched with hydroxyapatite (HAp) to create a rougher surface and larger pores to promote osteogenesis. In contrast, the upper layer was engineered to have smaller pores and aimed to promote cartilage tissue formation and mimic the physical properties of the cartilage. An electrospun ε-polycaprolactone (PCL) membrane with micrometer-range pores was incorporated between the layers to replicate the function of tidemark-a barrier to prevent vascularization of cartilage from subchondral bone tissue. In vitro cell studies confirmed the viability of the cells on the layers of the scaffolds and the ability of PCL mesh to prevent cellular migration. The fabricated scaffolds were thoroughly characterized, and their mechanical properties were compared to native OC tissue, demonstrating suitability for OC tissue engineering and graft modeling. The distance of gradient of mineral concentration was found to be 151 µm for grafts and the native OC interface. Component (thermodynamics) ; Materials science ; 3d printed ; In vitro ; Interface (matter) ; Biomedical engineering ; Composite material ; Wetting ; Chemistry ; Engineering Electrospun Nanofibers in Biomedical Applications ; Periodontal Regeneration and Treatments ; Osteoarthritis Treatment and Mechanisms
Authors: Elizabeth F. Bayne | Kevin M. Buck | Anna G. Towler | Yanlong Zhu | Melissa R. Pergande | Tianhua Zhou | Scott Price | Kalina J. Rossler | Vanessa Morales-Tirado | Sarah E. Lloyd | Fei Wang | Yupeng He | Yu Tian | Ying Ge
Source: Journal of Proteome Research (article, 2024-02-05)
Field: Chemistry — Spectroscopy

High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins. Extracellular matrix ; Proteome ; Proteomics ; Extracellular ; Pulmonary surfactant ; Biology ; Computational biology ; Chemistry ; Cell biology ; Bioinformatics ; Biochemistry ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Medical Imaging and Pathology Studies
Authors: Faezeh Dangkoub | Mehri Bemani Naeini | Shima Akar | Ali Badiee | Mahmoud Reza Jaafari | Mojtaba Sankian | Mohsen Tafaghodi | Seyed Ali Mousavi Shaegh
Source: International Journal of Pharmaceutics X (article, 2024-11-29)
Field: Materials Science — Biomaterials

Preparation of atorvastatin calcium-loaded liposomes using thin-film hydration and coaxial micromixing methods: A comparative study Development of techniques to produce nanoformulations in a controlled and reproducible manner is of great importance for research, clinical trials, and industrial scale-up. This research aimed to introduce a cost-effective micromixing approach for the nanoassembly of liposomes and compared with thin-film hydration (TFH) method. Numerical simulations and design of experiments (DOE) by response surface methodology (RSM) were used to evaluate the effects of input parameters on liposome properties, aiming to identify optimal conditions. Anionic liposomes without or with atorvastatin calcium (ATC) produced using TFH and the micromixing methods showed similar characteristics in size (150-190 nm), PDI (<0.2), and zeta potential (-50 to -60 mV). Both methods achieved about 70 % encapsulation efficiency with similar drug release profile for ATC-containing liposomes. Analysis of stability and DSC thermograms revealed comparable outcomes for liposomes prepared using both techniques. Nanoliposomes produced via both approaches indicated similar in vitro biological performance regarding cellular uptake and cell viability. The micromixing approach presented an alternative method to produce nanoliposomes in a one-step manner with high controllability and reproducibility without requiring specialized equipment. Compatibility of the micromixer with various solvents, including those detrimental to conventional microfluidic materials like PDMS and thermoplastics, enables exploration of a wide range of formulations. Micromixing ; Coaxial ; Liposome ; Materials science ; Calcium ; Chromatography ; Chemistry ; Nanotechnology ; Analytical Chemistry (journal) ; Mechanical engineering ; Engineering ; Metallurgy Nanoparticle-Based Drug Delivery ; Nanofabrication and Lithography Techniques ; Protein purification and stability
Authors: Daria Jóźwiak–Niedźwiedzka | Marta Choińska | Aneta Brachaczek | Mariusz Dąbrowski | Jakub Ośko | Michał Kuć
Source: Nuclear Engineering and Design (article, 2024-10-09)
Field: Materials Science — Materials Chemistry

Gas permeability and gamma ray shielding properties of concrete for nuclear applications • The presence of serpentinite aggregates emerged as the most influential factor affecting gas permeability. • Porous zones around serpentinite affected strength, gas permeability, ITZ and radiation shielding properties of concrete. • Slag cement concrete exhibited reduced radiation shielding capabilities compared to OPC. • The relationship between gas permeability, the Half-Value Layer (HVL), and the density of concrete was demonstrated. • Research results enable to create effective concrete shields through limiting leaks and boosting nuclear safety. Concrete used in nuclear applications faces significant durability challenges due to degradation from radiation, thermal stresses, and chemical reactions. These issues highlight the critical need for impermeable concrete shields to prevent radioactive leaks and protect against harmful radiation. This study examines how concrete composition affects gas permeability and gamma radiation shielding properties. Three coarse aggregates—amphibolite (reference), magnetite, and serpentine—and two cement types (ordinary and slag) were tested, with concrete densities ranging from 2309 to 3538 kg/m 3 . Gas permeability was measured using a Cembureau-type constant head permeameter, and gamma shielding was assessed through the linear attenuation coefficient (µ) and half-value layer (HVL) at 137 Cs decay energies. The results revealed significant variations in gas permeability and gamma ray shielding based on aggregate and cement type, with observable relationships between gas permeability, HVL, and concrete density. The results obtained from the presented research will contribute to increasing the safety, durability and cost-effectiveness of concrete constructions and maintenance of nuclear facilities. Electromagnetic shielding ; Materials science ; Nuclear engineering ; Gamma ray ; Permeability (electromagnetism) ; Nuclear physics ; Engineering ; Composite material ; Physics ; Chemistry Radiation Shielding Materials Analysis ; Graphite, nuclear technology, radiation studies ; Nuclear materials and radiation effects