jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Vira Raichenko | Nikolai Rosenthal | Michaela Eder | Myfanwy E. Evans
Source: Journal of The Royal Society Interface (article, 2024-11-01)
Field: Materials Science — Biomaterials

Cocoon microstructures through the lens of topological persistence Biological materials display a wide array of functionality, often dictated by complicated microstructures. New geometric and topological strategies allow one to describe the microstructures in a precise and systematic way. This article describes the application of topological persistence and other geometric methods to the microstructural analysis of three-dimensional X-ray micro-computed tomography scans of the <i>Bombyx mori</i> silkworm cocoons. These methods allow conclusions to be drawn about pore space gradients, silk fibre thickness gradients and fibre alignment within the cocoon. The study demonstrates the applicability of these topological and geometric methods to quantify and characterize fibrous materials. Persistence (discontinuity) ; Topology (electrical circuits) ; Persistent homology ; Microstructure ; Topological data analysis ; Lens (geology) ; Biological system ; Materials science ; Computer science ; Mathematics ; Physics ; Optics ; Biology ; Algorithm ; Composite material ; Geology Silk-based biomaterials and applications ; Cellular Mechanics and Interactions ; Neurobiology and Insect Physiology Research
Authors: Ondřej Michal | Jaroslav Hornak | Václav Mentlík
Source: AIP conference proceedings (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Semi-automated Havriliak-Negami analysis for the investigation of nanocomposite properties The complex permittivity of materials is a critical parameter in material diagnosis, as it describes their reaction to AC voltage. Researchers often use techniques such as the Cole-Cole diagram or the Havriliak-Negami equation to determine the frequency-dependence of complex permittivity. However, the interpretation of the Cole-Cole diagram can be challenging due to the overlapping contributions of multiple relaxation processes. In contrast, the Havriliak-Negami equation provides a more accurate and detailed characterization of the dielectric properties of amorphic materials. This paper presents a simple semi-automated application of the Havriliak-Negami equation to evaluate the influence of nanoscale fillers on the properties of polyester-imide resins. Nanocomposites, which are composite materials in which one or more components have a nanoscale dimension, are promising candidates for a wide range of applications due to their ability to significantly enhance the electrical, mechanical, and thermal properties of polymers. In this study, the researchers examined the influence of nanoscale fillers on the electrical properties of polyester-imide resins, which are commonly used as insulating materials in electrical rotating machines. The analysis presented in this paper provides an alternative indicator of the practical applications of nanocomposite dielectric materials. By examining the material in an unconventional manner, researchers can obtain new insights into their electrical properties and their potential for use in electrical rotating machines. The development of new dielectric composite materials can contribute to the improvement of the performance and efficiency of electrical machines, which is essential for the transition to a low-carbon energy system. Materials science ; Nanocomposite ; Permittivity ; Dielectric ; Polymer nanocomposite ; Polyester ; Polymer ; Composite material ; Characterization (materials science) ; Nanotechnology ; Optoelectronics High voltage insulation and dielectric phenomena ; Dielectric materials and actuators ; Power Transformer Diagnostics and Insulation
Authors: Cedric Landerer | Maxim Scheremetjew | HongKee Moon | Lena Hersemann | Ágnes Tóth-Petróczy
Source: Bioinformatics (article, 2024-06-27)
Field: Chemistry — Spectroscopy

deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets deTELpy is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://git.mpi-cbg.de/tothpetroczylab/detelpy and https://pypi.org/project/deTELpy/ and can be easily installed via pip install deTELpy. Computational biology ; Python (programming language) ; DNA sequencing ; Proteome ; Mass spectrometry ; Biology ; DNA ; Amino acid ; Genetics ; RNA ; Computer science ; Gene ; Chemistry ; Chromatography ; Programming language Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: Yuriy Tsapko | Аleksii Tsapko | Ruslan Likhnyovskyi | Maryna Sukhanevych | Leonid Zapolskiy | Павло Іллюченко | Olga Bedratiuk
Source: Eastern-European Journal of Enterprise Technologies (article, 2024-02-28)
Field: Materials Science — General Materials Science

Establishing patterns in reducing fire-dangerous properties of sip panels fire-protected with reactive coating An issue related to using SIP panels for building structures is to ensure their stability and durability during operation in wide ranges. Therefore, the object of research was the change in the properties of wood-polymer material in case of fire and its protection when applied with a reactive coating capable of forming a pinocoke layer under the influence of high temperature on the coating. It has been proven that in the process of thermal action on the fire-resistant coating, the heat insulation process of SIP panels involves the formation of soot-like products on the surface of the material. Thus, under the action of the radiation panel on the surface of the OSB sample, after 120 s of thermal exposure, the process of intensive formation of a layer of foam coke, which thermally insulated the wood-polymer material, began; instead, after the radiation panel was exposed to the fire-resistant polystyrene foam sample, the process of destruction began at a temperature of about 100 °C polystyrene foam. When determining the flammability of a fire-resistant SIP panel, it was established that the temperature of the flue gases during the tests was no more than 110 °C, the length of the damaged sample did not exceed 460 mm. At the same time, the mass loss did not exceed 200 g, and independent combustion of the SIP panel sample did not occur despite the high temperature. According to these data, the SIP panel, fire-resistant with a reaction coating, belongs to group G1 (low flammability) and is a non-flammable material. The practical significance is that the results were taken into account during the design of buildings from SIP panels. So, there are reasons to assert the possibility of targeted regulation of the fire protection processes of SIP panels through the use of reactive coatings capable of forming a protective layer on the surface of the material that inhibits the rate of heat transfer Coating ; Environmental science ; Fire protection ; Forensic engineering ; Materials science ; Engineering ; Composite material ; Civil engineering Material Properties and Applications ; Fire dynamics and safety research ; Flame retardant materials and properties
Authors: Shunsuke KOBAYASHI | Ryuichi Tarumi
Source: Royal Society Open Science (article, 2024-12-01)
Field: Materials Science — Materials Chemistry

Geometrical frustration in nonlinear mechanics of screw dislocation The existence of stress singularities and reliance on linear approximations pose significant challenges in comprehending the stress field generation mechanism around dislocations. This study employs differential geometry and calculus of variations to mathematically model and numerically analyse screw dislocations. The kinematics of the dislocation are expressed by the diffeomorphism of the Riemann-Cartan manifold, which includes both the Riemannian metric and affine connection. The modelling begins with a continuous distribution of dislocation density, which is transformed into torsion <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>τ</mml:mi></mml:math> through the Hodge duality. The plasticity functional is constructed by applying the Helmholtz decomposition to bundle isomorphism, which is equivalent to the Cartan first structure equation for the intermediate configuration <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>B</mml:mi></mml:math> . The current configuration is derived by the elastic embedding of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>B</mml:mi></mml:math> into the standard Euclidean space <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi>ℝ</mml:mi> <mml:mn>3</mml:mn></mml:msup> </mml:math> . The numerical analysis reveals that the elastic stress fields effectively eliminate the singularity along the dislocation line and exhibit excellent conformity with Volterra's theory beyond the dislocation core. Geometrical frustration is the direct source of dislocation stress fields, as demonstrated through the multiplicative decomposition of deformation gradients. By leveraging the mathematical properties of the Riemann-Cartan manifold, we demonstrate that the Ricci curvature determines the symmetry of stress fields. These results substantiate a long-standing mathematical hypothesis: the duality between stress and curvature. Algorithm ; Mathematics ; Geometry Nonlocal and gradient elasticity in micro/nano structures ; Microstructure and mechanical properties ; Elasticity and Material Modeling
Authors: Eslam Elhanafy | Amin Akbari Ahangar | Rebecca Roth | Tamer M. Gamal El-Din | John R. Bankston | Jing Li
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-09-10)
Field: Chemistry — Electrochemistry

Elucidating the Differential Impacts of Equivalent Gating-Charge Mutations in Voltage-Gated Sodium Channels Voltage-gated sodium (Na<sub>v</sub>) channels are pivotal for cellular signaling and mutations in Na<sub>v</sub> channels can lead to excitability disorders in cardiac, muscular, and neural tissues. A major cluster of pathological mutations localizes in the voltage-sensing domains (VSDs), resulting in either gain-of-function (GoF), loss-of-function (LoF) effects, or both. However, the mechanism behind this functional divergence of mutations at equivalent positions remains elusive. Through hotspot analysis, we identified three gating charges (R1, R2, and R3) as major mutational hotspots in VSDs. The same amino-acid substitutions at equivalent gating-charge positions in VSD<sub>I</sub> and VSD<sub>II</sub> of the cardiac sodium channel Na<sub>v</sub>1.5 show differential gating-property impacts in electrophysiology measurements. We conducted 120 μs molecular dynamics (MD) simulations on wild-type and six mutants to elucidate the structural basis of their differential impacts. Our μs-scale MD simulations with applied external electric fields captured VSD state transitions and revealed the differential structural dynamics between equivalent R-to-Q mutants. Notably, we observed transient leaky conformations in some mutants during structural transitions, offering a detailed structural explanation for gating-pore currents. Our salt-bridge network analysis uncovered VSD-specific and state-dependent interactions among gating charges, countercharges, and lipids. This detailed analysis elucidated how mutations disrupt critical electrostatic interactions, thereby altering VSD permeability and modulating gating properties. By demonstrating the crucial importance of considering the specific structural context of each mutation, our study represents a significant leap forward in understanding structure-function relationships in Na<sub>v</sub> channels. Our work establishes a robust framework for future investigations into the molecular basis of ion channel-related disorders. Sodium channel ; Gating ; Voltage ; Differential (mechanical device) ; Voltage-gated ion channel ; Sodium ; Charge (physics) ; Biophysics ; Chemistry ; Ion channel ; Physics ; Biology ; Electrical engineering ; Biochemistry ; Engineering ; Thermodynamics Electrochemical Analysis and Applications ; Ion channel regulation and function ; RNA and protein synthesis mechanisms
Authors: Maria Olga Varrà | Lenka Husáková | G. Lanza | Martina Piroutková | Jan Patočka | Sergio Ghidini | Emanuela Zanardi
Source: Food and Chemical Toxicology (article, 2024-04-16)
Field: Chemistry — Analytical Chemistry

Multi-elemental composition of botanical preparations and probabilistic evaluation of toxic metals and metalloids intake upon dietary exposure The aim of this study was to evaluate the inorganic elemental composition (49 elements) of 29 botanical preparations obtained from fruits, leaves, peels, seeds, roots, fungi, and spirulina by using inductively coupled-mass spectrometry and a mercury analyzer. Simultaneously, the risk associated with the chronic dietary exposure to 12 toxic metals and metalloids among the European population was evaluated by using a probabilistic approach based on Monte Carlo simulations. The analysis revealed worrying intake levels of Al, As, and Ni, primarily stemming from the consumption of spirulina-, peel-, and leaf-based botanicals by younger age groups. The intake of As from all analyzed botanicals posed a significant risk for infants, yielding margins of exposure (MOEs) below 1, while those deriving from peel-based botanicals raised concerns across all age groups (MOEs = 0.04-2.3). The consumption of peel-based botanicals contributed substantially (13-130%) also to the tolerable daily intake of Ni for infants, toddlers, and children, while that of spirulina-based botanicals raised concerns related to Al intake also among adults, contributing to 11-176% of the tolerable weekly intake of this element. The findings achieved underscore the importance of implementing a monitoring framework to address chemical contamination of botanicals, thus ensuring their safety for regular consumers. Reference dose ; Metalloid ; Spirulina (dietary supplement) ; Population ; Food science ; Inductively coupled plasma mass spectrometry ; Chemistry ; Environmental chemistry ; Contamination ; Mercury (programming language) ; Toxicology ; Ecotoxicology ; Environmental health ; Risk assessment ; Biology ; Medicine ; Mass spectrometry Heavy Metals in Plants ; Heavy metals in environment ; Radioactivity and Radon Measurements
Authors: Stanislav Naryzhny
Source: Proteomes (article, 2024-05-10)
Field: Chemistry — Spectroscopy

Puzzle of Proteoform Variety—Where Is a Key? One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different. Computer science ; Key (lock) ; Variety (cybernetics) ; Organism ; Proteome ; Posttranslational modification ; Computational biology ; Theoretical computer science ; Biology ; Artificial intelligence ; Computer security ; Bioinformatics ; Genetics Advanced Proteomics Techniques and Applications ; Ubiquitin and proteasome pathways ; Machine Learning in Bioinformatics
Authors: Gummalla Vijayamma | S. Nirmala
Source: Acta Chromatographica (article, 2024-12-12)
Field: Chemistry — Spectroscopy

Development of eco-friendly UPLC methods for metformin and empagliflozin by combining green chemistry with analytical quality by design Abstract The need to develop environmentally friendly analytical approaches has driven the pharmaceutical industry to seek greener alternatives. Ultra-Performance Liquid Chromatography (UPLC) is known for its efficiency but traditionally relies on toxic solvents. Integrating Green Analytical Chemistry (GAC) principles aims to address environmental concerns while maintaining analytical performance. This work aims to advance and authenticate a green, efficient UPLC method for the concurrent quantification of Metformin (MET) and Empagliflozin (EPI) in tablet formulations, adhering to green chemistry principles and ensuring high analytical accuracy. The method was optimized using a UPLC-PDA system with a phenyl column and a mobile phase of ethanol and perchloric acid. Analytical Quality by Design (AQbD) was employed to optimize critical method parameters. Environmental impact was assessed using metrics such as GAPI, AMGS, and AGREE. Degradation studies under various stress conditions were performed to test method robustness. The method achieved high recovery rates for MET and EPI, with minimal interference from excipients. The environmental evaluation showed a high Analytical Eco-Score (AES) of 97, indicating low environmental impact. The AGREE score of 0.89 confirmed excellent alignment with green chemistry principles. Degradation studies confirmed the method's stability and reliability under stress conditions. The developed UPLC method demonstrates a significant advancement in analytical sustainability, offering an eco-friendly, efficient, and precise approach to drug analysis. The method's high alignment with green chemistry principles and its effectiveness in quantifying MET and EPI highlight its potential as a model for sustainable analytical practices in pharmaceutical analysis. Empagliflozin ; Chemistry ; Biochemical engineering ; Environmentally friendly ; Chromatography ; Process engineering ; Diabetes mellitus ; Engineering ; Type 2 diabetes Analytical Chemistry and Chromatography ; Electrochemical sensors and biosensors ; Chemistry and Chemical Engineering
Authors: Hyeon‐Jeong Lee | Yoondam Seo | Yoon Park | Eugene C. Yi | Dohyun Han | Hophil Min
Source: Scientific Data (article, 2024-08-10)
Field: Chemistry — Spectroscopy

Comprehensive immune cell spectral library for large-scale human primary T, B, and NK cell proteomics Although proteomics is extensively used in immune research, there is currently no publicly accessible spectral assay library for the comprehensive proteome of immune cells. This study generated spectral assay libraries for five human immune cell lines and four primary immune cells: CD4 T, CD8 T, natural killer (NK) cells, and B cells. This was achieved by utilizing data-dependent acquisition (DDA) and employing fractionated samples from over 100 µg of proteins, which was applied to acquire the highest-quality MS/MS spectral data. In addition, Data-indedendent acquisition (DIA) was used to obtain sufficient data points for analyzing proteins from 10,000 primary CD4 T, CD8 T, NK, and B cells. The immune cell spectral assay library generated included 10,544 protein groups and 127,106 peptides. The proteomic profiles of 10,000 primary human immune cells obtained from 15 healthy volunteers analyzed using DIA revealed the highest heterogeneity of B cells among other immune cell types and the similarity between CD4 T and CD8 T cells. All data and spectral library are deposited in ProteomeXchange (PXD047742). Immune system ; Proteome ; Proteomics ; CD8 ; Biology ; Antibody ; Chemistry ; Immunology ; Bioinformatics ; Biochemistry Advanced Proteomics Techniques and Applications ; vaccines and immunoinformatics approaches ; Biosensors and Analytical Detection
Authors: H. R. Moustafa | Alexander Kovacs | Johann Fischbacher | Markus Gusenbauer | Qais Ali | Leoni Breth | Yuan Hong | W. Rigaut | Thibaut Devillers | Nora M. Dempsey | T. Schrefl | Harald Oezelt
Source: AIP Advances (article, 2024-02-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Reduced order model for hard magnetic films In the pursuit of rare earth-lean permanent magnets for green technologies, microstructural optimisation offers a promising strategy to enhance coercivity while minimising critical element content. For this approach, the combination of experimental work on hard magnetic films and numerical investigations is necessary. However, computational limitations restrict micromagnetics to small systems, motivating the development of a reduced order model for investigating large multigrain systems. The model is based on the embedded Stoner-Wohlfarth method and is used to investigate the influence of a nonmagnetic grain boundary phase thickness and the aspect ratio of the magnetic grains on the overall coercivity. It is possible to simulate large NdFeB multigrain structures which can be compared to hard magnetic films. We derive design recommendations to increase coercivity by increasing the grain boundary phase thickness and the aspect ratio of the grains in hard magnetic materials. Coercivity ; Micromagnetics ; Neodymium magnet ; Materials science ; Magnet ; Aspect ratio (aeronautics) ; Grain size ; Work (physics) ; Grain boundary ; Condensed matter physics ; Magnetic field ; Mechanical engineering ; Composite material ; Microstructure ; Magnetization ; Physics Magnetic Properties and Applications ; Magnetic Properties of Alloys ; Magnetic properties of thin films
Authors: Derseh Yilie Limeneh | Million Ayele | Mesfin Shiferaw Wubie | Addisu Ferede Tessema | Noureddine Abidi | Zelalem Adane Alemar
Source: Journal of Natural Fibers (article, 2024-05-26)
Field: Materials Science — Polymers and Plastics

Enhancing Textile Cotton Yarn Sizing: Investigating Factors Impacting Breaking Strength, Pick-Up Percentage, and Elongation Loss The paper investigates the effect of machine setting on breaking strength, breaking elongation, and pick-up percentage of sized yarn properties. The factors considered are concentration of size solution, squeezing pressure and counts of yarn, the aim to develop a regression model that shows the effect of factors on size pick-up percentage, breaking strength regain, and loss in breaking elongation. The experiment is conducted by using 16 Ne and 21 Ne of cotton yarn, 3 Bar and 5 Bar of squeezing pressure, and 1.9% and 6% of size concentration with maize starch as sizing agent. A factorial design with two factors and 5 replicants has been used to design the experiment and analyze the results. The result showed that a slight change in squeezing pressure and concentration significantly affects the pick-up percentage, breaking strength regain and breaking elongation loss while a change of yarn count would not have a significant effect on the pick-up percentage of sized yarn. Furthermore, for achieving optimum properties of the sized yarn the pressure of squeezing, the count of the yarn and the concentration of the solution should be adjusted, and a regression model is developed to investigate the properties of the sized yarn by considering considered factors. Sizing ; Breaking strength ; Yarn ; Elongation ; Textile ; Composite material ; Materials science ; Ultimate tensile strength ; Forensic engineering ; Pulp and paper industry ; Engineering ; Art ; Visual arts Textile materials and evaluations ; Additive Manufacturing and 3D Printing Technologies ; Natural Fiber Reinforced Composites