jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jing Zhang | Xuelei Kang | Xinghua Shi | C. Guedes Soares | Ming Song
Source: Journal of Marine Science and Engineering (article, 2023-03-22)
Field: Materials Science — Materials Chemistry

Low Temperature Effect on the Mechanical Properties of EH36 with Strain Rates With the expansion of the Arctic route, the safety of ship crossing the area in light of the low temperature and ice has become of focus, especially with regards to the ship’s structure. The mechanical properties of the material making up the ship’s structure may not be suitable for the Arctic environment. A series of quasi-static and dynamic tests were performed to investigate the behaviour of EH36 steel, which is used to build Arctic ships, at temperatures ranging from 20 °C to −60 °C. The yield and ultimate tensile stress increased more than 10% as the temperature decreased from 20 °C to −60 °C, whereas the toughness decreased as the temperature decreased. A formula was derived to illustrate the relationship between the temperature reduction and the yield strength by fitting the experimental data. Four common constitutive rigid-perfectly plastic, elastic-perfectly plastic, bilinear elastic-plastic, and multi-linear elastic plastic models were fitted to simulate the hull structure under static loading and low temperature. Additionally, the strain rate effect of EH36 steel at low temperatures was illustrated by quasi-static and high-speed impact tests. A constitutive model including the low temperature and strain rate was introduced based on a modified Cowper-Symonds model, in which the coefficients of the constitutive model are fitted by the test results. It is improved by an iterative numerical method used to obtain more accurate coefficients using a series of numerical analyses. Detailed finite element simulations of the experiment conditions revealed that the constitutive model accurately predicts the dynamic response at low temperatures. Materials science ; Constitutive equation ; Bilinear interpolation ; Yield (engineering) ; Strain rate ; Ultimate tensile strength ; Plasticity ; Series (stratigraphy) ; Finite element method ; Structural engineering ; Hull ; Stress (linguistics) ; Mechanics ; Composite material ; Mathematics ; Geology ; Physics ; Engineering High-Velocity Impact and Material Behavior ; Fluid Dynamics Simulations and Interactions ; Fatigue and fracture mechanics
Authors: Salah Chaji | Aadil Bajoub | Christian Cravotto | Mônica Voss | Silvia Tabasso | Hafida Hanine | Giancarlo Cravotto
Source: LWT (article, 2023-12-28)
Field: Chemistry — Organic Chemistry

Metabolomics in action: Towards producing authentic virgin olive oil rich in bioactive compounds and with distinctive organoleptic features Virgin olive oil (VOO) production is in a constant state of evolution as it adapts to meet the demands of an increasingly competitive global market. However, despite the significant research effort undertaken across multiple scientific disciplines, this vegetable oil still presents challenges and vulnerabilities that require continued research. Within this context, metabolomics has emerged, over the last twenty years, as a promising tool that can resolve several critical issues regarding VOO quality and authenticity. Advanced metabolomics approaches offer unparalleled insights into the molecular mechanisms that influence the sensorial and nutritional features of this vegetable oil in rapid and accurate analyses. This review highlights recent metabolomics applications that unlock the nutritional and sensorial potential of VOO by investigating the effects of various factors on its chemical composition, including environmental conditions, agricultural practices, harvesting time, oil-processing parameters and storage conditions. The principal studies on ensuring product authenticity and traceability are also discussed. Traceability ; Context (archaeology) ; Metabolomics ; Olive oil ; Biotechnology ; Quality (philosophy) ; Agriculture ; Food science ; Biochemical engineering ; Computer science ; Biology ; Engineering ; Ecology ; Bioinformatics Edible Oils Quality and Analysis ; Metabolomics and Mass Spectrometry Studies ; Essential Oils and Antimicrobial Activity
Authors: Simone Mathias | Daniel Burns | Tabatha Hambidge | Bryan J. McCullough | Chris Hopley | David Douce | Ashley Sage | Patrick Sears
Source: Drug Testing and Analysis (article, 2023-08-24)
Field: Chemistry — Spectroscopy

Assessment of atmospheric solids analysis probe as a tool for the rapid determination of drug purity The ability to determine the purity (% controlled compound) of drug-of-abuse samples is necessary for public health and law enforcement. Here, we describe the assessment of atmospheric solids analysis probe (ASAP) for the rapid determination of drug purity for a set of formulated pharmaceuticals, chosen due to their availability, uncontrolled status and consistency. Paracetamol and loratadine were used as models of high and low purity compounds being ~90% and ~10% active ingredient, respectively. Individual tablets were ground up and diluted in an internal standard solution. The resulting samples were analysed by ASAP coupled to a Waters QDa mass spectrometer followed by confirmatory testing by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The inclusion of a non-matched internal standard (quinine) improved linearity and repeatability of drug analysis by ASAP-MS. Levels of drug purity using formulated pharmaceutical tablets were found to be highly comparable with results produced by the 'gold standard' LC-MS/MS technique. Rapid determination of drug purity is therefore possible with ASAP-MS for highly concentrated samples with minimal sample preparation. It may be possible to use this deployable system to determine drug purity outside of a laboratory setting. Chromatography ; Repeatability ; Active ingredient ; Mass spectrometry ; Chemistry ; Drug ; Sample preparation ; Pharmacology ; Medicine Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Analytical chemistry methods development
Authors: Jiahui Zhang | Li Liu | Yuanfeng Chen | Yuan Rao | Xiaodan Zhang | Xiu Jin
Source: Agronomy (article, 2023-05-20)
Field: Chemistry — Analytical Chemistry

The Nondestructive Model of Near-Infrared Spectroscopy with Different Pretreatment Transformation for Predicting “Dangshan” Pear Woolliness Disease The “Dangshan” pear woolliness response is a physiological disease that mostly occurs in the pear growth process. The appearance of the disease is not obvious, and it is difficult to detect with the naked eye. Therefore, finding a way to quickly and nondestructively identify “Dangshan” pear woolliness disease is of great significance. In this paper, the near-infrared spectral (NIR) data of “Dangshan” pear samples were collected at 900–1700 nm reflectance spectra using a handheld miniature NIR spectrometer, and the data were modelled and analysed using random forest (RF), support vector machine (SVM) and boosting algorithms under the processing of 24 pretreatment methods. Considering the variations between different pretreatment methods, this work determined the relative optimality index of different pretreatment methods by evaluating their effects on model accuracy and Kappa and selected the best-performing first derivative with standard normal variate and Savitzky–Golay and first derivative with multiplicative scatter correction and Savitzky–Golay as the best pretreatment methods. With the best pretreatment method, all five models in the three categories showed good accuracy and stability after parameter debugging, with accuracy and F1 greater than 0.8 and Kappa floating at approximately 0.7, reflecting the good classification ability of the models and proving that near-infrared spectroscopy (NIRS) in the rapid identification of “Dangshan” pear woolliness response disease was feasible. By comparing the performance differences of the models before and after the pretreatment methods, it was found that the ensemble-learning models such as RF and boosting were more stringent on pretreatment methods in identifying “Dangshan” pear woolliness response disease than support vector machines, and the performance of the ensemble learning models was significantly improved under appropriate pretreatment methods. This experiment provided a relatively stable detection method for “Dangshan” pear woolliness response disease under nonideal detection conditions by analysing the impact of pretreatment methods and models on the prediction result. PEAR ; Artificial intelligence ; Chemistry ; Computer science ; Mathematics ; Pattern recognition (psychology) Spectroscopy and Chemometric Analyses ; Horticultural and Viticultural Research ; Plant Pathogens and Fungal Diseases
Authors: Jian Zhang | Abdul Mounem Mouazen
Source: Chemometrics and Intelligent Laboratory Systems (article, 2023-07-17)
Field: Chemistry — Analytical Chemistry

A novel non-integer order Savitzky–Golay derivative function of visible and near-infrared spectra for improving prediction accuracy of phosphorus in pig manure Binary Golay code ; Partial least squares regression ; Algorithm ; Manure ; Mathematics ; Integer (computer science) ; Second derivative ; Analytical Chemistry (journal) ; Statistics ; Chemistry ; Computer science ; Agronomy ; Environmental chemistry Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Soil Geostatistics and Mapping
Authors: Adam J. Simpkin | Iracema Caballero | Stuart McNicholas | Kyle Stevenson | Elisabet Jiménez | Filomeno Sánchez Rodríguez | Maria Fando | Ville Uski | Charles Ballard | Grzegorz Chojnowski | Andrey A. Lebedev | Eugene Krissinel | Isabel Usón | Daniel J. Rigden | Ronan M. Keegan
Source: Acta Crystallographica Section D Structural Biology (article, 2023-08-09)
Field: Materials Science — Materials Chemistry

Predicted models and <i>CCP</i>4 In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement. Exploit ; Computer science ; Focus (optics) ; Field (mathematics) ; Suite ; Phase (matter) ; Data science ; Operations research ; Data mining ; Engineering ; Mathematics ; Computer security ; Physics ; Political science ; Law Enzyme Structure and Function ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: Shishun Wang | Zhengmin Wu | Chengmao Cao | Minhui An | Kun Luo | Liang Sun | Xiaoran Wang
Source: Sensors (article, 2023-01-06)
Field: Chemistry — Analytical Chemistry

Design and Experiment of Online Detection System for Water Content of Fresh Tea Leaves after Harvesting Based on Near Infra-Red Spectroscopy Fresh tea leaves continuously lose water after harvesting, and the level of water content directly affects the configuration of tea processing parameters. To address this problem, this study established an online detection system for the water content of fresh tea leaves after harvesting based on near-infrared spectroscopy. The online acquisition and analysis system of the temperature and humidity sensor signal data was developed based on LabVIEW and Python software platforms. Near-infrared spectral data, environmental temperature, and humidity were collected from fresh leaves after harvesting. Spectral data were combined with PLS (partial least squares) to develop a prediction model for the water content of fresh tea leaves. Simultaneously, data communication between LabVIEW and PLC was established, laying the foundation for establishing a feedback mechanism to send the prediction results to the main platform of the lower computer. This provides a more objective and accurate basis for the detection of fresh leaves before processing and regulation during processing, thereby effectively promoting the standardisation and intelligent development of tea-processing equipment. Water content ; Python (programming language) ; Near-infrared spectroscopy ; Data acquisition ; Computer science ; Environmental science ; Remote sensing ; Engineering ; Physics ; Geography ; Operating system Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Nathan V. Roblin | Megan K. DeBari | Sandra L. Shefter | Erica Iizuka | Rosalyn D. Abbott
Source: Journal of Functional Biomaterials (article, 2023-04-18)
Field: Materials Science — Biomaterials

Development of a More Environmentally Friendly Silk Fibroin Scaffold for Soft Tissue Applications A push for environmentally friendly approaches to biomaterials fabrication has emerged from growing conservational concerns in recent years. Different stages in silk fibroin scaffold production, including sodium carbonate (Na<sub>2</sub>CO<sub>3</sub>)-based degumming and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)-based fabrication, have drawn attention for their associated environmental concerns. Environmentally friendly alternatives have been proposed for each processing stage; however, an integrated green fibroin scaffold approach has not been characterized or used for soft tissue applications. Here, we show that the combination of sodium hydroxide (NaOH) as a substitute degumming agent with the popular "aqueous-based" alternative silk fibroin gelation method yields fibroin scaffolds with comparable properties to traditional Na<sub>2</sub>CO<sub>3</sub>-degummed aqueous-based scaffolds. The more environmentally friendly scaffolds were found to have comparable protein structure, morphology, compressive modulus, and degradation kinetics, with increased porosity and cell seeding density relative to traditional scaffolds. Human adipose-derived stem cells showed high viability after three days of culture while seeded in each scaffold type, with uniform cell attachment to pore walls. Adipocytes from human whole adipose tissue seeded into scaffolds were found to have similar levels of lipolytic and metabolic function between conditions, in addition to a healthy unilocular morphology. Results indicate that our more environmentally friendly methodology for silk scaffold production is a viable alternative and well suited to soft tissue applications. Fibroin ; Environmentally friendly ; Scaffold ; Materials science ; SILK ; Tissue engineering ; Chemical engineering ; Aqueous solution ; Biomedical engineering ; Composite material ; Chemistry ; Organic chemistry Silk-based biomaterials and applications ; Electrospun Nanofibers in Biomedical Applications ; Bone Tissue Engineering Materials
Authors: M. C. Rodriguez Gallo | Qiaomu Li | Mohana Talasila | R. Glen Uhrig
Source: Molecular & Cellular Proteomics (article, 2023-09-12)
Field: Chemistry — Spectroscopy

Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants. Proteome ; Arabidopsis ; Arabidopsis thaliana ; Seedling ; Shoot ; Osmotic shock ; Proteomics ; Quantitative proteomics ; Biology ; Chemistry ; Computational biology ; Botany ; Mutant ; Bioinformatics ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Plant Stress Responses and Tolerance
Authors: Tiantian Chen | Bin Gong | Chun’an Tang
Source: Materials (article, 2023-08-08)
Field: Materials Science — Ceramics and Composites

Origin and Evolution of Cracks in the Glaze Surface of a Ceramic during the Cooling Process Because of the significant difference between the thermal expansion coefficients of ceramic blank and glaze, the glaze typically undergoes more pronounced shrinkage than the blank during ceramic cooling, which results in high stress concentrations and cracking. In this study, the mechanical mechanism of glaze cracking is studied, based on the statistical strength theory, damage mechanics, and continuum mechanics. Furthermore, the influence of the glaze layer thickness, heat transfer coefficient, expansion coefficient, and temperature difference on the creation and propagation of inner microcracks is systematically investigated, and the final discrete fracture network of ceramics is discussed at the specific crack saturation state. The results show that (1) a higher heat transfer coefficient will lead to a more uniform distribution of the surface temperature and a faster cooling process of the ceramics, reducing the number of microcracks when the ambient temperature is reached; (2) the thinner glaze layer is less prone to cracking when its thickness is smaller than that of the blank. However, when the thickness of the glaze layer is similar to that of the blank, the increased thickness of the glaze layer will increase the number of cracks on its surface; and (3) when the expansion coefficient of the glaze layer is smaller than that of the blank, cracks will not occur inside the glaze layer. However, as the coefficient of the thermal expansion of the glaze layer continuously rises, the number of cracks on its surface will first increase and then decrease. Glaze ; Materials science ; Blank ; Composite material ; Thermal expansion ; Ceramic ; Cracking ; Layer (electronics) ; Metallurgy ; Mineralogy ; Chemistry Advanced ceramic materials synthesis ; Recycling and utilization of industrial and municipal waste in materials production ; Concrete and Cement Materials Research
Authors: Noah M. Lancaster | Pavel Sinitcyn | Patrick Forny | Trenton M. Peters-Clarke | Caroline Fecher | Andrew J. H. Smith | Evgenia Shishkova | Tabiwang N. Arrey | Anna Pashkova | Margaret Lea Robinson | Nicholas L. Arp | Jing Fan | J N Hansen | Andrea Galmozzi | Lia R. Serrano | Julie Rojas | Audrey P. Gasch | Michael S. Westphall | Hamish Stewart | Christian Hock | Eugen Damoc | David J. Pagliarini | Vlad Zabrouskov | Joshua J. Coon
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-11-21)
Field: Chemistry — Spectroscopy

Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer ABSTRACT Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology was benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We applied this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detected 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of novel phosphorylation events relevant to mitochondrial and brain biology. Orbitrap ; Mass spectrometry ; Computer science ; Chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Mengwen Mei | Zhonglei Cai | Xinran Zhang | Chanjun Sun | Junyi Zhang | Huijie Peng | Jiangbo Li | Ruiyao Shi | Wei Zhang
Source: Frontiers in Plant Science (article, 2023-11-16)
Field: Chemistry — Analytical Chemistry

Early bruising detection of ‘Korla’ pears by low-cost visible-LED structured-illumination reflectance imaging and feature-based classification models It was found that RT images consistently outperformed AC images regardless of type of model, and LS-SVM model exhibited the highest detection accuracy and stability. Across mild, moderate, severe and mixed bruises, the LS-SVM model with RT images achieved classification accuracies of 98.6%, 98.9%, 98.5%, and 98.8%, respectively. This study showed that visible-LED SIRI technique could effectively detect early bruising of 'Korla' pears, providing a valuable reference for using low-cost visible LED SIRI to detect fruit damage. Artificial intelligence ; Reflectivity ; Support vector machine ; Pattern recognition (psychology) ; Computer science ; Feature (linguistics) ; Mathematics ; Computer vision ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Plant Surface Properties and Treatments ; Industrial Vision Systems and Defect Detection