jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ali Khadivi | Farhad Mirheidari | Younes Moradi | Simin Paryan
Source: Food Science & Nutrition (article, 2022-02-07)
Field: Chemistry — Organic Chemistry

Identification of the promising olive (<i>Olea europaea</i> L.) cultivars based on morphological and pomological characters Olive (<i>Olea europaea</i> L.) is an ancient tree and can tolerate drought very well. In the present study, morphological and pomological diversity of 24 olive cultivars (5-15 replications for each cultivar, 243 trees in total) was evaluated. There were significant differences among the cultivars studied based on the characters recorded. The CV was more than 20.00% in 46 of 50 characters measured. Leaf length ranged from 27.07 to 78.54 mm, and leaf width varied from 5.42 to 23.06 mm. Ripening date ranged from late-August to early-October. Fruit length ranged from 13.04 to 33.72 mm, fruit diameter varied from 10.24 to 23.71 mm, fruit weighted from 0.97 to 9.61 g, and the range of fruit flesh thickness was 1.63-7.65 mm. There was high variability in terms of fruit color, ranging from light green to black. Hierarchical cluster analysis (HCA) performed based on the mean of replications with Euclidean distance and Ward method grouped the cultivars into two major clusters. Differences in many of the morphological traits were observed across the cultivars. These sets of data were used to identify unique and desirable cultivars morphologically. The present research demonstrates that local olive cultivars have unique characteristics that differentiate them from imported cultivars. Thus, local cultivars provide novel genetic resources that should be conserved. Olea ; Identification (biology) ; Cultivar ; Biology ; Oleaceae ; Botany ; Horticulture Edible Oils Quality and Analysis ; Essential Oils and Antimicrobial Activity ; Plant Physiology and Cultivation Studies
Authors: Genki Terashi | Xiao Wang | Daisuke Kihara
Source: Acta Crystallographica Section D Structural Biology (article, 2022-12-13)
Field: Materials Science — Materials Chemistry

Protein model refinement for cryo-EM maps using <i>AlphaFold</i>2 and the DAQ score As more protein structure models have been determined from cryogenic electron microscopy (cryo-EM) density maps, establishing how to evaluate the model accuracy and how to correct models in cases where they contain errors is becoming crucial to ensure the quality of the structural models deposited in the public database, the PDB. Here, a new protocol is presented for evaluating a protein model built from a cryo-EM map and applying local structure refinement in the case where the model has potential errors. Firstly, model evaluation is performed using a deep-learning-based model-local map assessment score, DAQ, that has recently been developed. The subsequent local refinement is performed by a modified AlphaFold2 procedure, in which a trimmed template model and a trimmed multiple sequence alignment are provided as input to control which structure regions to refine while leaving other more confident regions of the model intact. A benchmark study showed that this protocol, DAQ-refine, consistently improves low-quality regions of the initial models. Among 18 refined models generated for an initial structure, DAQ shows a high correlation with model quality and can identify the best accurate model for most of the tested cases. The improvements obtained by DAQ-refine were on average larger than other existing methods. Computer science ; Data acquisition ; Artificial intelligence ; Programming language Enzyme Structure and Function ; Advanced Electron Microscopy Techniques and Applications ; Protein Structure and Dynamics
Authors: Ayman Ibrahim | Hussein G. Daood | Márton Égei | Sándor Takács | Lájos Helyes
Source: Horticulturae (article, 2022-06-08)
Field: Chemistry — Analytical Chemistry

A Comparative Study between Vis/NIR Spectroradiometer and NIR Spectroscopy for the Non-Destructive Quality Assay of Different Watermelon Cultivars In light of the great technological progress in non-destructive quality detection methods, sweetness is no longer the essential parameter in evaluating watermelon quality. There is an aspiration to determine physicochemical quality characteristics to enable us to select the best cultivars, agricultural practices, and harvest dates. In the present work, three different watermelon cultivars (Lady, Galander, and Style) were harvested at three consecutive harvest times. Two pieces were taken from each watermelon sample, one from the middle (part A) and the other from the ends (part B), to track the intensity of quality parameters inside the watermelon. Parts A and B were subjected to Vis/NIR spectroradiometer (475:1075 nm), near-infrared spectroscopy (NIRS) (950:1650 nm), and high-performance liquid chromatography to assess the physicochemical quality. Calibration and prediction models were conducted using partial least squares regressions (PLS). The results indicated that the harvesting time significantly influenced the color and chemical parameters. Quality parameters concentrations markedly degraded towards late harvest. The highest concentrations of quality parameters were sighted for the middle zone (part A), especially in the Galander cultivar. Spectroradiometer achieved the best coefficient of prediction (R2P) ≃ 0.88 and 0.81 attached with the lowest value of the standard error of prediction (SEP) ≃ 0.03 and 1.06 for chroma (C*) and yellowness index (YI). However, the findings showed the superiority of the NIRS compared to the Vis-NIR method. The highest R2P was achieved by values 0.92, 0.91, 0.90, 0.89, 0.85, and 0.85 for lycopene, total carotenoids, vitamin C, β-carotene, γ-content, and TSS, respectively. It could be concluded that the NIRS has the ability to monitor the maturity development and determine the harvest dates practically and reliably. Cultivar ; Spectroradiometer ; Partial least squares regression ; Coefficient of determination ; Horticulture ; Sweetness ; Near-infrared spectroscopy ; Chemistry ; Mathematics ; Botany ; Food science ; Biology ; Statistics ; Reflectivity ; Flavor ; Physics Spectroscopy and Chemometric Analyses ; Phytochemicals and Antioxidant Activities ; Advances in Cucurbitaceae Research
Authors: Fuxiang Wang | Chunguang Wang | Shiyong Song
Source: Foods (article, 2022-06-22)
Field: Chemistry — Analytical Chemistry

Rapid and Low-Cost Detection of Millet Quality by Miniature Near-Infrared Spectroscopy and Iteratively Retaining Informative Variables Traditional chemical methods for testing the fat content of millet, a widely consumed grain, are time-consuming and costly. In this study, we developed a low-cost and rapid method for fat detection and quantification in millet. A miniature NIR spectrometer connected to a smartphone was used to collect spectral data from millet samples of different origins. The standard normal variate (SNV) and first derivative (1D) methods were used to preprocess spectral signals. Variable selection methods, including bootstrapping soft shrinkage (BOSS), the variable iterative space shrinkage approach (VISSA), iteratively retaining informative variables (IRIV), iteratively variable subset optimization (IVSO), and competitive adaptive reweighted sampling (CARS), were used to select characteristic wavelengths. The partial least squares regression (PLSR) algorithm was employed to develop the regression models aimed at predicting the fat content in millet. The results showed that the proposed 1D-IRIV-PLSR model achieved optimal accuracy for fat detection, with a correlation coefficient for prediction (Rp) of 0.953, a root mean square error for prediction (RMSEP) of 0.301 g/100 g, and a residual predictive deviation (RPD) of 3.225, by using only 18 characteristic wavelengths. This result highlights the feasibility of using this low-cost and high-portability assessment tool for millet quality testing, which provides an optional solution for in situ inspection of millet quality in different scenarios, such as production lines or sales stores. Partial least squares regression ; Mathematics ; Residual ; Feature selection ; Statistics ; Coefficient of determination ; Computer science ; Mean squared error ; Correlation coefficient ; Algorithm ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Water Quality Monitoring and Analysis
Authors: Nan Meng | Fangfang Fu | Jing Sun | Pengyang Feng | Yu Luo | Yaping Wu | Xiaochen Li | Jianmin Yuan | Yang Yang | Hui Liu | Zhe Wang | Meiyun Wang
Source: Quantitative Imaging in Medicine and Surgery (article, 2022-07-12)
Field: Materials Science — Materials Chemistry

Sensitivity and specificity of amide proton transfer-weighted imaging for assessing programmed death-ligand 1 status in non-small cell lung cancer: a comparative study with intravoxel incoherent motion and 18F-FDG PET Multi-parametric <sup>18</sup>F-FDG PET/MRI is beneficial for the non-invasive assessment of PD-L1 status in NSCLC patients, and the combination of SUV<sub>max</sub>, D, and MTRasym (3.5 ppm) may serve as a prognostic biomarker to guide immunotherapy. Sensitivity (control systems) ; Lung cancer ; Medicine ; Intravoxel incoherent motion ; Pathology ; Nuclear medicine ; Nuclear magnetic resonance ; Cancer research ; Chemistry ; Radiology ; Magnetic resonance imaging ; Physics ; Diffusion MRI Lanthanide and Transition Metal Complexes ; Medical Imaging Techniques and Applications ; Radiopharmaceutical Chemistry and Applications
Authors: I. O. Bondarenko | Tiziana Campisi | Giovanni Tesoriere | Larysa Neduzha
Source: Sustainability (article, 2022-12-20)
Field: Materials Science — Materials Chemistry

Using Detailing Concept to Assess Railway Functional Safety The ability to assess the risks of the functional safety of railway tracks allows harmonizing characteristics of track elements under certain operating conditions under certain maintenance for the efficient use of the track structure throughout its life cycle. The concept of detailing conditions of the interaction of the rolling stock and railway track was used for the productive solution of tasks of infrastructure functional safety assessment. The paper formed an approach to the analytical solution of determination problems of deformability parameters over time using the elastic waves theory. The formation method of interconnections between the technical and economic aspects of the operation of railway infrastructure was proposed. The criteria of deformability work and intensity of use were utilized for the effective use of the track structure through its life cycle. The results of calculations are presented to assess changes in the deformability behaviour of the track elements and structure when the force and speed parameters of the operating conditions change, as well as the algorithm of the method for estimating the operation deformability of the railway track. Thus, the proposed approach can be adapted to optimize objects by railway functional safety assessment at the stage of object operation simulation. Track (disk drive) ; Functional safety ; Work (physics) ; Computer science ; Research Object ; Engineering ; Reliability engineering ; Mechanical engineering Material Properties and Failure Mechanisms ; Railway Engineering and Dynamics ; Transportation Systems and Logistics
Authors: Firas Hamood | Florian Bayer | Mathias Wilhelm | Bernhard Küster | Matthew The
Source: Molecular & Cellular Proteomics (article, 2022-04-21)
Field: Chemistry — Spectroscopy

SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering Isobaric stable isotope labeling techniques such as tandem mass tags (TMTs) have become popular in proteomics because they enable the relative quantification of proteins with high precision from up to 18 samples in a single experiment. While missing values in peptide quantification are rare in a single TMT experiment, they rapidly increase when combining multiple TMT experiments. As the field moves toward analyzing ever higher numbers of samples, tools that reduce missing values also become more important for analyzing TMT datasets. To this end, we developed SIMSI-Transfer (Similarity-based Isobaric Mass Spectra 2 [MS2] Identification Transfer), a software tool that extends our previously developed software MaRaCluster (© Matthew The) by clustering similar tandem MS2 from multiple TMT experiments. SIMSI-Transfer is based on the assumption that similarity-clustered MS2 spectra represent the same peptide. Therefore, peptide identifications made by database searching in one TMT batch can be transferred to another TMT batch in which the same peptide was fragmented but not identified. To assess the validity of this approach, we tested SIMSI-Transfer on masked search engine identification results and recovered >80% of the masked identifications while controlling errors in the transfer procedure to below 1% false discovery rate. Applying SIMSI-Transfer to six published full proteome and phosphoproteome datasets from the Clinical Proteomic Tumor Analysis Consortium led to an increase of 26 to 45% of identified MS2 spectra with TMT quantifications. This significantly decreased the number of missing values across batches and, in turn, increased the number of peptides and proteins identified in all TMT batches by 43 to 56% and 13 to 16%, respectively. Isobaric labeling ; Tandem mass tag ; Proteome ; Tandem mass spectrometry ; Chemistry ; Isobaric process ; Cluster analysis ; Peptide ; Tandem ; Computer science ; Similarity (geometry) ; Proteomics ; Data mining ; Computational biology ; Chromatography ; Quantitative proteomics ; Mass spectrometry ; Artificial intelligence ; Biology ; Protein mass spectrometry ; Biochemistry Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: Thi Ngoc Mai Pham | Thi Hieu Hoang | Nguyễn Thu Phương | Quang Khánh Nguyễn | Bach Pham | Quoc Anh Hoang | Tien Duc Pham | Thi Anh Huong Nguyen | Anh‐Tuan Le | Duc Thang Pham
Source: Adsorption Science & Technology (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

Adsorption Characteristics of Antibiotic Meropenem on Magnetic CoFe<sub>2</sub>O<sub>4</sub>@Au Nanoparticles Adsorption characteristics of the antibiotic meropenem on a novel magnetic material synthesized by surface coating cobalt iron oxide (CFO) with gold nanoparticles (AuNPs) were systematically investigated. The AuNPs can enhance material adsorption capacity by having high affinity towards the thioether and amine groups in the meropenem structure. Au coverage on the CFO surface decreased the saturation magnetization from 55.8 emu/g to 48.8 emu/g, still allowing synthesized CFO@Au nanomaterials to be magnetically recoverable. The CFO@Au nanomaterials showed enhanced adsorption capacity of 25.5 mg/g at optimum conditions of pH 4.0 adsorption time 120 min, and adsorbent mass 0.05 g. Adsorption equilibrium was in accordance with a monolayer Langmuir isotherm, while the adsorption kinetics followed pseudo-first-order kinetics and intraparticle diffusion models. This work provides a simple method to prepare a magnetic composite material with high adsorption efficiency for meropenem and probably other thioether-containing substances. Adsorption ; Chemistry ; Langmuir adsorption model ; Nanomaterials ; Magnetic nanoparticles ; Chemical engineering ; Nanoparticle ; Monolayer ; Nuclear chemistry ; Kinetics ; Langmuir ; Organic chemistry Nanomaterials for catalytic reactions ; Nanoparticle-Based Drug Delivery ; Iron oxide chemistry and applications
Authors: Mohammad Khazaei | Dariush Bastani | Aliasghar Mohammadi | Azadeh Kordzadeh
Source: Langmuir (article, 2022-09-30)
Field: Chemistry — Organic Chemistry

Adsorption Dynamics of Surface-Modified Silica Nanoparticles at Solid–Liquid Interfaces Understanding the adsorption dynamics of nanoparticles at solid-liquid interfaces is of paramount importance to engineer nanoparticles for a variety of applications. The nanoparticle surface chemistry is significant for controlling the adsorption dynamics. This study aimed to experimentally examine the adsorption of surface-modified round-shaped silica nanoparticles (with an average diameter of 12 nm), grafted with hydrophobic (propyl chains) and/or hydrophilic (polyethylene glycol chains) agents, at an aqueous solution-silica interface with spherical soda-lime glass beads (diameter of 3 mm) being used as adsorbents. While no measurable adsorption was observed for solely hydrophobic or hydrophilic nanoparticles, a considerable level of adsorption was detected for nanoparticles comprising both hydrophobic and hydrophilic agents. Various kinetic models were employed to model the adsorption dynamics of the responsive nanoparticles. The results demonstrated that the mixed diffusion-kinetics models could predict the dynamics better than the adsorption diffusion models, indicating that the dynamics is controlled by a combination of liquid film diffusion, intra-particle diffusion, and mass action. Additionally, the adsorption of the surface-modified silica nanoparticles onto a mineral silica surface was examined using molecular dynamics simulations. The interaction energy for nanoparticles comprising both hydrophobic and hydrophilic agents was evaluated to be more favorable than that of solely hydrophobic or hydrophilic nanoparticles. Adsorption ; Nanoparticle ; Chemical engineering ; Hydrophobic silica ; Diffusion ; Aqueous solution ; Materials science ; Particle (ecology) ; Molecular dynamics ; Chemistry ; Nanotechnology ; Organic chemistry ; Computational chemistry ; Thermodynamics Surfactants and Colloidal Systems ; Iron oxide chemistry and applications ; Pickering emulsions and particle stabilization
Authors: Valentina Guccini | Shun Yu | Zhoujun Meng | Eero Kontturi | F. Demmel | Germán Salazar‐Alvarez
Source: Biomacromolecules (article, 2022-07-05)
Field: Materials Science — Biomaterials

The Impact of Surface Charges of Carboxylated Cellulose Nanofibrils on the Water Motions in Hydrated Films Cellulose nanofibrils (CNFs) with carboxylated surface ligands are a class of materials with tunable surface functionality, good mechanical properties, and bio-/environmental friendliness. They have been used in many applications as scaffold, reinforcing, or functional materials, where the interaction between adsorbed moisture and the CNF could lead to different properties and structures and become critical to the performance of the materials. In this work, we exploited multiple experimental methods to study the water movement in hydrated films made of carboxylated CNFs prepared by TEMPO oxidation with two different surface charges of 600 and 1550 μmol·g<sup>-1</sup>. A combination of quartz crystal microbalance with dissipation (QCM-D) and small-angle X-ray scattering (SAXS) shows that both the surface charge of a single fibril and the films' network structure contribute to the moisture uptake. The films with 1550 μmol·g<sup>-1</sup> surface charges take up twice the amount of moisture per unit mass, leading to the formation of nanostructures with an average radius of gyration of 2.1 nm. Via the nondestructive quasi-elastic neutron scattering (QENS), a faster motion is explained as a localized movement of water molecules inside confined spheres, and a slow diffusive motion is found with the diffusion coefficient close to bulk water at room temperature via a random jump diffusion model and regardless of the surface charge in films made from CNFs. Quartz crystal microbalance ; Materials science ; Small-angle X-ray scattering ; Radius of gyration ; Surface charge ; Chemical physics ; Chemical engineering ; Cellulose ; Composite material ; Moisture ; Adsorption ; Diffusion ; Neutron scattering ; Scattering ; Polymer chemistry ; Polymer ; Chemistry ; Physical chemistry ; Thermodynamics ; Optics Advanced Cellulose Research Studies ; Polysaccharides and Plant Cell Walls ; Lignin and Wood Chemistry
Authors: Jianwei Zhang | Hongguang Wang | Yongdong Li | Chunliang Liu | Wei Luo | Jia‐Wei Zhang
Source: Physics of Plasmas (article, 2022-04-01)
Field: Materials Science — Materials Chemistry

Evolution of vacuum surface flashover for angled dielectric insulators with particle-in-cell simulation With the introduction of the gas diffusion model, the surface flashover at the insulator–vacuum interface perpendicular to electrodes is simulated with the particle-in-cell method. The distributions of density of electrons, ions, and neutral gas molecules are obtained, which is consistent with images diagnosed in the experiment. The gas pressure at the dielectric surface near electrodes is much higher than it is at other locations. Furthermore, the processes of vacuum surface flashover for angled dielectric insulators are analyzed. The results show that negative charges will accumulate on the dielectric surface when the negative angle is large. The electric field produced by negative charges weakens the normal electric field and emission current on the cathode triple junction. Moreover, the process of secondary electron emission is completely suppressed when the negative angle is large. With the development of gas desorption, the breakdown will evolve from field emission into gas ionization. Therefore, when the angle is negative, the threshold of surface flashover first decreases then increases with the angle, which is in good agreement with laws obtained in experiments. This study can provide a deep understanding to the vacuum surface flashover. Electric field ; Dielectric ; Insulator (electricity) ; Arc flash ; Atomic physics ; Electron ; Particle-in-cell ; Electrode ; Cathode ; Secondary emission ; Ionization ; Perpendicular ; Triple junction ; Ion ; Physics ; Materials science ; Chemistry ; Optoelectronics High voltage insulation and dielectric phenomena ; Plasma Diagnostics and Applications ; Semiconductor materials and devices
Authors: Martinus Heru Palmiyanto | Eko Surojo | Dody Ariawan | Fitrian Imaduddin
Source: Scientific Reports (article, 2022-11-25)
Field: Materials Science — Polymers and Plastics

E-glass/kenaf fibre reinforced thermoset composites fiiled with MCC and immersion in a different fluid It is important to examine the long-term durability of glass-kenaf fibre reinforced phenolic resin composites when they are exposed to humid environments or submerged in water. Furthermore, the durability of such composites when immersed in different pH solutions have yet to be examined. As such, this present study examined the use of 4%, 8%, and 12% volume fractions (vfs) of microcrystalline cellulose (MCC) as a filler and reinforcement to improve the properties of glass fibre-kenaf reinforced phenolic resin composites. The flexural strength of these composites was examined both pre- and post-immersion in distilled water (pH 7), seawater (pH 8), and an acidic solution (pH 3) for 60 days. The diffusion mechanism, difussion coefficient, and water absorption concentration were also examined. The difussion coefficient and water absorption concentration occurred post-immersion in distilled water (pH7) and seawater (pH8) while the acidic solution (pH3) resulted in the highest loss of mass and size. Scanning electron microscopy (SEM) of the surfaces of the saturated composites indicated that fibre-matrix interfacial bonding was weak. However, composites that contained a higher vf of MCC exhibited stronger interfacial bonding between the matrix and constituents, thereby, reducing water absorption and diffusion. The flexural strength of the composite pre- and post-immersion was MCC12 > MCC8 > MCC4 > MCC0, in descending order of strength. Kenaf ; Distilled water ; Composite material ; Materials science ; Absorption of water ; Flexural strength ; Immersion (mathematics) ; Thermosetting polymer ; Composite number ; Durability ; Glass fiber ; Seawater ; Scanning electron microscope ; Epoxy ; Chemistry ; Fiber Natural Fiber Reinforced Composites ; Advanced Cellulose Research Studies ; Fiber-reinforced polymer composites