jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ponlapath Tipboonsri | Supaaek Pramoonmak | Putinun Uawongsuwan | Anin Memon
Source: Preprints.org (preprint, 2023-12-12)
Field: Materials Science — Polymers and Plastics

Optimization of Thermoplastic Pultrusion Parameters of Jute and Glass Fiber-Reinforced Polypropylene Composite Thermoplastic pultrusion is a suitable process for fabricating continuous unidirectional thermoplastics with a uniform cross-section, high mechanical properties due to continuous fiber reinforcement, low cost, and suitability for mass production. In this paper, jute and glass fibers were reinforced with a polypropylene matrix and fabricated using the thermoplastic pultrusion process. The volumetric fraction of the composite was designed by controlling the filling ratio of the reinforcing fiber and matrix. The effects of molding parameters were investigated, such as pulling speed and molding temperature, on the mechanical properties and microstructure of the final rectangular profile composite. The pulling speed and molding temperature were varied from 40 to 140 mm/min and 190 to 220°C, respectively. The results show that an increase in molding temperature initially led to an increase in mechanical properties, up to a certain point. Beyond that point, they started to decrease. The increase in molding temperature also led to an increase in void content. Meanwhile, un-impregnation decreased with the increase in molding temperature, and the jute fiber began to degrade at high temperatures. In the next step, with varying pulling speed, the mechanical properties decreased as the pulling speed increased, with a corresponding increase in void content and un-impregnation. The decrease in mechanical properties was influenced by the increase in void content and un-impregnation, as the jute fiber degraded at higher temperatures. Materials science ; Composite material ; Pultrusion ; Polypropylene ; Composite number ; Thermoplastic ; Void (composites) ; Molding (decorative) ; Glass fiber ; Fiber Natural Fiber Reinforced Composites ; Textile materials and evaluations ; Mechanical Behavior of Composites
Authors: А. Ф. Чешкова
Source: E3S Web of Conferences (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Application of machine learning methods for the differentiation of fungal diseases in strawberry based on hyperspectral image analysis Fungal diseases have a significant negative impact on strawberry yield. Their detection and differentiation using hyperspectral measurements is a possible alternative to traditional methods. In this study, strawberry leaves infected with Ramularia Tulasnei, Marssonina potentillae and Dendrophoma obscurans with visible symptoms of the disease were used for hyperspectral analysis. The reflection spectrum of leaves was recorded with a Photonfocus hyperspectral camera (wavelength range 475–900 nm, 149 channels) under laboratory conditions using the line scanning method. This research has aimed to compare four machine learning methods: spectral angle mapper (SAM), support vector machine (SVM), k-nearest neighbors (KNN) and linear discriminant analysis (LDA). Classification models were built based on the full spectrum, as well as on 12 vegetation indices (VI) as spectral features. The results demonstrated that the SVM model based on full spectra reached highest classification accuracy 94%. The KNN model performed slightly worse with 91% accuracy. The performance of models based on VIs was lower than that of models based on full spectra with an accuracy range of 78–85%. Hyperspectral imaging ; Support vector machine ; Linear discriminant analysis ; Artificial intelligence ; Pattern recognition (psychology) ; Computer science ; Mathematics ; Remote sensing ; Biological system ; Biology ; Geography Spectroscopy and Chemometric Analyses ; Plant Pathogens and Fungal Diseases ; Remote Sensing in Agriculture
Authors: Andrew Hong | M. A. Gallis
Source: Physics of Fluids (article, 2023-06-01)
Field: Materials Science — Materials Chemistry

Optimized collision-specific parameters for binary mixtures of nitrogen, oxygen, argon, and helium Recently proposed collision-specific parameters for direct simulation Monte Carlo simulations are tested for binary mixtures of nitrogen, oxygen, and argon. Near ambient conditions, the traditional collision-averaged parameters are highly accurate, whereas the collision-specific parameters are not. The simulated transport using the collision-averaged parameters for mixtures with helium, however, is found to be inaccurate. Hence, we propose a novel method to determine molecular parameters by combining the Chapman–Enskog theory with empirical mixing rules and experimental data. The optimized parameters are highly accurate for the binary mixtures of nitrogen, oxygen, and argon and greatly improve the simulated transport for the helium mixtures. Argon ; Helium ; Collision ; Binary number ; Physics ; Nitrogen ; Mixing (physics) ; Monte Carlo method ; Atomic physics ; Oxygen ; Statistical physics ; Thermodynamics ; Computer science ; Statistics Catalytic Processes in Materials Science ; Gas Dynamics and Kinetic Theory ; Plasma Diagnostics and Applications
Authors: Xuqing Fan | Sai Deng | Zhengxing Wu | Junfeng Fan | Chao Zhou
Source: Biomimetics (article, 2023-10-17)
Field: Chemistry — Analytical Chemistry

Spatial Domain Image Fusion with Particle Swarm Optimization and Lightweight AlexNet for Robotic Fish Sensor Fault Diagnosis Safety and reliability are vital for robotic fish, which can be improved through fault diagnosis. In this study, a method for diagnosing sensor faults is proposed, which involves using Gramian angular field fusion with particle swarm optimization and lightweight AlexNet. Initially, one-dimensional time series sensor signals are converted into two-dimensional images using the Gramian angular field method with sliding window augmentation. Next, weighted fusion methods are employed to combine Gramian angular summation field images and Gramian angular difference field images, allowing for the full utilization of image information. Subsequently, a lightweight AlexNet is developed to extract features and classify fused images for fault diagnosis with fewer parameters and a shorter running time. To improve diagnosis accuracy, the particle swarm optimization algorithm is used to optimize the weighted fusion coefficient. The results indicate that the proposed method achieves a fault diagnosis accuracy of 99.72% when the weighted fusion coefficient is 0.276. These findings demonstrate the effectiveness of the proposed method for diagnosing depth sensor faults in robotic fish. Particle swarm optimization ; Gramian matrix ; Computer science ; Fault (geology) ; Artificial intelligence ; Image fusion ; Fusion ; Zernike polynomials ; Computer vision ; Algorithm ; Control theory (sociology) ; Pattern recognition (psychology) ; Image (mathematics) ; Physics ; Optics Spectroscopy and Chemometric Analyses ; Fault Detection and Control Systems ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Stefan C. Mueller | Jan Kubíček | Felipe Merino | Philipp Hanisch | Barbara Maertens | Jan‐Wilm Lackmann
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-07-11)
Field: Chemistry — Spectroscopy

The bigger picture: global analysis of solubilization performance of classical detergents versus new synthetic polymers utilizing shotgun proteomics Abstract Integral membrane proteins are critical for many cellular functions. Roughly 25% of all human genes code for membrane proteins, and about 70% of all approved drugs target them. Despite their importance, laborious and harsh purification conditions often hinder their characterization. Traditionally, they are removed from the membrane using detergents, thereby taking the proteins out of their native environment, affecting their function. Recently, a variety of synthetic polymers have been introduced, which can extract membrane proteins together with their native lipids into a so-called native nanodisc. However, they usually show lesser solubilization capacity than detergents, and their general applicability for membrane protein biochemistry is poorly understood. Here, we used Hek293 cell membrane extracts and LC-MS-based proteomics to compare the ability of nanodisc-forming polymers against state-of-the- art detergents to solubilize the membrane proteome. Our data demonstrates the general ability of synthetic co-polymers to extract membrane proteins, rivaling the efficacy of commonly used detergents. Interestingly, each class of solubilization agent presents specific solubilization profiles. We found no correlation between efficiency and number of transmembrane domains, isoelectric point, or GRAVY score for any compound. Our data shows that these polymers are a versatile alternative to detergents for the biochemical and structural study of membrane proteins, functional proteomics, or as components of native lysis/solubilization buffers. Our work here represents the first attempt at a proteome-scale comparison of the efficacy of nanodisc-forming polymers. These data should serve as starting reference for researchers looking to purify membrane proteins in near native conditions. Nanodisc ; Membrane protein ; Proteome ; Proteomics ; Membrane ; Transmembrane protein ; Lysis ; Human proteome project ; Chemistry ; Integral membrane protein ; Solubilization ; Biochemistry ; Gene Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ahmed Warshanna | Benjamin C. Orsburn
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-29)
Field: Chemistry — Spectroscopy

SCP Viz – A universal graphical user interface for single protein analysis in single cell proteomics datasets Single cell proteomics (SCP) requires the analysis of dozens to thousands of single human cells to draw biological conclusions. However, assessing of the abundance of single proteins in output data presents a considerable challenge, and no simple universal solutions currently exist. To address this, we developed SCP Viz, a statistical package with a graphical user interface that can handle small and large scale SCP output from any instrument or data processing software. In this software, the abundance of individual proteins can be plotted in a variety of ways, using either unadjusted or normalized outputs. These outputs can also be transformed or imputed within the software. SCP Viz offers a variety of plotting options which can help identify significantly altered proteins between groups, both before and after quantitative transformations. Upon the discovery of subpopulations of single cells, users can easily regroup the cells of interest using straightforward text-based filters. When used in this way, SCP Viz allows users to visualize proteomic heterogeneity at the level of individual proteins, cells, or identified subcellular populations. SCP Viz is compatible with output files from MaxQuant, FragPipe, SpectroNaut, and Proteome Discoverer, and should work equally well with other formats. SCP Viz is publicly available at https://github.com/orsburn/SCPViz. For demonstrations, users can download our test data from GitHub and use an online version that accepts user input for analysis at https://orsburnlab.shinyapps.io/SCPViz/. Computer science ; Software ; Graphical user interface ; Proteome ; Download ; Interface (matter) ; Variety (cybernetics) ; Proteomics ; Data mining ; Bioinformatics ; Operating system ; Biology ; Artificial intelligence Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Biosensors and Analytical Detection
Authors: S. Mohamed Mansoor Roomi | B. Sathya Bama | Vijaya Lakshmi | M. Vaishnavi
Source: Data in Brief (article, 2023-06-16)
Field: Chemistry — Analytical Chemistry

Hyperspectral dataset of pure and pesticide-coated apples for measuring the level of fertilizers used This dataset provides three classes of hyperspectral images: pure, insecticide-immersed, and fungicide-immersed apples with different concentrations of fertilizers. The hyperspectral images were calibrated under white and dark correction and enhanced using contrast enhancement. In order to know the variations in the level of fertilizers used, we soaked the apples in 2 different concentrations of chemicals i.e., 1ml or 1g of fertilizer in 1 liter of water as low concentration, and 3ml or 3g of fertilizer in 1 liter of water as high concentration. The proposed dataset will help in finding the consumption level of fertilizers (pesticides) in apples. Hyperspectral imaging ; Fertilizer ; Pesticide ; Environmental science ; Remote sensing ; Agronomy ; Biology ; Geology Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Water Quality Monitoring and Analysis
Authors: Ipek Caliskanelli
Source: Robotics & Automation Engineering Journal (article, 2023-11-14)
Field: Materials Science — Materials Chemistry

Digital Mock-Ups for Nuclear Decommissioning: A Survey on Existing Simulation Tools for Industry Applications The maturation of Virtual Reality software introduces new avenues of nuclear decommissioning research. Digital Mockups are an emerging technology which provide a virtual representation of the environment, objects or processes, supporting the whole lifecycle of product development and operations. This paper provides a survey on currently available simulation tools to design digital mock-ups required for safe remote decommissioning activities in the nuclear industry. The survey looks at eleven simulation tools; CoppeliaSim, Gazebo Classic, Gazebo (Ignition), Nvidia Omniverse Isaac Sim, WeBots, Choreonoid, AGX Dynamics, MORSE, VR4Robots, RoboDK, and Toia. Using the available documentation, the different capabilities of these software packages were assessed for their suitability to nuclear decommissioning, such as environment simulation, haptic interfaces, and general usability. Nuclear decommissioning ; Nuclear industry ; Engineering ; Construction engineering ; Systems engineering ; Computer science ; Nuclear engineering ; Manufacturing engineering ; Waste management Graphite, nuclear technology, radiation studies ; Nuclear and radioactivity studies
Authors: Vineel Kondiboyina | Timothy J. Duerr | James R. Monaghan | Sandra J. Shefelbine
Source: Journal of the mechanical behavior of biomedical materials/Journal of mechanical behavior of biomedical materials (article, 2023-12-24)
Field: Materials Science — Biomaterials

Material properties in regenerating axolotl limbs using inverse finite element analysis Axolotl ; Finite element method ; Inverse ; Regeneration (biology) ; Mathematics ; Computer science ; Geology ; Anatomy ; Structural engineering ; Engineering ; Geometry ; Biology ; Cell biology Electrospun Nanofibers in Biomedical Applications ; Tendon Structure and Treatment ; Silk-based biomaterials and applications
Authors: Filip Mundt | Annelaura Bach Nielsen | Juanjuan Wang | Josephine Kerzel Duel | Christina W. Yde | Martina Eriksen | Ulrik Lassen | Finn Cilius Nielsen | Kristoffer Staal Rohrberg | Matthias Mann
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-05-14)
Field: Chemistry — Spectroscopy

In depth profiling of the cancer proteome from the flowthrough of standard RNA- preparation kits for precision oncology Abstract Cancer is a highly heterogeneous disease, even within the same patient. Biopsies taken from different regions of a tumor may stand in stark molecular contrast to each other. Therefore, the ability to generate meaningful data from multiple platforms using the same biopsy is crucial for translating multi-omics characterizations into the clinic. However, it is generally a cumbersome and lengthy procedure to generate DNA, RNA and protein material from the same biopsy. The Qiagen AllPrep kit is an accessible, straightforward, and widely used kit in clinics worldwide to process biopsies and generate genomic and transcriptomic data from tumors. We aimed to determine if high-quality proteomics data could also be obtained from the remaining material. Here, we investigated procedures for generating deep and quantitatively accurate proteomic information in high throughput from Qiagen AllPrep flowthroughs. With a number of refinements, we obtain in excess of 10,000 quantified proteins, from 60 samples per day, achieving a substantial coverage of the total proteome. Additionally, we successfully characterize the tumors using phosphoproteomics. Combining a standard kit with in-depth proteomics will be an attractive approach for clinics seeking to implement multi-omics-based precision oncology. Precision oncology ; Proteome ; Computational biology ; Proteomics ; Transcriptome ; Omics ; RNA ; Liquid biopsy ; Biopsy ; Precision medicine ; Profiling (computer programming) ; Bioinformatics ; Computer science ; Cancer ; Biology ; Medicine ; Pathology ; Gene ; Internal medicine ; Genetics ; Gene expression Advanced Proteomics Techniques and Applications ; RNA modifications and cancer ; Genomics and Phylogenetic Studies
Authors: Quentin Drouhet | Fabienne Touchard | Laurence Chocinski‐Arnault
Source: Micro (article, 2023-05-02)
Field: Materials Science — Polymers and Plastics

Tensile Behavior of [0/90]7 Hemp/Elium Biocomposites after Water Aging: In-Situ Micro-CT Testing and Numerical Analysis This paper aims to study the tensile behavior of a woven [0/90]7 hemp/Elium composite after three different conditionings: “Ambient storage”, “Saturated at 60 °C” and “15 wet/dry cycles”. Instrumented repeated progressive tensile loading tests were carried out and showed an unexpected increase in the secant modulus for the aged samples at the end of the test. An in-situ micro-CT tensile test was then performed on a “15 wet/dry cycles” aged sample. The analysis of the tomographic images showed the damage development with interfacial debonding and matrix cracks in the specimen volume, and also the decrease in the curvature radius of the warp yarns during tensile loading facilitated by the plasticization of the resin. Finite element calculations were thus performed and demonstrated that the increase in the modulus is directly linked to the straightening of warp yarns, showing that the evolution of the modulus on a macroscopic scale can be explained by the deformations of the yarns on a microscopic level. These results allow us to better understand the mechanical behavior and the damage mechanisms that occur in biocomposites during tensile testing after water aging. Ultimate tensile strength ; Materials science ; Composite material ; Modulus ; Tensile testing ; Composite number ; Young's modulus ; In situ Natural Fiber Reinforced Composites ; Textile materials and evaluations ; Additive Manufacturing and 3D Printing Technologies
Authors: Andrew Leduc | Hannah Harens | Nikolai Slavov
Source: arXiv (Cornell University) (preprint, 2023-08-14)
Field: Chemistry — Spectroscopy

Modeling and interpretation of single-cell proteogenomic data Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable data-driven modeling of the molecular mechanisms coordinating proteins and nucleic acids at single-cell resolution. This promising potential requires estimating the reliability of measurements and computational analysis so that models can distinguish biological regulation from technical artifacts. We highlight different measurement modes that can support single-cell proteogenomic analysis and how to estimate their reliability. We then discuss approaches for developing both abstract and mechanistic models that aim to biologically interpret the measured differences across modalities, including specific applications to directed stem cell differentiation and to inferring protein interactions in cancer cells from the buffing of DNA copy-number variations. Single-cell proteogenomic data will support mechanistic models of direct molecular interactions that will provide generalizable and predictive representations of biological systems. Proteogenomics ; Computational biology ; Computer science ; Proteomics ; Biological data ; Reliability (semiconductor) ; Genomics ; Biology ; Bioinformatics ; Genome ; Biochemistry Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Bioinformatics and Genomic Networks
Authors: Maylin Acosta | Fernando Visconti | Ana Quiñones | J. Blasco | José Miguel de Paz
Source: Agronomy (article, 2023-04-12)
Field: Chemistry — Analytical Chemistry

Estimation of Macro and Micronutrients in Persimmon (Diospyros kaki L.) cv. ‘Rojo Brillante’ Leaves through Vis-NIR Reflectance Spectroscopy The nutritional diagnosis of crops is carried out through costly elemental analyses of different plant organs, particularly leaves, in the laboratory. However, visible and near-infrared (Vis-NIR) spectroscopy of unprocessed plant samples has a high potential as a faster, non-destructive, environmental-friendly alternative to elemental analyses. In this work, the potential of this technique to estimate the concentrations of macronutrients such as nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg), and micronutrients such as iron (Fe), manganese (Mn) and boron (B), in persimmon (Diospyros kaki L.) ‘Rojo Brillante’ leaves, has been investigated. Throughout the crop cycle variable rates of N and K were applied to obtain six nutritional status levels in persimmon trees in an experimental orchard. Then, leaves were systematically sampled throughout the cropping season from the different nutritional levels and spectral reflectance measurements were acquired in the 430–1040 nm wavelength range. The concentrations of nutrients were determined by inductively coupled plasma optical emission spectrometry (ICP-OES) for P, K, Ca, Mg, Fe, Mn and B after microwave digestion, while the Kjeldahl method was used for N. Then, partial least squares regression (PLS-R) was used to model the concentrations of these nutrients from the reflectance measurements of the leaves. The model was calibrated using 75% of the samples while the remaining 25% were left as the independent test set for external validation. The results of the test set indicated an acceptable validation for most of the nutrients, with determination coefficients (R2) of 0.74 for N and P, 0.54 for K, 0.77 for Ca, 0.60 for Mg, 0.39 for Fe, 0.69 for Mn and 0.83 for B. These findings support the potential use of Vis-NIR spectrometric techniques as an alternative to conventional laboratory methods for the persimmon nutritional status diagnosis although more research is needed to know how the models developed one year perform in ensuing years. Diospyros kaki ; Nutrient ; Chemistry ; Horticulture ; Micronutrient ; Phosphorus ; Potassium ; Botany ; Nitrogen ; Kjeldahl method ; Biology Spectroscopy and Chemometric Analyses ; Heavy Metals in Plants ; Leaf Properties and Growth Measurement