jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Andrew J. Carradus | Joe M. P. Bradley | Penny Gowland | Olivier Mougin
Source: NMR in Biomedicine (article, 2023-07-14)
Field: Materials Science — Materials Chemistry

Measuring chemical exchange saturation transfer exchange rates in the human brain using a particle swarm optimisation algorithm The z-spectrum contains many pools with different exchange rates and T<sub>2</sub> values, which can make it difficult to interpret in vivo data and complicates the design of experiments aimed at providing sensitivity to one pool. This work aims to characterise the main pools observable with MRI at 7T in the human brain. To achieve this, we acquired z-spectra at multiple saturation powers in the human brain at 7T. We used simulations to optimise the use of particle swarm optimisation (PSO) to fit these data, validating this approach using further simulations and creatine phantoms. We then used the PSO to fit data from grey and white matter for the pool size, exchange rate, and T<sub>2</sub> of five proton pools (magnetisation transfer, amides, amines, nuclear Overhauser enhancement NOE<sub>-3.5ppm</sub> and NOE<sub>-1.7ppm</sub> in addition to water). We then devised an approach for using PSO to fit z-spectra while limiting the computational burden, and we investigated the sensitivity of the fit to T<sub>2</sub> and k for three overlapping pools. We used this to measure the exchange rate of creatine and to show that it varied with temperature, as expected. In the brain we measured a significantly larger pool size in white matter than in grey matter for the magnetisation transfer pool and the NOE<sub>-3.5ppm</sub> pool. For all other parameters we found no significant difference between grey and white matter. We showed that PSO can be used to fit z-spectra acquired at a range of B<sub>1</sub> to provide information about peak position, amplitude, exchange rate, and T<sub>2</sub> in vivo in the human brain. These data could provide more sensitivity to change in some clinical conditions and will also provide key information for further experimental design. Magnetization transfer ; White matter ; Particle swarm optimization ; Nuclear magnetic resonance ; Biological system ; Chemistry ; Limiting ; Saturation (graph theory) ; Spectral line ; Algorithm ; Physics ; Computer science ; Magnetic resonance imaging ; Mathematics Lanthanide and Transition Metal Complexes ; Advanced MRI Techniques and Applications ; Electron Spin Resonance Studies
Authors: Fan ZHAO | Jiawei Zhang | Jihao ZHI | Zhaoru YAN
Source: Food Science and Technology (article, 2023-07-11)
Field: Chemistry — Analytical Chemistry

Effect of different spectral processing methods on the quantitative model of Astragalus polysaccharides detected by NIR spectroscopy Quality control of Chinese herbal medicines requires reliable and rapid detection techniques, Many scholars have used NIR spectroscopy for research in Chinese herbal medicine industry. The aim of this study was to evaluate the feasibility of combining NIR spectroscopy and machine learning to predict the adulteration content of Astragalus polysaccharides. The astragalus polysaccharide and rice flour were mixed to form astragalus polysaccharide adulterant with different concentration. the Quantitative prediction models are built using the support vector machine (SVM). Different pre-processing methods of SG, SNV, WT, SG+SNV, SG+WT were used to process the spectra, and then the continuous projection algorithm (SPA) and uninformative variable elimination (UVE) were used to select the characteristic wavelengths. The SVM prediction model based on SG+SNV+SPA is optimal with an RPD of 2.653, indicating that the model has good predictive ability. The results showed that NIR technique could be used for quantitative analysis of Astragalus polysaccharides. Polysaccharide ; Adulterant ; Astragalus ; Support vector machine ; Near-infrared spectroscopy ; Artificial intelligence ; Traditional medicine ; Pattern recognition (psychology) ; Chemistry ; Computer science ; Chromatography ; Biology ; Traditional Chinese medicine ; Medicine ; Biochemistry Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Traditional Chinese Medicine Analysis
Authors: Raquel Peron-Danaher | Lorenzo Cotrozzi | Ali Masjedi | Laramy Enders | Christian H. Krupke | Michael V. Mickelbart | John J. Couture
Source: Agronomy (article, 2023-10-05)
Field: Chemistry — Analytical Chemistry

Drought Stress Affects Spectral Separation of Maize Infested by Western Corn Rootworm Root-feeding herbivores present challenges for insect scouting due to the reliance on aboveground visual cues. These challenges intensify in multi-stress environments, where one stressor can mask another. Pre-visual identification of plant stress offers promise in addressing this issue. Hyperspectral data have emerged as a measurement able to identify plant stress before visible symptoms appear. The effectiveness of spectral data to identify belowground stressors using aboveground vegetative measurements, however, remains poorly understood, particularly in multi-stress environments. We investigated the potential of hyperspectral data to detect Western corn rootworm (WCR; Diabrotica virgifera virgirefa) infestations in resistant and susceptible maize genotypes in the presence and absence of drought. Under well-watered conditions, the spectral profiles separated between WCR treatments, but the presence of drought eliminated spectral separation. The foliar spectral profiles separated under drought conditions, irrespective of WCR presence. Spectral data did not classify WCR well; drought was well classified, and the presence of drought further reduced WCR classification accuracy. We found that multiple plant traits were not affected by WCR but were negatively affected by drought. Our study highlights the possibility of detecting WCR and drought stress in maize using hyperspectral data but highlights limitations of the approach for assessing plant health in multi-stress conditions. Western corn rootworm ; Hyperspectral imaging ; Agronomy ; Drought stress ; Biology ; Zea mays ; Environmental science ; Remote sensing ; Geography Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Date Palm Research Studies
Authors: Rekha Lakshmanan
Source: Journal of Informatics Electrical and Electronics Engineering (JIEEE) (article, 2023-01-01)
Field: Chemistry — Inorganic Chemistry

Inspection and Grading of Dried Coconut – an Automatic Method Using SVM Classification Coconut production and consumption rate of India being very high, contributes significantly towards the Indian economy; thus, ensuring the quality of allied products proves to be a necessity. Intelligent quality evaluation and grading system for copra images is proposed to classify copra, the dried coconut kernel into various categories using an image processing approach. The proposed method is useful in the current scenario, as quality deterioration during drying and storing of copra is a challenging task. Inferior quality of copra due to the presence of moisture, mold, fungi, bacteria and sulphur may adversely affect the shelf life thus deteriorating the quality of final products and human health. The grading system automatically segments the region of interest of copra images using SUSAN filter and classifies them into usable and unusable categories. The unusable categories of copra considered in the proposed method include copra with moisture, mold, wrinkles and sulphur. Various features of copra images were collected and analyzed. The selected features of copra images were used for training and classification using SVM classifier. The proposed method has been evaluated using a real database and the results are promising. Copra ; Grading (engineering) ; Support vector machine ; Computer science ; Coconut oil ; Agricultural engineering ; Artificial intelligence ; Pattern recognition (psychology) ; Engineering ; Food science ; Biology Coconut Research and Applications ; Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies
Authors: Ethan A. Chen | Lauren L. Porter
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-27)
Field: Materials Science — Materials Chemistry

SSDraw: software for generating comparative protein secondary structure diagrams The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded (https://github.com/ethanchen1301/SSDraw) and run locally for rapid structure generation, while a Google Colab notebook allows easy use. Protein superfamily ; Computer science ; Protein secondary structure ; Diagram ; Visualization ; Sequence (biology) ; Software ; Computational biology ; Protein structure ; Data mining ; Crystallography ; Biology ; Programming language ; Genetics ; Chemistry ; Database Enzyme Structure and Function ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: C. Bruno | Ernesto Tripodi | D. Werner | Kit Windows‐Yule | Fotis Spyropoulos
Source: Chemical Engineering Science (article, 2023-11-10)
Field: Materials Science — Materials Chemistry

The performance of rotating membrane emulsification in the presence of baffles: Insights from flux experiments, microstructural analysis, and positron emission particle tracking Rotating Membrane Emulsification (RME) is a bottom-up emulsification technique developed to circumvent the significant energy requirements of conventional methods; however, its implementation has been hindered by low emulsion throughputs. This work presents a novel baffled-RME setup and investigates the potential improvement to emulsion throughput and droplet microstructure, whilst employing both surface-active and Pickering particle emulsifiers to assess whether any advantages are emulsifier-specific. Overall, baffle addition improves emulsion throughputs, however the droplet microstructure was positively influenced only when using surfactant-based emulsifiers. Positron Emission Particle Tracking (PEPT) was utilised to demonstrate that these advantages result from improved hydrodynamic conditions instigated by the break-up of streamlines, inducing higher turbulence near the membrane surface, and by increasing the transmembrane pressure drop and drag force through flow restrictions. Overall, by detailing the first baffled-RME setup and first application PEPT analysis to such equipment, this work lays the foundation for further optimisation of bottom-up emulsification approaches. Baffle ; Membrane emulsification ; Streamlines, streaklines, and pathlines ; Particle (ecology) ; Emulsion ; Materials science ; Microstructure ; Drag ; Membrane ; Tracking (education) ; Turbulence ; Work (physics) ; Oil droplet ; Flux (metallurgy) ; Mechanics ; Chemical engineering ; Composite material ; Chemistry ; Mechanical engineering ; Engineering ; Physics Pickering emulsions and particle stabilization ; Micro and Nano Robotics ; Characterization and Applications of Magnetic Nanoparticles
Authors: Boyang Jason Wu | Fei Sun | Yichao Liu | Xin Liu | Xiaodan Zhao | Hongming Fei | Yibiao Yang | Zhihui Chen | Shaowei Liang | Zheng Wang | Bingjie Wang
Source: Frontiers in Materials (article, 2023-08-02)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Simultaneously focusing electromagnetic and acoustic waves by double-physical-fields null medium A novel double-physical-fields lens that can simultaneously focus acoustic and electromagnetic waves into a given region is designed based on double-physical-fields null medium, which can be realized by metal plates with subwavelength separations/thicknesses and precisely designed lengths. Numerical simulations show the proposed double-physical-fields lens can create exactly the same focusing effect for both electromagnetic and acoustic waves, i.e., the same focal spot size and efficiency at the same focal length. Four typical lens with different output surfaces are studied, which shows different focusing characteristics, e.g., noodle-shaped focal spot, tiny focal spot, and capsule-shaped focal spot. With the help of the designed double-physical-fields lens, an additional degree of freedom for control can be provided by simultaneously focusing acoustic and electromagnetic waves, which may lead to wider range of applications than single-field focusing. Optics ; Lens (geology) ; Physics ; Focal length ; Near and far field ; Null (SQL) ; Cardinal point ; Focus (optics) ; Electromagnetic radiation ; Focal point ; Electromagnetic field ; Acoustics ; Computer science Metamaterials and Metasurfaces Applications ; Acoustic Wave Phenomena Research ; Antenna Design and Analysis
Authors: Javier Reyes | Mareike Ließ
Source: Preprints.org (preprint, 2023-07-12)
Field: Chemistry — Analytical Chemistry

On-the-Go Vis-NIR Spectroscopy for Field-Scale Spatial-Temporal Monitoring of Soil Organic Carbon Agricultural soils serve as crucial storage sites for soil organic carbon (SOC). Their appropriate management is pivotal for mitigating climate change. To evaluate spatial and temporal changes in SOC within agricultural fields, continuous monitoring is imperative. In-field data sets of Vis-NIR soil spectra were collected on a long-term experimental site using an on-the-go spectrophotometer. Data processing for continuous SOC prediction involves a two-steps modelling approach. In Step 1, a Partial Least Square (PLSR) regression model is trained to establish a relationship between the SOC content and the spectral information also including spectral preprocesisng. In Step 2, the predicted SOC content obtained from the PLSR models is interpolated using ordinary kriging. Among the tested spectral preprocessing techniques and semivariogram models, SG and gapDer preprocessing along with a Gaussian semivariogram model, yielded the best performance resulting in a root mean square error of of 1.24 and 1.26 g kg-1. A striping effect due to the transect-based data collection was addressed by testing the effectiveness of extending the spatial separation distance, employing data aggregation, and defining the distribution based on treatment plots using block kriging. Overall, the results highlight the immense potential of on-the-go spectral Vis-NIR data for field-scale spatial-temporal monitoring of SOC. Kriging ; Soil carbon ; Environmental science ; Remote sensing ; Variogram ; Mean squared error ; Soil science ; Partial least squares regression ; Soil water ; Mathematics ; Statistics ; Geography Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Soil Geostatistics and Mapping
Authors: Grazia Cecchi | Simone Di Piazza | Ester Rosa | Furio De Vecchis | Milena Sara Silvagno | Junio Valerio Rombi | Micaela Tiso | Mirca Zotti
Source: Fermentation (article, 2023-07-19)
Field: Chemistry — Organic Chemistry

Autochthonous Microbes to Produce Ligurian Taggiasca Olives (Imperia, Liguria, NW Italy) in Brine Table olives are considered high-quality food, and Italy has a wealth of varieties and typical features that are truly unique in the world (about eighty cultivars of table olives or dual-purpose olives, four of which are protected by the protected designation of origin—PDO), and it is the second largest European consumer, behind Spain. The Taggiasca olive does not have a PDO, but it is very appreciated not only in the region of production (Liguria), but also in all the Italian regions and abroad. Autochthonous microbes (bacteria, yeasts, and filamentous fungi) are essential in the fermentative processes for brine olive production. However, these microbial communities that colonised the olive drupes are affected by the environmental conditions and the fermentation treatments. Hence the importance of studying and comparing olive microbes from different farms and investigating the relationships between bacteria, yeasts, and filamentous fungi to speed up the deamarisation process. Our results showed that yeasts are dominant relative to lactobacteria in all three brines studied, and Wickerhamomyces anomalus was the most performant fungus for the oleuropein degradation. The latter represents the best candidate for the realisation of a microbial starter. Oleuropein ; Brine ; Biology ; Starter ; Table grape ; Olive oil ; Geography ; Botany ; Food science ; Cultivar Edible Oils Quality and Analysis ; Fermentation and Sensory Analysis ; Essential Oils and Antimicrobial Activity
Authors: Shahid Aziz | Faisal Rasheed | Rabaab Zahra | Simone König
Source: Life (article, 2023-02-15)
Field: Chemistry — Spectroscopy

Mass Spectrometry-Based Proteomics of Minor Species in the Bulk: Questions to Raise with Respect to the Untargeted Analysis of Viral Proteins in Human Tissue (1) Background: Untargeted mass spectrometry (MS)-based proteomic analysis is highly amenable to automation. Software algorithms translate raw spectral data into protein information obtained by a comparison to sequence databases. However, the technology has limitations, especially for analytes measured at the limit of detection. In a protein expression study of human gastric biopsies, the question arose whether or not it is possible, as well as sensible, to search for viral proteins in addition to those from the human host. (2) Methods: Experimental data-independent MS data were analyzed using protein sequences for oncoviruses, and BLAST analyses were performed to elucidate the level of sequence homology to host proteins. (3) Results: About one hundred viral proteins were assigned, but there was also up to 43% sequence homology to human proteins. (4) Conclusions: There are at least two reasons why the matches to viral proteins should be used with care. First, it is not plausible that large amounts of viral proteins should be present in human gastric biopsies, so the spectral quality of the peptides derived from viral proteins is likely low. As a consequence, the number of false assignments is high. Second, homologous peptides found both in human and virus proteomes contribute to matching errors. Thus, though shotgun proteomics raw data can technically be analyzed using any database, meaningful results cannot be always expected and a sanity check must be performed. Both instrumentation and bioinformatic processing in MS-based proteomics are continuously improving at lowering the limit of detection even further. Nevertheless, data output should always be controlled in order to avoid the over-interpretation of results. Proteomics ; UniProt ; Shotgun proteomics ; Computational biology ; Proteome ; Biology ; Sequence database ; Human proteins ; Mass spectrometry ; Human proteome project ; Protein sequencing ; Tandem mass spectrometry ; Bioinformatics ; Peptide sequence ; Biochemistry ; Chemistry ; Chromatography ; Gene Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Enzyme Structure and Function
Authors: Tom Szwagier | Xavier Pennec
Source: arXiv (Cornell University) (preprint, 2023-07-28)
Field: Chemistry — Analytical Chemistry

The curse of isotropy: from principal components to principal subspaces Principal component analysis is a ubiquitous tool in exploratory data analysis. It is widely used by applied scientists for visualization and interpretability purposes. We raise an important issue (the curse of isotropy) about the interpretation of principal components with close eigenvalues. They may indeed suffer from an important rotational variability, which is a pitfall for interpretation. Through the lens of a probabilistic covariance model parameterized with flags of subspaces, we show that the curse of isotropy cannot be overlooked in practice. In this context, we propose to transition from ill-defined principal components to more-interpretable principal subspaces. The final methodology (principal subspace analysis) is extremely simple and shows promising results on a variety of datasets from different fields. Eigenvalues and eigenvectors ; Principal component analysis ; Identifiability ; Covariance ; Mathematics ; Applied mathematics ; Probabilistic logic ; Goodness of fit ; Statistics ; Physics Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models
Authors: Gyeong-Yeol Lee | Nam Hoon Kim | Dong-Eon Kim | Gyung-Suk Kil | Sung-Wook Kim
Source: Preprints.org (preprint, 2023-11-16)
Field: Materials Science — Materials Chemistry

Design, Fabrication, and Evaluation of a Phase-Resolved Partial Discharge Sensor embedded in MV-Class Bushing This paper proposes a novel phase-resolved partial discharge (PRPD) sensor embedded in MV-class bushing for high-accuracy insulation analysis. The design, fabrication, and evaluation of a PRPD sensor embedded in MV-class bushing aimed to detect partial discharge (PD) pulses that are phase-synchronized with the applied primary HV signals. A prototype PRPD sensor was composed of a flexible printed circuit board (PCB) with dual-sensing electrodes, utilizing a capacitive voltage divider (CVD) principle for voltage measurement and D-dot principle for PD detection, and a signal transducer with passive elements. A PD simulator was prepared to emulate typical PD defects, i.e., a metal protrusion. The voltage measurement precision of the prototype PRPD sensor was satisfied with the accuracy class of 0.2 specified in IEC 61869-11, as the maximum corrected voltage error ratios and corrected phase errors in 80%, 100%, and 120% of the rated voltage (13.2 kV) were less than 0.2% and 10 minutes, respectively. In addition, the prototype PRPD sensor had good linearity and high sensitivity for PD detection compared with a conventional electrical detection method. According to performance evaluation tests, the prototype PRPD sensor embedded in the MV-class bushing can measure PRPD patterns phase-synchronized with the primary voltage without any additional synchronization equipment or system. Therefore, the prototype PRPD sensor holds potential as a substitute for conventional commercial PD sensors. Consequently, this advancement could lead to the enhancement of power system monitoring and maintenance, contributing to the digitalization and minimization of power apparatus. Bushing ; Partial discharge ; Voltage ; Materials science ; Phase (matter) ; Capacitive sensing ; High voltage ; Sensitivity (control systems) ; Electrical engineering ; SIGNAL (programming language) ; Acoustics ; Electronic engineering ; Computer science ; Engineering High voltage insulation and dielectric phenomena ; Advanced Fiber Optic Sensors ; Thermal Analysis in Power Transmission