jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Haijun Du | Yaru Zhang | Yanhua Ma | Jiao Wei | Ting Lei | Su He
Source: Foods (article, 2024-07-11)
Field: Chemistry — Analytical Chemistry

Rapid Determination of Crude Protein Content in Alfalfa Based on Fourier Transform Infrared Spectroscopy The crude protein (CP) content is an important determining factor for the quality of alfalfa, and its accurate and rapid evaluation is a challenge for the industry. A model was developed by combining Fourier transform infrared spectroscopy (FTIS) and chemometric analysis. Fourier spectra were collected in the range of 4000~400 cm<sup>-1</sup>. Adaptive iteratively reweighted penalized least squares (airPLS) and Savitzky-Golay (SG) were used for preprocessing the spectral data; competitive adaptive reweighted sampling (CARS) and the characteristic peaks of CP functional groups and moieties were used for feature selection; partial least squares regression (PLSR) and random forest regression (RFR) were used for quantitative prediction modelling. By comparing the combined prediction results of CP content, the predictive performance of airPLST-cars-PLSR-CV was the best, with an RP2 of 0.99 and an RMSEP of 0.053, which is suitable for establishing a small-sample prediction model. The research results show that the combination of the PLSR model can achieve an accurate prediction of the crude protein content of alfalfa forage, which can provide a reliable and effective new detection method for the crude protein content of alfalfa forage. Partial least squares regression ; Feature selection ; Fourier transform ; Content (measure theory) ; Forage ; Random forest ; Mathematics ; Biological system ; Chemistry ; Artificial intelligence ; Pattern recognition (psychology) ; Statistics ; Analytical Chemistry (journal) ; Computer science ; Chromatography ; Agronomy ; Biology Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Meat and Animal Product Quality
Authors: Piero Gasparotto | Luis Barba | Hans-Christian Stadler | Greta Aßmann | Henrique Mendonça | Alun Ashton | M. Janousch | Filip Leonarski | Benjamı́n Béjar
Source: Journal of Applied Crystallography (article, 2024-05-07)
Field: Materials Science — Materials Chemistry

<i>TORO Indexer</i> : a <i>PyTorch</i> -based indexing algorithm for kilohertz serial crystallography Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (<i>i.e.</i> their orientation determined), integrated and merged. Introduced here is <i>TORO</i> (<i>Torch</i>-powered robust optimization) <i>Indexer</i>, a robust and adaptable indexing algorithm developed using the <i>PyTorch</i> framework. <i>TORO</i> is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by <i>PyTorch</i>, ensuring compatibility with a wide variety of computational setups. In tests, <i>TORO</i> outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like <i>DIALS</i> real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). <i>Acta Cryst.</i> D<b>70</b>, 2652-2666] and <i>XGandalf</i> [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). <i>Acta Cryst.</i> A<b>75</b>, 694-704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, <i>TORO</i> consistently matches, and in certain instances outperforms, established algorithms such as <i>XGandalf</i> and <i>MOSFLM</i> [Powell (1999). <i>Acta Cryst.</i> D<b>55</b>, 1690-1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of <i>TORO</i> and the versatility of <i>PyTorch</i> code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX. Search engine indexing ; Computer science ; Algorithm ; Crystallography ; Chemistry ; Artificial intelligence Enzyme Structure and Function ; Crystallization and Solubility Studies ; Crystallography and molecular interactions
Authors: Linda Berg Luecke | Roneldine Mesidor | Jack Littrell | Morgan Carpenter | Melinda Wojtkiewicz | Rebekah L. Gundry
Source: Journal of Proteome Research (article, 2024-02-27)
Field: Chemistry — Spectroscopy

Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface <i>N</i>-Glycocapture Data Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface <i>N</i>-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface <i>N</i>-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories. Proteome ; Computer science ; Workflow ; Proteomics ; Annotation ; Data set ; Set (abstract data type) ; Information retrieval ; Data mining ; Database ; Artificial intelligence ; Bioinformatics ; Biology Advanced Proteomics Techniques and Applications ; Glycosylation and Glycoproteins Research ; Machine Learning in Bioinformatics
Authors: Shouryya Ray
Source: Physical review. B./Physical review. B (article, 2024-04-19)
Field: Chemistry — Spectroscopy

Unconventional Gross-Neveu quantum criticality: Interaction-induced SO(3)-biadjoint insulator and emergent SU(3) symmetry I point out that Gross-Neveu theory with SO(3) isospin in three space-time dimensions---proposed recently, for instance, as an effective description of the N\'eel transition in certain spin-orbital liquids---also hosts quantum criticality of a more exotic kind. The ordered phase breaks SO(3) spontaneously, but the SO(3)-N\'eel order parameter vanishes. The fermionic bilinear order parameter is instead a biadjoint with respect to SO(3); unlike its N\'eel cousin, it constitutes an interaction-induced insulator. Furthermore, I show that the N\'eel and biadjoint order parameters can be combined to transform as an adjoint under SU(3) symmetry; the symmetry is emergent at the critical point separating the symmetric semimetal and the biadjoint insulator, but only if the flavor number is small enough, suggesting order-parameter fluctuations and the interplay between different channels play a crucial role in stabilizing the enlarged symmetry. In candidate SO(3) spin-orbital liqiuds, thermodynamic critical exponents carry fingerprints of ``spinons.'' The existence of an independent universality class in addition to the N\'eel transition opens the possibility of posing further constraints on spinon properties from thermodynamic measurements near criticality alone. Criticality ; Quantum ; Symmetry (geometry) ; Self-organized criticality ; Theoretical physics ; Gross–Neveu model ; Physics ; Mott insulator ; Quantum mechanics ; Condensed matter physics ; Mathematics ; Nuclear physics ; Fermion Advanced NMR Techniques and Applications ; Organic and Molecular Conductors Research ; Solid-state spectroscopy and crystallography
Authors: Larry K. Heki | Yahya Mohtashami | R. Chao | Jacob Ewing | Alejandro M. Quevedo | Shuji Nakamura | Steven P. DenBaars | Jon A. Schuller
Source: Advanced Optical Materials (article, 2024-02-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optimizing Polarization Selective Unidirectional Photoluminescence from Phased‐Array Metasurfaces Abstract Metasurface‐based optical elements offer a wide design space for miniature and lightweight optical applications. Typically, metasurface optical elements transform an incident light beam into a desired output waveform. Recent demonstrations of light‐emitting metasurfaces highlight the potential for directly producing desired output waveforms via metasurface‐mediated spontaneous emission. In this work, reciprocal finite‐difference time‐domain (FDTD) simulations and machine learning are used to enable the inverse design of highly unidirectional photoluminescent III‐Nitride quantum well metasurfaces capable of directive p ‐, s ‐, or combined p ‐ and s ‐ polarized emission at arbitrary angles. In comparison with previous intuition‐guided designs using the same quantum well architectures, the inverse design approach enables new polarization capabilities and experimentally demonstrated improvements in directivity of 54%. An analysis of ways in which the inverse design both validates and contradicts previous intuition‐guided design heuristics is presented. Ultimately, the combination of reciprocal simulations and efficient global optimization (EGO) grants remarkable improvements in emission directivity and results in full control over the polarization and momentum of emitted light, including simultaneous directional emission of s ‐ and p ‐polarized light. Directivity ; Polarization (electrochemistry) ; Optics ; Finite-difference time-domain method ; Quantum ; Materials science ; Optoelectronics ; Physics ; Computer science ; Telecommunications Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Plasmonic and Surface Plasmon Research
Authors: Heng Li | Lorenzo Botto
Source: Journal of Fluid Mechanics (article, 2024-12-12)
Field: Materials Science — Materials Chemistry

Hindered settling of a log-normally distributed Stokesian suspension Settling velocity statistics for dilute, non-Brownian homogeneous suspensions of polydisperse spheres having a log-normal size distribution are generated from Stokesian dynamics simulations, as a function of the total volume fraction $\phi$ and normalised width $\alpha$ of the particle size distribution. Several hundred instantaneous configurations are averaged to obtain reliable statistics. The paper reports data for the average and fluctuating settling velocity of each particle class in a suspension that is widely polydisperse – previous work was limited to only two or three classes, and the average settling velocity of each particle class was in most cases not reported – and provides an assessment of the accuracy of the analytical models proposed by Batchelor, Richardson &amp; Zaki, Davis &amp; Gecol and Masliyah–Lockett–Bassoon in predicting the simulation data. A limited comparison with dynamic simulations in which the particle microstructure is allowed to evolve in time is also included. Settling ; Suspension (topology) ; Brownian motion ; Mechanics ; Volume fraction ; SPHERES ; Particle (ecology) ; Statistical physics ; Homogeneous ; Physics ; Statistics ; Materials science ; Mathematics ; Thermodynamics ; Geology Material Dynamics and Properties ; Electrostatics and Colloid Interactions ; Rheology and Fluid Dynamics Studies
Authors: John‐Lewis Zinia Zaukuu | Sheila Mensah | Eric Tetteh Mensah | Florence Akomanin-Mensah | Solomon Wiredu | Zoltán Kovács
Source: npj Science of Food (article, 2024-10-26)
Field: Chemistry — Analytical Chemistry

Combining NIR spectroscopy with chemometrics for discriminating naturally ripened banana and calcium carbide ripened banana Calcium carbide is prohibited as a fruit ripening agent in many countries due to its harmful effects. Current methods for detecting calcium carbide in fruit involve time-consuming and destructive chemical analysis techniques, necessitating the need for non-destructive and rapid detection techniques. This study combined near infrared (NIR) spectroscopy with chemometrics to detect two banana varieties ripened with calcium carbide in different forms when they are peeled or unpeeled. Sixteen linear discriminant analysis (LDA) models were developed with high average classification accuracies for classifying banana based on the mode used to ripen banana, type of carbide treatment and the duration of soaking banana in carbide solution. Banana colour was predicted with partial least squared regression (PLSR) models with R<sup>2</sup>CV > 0.74, RMSECV and <5.4 and RPD close to 3. NIR coupled with chemometrics has good potential as a technique for detecting carbide ripened banana even if the banana is peeled or not. Chemometrics ; Calcium carbide ; Banana peel ; Spectroscopy ; Materials science ; Chemistry ; Food science ; Chromatography ; Metallurgy ; Physics Spectroscopy and Chemometric Analyses ; Sensory Analysis and Statistical Methods ; Food composition and properties
Authors: J. M. Li | Xiaoqiang Bian
Source: Energy Technology (article, 2024-01-24)
Field: Chemistry — Analytical Chemistry

Improved Least Squares Support Vector Machine Model Based on Grey Wolf Optimizer Algorithm for Predicting CO<sub>2</sub>–Crude Oil Minimum Miscibility Pressure The minimum miscibility pressure (MMP) is an important reference parameter in the study of CO 2 oil drive systems. In response to the problems of time‐consuming and costly prediction of MMP by conventional experimental methods, an improved least squares support vector machine (LSSVM) model based on grey wolf optimizer (GWO) algorithm is proposed to predict the CO 2 –crude oil MMP. Based on Pearson correlation analysis, reservoir temperature, C 5+ molecular weight, intermediate component mole fraction, and volatile component mole fraction are selected as independent variables of the model, and MMP is the dependent variable. A total of 51 MMP experimental data are collected, of which 35 are used to fine‐tune the model's parameters and 16 are used to verify the model's reliability. The high leverage point method is used to detect anomalies in all experimental data to check the reliability of the model, and the abnormality of only one piece of experimental data is identified. Finally, a comparison of the model with other intelligent models is found. The absolute relative deviation of the GWO‐LSSVM model is 2.24% for the training data and 3.48% for the test data, which provides high adaptability and accuracy. Miscibility ; Crude oil ; Least squares support vector machine ; Algorithm ; Least-squares function approximation ; Support vector machine ; Mathematics ; Petroleum engineering ; Mathematical optimization ; Computer science ; Engineering ; Chemistry ; Artificial intelligence ; Statistics Petroleum Processing and Analysis ; Enhanced Oil Recovery Techniques ; Hydrocarbon exploration and reservoir analysis
Authors: Tian‐Ye Du | Saowaluck Tibpromma | Kevin D. Hyde | Ausana Mapook | Dong‐Qin Dai | Guiqing Zhang | Steven L. Stephenson | Nakarin Suwannarach | Jaturong Kumla | Abdallah M. Elgorban | Kunhiraman C. Rajeshkumar | Sajeewa S. N. Maharachchikumbura | Qiang Li | Samantha C. Karunarathna
Source: Journal of Systematics and Evolution (article, 2024-09-30)
Field: Chemistry — Organic Chemistry

The polyphasic approach reveals ten novel and one known Ascomycota taxa from terrestrial agarwood‐producing trees Abstract Aquilaria (Thymelaeaceae), a tropical and subtropical plant, is one of the main genera that can produce agarwood. Aquilaria sinensis and Aquilaria yunnanensis are native Chinese tree species, and A. sinensis is China's main agarwood source. Agarwood is a nontimber forest product with high economic and medicinal value. First‐grade agarwood is sold as much as $100 000 per kilogram. There has been little research on the saprobic fungi associated with Aquilaria , with only 11 records having been reported. In the present study, 10 terrestrial saprobic fungi associated with A. sinensis and A. yunnanensis were collected in China. Based on morphological and phylogenetic studies, these 10 collections are introduced herein as one new genus ( Aquilariomyces ), nine new species – Aquilariomyces aquilariae , Corynespora aquilariae , Melomastia maomingensis , Nigrograna aquilariae , Parathyridariella aquilariae , Peroneutypa maomingensis , Phaeoseptum aquilariae , Pseudothyridariella aquilariae , and Triangularia aquilariae , and one known species ( Camarographium clematidis ). Descriptions, illustrations of morphological characteristics, photo plates, phylogenetic trees, and the results of a pairwise homoplasy index test (PHI) test results are provided. Agarwood ; Ascomycota ; Taxon ; Botany ; Biology Wood and Agarwood Research ; Forest Ecology and Biodiversity Studies ; Plant Pathogens and Fungal Diseases
Authors: Shahid Iqbal | Ahsan Noor | Naeem Ullah | Yasir Saifullah | Shehzad Ahmed | Muhammad Shemyal Nisar | Sai‐Wai Wong
Source: Scientific Reports (article, 2024-09-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Polarization insensitive non-interleaved frequency multiplexed dual-band Terahertz coding metasurface for independent control of reflected waves Independent control of electromagnetic (EM) waves by metasurfaces for multiple tasks are highly desired and is the recent hot topic of research. In this work we contribute a polarization insensitive frequency multiplexed 2-bit coding metasurface to control the Terahertz (THz) waves in the two operating bands independently. In this regard, as a first step a cascaded meta-atom composed of square rings and/or square metallic patches separated by two polyimide substrates is designed and optimized that provides sixteen independent distinct discrete phases in the reflection geometry. These meta-atoms are then distributed with distinct coding sequences in the two-dimensional spatial plane to realize various bi-functional metasurfaces. As a proof of the concept various full structures are designed and simulated to realize a series of bi-functionalities including anomalous reflection/beam shaping, beam shaping/anomalous reflection, beam deflection/Orbital angular momentum (OAM) beam generation with distinct modes and propagating wave to surface wave (PW-SW) conversion/PW beam manipulation in the lower and higher THz bands, respectively. All the simulation results are in excellent agreement with their theoretical equivalents. We envision that the proposed meta-designs have potential applications for the multi-spectral control of EM waves in THz band. The idea can be further extended to design frequency dependent tri-functional and multi-functional THz meta-devices. Terahertz radiation ; Multiplexing ; Polarization (electrochemistry) ; Optics ; Physics ; Multi-band device ; Optoelectronics ; Telecommunications ; Computer science ; Chemistry Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Millimeter-Wave Propagation and Modeling
Authors: Nichlas Vous Christensen | Christoffer Laustsen | Lotte Bonde Bertelsen
Source: NMR in Biomedicine (article, 2024-09-25)
Field: Chemistry — Spectroscopy

Differentiating leukemia subtypes based on metabolic signatures using hyperpolarized <sup>13</sup>C NMR Leukemia is a group of blood cancers that are classified in four major classes. Within these four classes, many different subtypes exists with similar origin, genetic mutations, and level of maturity, which can make them difficult to distinguish. Despite their similarities, they might respond differently to treatment, and therefore distinguishing between them is of crucial importance. A deranged metabolic phenotype (Warburg effect) is often seen in cancer cells, leukemia cells included, and is increasingly a target for improved diagnosis and treatment. In this study, hyperpolarized <sup>13</sup>C NMR spectroscopy was used to characterize the metabolic signatures of the six leukemia cell lines ML-1, CCRF-CEM, THP-1, MOLT-4, HL-60, and K562. This was done using [1-<sup>13</sup>C]pyruvate and [1-<sup>13</sup>C]alanine as bioprobes for downstream metabolite quantification and kinetic analysis on cultured cells with and without 2-deoxy-D-glucose treatment. The metabolic signatures of similar leukemia subtypes could be readily distinguished. This includes ML-1 and THP-1, which are of the similar M4 and M5 AML subtypes, CCRF-CEM and MOLT-4, which are of the similar T-ALL lineage at different maturation states, and HL-60 and K562, which are of the closely related M1 and M2 AML subtypes. The data presented here demonstrate the potential of hyperpolarized <sup>13</sup>C NMR spectroscopy as a method to differentiate between leukemia subtypes of similar origin. Combining this method with bioreactor setups could potentially allow for better leukemia disease management as metabolic signatures could be acquired from a single biopsy through repeated experimentation and intervention. Nuclear magnetic resonance ; Chemistry ; Radiochemistry ; Physics Advanced NMR Techniques and Applications ; Biochemical and Molecular Research ; Advanced MRI Techniques and Applications
Authors: Alba Agenjos-Moreno | Constanza Rubio | Antonio Uris | Rubén Simeón | B. Franch | Concha Domingo | A. San Bautista
Source: Agriculture (article, 2024-08-16)
Field: Chemistry — Analytical Chemistry

Strategy for Monitoring the Blast Incidence in Crops of Bomba Rice Variety Using Remote Sensing Data In this paper, we investigated the monitoring and characterization of the pest Magnaporthe oryzae, known as rice blast, in the Bomba rice variety at the Albufera Natural Park, located in Valencia, Spain during the 2022 and 2023 seasons. Using reflectance data from different Sentinel-2 satellite bands, various vegetative indices were calculated for each year. Significant differences in reflectance in the visible (B4), infrared (B8), red-edge (B6 and B7), and SWIR (B11) bands were detected between healthy and unhealthy fields. Additionally, variations were observed in the vegetation indices, with RVI and IRECI standing out for their higher accuracy in identifying blast-affected plots compared to NDVI and NDRE. Early differences in band values, vegetative indices, and spectral signatures were observed between the unhealthy and healthy plots, allowing for the anticipation of control treatments, whose effectiveness relies on timely intervention. Rice plant ; Remote sensing ; Agronomy ; Environmental science ; Biology ; Geography Spectroscopy and Chemometric Analyses