jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ziyi Li | Cory A. Weller | Syed Nisar Hussain Shah | Nicholas L. Johnson | Ying Hao | Jessica Roberts | Colleen Bereda | Sydney Klaisner | Pedro Machado | Pietro Fratta | Leonard Petrucelli | Mercedes Prudencio | Björn Oskarsson | Nathan P. Staff | Dennis W. Dickson | Mark Cookson | Michael E. Ward | Andrew Singleton | Mike A. Nalls | Yue Qi
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-12-13)
Field: Chemistry — Spectroscopy

ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, personalized medicine, systems biology and biomedical applications. By combining MS with different proteomics approaches such as immunopurification MS, immunopeptidomics, and total protein proteomics, researchers can gain insights into protein-protein interactions, immune responses, cellular processes, and disease mechanisms. The application of MS-based proteomics in these areas continues to advance our understanding of protein function, cellular signaling, and complex biological systems. Data analysis for mass spectrometry is a critical process that includes identifying and quantifying proteins and peptides and exploring biological functions for these proteins in downstream analysis. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analysis. ProtPipe provides downstream analysis including identifying differential abundance proteins and peptides, pathway enrichment analysis, protein-protein interaction analysis, and MHC1-peptide binding affinity. ProtPipe generates annotated tables and diagnostic visualizations from statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. ProtPipe is well-documented open-source software and is available at https://github.com/NIH-CARD/ProtPipe , accompanied by a web interface. Pipeline (software) ; Proteomics ; Computer science ; Computational biology ; Data science ; Data mining ; Biology ; Programming language ; Genetics Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Ubiquitin and proteasome pathways
Authors: Yanjing Fan | Jian Pan | Zhixiao Wu | Bin Li | Zhan Wang
Source: Buildings (article, 2023-01-16)
Field: Materials Science — Materials Chemistry

A Method for Predicting the Corrosion Behavior of Structural Steel under Atmosphere The durability and safety of steel structures during their life cycle are affected by steel corrosion. Limited test conditions and time hinder the reproduction of actual atmospheric steel corrosion. Most test studies have focused on the effect of pitting or uniform corrosion of steel structures, leading to the development of vague engineering methods that make it difficult to design steel structures with excellent corrosion resistance. In this study, a method involving three-dimensional cellular automata and a genetic algorithm was developed for predicting the corrosion behavior of structural steel. The calculation efficiency of three-dimensional cellular automata was improved by small iterative steps and adaptive activation for potential corrosion. Furthermore, the proposed method was tested with published tests, and the results showed that the method can simulate atmospheric corrosion with excellent accuracy and efficiency. The simulation results were used to calculate the structural steel cross-sectional performance with greater accuracy than that of the method of assuming uniform corrosion. Meanwhile, with accurate material parameters, the proposed method can also simulate the atmospheric corrosion of high-performance steel of different strengths and properties. Corrosion ; Durability ; Materials science ; Cellular automaton ; Structural material ; Structural engineering ; Atmosphere (unit) ; Metallurgy ; Composite material ; Computer science ; Engineering ; Algorithm Corrosion Behavior and Inhibition ; Structural Integrity and Reliability Analysis ; Concrete Corrosion and Durability
Authors: Gull Rimsha | Muhammad Shahbaz | Muhammad Irfan Majeed | Haq Nawaz | Nosheen Rashid | Muhammad Waseem Akram | Ifra Shabbir | Kiran Kainat | Aiman Amir | Eiman Sultan | Mulja Munir | Muhammad Imran
Source: ACS Omega (article, 2023-10-27)
Field: Chemistry — Analytical Chemistry

Raman Spectroscopy for the Quantitative Analysis of Solid Dosage Forms of the Active Pharmaceutical Ingredient of Febuxostat Raman spectroscopy has been used to characterize and quantify the solid dosage forms of the commercially available drug febuxostat. For this purpose, different formulations consisting of the febuxostat (API) and excipients with different concentrations of the API are prepared and analyzed by Raman spectroscopy to identify different spectral features related to the febuxostat API and excipients. Multivariate data analysis tools such as principal component analysis (PCA) and partial least-squares regression (PLSR) analysis are used for qualitative and quantitative analyses. PCA has been found to be useful for the qualitative monitoring of various solid dosage forms. PLSR analysis has led to the successful prediction of API concentration in the unknown samples with a sensitivity and a selectivity of 98 and 99%, respectively. Moreover, the root-mean-square error (RMSE) of calibration and validation of the PLSR model has been found to be 2.9033 and 1.35, respectively. Notably, it is found to be very helpful for the comparison between the self-made formulations of febuxostat and commercially available febuxostat tablets (40 and 80 mg) of two different brands (Gouric and Zurig). These results showed that Raman spectroscopy can be a useful and reliable technique for identifying and quantifying the active pharmaceutical ingredient (API) in commercially available solid dosage forms. Febuxostat ; Partial least squares regression ; Active ingredient ; Raman spectroscopy ; Principal component analysis ; Dosage form ; Chemometrics ; Chemistry ; Principal component regression ; Ingredient ; Calibration ; Analytical Chemistry (journal) ; Chromatography ; Mathematics ; Statistics ; Pharmacology ; Medicine ; Food science Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Analytical Methods in Pharmaceuticals
Authors: Д. С. Лобанов | S. V. Slovikov | Ekaterina Lunegova
Source: Frattura ed Integrità Strutturale (article, 2023-06-22)
Field: Materials Science — General Materials Science

Influence of Internal Technological Defects on the Mechanical Properties of Structural CFRP The use of carbon-fiber composite materials (CFRP) in critical cases implies an increase in the resistance to the stability of their mechanical properties. For the purpose of in-depth analysis of defects in the experiments, an integrated approach to mechanical flaw detection and testing of CFRP is used. To determine the parameters of defects in ultrasonic diagnostic sensors and the method of infrared thermography. The main technological defects of structural carbon fiber in samples of the internal "glueline defect", are three geometric shapes (circle, square, rectangle) and a "buckling" inner layer. As a result of flaw detection of individual samples by ultrasonic diagnostics, data were obtained on the shape and size of defects such as "glueline defect" and "buckling". As a result of the study, tensile testing of the samples with and without defects was carried out using the Vic 3D system, the AMSY-6 acoustic emission system, and the FLIR SC7700M thermal imaging system. The tensile strength, elastic modulus, Poisson's ratio, and maximum fracture strains of the studied CFRP without defects and with defects are obtained. The effect of defective zones on the main mechanical parameters is determined. The investigated defects lead to a decrease in strength and elastic characteristics by at least 15% and 5%, respectively. Materials science ; Composite material ; Ultimate tensile strength ; Buckling ; Thermography ; Elastic modulus ; Ultrasonic sensor ; Modulus ; Acoustic emission ; Nondestructive testing ; Poisson's ratio ; Composite number ; Fracture (geology) ; Structural engineering ; Infrared ; Poisson distribution ; Acoustics ; Optics Material Properties and Applications ; Thermography and Photoacoustic Techniques ; Engineering Diagnostics and Reliability
Authors: Glen P. Jackson | Samantha A. Mehnert | J. Tyler Davidson | Brandon D. Lowe | E. Ruiz | Jacob King
Source: Journal of the American Society for Mass Spectrometry (article, 2023-05-31)
Field: Chemistry — Spectroscopy

Expert Algorithm for Substance Identification Using Mass Spectrometry: Statistical Foundations in Unimolecular Reaction Rate Theory This study aims to resolve one of the longest-standing problems in mass spectrometry, which is how to accurately identify an organic substance from its mass spectrum when a spectrum of the suspected substance has not been analyzed contemporaneously on the same instrument. Part one of this two-part report describes how Rice-Ramsperger-Kassel-Marcus (RRKM) theory predicts that many branching ratios in replicate electron-ionization mass spectra will provide approximately linear correlations when analysis conditions change within or between instruments. Here, proof-of-concept general linear modeling is based on the 20 most abundant fragments in a database of 128 training spectra of cocaine collected over 6 months in an operational crime laboratory. The statistical validity of the approach is confirmed through both analysis of variance (ANOVA) of the regression models and assessment of the distributions of the residuals of the models. General linear modeling models typically explain more than 90% of the variance in normalized abundances. When the linear models from the training set are applied to 175 additional known positive cocaine spectra from more than 20 different laboratories, the linear models enabled ion abundances to be predicted with an accuracy of <2% relative to the base peak, even though the measured abundances vary by more than 30%. The same models were also applied to 716 known negative spectra, including the diastereomers of cocaine: allococaine, pseudococaine, and pseudoallococaine, and the residual errors were larger for the known negatives than for known positives. The second part of the manuscript describes how general linear regression modeling can serve as the basis for binary classification and reliable identification of cocaine from its diastereomers and all other known negatives. Chemistry ; Linear regression ; Linear model ; Mass spectrum ; Statistics ; Mass spectrometry ; Chromatography ; Mathematics Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Analytical Chemistry and Chromatography
Authors: Hang Xue | Yang Yang | Xiping Xu | Ning Zhang | Yaowen Lv
Source: Applied Sciences (article, 2023-03-09)
Field: Chemistry — Analytical Chemistry

Application of Near Infrared Hyperspectral Imaging Technology in Purity Detection of Hybrid Maize Seed purity has an important impact on the yield and quality of maize. Studying the spectral characteristics of hybrid maize and exploring the rapid and non-destructive detection method of seed purity are conducive to the development of maize seed breeding and planting industry. The near-infrared spectral data of five hybrid maize seeds were collected in the laboratory. After eliminating the obvious noises, the multiple scattering correction (MSC) was applied to pretreat the spectra. PLS-DA, KNN, NB, RF, SVM-Linear, SVM-Polynomial, SVM-RBF, and SVM-Sigmaid were used as pattern recognition methods to classify five different types of maize seeds. The recognition accuracy of the models established by different algorithms was 84.4%, 97.6, 100%, 96.4, 99.2%, 100%, 98.4%, and 91.2%, respectively. The results indicated that hyperspectral imaging technology could be used for variety classification and the purity detection of maize seeds. To improve the calculation speed, using the principal component analysis (PCA) to reduce the dimension of hyperspectral data, we then established classification models based on characteristic wavelengths. The recognition accuracy of the models established by different algorithms was 80.8%, 86.8%, 98%, 94%, 96.8%, 98.4%, 94.4%, and 88.2%, respectively. The results showed that the selected sensitive wavelengths could be used to detect the purity of maize seeds. The overall results indicated that it was feasible to use near-infrared hyperspectral imaging technology for the variety identification and purity detection of maize seeds. This study also provides a new method for rapid and non-destructive detection of seed purity. Hyperspectral imaging ; Principal component analysis ; Support vector machine ; Pattern recognition (psychology) ; Artificial intelligence ; Mathematics ; Computer science Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Smart Agriculture and AI
Authors: Ewa Napiórkowska
Source: Prospects in Pharmaceutical Sciences (article, 2023-08-03)
Field: Chemistry — Spectroscopy

Overview of cyclodextrins and medicinal products containing cyclodextrins currently registered in Poland Cyklodekstryny należą do cyklicznych oligosacharydów o unikalnych zdolnościach do tworzenia niekowalencyjnych kompleksów inkluzyjnych typu gospodarz-gość z wieloma cząsteczkami o właściwościach hydrofobowych, w tym także lekami. W efekcie mogą poprawiać rozpuszczalność wiązanych cząsteczek, a także zwiększać ich stabilność. Liczne zastosowania cyklodekstryn, m.in. w produkcji żywności, przemyśle kosmetycznym oraz naukach farmaceutycznych, świadczą o ich uniwersalności. Przeanalizowanie potencjału cyklodekstryn w naukach farmaceutycznych stwarza nowe możliwości poprawy właściwości fizykochemicznych leków, tworzenia nowych formulacji, projektowania systemów dostarczania leków, a także rozwoju innowacyjnych metod leczenia. Celem pracy było zebranie najważniejszych aspektów dotyczących cyklodekstryn, w tym ich budowy, sposobu tworzenia kompleksów inkluzyjnych, zastosowania w przemyśle farmaceutycznym, a także bezpieczeństwa stosowania cyklodekstryn. Artykuł obejmuje także przegląd dostępnych produktów leczniczych zarejestrowanych w Polsce zawierających w swoim składzie cyklodekstryny, wraz ze wskazaniami do ich stosowania oraz podaniem postaci farmaceutycznych. Różnorodność dostępnych produktów leczniczych podkreśla potencjał wykorzystania cyklodekstryn w projektowaniu nowych leków. Gynecology ; Philosophy ; Medicine Analytical Chemistry and Chromatography ; Drug Solubulity and Delivery Systems ; Chemical Reactions and Isotopes
Authors: Andrea Bocchieri | Lorenzo V. Mugnai | E. Pascale | Quentin Changeat | G. Tinetti
Source: Experimental Astronomy (article, 2023-09-13)
Field: Chemistry — Spectroscopy

Detecting molecules in Ariel low resolution transmission spectra Abstract The Ariel Space Mission aims to observe a diverse sample of exoplanet atmospheres across a wide wavelength range of 0.5 to 7.8 microns. The observations are organized into four Tiers, with Tier 1 being a reconnaissance survey. This Tier is designed to achieve a sufficient signal-to-noise ratio (S/N) at low spectral resolution in order to identify featureless spectra or detect key molecular species without necessarily constraining their abundances with high confidence. We introduce a P -statistic that uses the abundance posteriors from a spectral retrieval to infer the probability of a molecule’s presence in a given planet’s atmosphere in Tier 1. We find that this method predicts probabilities that correlate well with the input abundances, indicating considerable predictive power when retrieval models have comparable or higher complexity compared to the data. However, we also demonstrate that the P -statistic loses representativity when the retrieval model has lower complexity, expressed as the inclusion of fewer than the expected molecules. The reliability and predictive power of the P -statistic are assessed on a simulated population of exoplanets with H $$_2$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mrow/> <mml:mn>2</mml:mn> </mml:msub> </mml:math> -He dominated atmospheres, and forecasting biases are studied and found not to adversely affect the classification of the survey. Exoplanet ; Statistic ; Spectral resolution ; Population ; Spectral line ; Astrophysics ; Range (aeronautics) ; Physics ; Sampling (signal processing) ; Computer science ; Planet ; Astronomy ; Statistics ; Optics ; Mathematics ; Detector ; Materials science Spectroscopy and Laser Applications ; Spectroscopy and Chemometric Analyses ; Atmospheric Ozone and Climate
Authors: Puneet Mishra | Aneesh Chauhan | Tobias Pettersson
Source: Food Control (article, 2023-03-20)
Field: Chemistry — Analytical Chemistry

Seeing through plastics: A novel combination of NIR hyperspectral imaging and spectral orthogonalization for detecting fresh fruit inside plastic packaging to support automated barcode less checkouts in supermarkets Fully automated barcode less checkouts in supermarkets utilising machine vision and advanced image recognition algorithms are gaining popularity. A main step in the barcode less automated checkout machines is to recognise objects such that they can be added to the inventory list before the billing and payment by the consumers. For pre-packaged products, the task of image recognition is relatively well addressed in scientific literature and industrial applications. A key challenge arises when the object detection and recognition must be carried out for fresh produce, inside semi-transparent plastic packaging, which is often the case when consumer selects fresh fruits and uses plastic packaging to collect them. To address this, the study proposes a novel solution based on near-infrared hyperspectral imaging and spectral orthogonalization to remove the plastic contribution from the imaged scene. The aim is to use the independent pure spectra of plastics to define a detrimental sub-space on which the imaged hyperspectral scene is orthogonally projected. By doing this, it is demonstrated that, the contribution of the plastic from the imaged scene can be removed and an enhanced insight of the fruits inside the plastic bags is gained. Such technique can facilitate the automated checkout process, improving the recognition performance of fresh products. Barcode ; Hyperspectral imaging ; Computer science ; Plastic bag ; Artificial intelligence ; Computer vision ; Pattern recognition (psychology) ; Materials science Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Identification and Quantification in Food
Authors: Naoya Yamaguchi | Toshio Osada | Yen-Ling Kuo | Makoto Nanko
Source: Journal of the Ceramic Society of Japan (article, 2023-03-31)
Field: Materials Science — Materials Chemistry

Influence of cutting damage on the bending strength of Ti&lt;sub&gt;2&lt;/sub&gt;AlC MAX phase machinable ceramics Ti2AlC MAX phase ceramics are excellent candidates for high-temperature heat resistant materials. In addition, they are machinable using cemented carbide tools. However, heavy machining induces many surface cracks, reducing the mechanical strength and reliability of ceramic parts. Herein, we investigated the influence of the machining process on the bending strength and microstructure of Ti2AlC ceramics. Nearly fully dense Ti2AlC ceramics with elongated grains were machined using a carbide end mill in brittle mode, producing numerous cracks; however, the roughness of the ceramic was similar to that of tool steel cut in ductile mode. Despite its rough surface, the bending strength of the machined Ti2AlC was only slightly lower than that of polished Ti2AlC. The cracks in the machined Ti2AlC ceramics were induced with a kinking structure; however, they stopped at a length equivalent to one grain. The minimum strength of the machined Ti2AlC ceramics with a fracture toughness of 6.9 MPa·m1/2 was estimated by assuming a machining through-crack shape that was as deep as the maximum grain size. Cutting damage was limited to a single grain; thus, the bending strength of the machined Ti2AlC was not significantly reduced. Materials science ; Ceramic ; Machining ; Composite material ; Microstructure ; Brittleness ; Flexural strength ; Fracture toughness ; Carbide ; Surface roughness ; Bending ; Surface finish ; Grain size ; Toughness ; Phase (matter) ; Cemented carbide ; Metallurgy MXene and MAX Phase Materials ; Aluminum Alloys Composites Properties ; Advanced materials and composites
Authors: Cassandra K. Walker | Joe Panozzo
Source: Cereal Chemistry (article, 2023-09-20)
Field: Chemistry — Analytical Chemistry

Near‐infrared spectroscopy enables quality selection in wheat breeding Abstract Background and Objectives Near‐infrared spectroscopy (NIRS) and small‐scale testing are used to evaluate wheat germplasm is a cost‐effective strategy to reduce thousands of wheat lines to hundreds and then to tens of lines. Identification of high‐quality germplasm among thousands of lines is dependent on the accuracy of the tests that are used and how well these data correlate with the large‐scale tests that are used to confirm the end‐use quality before commercial release of a new wheat variety. In this study, NIR‐based testing was investigated to determine the effectiveness of this high‐throughput, nondestructive technology. Findings To demonstrate the effectiveness of NIRS and small‐scale testing as a selection strategy, interpretive population statistics evaluating three consecutive generations (F 4 , F 5 , and F 6 ) from a wheat breeding program were compared. The F 4 (early stage) generation (2019) was predicted for milling yield with a proportion of 13.9% of lines above 74% (w/w) milling yield. From those lines that progressed to F 5 (mid‐generation in 2020), the proportion increased to 26.2% of lines above 74% (w/w) milling yield. Selected lines from F 5 were progressed to F 6 (advanced generation in 2021), where 62.4% of lines were above 74% (w/w) milling yield. Conclusions Each time the set progressed through the selection strategy, the portion of lines above 74% (w/w) milling yield increased. Significance and Novelty This study demonstrates the value and efficiency of high‐throughput selection strategies using nondestructive NIRS at the F 4 (early‐stage generation) stage and small‐scale testing at the F 5 stage of a wheat breeding program. Germplasm ; Selection (genetic algorithm) ; Yield (engineering) ; Population ; Biotechnology ; Chemistry ; Agronomy ; Biology ; Materials science ; Computer science ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Genetics and Plant Breeding ; Wheat and Barley Genetics and Pathology