jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Atiqah Zaid | Norfarizah Hanim Hassan | Philip J. Marriott | Yong Foo Wong
Source: Pharmaceutics (review, 2023-03-31)
Field: Chemistry — Spectroscopy

Comprehensive Two-Dimensional Gas Chromatography as a Bioanalytical Platform for Drug Discovery and Analysis Over the last decades, comprehensive two-dimensional gas chromatography (GC×GC) has emerged as a significant separation tool for high-resolution analysis of disease-associated metabolites and pharmaceutically relevant molecules. This review highlights recent advances of GC×GC with different detection modalities for drug discovery and analysis, which ideally improve the screening and identification of disease biomarkers, as well as monitoring of therapeutic responses to treatment in complex biological matrixes. Selected recent GC×GC applications that focus on such biomarkers and metabolite profiling of the effects of drug administration are covered. In particular, the technical overview of recent GC×GC implementation with hyphenation to the key mass spectrometry (MS) technologies that provide the benefit of enhanced separation dimension analysis with MS domain differentiation is discussed. We conclude by highlighting the challenges in GC×GC for drug discovery and development with perspectives on future trends. Bioanalysis ; Drug discovery ; Metabolomics ; Chromatography ; Profiling (computer programming) ; Chemistry ; Gas chromatography ; Computational biology ; Gas chromatography–mass spectrometry ; Mass spectrometry ; Computer science ; Biology Analytical Chemistry and Chromatography ; Advanced Chemical Sensor Technologies ; Mass Spectrometry Techniques and Applications
Authors: Leiming Yuan | Xueping Fu | Xiaofeng Yang | Xiaojing Chen | Guangzao Huang | Xi Chen | Wen Shi | Limin Li
Source: Foods (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Non-Destructive Measurement of Egg’s Haugh Unit by Vis-NIR with iPLS-Lasso Selection Egg freshness is of great importance to daily nutrition and food consumption. In this work, visible near-infrared (vis-NIR) spectroscopy combined with the sparsity of interval partial least square regression (iPLS) were carried out to measure the egg's freshness by semi-transmittance spectral acquisition. A fiber spectrometer with a spectral range of 550-985 nm was embedded in the developed spectral scanner, which was designed with rich light irradiation mode from another two reflective surfaces. The semi-transmittance spectra were collected from the waist of eggs and monitored every two days. Haugh unit (HU) is a key indicator of egg's freshness, and ranged 56-91 in 14 days after delivery. The profile of spectra was analyzed the relation to the changes of egg's freshness. A series of iPLS models were constructed on the basis of spectral intervals at different divisions of the spectral region to predict the egg's HU, and then the least absolute shrinkage and selection operator (Lasso) was used to sparse the number of iPLS member models acting as a role of model selection and fusion regression. By optimization of the number of spectral intervals in the range of 1 to 40, the 26<sup>th</sup> fusion model obtained the best performance with the minimum root mean of squared error of prediction (RMSEP) of 5.161, and performed the best among the general PLS model and other intervals-combined PLS models. This study provided a new, rapid, and reliable method for the non-destructive and in-site determination of egg's freshness. Partial least squares regression ; Lasso (programming language) ; Mean squared error ; Mathematics ; Spectrometer ; Haugh unit ; Transmittance ; Statistics ; Computer science ; Optics ; Biology ; Physics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Advanced Chemical Sensor Technologies
Authors: Shun Lu | Yu Hu | Peihao Wang | Yan Han | Jianchao Tan | Jixiang Li | Sen Yang | Ji Liu
Source: Proceedings of the AAAI Conference on Artificial Intelligence (article, 2023-06-26)
Field: Materials Science — Materials Chemistry

PINAT: A Permutation INvariance Augmented Transformer for NAS Predictor Time-consuming performance evaluation is the bottleneck of traditional Neural Architecture Search (NAS) methods. Predictor-based NAS can speed up performance evaluation by directly predicting performance, rather than training a large number of sub-models and then validating their performance. Most predictor-based NAS approaches use a proxy dataset to train model-based predictors efficiently but suffer from performance degradation and generalization problems. We attribute these problems to the poor abilities of existing predictors to character the sub-models' structure, specifically the topology information extraction and the node feature representation of the input graph data. To address these problems, we propose a Transformer-like NAS predictor PINAT, consisting of a Permutation INvariance Augmentation module serving as both token embedding layer and self-attention head, as well as a Laplacian matrix to be the positional encoding. Our design produces more representative features of the encoded architecture and outperforms state-of-the-art NAS predictors on six search spaces: NAS-Bench-101, NAS-Bench-201, DARTS, ProxylessNAS, PPI, and ModelNet. The code is available at https://github.com/ShunLu91/PINAT. Computer science ; Graph embedding ; Machine learning ; Embedding ; Bottleneck ; Transformer ; Data mining ; Artificial intelligence ; Theoretical computer science ; Engineering Machine Learning in Materials Science ; Advanced Graph Neural Networks ; Machine Learning in Bioinformatics
Authors: Yiming Peng | Cise Unluer
Source: Cement and Concrete Composites (article, 2023-06-21)
Field: Materials Science — Materials Chemistry

Investigation of the viscoelastic evolution of reactive magnesia cement pastes with accelerated hydration mechanisms Viscoelasticity of reactive magnesia cement (RMC) pastes containing 3 different hydration agents (HCl, Mg(CH3COO)2 and MgCl2) were investigated. Amplitude sweep, frequency sweep and time sweep of RMC pastes were examined within 3 h of hydration. Time-dependent evolution of storage modulus, loss modulus, phase angle, and shear stress were recorded. Measurements of pH, isothermal calorimetry, XRD, TG-DTG and FTIR were used to analyze hydration reaction and products. Addition of hydration agents (HAs) accelerated the growth rate of storage modulus/loss modulus over time. MgCl2 demonstrated the greatest acceleration influence, also reflected in non-destructive structural build-up and buildability related to 3D printing applications. Addition of MgCl2 and HCl advanced the initial setting time of RMC pastes to 100–110 min, during which yield stress reached maximum, and decreased afterwards. Within 3 h of hydration, pastes containing MgCl2 revealed lowest pH, highest heat release and brucite concentration. HAs inclusion precipitated brucite away from MgO particles in the bulk solution, creating a bridge between MgO particles and enabling denser microscopic network structure. Brucite ; Materials science ; Viscoelasticity ; Rheometry ; Dynamic mechanical analysis ; Magnesium ; Composite material ; Cement ; Isothermal process ; Dynamic modulus ; Chemical engineering ; Metallurgy ; Polymer ; Thermodynamics Magnesium Oxide Properties and Applications ; Concrete and Cement Materials Research ; Innovations in Concrete and Construction Materials
Authors: Ian Jones | Lucas Dent | Tomoaki Higo | Theodoros I. Roumeliotis | Mar Arias-García | Hansa Shree | Jyoti S. Choudhary | Malin Pedersen | Chris Bakal
Source: Science Advances (article, 2023-01-25)
Field: Chemistry — Spectroscopy

Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer Almost all living cells maintain size uniformity through successive divisions. Proteins that over and underscale with size can act as rheostats, which regulate cell cycle progression. Using a multiomic strategy, we leveraged the heterogeneity of melanoma cell lines to identify peptides, transcripts, and phosphorylation events that differentially scale with cell size. Subscaling proteins are enriched in regulators of the DNA damage response and cell cycle progression, whereas super-scaling proteins included regulators of the cytoskeleton, extracellular matrix, and inflammatory response. Mathematical modeling suggested that decoupling growth and proliferative signaling may facilitate cell cycle entry over senescence in large cells when mitogenic signaling is decreased. Regression analysis reveals that up-regulation of TP53 or CDKN1A/p21CIP1 is characteristic of proliferative cancer cells with senescent-like sizes/proteomes. This study provides one of the first demonstrations of size-scaling phenomena in cancer and how morphology influences the chemistry of the cell. Cell cycle ; Proteome ; Biology ; Cell biology ; Cell growth ; Senescence ; Cell ; Extracellular matrix ; Cancer cell ; Signal transduction ; Cancer ; Computational biology ; Bioinformatics ; Genetics Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Protein Structure and Dynamics
Authors: A. S. Shankar | D. O. Oriekhov | Andrew K. Mitchell | Lars Fritz
Source: Physical review. B./Physical review. B (article, 2023-06-01)
Field: Materials Science — Materials Chemistry

Kondo effect in twisted bilayer graphene The emergence of flat bands in twisted bilayer graphene at the magic angle can be understood in terms of a vanishing Fermi velocity of the Dirac cone. This is associated with van Hove singularities approaching the Fermi energy and becoming higher-order. In the density of states, this is reflected by flanking logarithmic van Hove divergences pinching off the central Dirac cone in energy space. The low-energy pseudogap of the Dirac cone away from the magic angle is replaced by a power-law divergence due to the higher-order van Hove singularity at the magic angle. This plays an important role in the exotic phenomena observed in this material, such as superconductivity and magnetism, by amplifying electronic correlation effects. Here we investigate one such correlation effect---the Kondo effect due to a magnetic impurity embedded in twisted bilayer graphene. We use the Bistritzer-MacDonald model to extract the low-energy density of states of the material as a function of twist angle and study the resulting quantum impurity physics using perturbative and numerical renormalization group methods. Although at zero temperature the impurity is only Kondo screened precisely at the magic angle, we find highly nontrivial behavior at finite temperatures relevant to experiments, due to the complex interplay between Dirac, van Hove, and Kondo physics. Van Hove singularity ; Physics ; Condensed matter physics ; Bilayer graphene ; Pseudogap ; Density of states ; Fermi energy ; Anderson impurity model ; Kondo effect ; Dirac fermion ; Fermi level ; Superconductivity ; Quantum mechanics ; Graphene ; Impurity ; Cuprate ; Electron Graphene research and applications ; Quantum and electron transport phenomena ; Topological Materials and Phenomena
Authors: Bilkis Mitu | M. E. Barrera Cerda | Radovan Hřib | Václav Trojan | Lenka Halámková
Source: ACS Omega (article, 2023-06-06)
Field: Chemistry — Analytical Chemistry

Attenuated Total Reflection Fourier Transform Infrared Spectroscopy for Forensic Screening of Long-Term Alcohol Consumption from Human Nails Fourier transform infrared (FT-IR) spectroscopy is used throughout forensic laboratories for many applications. FT-IR spectroscopy can be useful with ATR accessories in forensic analysis for several reasons. It provides excellent data quality combined with high reproducibility, with minimal user-induced variations and no sample preparation. Spectra from heterogeneous biological systems, including the integumentary system, can be associated with hundreds or thousands of biomolecules. The nail matrix of keratin possesses a complicated structure with captured circulating metabolites whose presence may vary in space and time depending on context and history. We developed a new approach by using machine-learning (ML) tools to leverage the potential and enhance the selectivity of the instrument, create classification models, and provide invaluable information saved in human nails with statistical confidence. Here, we report chemometric analysis of ATR FT-IR spectra for the classification and prediction of long-term alcohol consumption from nail clippings in 63 donors. A partial least squares discriminant analysis (PLS-DA) was used to create a classification model that was validated against an independent data set which resulted in 91% correctly classified spectra. However, when considering the prediction results at the donor level, 100% accuracy was achieved, and all donors were correctly classified. To the best of our knowledge, this proof-of-concept study demonstrates for the first time the ability of ATR FT-IR spectroscopy to discriminate donors who do not drink alcohol from those who drink alcohol on a regular basis. Attenuated total reflection ; Artificial intelligence ; Chemometrics ; Computer science ; Infrared spectroscopy ; Pattern recognition (psychology) ; Fourier transform infrared spectroscopy ; Spectroscopy ; Linear discriminant analysis ; Fourier transform ; Machine learning ; Chemistry ; Mathematics ; Optics ; Physics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Bee Products Chemical Analysis
Authors: M.S. Dhanoa | Secundino López | R. Sanderson | Sue J. Lister | Ralph J. Barnes | J.L. Ellis | J. France
Source: Journal of Chemometrics (article, 2023-08-03)
Field: Chemistry — Analytical Chemistry

Methodology adjusting for least squares regression slope in the application of multiplicative scatter correction to near‐infrared spectra of forage feed samples Abstract Scatter corrections are commonly applied to refine near‐infrared (NIR) spectra. The aim of this study is to assess the impact of measurement errors when using ordinary least squares (OLS) for multiplicative scatter correction (MSC). Any measurement errors attached to the set‐mean spectrum may attenuate the OLS slope and that in turn will affect the estimate of the intercept and the adjustment of the spectra when using MSC methods to mitigate scattering. A corrected least squares slope may be used instead to prevent this problem, although the impact of this approach on the final outcome will depend on the relative size of the measurement errors in the individual spectra and the set‐mean spectrum. The errors‐in‐variables or type II regression model (also known as Deming regression) and its special cases, major axis (MA) and reduced major axis (RMA), are discussed and illustrated. The extent of OLS slope bias or attenuation is demonstrated as is the resulting MSC spectral distortion. Further modification to the MSC transformation method is also suggested. The influence of scattering correction (by MSC, standard normal variate (SNV) and detrending) and of using the maximum likelihood estimate of the slope for MSC on the prediction of chemical composition of Lucerne herbage from NIR spectra was assessed. The predictive performance was slightly improved by the use of scattering corrections with fairly minor differences among methods. Nonetheless, it seems well worth considering the use of type II regression models for assessing MSC application aiming at improving the goodness of prediction from NIR spectra. Statistics ; Partial least squares regression ; Mathematics ; Least-squares function approximation ; Ordinary least squares ; Regression ; Multiplicative function ; Spectral line ; Regression analysis ; Linear regression ; Goodness of fit ; Physics ; Mathematical analysis Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Animal Nutrition and Physiology
Authors: Youkai Yu | Zhiqin Yuan | Chao Lu
Source: Aggregate (article, 2023-04-27)
Field: Materials Science — Materials Chemistry

Long‐lasting chemiluminescence by aggregation‐induced emission surfactant with ultralow critical micelle concentration Abstract The development of green and simple chemiluminescence (CL) systems with intensive and long‐lasting emission is highly desirable in lighting and extension of their applications. In this study, it is found that the involvement of aggregation‐induced emission (AIE) surfactant could greatly enhance the CL of luminol–H 2 O 2 –Co 2+ system. The inserted hydrophobic tetraphenylethylene fluorophore in AIE is able to increase the hydrophobicity of alkyl chain and decrease the critical micelle concentration (CMC) of surfactant. The synergistic effect of micelle‐improved enrichment and CL resonance energy transfer endows luminol–H 2 O 2 –Co 2+ system intensive and long‐lasting emission under neutral pH conditions (pH 7.4). The visible emission is still observed even after 60 min. Our study has opened a new avenue for exploring green and simple effective CL systems through AIE surfactant with unltralow CMC toward various applications in lighting, optical sensing, and photocatalysis, etc. Chemiluminescence ; Pulmonary surfactant ; Micelle ; Critical micelle concentration ; Fluorophore ; Chemistry ; Tetraphenylethylene ; Photochemistry ; Alkyl ; Luminol ; Chemical engineering ; Aggregation-induced emission ; Organic chemistry ; Fluorescence ; Optics ; Aqueous solution Luminescence and Fluorescent Materials ; Molecular Sensors and Ion Detection ; Nanocluster Synthesis and Applications
Authors: Longke He | Cheng Xiao | Aying Jiwa | Dan Li | Jing Fang | Zhencong Du
Source: IEEE Sensors Journal (article, 2023-05-25)
Field: Chemistry — Analytical Chemistry

Zanthoxylum bungeanum Fruit Detection by Adaptive Thresholds in HSV Space for an Automatic Picking System Zanthoxylum bungeanum is widely cultivated, and some automatic picking systems or robots are researched to pick the pepper fruit instead of human hands. The detection algorithm is very important to an automatic picking system. HSV color space is widely used in color image segmentation. There is a fixed threshold based on HSV color space, or there is a dynamic threshold based on the Otsu method after the color images are converted into the gray images, because the Otsu method is very popular for the gray pictures. After the evaluation of the fixed threshold and the Otsu method for the pepper fruit detection, we propose an adaptive threshold method directly based on the HSV color space, called AHT and BBSV, which means Adaptive Hue Threshold, and Balance Between Saturation and Value. There is an adaptive threshold of separate hue, saturation, and luminance component. The hue threshold is obtained according to the conditions of whether there is soil, rock, and the pepper fruit in the image. The saturation and luminance thresholds are obtained by keeping the sum of saturation and luminance unchangeable. There are many hundreds of pictures for the test dataset. Our proposed method works very well, and the recall rate, accuracy and false alarm can separately achieve 100%, 100%, and 0%. And to evaluate the location precision, we address two metrics: the ratio of the overlap area between the detection region and the ideal region, and the location error. The ratio of the overlap area of our method is above 64%, and the location error is about 8%. All performance has been greatly improved compared with the fixed threshold. Hue ; Artificial intelligence ; HSL and HSV ; Luminance ; Otsu's method ; Computer vision ; Computer science ; Color space ; Pattern recognition (psychology) ; Mathematics ; Segmentation ; Image segmentation ; Image (mathematics) Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Smart Agriculture and AI
Authors: Juan Wei | Dimitris Papanastasiou | Mariangela Kosmopoulou | Athanasios Smyrnakis | Pengyu Hong | Nafisa Tursumamat | Joshua Klein | Chaoshuang Xia | Yang Tang | Joseph Zaia | Catherine E. Costello | Cheng Lin
Source: Chemical Science (article, 2023-01-01)
Field: Chemistry — Spectroscopy

<i>De novo</i> glycan sequencing by electronic excitation dissociation MS <sup>2</sup> -guided MS <sup>3</sup> analysis on an Omnitrap-Orbitrap hybrid instrument Comprehensive <i>de novo</i> glycan sequencing remains an elusive goal due to the structural diversity and complexity of glycans. Present strategies employing collision-induced dissociation (CID) and higher energy collisional dissociation (HCD)-based multi-stage tandem mass spectrometry (MS<sup><i>n</i></sup>) or MS/MS combined with sequential exoglycosidase digestions are inherently low-throughput and difficult to automate. Compared to CID and HCD, electron transfer dissociation (ETD) and electron capture dissociation (ECD) each generate more cross-ring cleavages informative about linkage positions, but electronic excitation dissociation (EED) exceeds the information content of all other methods and is also applicable to analysis of singly charged precursors. Although EED can provide extensive glycan structural information in a single stage of MS/MS, its performance has largely been limited to FTICR MS, and thus it has not been widely adopted by the glycoscience research community. Here, the effective performance of EED MS/MS was demonstrated on a hybrid Orbitrap-Omnitrap QE-HF instrument, with high sensitivity, fragmentation efficiency, and analysis speed. In addition, a novel EED MS<sup>2</sup>-guided MS<sup>3</sup> approach was developed for detailed glycan structural analysis. Automated topology reconstruction from MS<sup>2</sup> and MS<sup>3</sup> spectra could be achieved with a modified GlycoDeNovo software. We showed that the topology and linkage configurations of the Man<sub>9</sub>GlcNAc<sub>2</sub> glycan can be accurately determined from first principles based on one EED MS<sup>2</sup> and two CID-EED MS<sup>3</sup> analyses, without reliance on biological knowledge, a structure database or a spectral library. The presented approach holds great promise for autonomous, comprehensive and <i>de novo</i> glycan sequencing. Orbitrap ; Chemistry ; Mass spectrometry ; Dissociation (chemistry) ; Glycan ; Analytical Chemistry (journal) ; Chromatography ; Physical chemistry ; Biochemistry Mass Spectrometry Techniques and Applications ; Glycosylation and Glycoproteins Research ; Genomics and Phylogenetic Studies
Authors: Lü Yang | Lei Wang | Yuchuan Tan | Hanli Dan | Xian Peng | Y. Zhang | Yong Tan | Meng Lin | Jiuquan Zhang
Source: Cancer Imaging (article, 2023-01-07)
Field: Materials Science — Materials Chemistry

Amide Proton Transfer-weighted MRI combined with serum prostate-specific antigen levels for differentiating malignant prostate lesions from benign prostate lesions: a retrospective cohort study APTmax, APTmean, ADCmean, ADCmin, tPAD, FPSA, and PSAD showed to have a high value in differentiating malignant prostate lesions from benign prostate lesions in the separate assessment of indexes. The combination of APTmax, APTmean, ADCmean, and PSAD had the highest diagnostic value. Medicine ; Prostate ; Prostate cancer ; Receiver operating characteristic ; Prostate-specific antigen ; Magnetic resonance imaging ; Effective diffusion coefficient ; Urology ; Diffusion MRI ; Retrospective cohort study ; Radiology ; Nuclear medicine ; Cancer ; Pathology ; Internal medicine Lanthanide and Transition Metal Complexes ; MRI in cancer diagnosis ; Prostate Cancer Diagnosis and Treatment