jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mohammad Shahbazy | Sri H. Ramarathinam | Patricia T. Illing | Emma Christine Jappe | Pouya Faridi | Nathan P. Croft | Anthony W. Purcell
Source: Molecular & Cellular Proteomics (article, 2023-02-14)
Field: Chemistry — Spectroscopy

Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex [human leukocyte antigen (HLA) in humans]. These HLA-peptide complexes are presented on the cell surface for immune T-cell recognition. Immunopeptidomics denotes the utilization of tandem mass spectrometry to identify and quantify peptides bound to HLA molecules. Data-independent acquisition (DIA) has emerged as a powerful strategy for quantitative proteomics and deep proteome-wide identification; however, DIA application to immunopeptidomics analyses has so far seen limited use. Further, of the many DIA data processing tools currently available, there is no consensus in the immunopeptidomics community on the most appropriate pipeline(s) for in-depth and accurate HLA peptide identification. Herein, we benchmarked four commonly used spectral library-based DIA pipelines developed for proteomics applications (Skyline, Spectronaut, DIA-NN, and PEAKS) for their ability to perform immunopeptidome quantification. We validated and assessed the capability of each tool to identify and quantify HLA-bound peptides. Generally, DIA-NN and PEAKS provided higher immunopeptidome coverage with more reproducible results. Skyline and Spectronaut conferred more accurate peptide identification with lower experimental false-positive rates. All tools demonstrated reasonable correlations in quantifying precursors of HLA-bound peptides. Our benchmarking study suggests a combined strategy of applying at least two complementary DIA software tools to achieve the greatest degree of confidence and in-depth coverage of immunopeptidome data. Benchmarking ; Mass spectrometry ; Computer science ; Chemistry ; Data mining ; Computational biology ; Chromatography ; Biology ; Business Advanced Proteomics Techniques and Applications ; vaccines and immunoinformatics approaches ; Advanced Biosensing Techniques and Applications
Authors: Jason D. Weaver | Grazziela M. Sena | Kenneth I. Aycock | Andrew Roiko | Wayne M. Falk | Shiril Sivan | B. T. Berg
Source: Shape Memory and Superelasticity (article, 2023-01-18)
Field: Materials Science — Materials Chemistry

Rotary Bend Fatigue of Nitinol to One Billion Cycles Fatigue testing ; Durability ; Structural engineering ; Materials science ; Low-cycle fatigue ; Finite element method ; Fatigue limit ; Work (physics) ; Forensic engineering ; Mechanical engineering ; Engineering ; Composite material Shape Memory Alloy Transformations ; Titanium Alloys Microstructure and Properties ; Metal and Thin Film Mechanics
Authors: Hossein Kashani Zadeh | Mike Hardy | Mitchell Sueker | Yicong Li | Angelis Tzouchas | Nicholas MacKinnon | Gregory H. Bearman | Simon A. Haughey | Alireza Akhbardeh | Insuck Baek | Chansong Hwang | Jianwei Qin | Amanda M. Tabb | Rosalee S. Hellberg | Shereen Ismail | Hassan Reza | Fartash Vasefi | Moon J. Kim | Kouhyar Tavakolian | Christopher T. Elliott
Source: Sensors (article, 2023-05-28)
Field: Chemistry — Analytical Chemistry

Rapid Assessment of Fish Freshness for Multiple Supply-Chain Nodes Using Multi-Mode Spectroscopy and Fusion-Based Artificial Intelligence This study is directed towards developing a fast, non-destructive, and easy-to-use handheld multimode spectroscopic system for fish quality assessment. We apply data fusion of visible near infra-red (VIS-NIR) and short wave infra-red (SWIR) reflectance and fluorescence (FL) spectroscopy data features to classify fish from fresh to spoiled condition. Farmed Atlantic and wild coho and chinook salmon and sablefish fillets were measured. Three hundred measurement points on each of four fillets were taken every two days over 14 days for a total of 8400 measurements for each spectral mode. Multiple machine learning techniques including principal component analysis, self-organized maps, linear and quadratic discriminant analyses, k-nearest neighbors, random forest, support vector machine, and linear regression, as well as ensemble and majority voting methods, were used to explore spectroscopy data measured on fillets and to train classification models to predict freshness. Our results show that multi-mode spectroscopy achieves 95% accuracy, improving the accuracies of the FL, VIS-NIR and SWIR single-mode spectroscopies by 26, 10 and 9%, respectively. We conclude that multi-mode spectroscopy and data fusion analysis has the potential to accurately assess freshness and predict shelf life for fish fillets and recommend this study be expanded to a larger number of species in the future. Quadratic classifier ; Sensor fusion ; Spectroscopy ; Chemometrics ; Principal component analysis ; Support vector machine ; Linear discriminant analysis ; Artificial intelligence ; Artificial neural network ; Computer science ; Random forest ; Fluorescence spectroscopy ; Environmental science ; Remote sensing ; Pattern recognition (psychology) ; Machine learning ; Optics ; Physics ; Geology ; Fluorescence Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Cheng Li | Mengyu He | Zeyi Cai | Hengnian Qi | Jianhong Zhang | Chu Zhang
Source: Foods (article, 2023-01-05)
Field: Chemistry — Analytical Chemistry

Hyperspectral Imaging with Machine Learning Approaches for Assessing Soluble Solids Content of Tribute Citru Tribute Citru is a natural citrus hybrid with plenty of vitamins and nutrients. Fruits' soluble solids content (SSC) is a critical quality index. This study used hyperspectral imaging at two spectral ranges (400-1000 nm and 900-1700 nm) to determine SSC in Tribute Citru. Partial least squares regression (PLSR) and support vector regression (SVR) models were established in order to determine SSC using the spectral information of the calyx and blossom ends. The average spectra of both ends as well as their fusion was studied. The successive projections algorithm (SPA) and the correlation coefficient analysis (CCA) were used to examine the differences in characteristic wavelengths between the two ends. Most models achieved performances with the correlation coefficient of the training, validation, and testing sets over 0.6. Results showed that differences in the performances among the models using the one-sided and two-sided spectral information. No particular regulation could be found for the differences in model performances and characteristic wavelengths. The results illustrated that the sampling side was an influencing factor but not the determinant factor for SSC determination. These results would help with the development of real-world applications for citrus quality inspection without concerning the sampling sides and the spectral ranges. Hyperspectral imaging ; Partial least squares regression ; Sampling (signal processing) ; Support vector machine ; Correlation coefficient ; Regression ; Mathematics ; Artificial intelligence ; Quality (philosophy) ; Biological system ; Statistics ; Pattern recognition (psychology) ; Computer science ; Physics ; Biology ; Computer vision Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Smart Agriculture and AI
Authors: Marco Schiavina | Lorenzo Bracaglia | Tessa Bolognesi | Maria Anna Rodella | Giuseppe Tagliaferro | Angela Tino | Roberta Pierattelli | Isabella C. Felli
Source: Journal of Magnetic Resonance Open (article, 2023-12-24)
Field: Chemistry — Spectroscopy

Intrinsically disordered proteins studied by NMR spectroscopy Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of complex multi-domain proteins are now identified as a trend topic by the scientific community. NMR constitutes a unique investigation tool to access atom resolved information on their structural and dynamic properties, in isolation or upon interaction with potential partners (metal ions, small molecules, proteins, nucleic acids, membrane mimetics etc.). Their high flexibility and disorder, in contrast to more compact structures of globular protein domains, has a strong impact on NMR observables and NMR experiments should be tailored for their investigation. In this context, 13C direct detection NMR has become a very useful tool to contribute to IDPs/IDRs characterization at atomic resolution. 2D CON spectra can now be collected in parallel to 2D HN ones, and reveal information, which in some cases is not accessible through 2D HN spectra only, particularly when studying proteins in experimental conditions approaching physiological pH and temperature. The 2D HN/CON spectra are thus becoming a sort of identity card of an IDP/IDR in solution. Their simultaneous acquisition through multiple receiver NMR experiments is particularly useful to investigate the properties of highly flexible intrinsically disordered regions within complex multi-domain proteins, rather than in isolation as often performed to reduce the complexity of the system, an interesting perspective in the field. Intrinsically disordered proteins ; Context (archaeology) ; Nuclear magnetic resonance spectroscopy ; Chemistry ; Nucleic acid ; NMR spectra database ; Crystallography ; Chemical physics ; Nanotechnology ; Spectral line ; Materials science ; Physics ; Biology ; Biochemistry ; Stereochemistry Advanced NMR Techniques and Applications ; Protein Structure and Dynamics ; NMR spectroscopy and applications
Authors: Kasper Krijnen | Joel D. Keelor | Sebastian Böhm | Shane R. Ellis | Claus Köster | Jens Höhndorf | Ron M. A. Heeren | Ian G. M. Anthony
Source: Journal of the American Society for Mass Spectrometry (article, 2023-03-09)
Field: Chemistry — Spectroscopy

A Multimodal SIMS/MALDI Mass Spectrometry Imaging Source with Secondary Electron Imaging Capabilities for Use with timsTOF Instruments Mass spectrometry imaging (MSI) is a surface analysis technique that produces chemical images and is commonly used for biological and biomedical research. Multimodal imaging combines multiple imaging modes in order to get a more comprehensive view of a sample. Multimodal MSI images are often acquired using multiple MSI instruments, which leads to issues regarding image registration and increases the chance of sample damage or degradation during sample transfer. These problems can be solved by using a single instrument that can image in multiple modes. In order to improve the efficiency of multimodal imaging and investigate complementary modes of MSI, we have modified a prototype Bruker timsTOF fleX by adding secondary ion mass spectrometry (SIMS) and secondary electron (SE) imaging capabilities while preserving the ability to perform matrix-assisted laser desorption/ionization (MALDI). We show multimodal images collected on this instrument that required only trivial registration and were acquired without sample transfer between imaging trials. Furthermore, we characterize the performance of SIMS, SE, and MALDI imaging and compare the performance of the modified instrument to a commercial timsTOF fleX. Mass spectrometry imaging ; MALDI imaging ; Chemistry ; Mass spectrometry ; Sample (material) ; Sample preparation ; Desorption electrospray ionization ; Matrix-assisted laser desorption/ionization ; Analytical Chemistry (journal) ; Ionization ; Desorption ; Ion ; Chromatography ; Chemical ionization Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis ; Nuclear Physics and Applications
Authors: Jongmin Jacob Woo | Qibin Zhang
Source: Journal of the American Society for Mass Spectrometry (article, 2023-03-28)
Field: Chemistry — Spectroscopy

A Streamlined High-Throughput Plasma Proteomics Platform for Clinical Proteomics with Improved Proteome Coverage, Reproducibility, and Robustness Mass spectrometry-based clinical proteomics requires high throughput, reproducibility, robustness, and comprehensive coverage to serve the needs of clinical diagnosis, prognosis, and personalized medicine. Oftentimes these requirements are contradictory to each other. We report the development of a streamlined High-Throughput Plasma Proteomics (sHTPP) platform for untargeted profiling of the blood plasma proteome, which includes 96-well plates and simplified procedures for sample preparation, disposable trap column for peptide loading, robust liquid chromatographic system for separation, data-independent acquisition in tandem mass spectrometry, and DIA-NN, FragPipe, and in-house peptide spectral library-based data analysis. Using the optimized platform at a throughput of 60 samples per day, over 600 protein groups including 57 FDA-approved biomarkers can be consistently identified from whole human plasma, and more than 85% of the detected proteins have 100% completeness in quantitative values across 300 samples. The balance achieved between proteome coverage, throughput, and reproducibility of this sHTPP platform makes it promising in clinical settings, where a large number of samples are to be measured quickly and reliably to support various needs of clinical medicine. Proteomics ; Proteome ; Reproducibility ; Chemistry ; Tandem mass spectrometry ; Mass spectrometry ; Chromatography ; Biomarker discovery ; Quantitative proteomics ; Throughput ; Computational biology ; Computer science ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Ting Huang | Jian Wang | Alexey Stukalov | Margaret K. R. Donovan | Shadi Ferdosi | Lucy Williamson | Seth Just | Gabriel Castro | Lee S. Cantrell | Eltaher M. Elgierari | Ryan W. Benz | Yingxiang Huang | Khatereh Motamedchaboki | Amirmansoor Hakimi | Tabiwang N. Arrey | Eugen Damoc | Simion Kreimer | Omid C. Farokhzad | Serafim Batzoglou | Asim Siddiqui | Jennifer E. Van Eyk | Daniel Hornburg
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-29)
Field: Chemistry — Spectroscopy

Protein Coronas on Functionalized Nanoparticles Enable Quantitative and Precise Large-Scale Deep Plasma Proteomics The automated NP workflow enables high-throughput, deep, and quantitative plasma proteomics investigation with sufficient power to discover new biomarker signatures with a peptide level resolution. Proteomics ; Plasma ; Nanoparticle ; Nanotechnology ; Quantitative proteomics ; Scale (ratio) ; Chemistry ; Materials science ; Physics ; Biochemistry ; Nuclear physics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Biosensors and Analytical Detection
Authors: Irena Senkovska | Volodymyr Bon | Leila Abylgazina | Matthias Mendt | Jan Berger | Gregor Kieslich | Petko St. Petkov | Jhonatan Luiz Fiorio | Jan‐Ole Joswig | Thomas Heine | Larissa Schaper | Christopher Bachetzky | Rochus Schmid | Roland A. Fischer | Andreas Pöppl | Eike Brunner | Stefan Kaskel
Source: Angewandte Chemie (article, 2023-04-13)
Field: Chemistry — Inorganic Chemistry

Understanding MOF Flexibility: An Analysis Focused on Pillared Layer MOFs as a Model System Abstract Flexible porous frameworks are at the forefront of materials research. A unique feature is their ability to open and close their pores in an adaptive manner induced by chemical and physical stimuli. Such enzyme‐like selective recognition offers a wide range of functions ranging from gas storage and separation to sensing, actuation, mechanical energy storage and catalysis. However, the factors affecting switchability are poorly understood. In particular, the role of building blocks, as well as secondary factors (crystal size, defects, cooperativity) and the role of host–guest interactions, profit from systematic investigations of an idealized model by advanced analytical techniques and simulations. The review describes an integrated approach targeting the deliberate design of pillared layer metal–organic frameworks as idealized model materials for the analysis of critical factors affecting framework dynamics and summarizes the resulting progress in their understanding and application. Nanotechnology ; Metal-organic framework ; Cooperativity ; Flexibility (engineering) ; Materials science ; Computer science ; Chemistry Metal-Organic Frameworks: Synthesis and Applications ; Advanced Nanomaterials in Catalysis ; Polyoxometalates: Synthesis and Applications
Authors: Saroj B. Chand | John M. Woods | Jiamin Quan | Enrique Mejía‐Ospino | Takashi Taniguchi | Kenji Watanabe | Andrea Alù | Gabriele Grosso
Source: Nature Communications (article, 2023-06-22)
Field: Materials Science — Materials Chemistry

Interaction-driven transport of dark excitons in 2D semiconductors with phonon-mediated optical readout The growing field of quantum information technology requires propagation of information over long distances with efficient readout mechanisms. Excitonic quantum fluids have emerged as a powerful platform for this task due to their straightforward electro-optical conversion. In two-dimensional transition metal dichalcogenides, the coupling between spin and valley provides exciting opportunities for harnessing, manipulating, and storing bits of information. However, the large inhomogeneity of single layers cannot be overcome by the properties of bright excitons, hindering spin-valley transport. Nonetheless, the rich band structure supports dark excitonic states with strong binding energy and longer lifetime, ideally suited for long-range transport. Here we show that dark excitons can diffuse over several micrometers and prove that this repulsion-driven propagation is robust across non-uniform samples. The long-range propagation of dark states with an optical readout mediated by chiral phonons provides a new concept of excitonic devices for applications in both classical and quantum information technology. Exciton ; Physics ; Spin (aerodynamics) ; Phonon ; Photonics ; Coupling (piping) ; Condensed matter physics ; Semiconductor ; Quantum ; Optoelectronics ; Materials science ; Quantum mechanics 2D Materials and Applications ; Perovskite Materials and Applications ; Topological Materials and Phenomena
Authors: Priteshkumar M. Thakor | Rajesh Patel | Ranjan Kr. Giri | Sunil H. Chaki | Ankurkumar J. Khimani | Yati H. Vaidya | Parth Thakor | Anjali B. Thakkar | Jatin D. Patel
Source: ACS Omega (article, 2023-08-25)
Field: Chemistry — Organic Chemistry

Synthesis, Spectral Characterization, Thermal Investigation, Computational Studies, Molecular Docking, and <i>In Vitro</i> Biological Activities of a New Schiff Base Derived from 2-Chloro Benzaldehyde and 3,3′-Dimethyl-[1,1′-biphenyl]-4,4′-diamine The current research involves the synthesis of a new Schiff base through the reaction between 2-chlorobenzaldehyde and 3,3'-dimethyl-[1,1'-biphenyl]-4,4'-diamine by using a natural acid catalyst and a synthesized compound physicochemically characterized by X-ray diffraction, Fourier transform infrared spectroscopy, <sup>1</sup>H- and <sup>13</sup>C-nuclear magnetic resonance, and liquid chromatography-mass spectrometry. Thermal studies were conducted using thermogravimetric, differential thermal analysis, and differential thermogravimetric curves. These curves were obtained in an inert nitrogen environment from ambient temperature to 1263 K using heating rates of 10, 15, and 20 K·min<sup>-1</sup>. Using thermocurve data, model-free isoconversional techniques such as Kissinger-Akahira-Sunose, Flynn-Wall-Ozawa, and Friedman are used to determine kinetic parameters. These parameters include activation energy, phonon frequency factor, activation enthalpy, activation entropy, and Gibb's free energy change. All of the results have been thoroughly investigated. The molecule's anti-inflammatory and antidiabetic properties were also examined. To learn more about the potential of the Schiff base and how successfully it can suppress the amylase enzyme, a molecular docking experiment was also conducted. For <i>in silico</i> research, the Swiss Absorption, Distribution, Metabolism, Excretion, and Toxicity algorithms were used to calculate the theoretical pharmacokinetic properties, oral bioavailability, toxic effects, and biological activities of the synthesized molecule. Moreover, the cytotoxicity tests against a human lung cancer cell line (A549) using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay demonstrated that the synthesized Schiff base exhibited significant anticancer properties. Thermogravimetric analysis ; Schiff base ; Chemistry ; Differential scanning calorimetry ; Enthalpy ; Gibbs free energy ; Physical chemistry ; Nuclear chemistry ; Organic chemistry ; Polymer chemistry Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Metal complexes synthesis and properties
Authors: Soham Maity | Marco A. Lopez | Desiree M. Bates | Shishi Lin | Shane W. Krska | Shannon S. Stahl
Source: Journal of the American Chemical Society (article, 2023-08-29)
Field: Chemistry — Organic Chemistry

Polar Heterobenzylic C(sp<sup>3</sup>)–H Chlorination Pathway Enabling Efficient Diversification of Aromatic Nitrogen Heterocycles Site-selective radical reactions of benzylic C-H bonds are now highly effective methods for C(sp<sup>3</sup>-H) functionalization and cross-coupling. The existing methods, however, are often ineffective with heterobenzylic C-H bonds in alkyl-substituted pyridines and related aromatic heterocycles that are prominently featured in pharmaceuticals and agrochemicals. Here, we report new synthetic methods that leverage polar, rather than radical, reaction pathways to enable the selective heterobenzylic C-H chlorination of 2- and 4-alkyl-substituted pyridines and other heterocycles. Catalytic activation of the substrate with trifluoromethanesulfonyl chloride promotes the formation of enamine tautomers that react readily with electrophilic chlorination reagents. The resulting heterobenzyl chlorides can be used without isolation or purification in nucleophilic coupling reactions. This chlorination-diversification sequence provides an efficient strategy to achieve heterobenzylic C-H cross-coupling with aliphatic amines and a diverse collection of azoles, among other coupling partners. Chemistry ; Electrophile ; Nucleophile ; Alkyl ; Enamine ; Reagent ; Catalysis ; Combinatorial chemistry ; Umpolung ; Organic chemistry ; Coupling reaction ; Medicinal chemistry Catalytic C–H Functionalization Methods ; Radical Photochemical Reactions ; Oxidative Organic Chemistry Reactions
Authors: Saruchi Saruchi | Vaneet Kumar | Diksha Bhatt | Sadanand Pandey | Ayman A. Ghfar
Source: RSC Advances (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Synthesis and characterization of silver nanoparticle embedded cellulose–gelatin based hybrid hydrogel and its utilization in dye degradation The present work describes the synthesis of a cellulose and gelatin based hydrogel by the grafting of poly(acrylic acid) using ammonium persulphate (APS)-glutaraldehyde as the initiator-crosslinker system. The structure of the hydrogel was studied through scanning electron microscopy (SEM) and FTIR. The maximum swelling rate of C-G-g-poly(AA) was found to be 92 g g<sup>-1</sup> at pH 10. The size and structure of the prepared silver nanoparticles (AgNPs) were studied through TEM and zeta potential, and it was found that the synthesized AgNPs were spherical and the size range was 11-30 nm. The reduction process followed pseudo 1st order kinetics. EtBr and eosin dye degradation were more than 4 times faster, when AgNPs were used with sodium borohydride. Thus, it can be concluded that the synthesized C-G-g-poly(AA) AgNPs hybrid hydrogel is effective for the reduction and degradation of carcinogenic dyes in wastewater. Gelatin ; Degradation (telecommunications) ; Cellulose ; Characterization (materials science) ; Nanoparticle ; Chemical engineering ; Materials science ; Silver nanoparticle ; Chemistry ; Nanotechnology ; Organic chemistry ; Computer science Nanomaterials for catalytic reactions ; Dyeing and Modifying Textile Fibers