jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Addison Bralick | Erica C. Mitchell | Anna C. Doner | Annabelle R. Webb | Matthew G. Christianson | Justin M. Turney | Brandon Rotavera | Henry F. Schaefer
Source: The Journal of Physical Chemistry A (article, 2023-04-25)
Field: Chemistry — Organic Chemistry

Simulation of the VUV Absorption Spectra of Oxygenates and Hydrocarbons: A Joint Theoretical–Experimental Study Vacuum UV absorption spectroscopy is regularly used to provide unambiguous identification of a target species, insight into the electronic structure of molecules, and quantitative species concentrations. As molecules of interest have become more complex, theoretical spectra have been used in tandem with laboratory spectroscopic analysis or as a replacement when experimental data is unavailable. However, it is difficult to determine which theoretical methodologies can best simulate experiment. This study examined the performance of EOM-CCSD and 10 TD-DFT functionals (B3LYP, BH&HLYP, BMK, CAM-B3LYP, HSE, M06-2X, M11, PBE0, ωB97X-D, and X3LYP) to produce reliable vacuum UV absorption spectra for 19 small oxygenates and hydrocarbons using vertical excitation energies. The simulated spectra were analyzed against experiment using both a qualitative analysis and quantitative metrics, including cosine similarity, relative integral change, mean signed error, and mean absolute error. Based on our ranking system, it was determined that M06-2X was consistently the top performing TD-DFT method with BMK, CAM-B3LYP, and ωB97X-D also producing reliable spectra for these small combustion species. Absorption spectroscopy ; Spectral line ; Oxygenate ; Chemistry ; Absorption (acoustics) ; Spectroscopy ; Molecule ; Analytical Chemistry (journal) ; Optics ; Physics Free Radicals and Antioxidants ; Atmospheric chemistry and aerosols ; Spectroscopy and Laser Applications
Authors: S. S. Mahtab | Peker Milas | D. Tim Veal | Michael G. Spencer | Birol Ozturk
Source: Review of Scientific Instruments (article, 2023-04-01)
Field: Materials Science — Materials Chemistry

High efficiency radio frequency antennas for amplifier free quantum sensing applications Radio frequency (RF) signals are frequently used in emerging quantum applications due to their spin state manipulation capability. Efficient coupling of RF signals into a particular quantum system requires the utilization of carefully designed and fabricated antennas. Nitrogen vacancy (NV) defects in diamond are commonly utilized platforms in quantum sensing experiments with the optically detected magnetic resonance (ODMR) method, where an RF antenna is an essential element. We report on the design and fabrication of high efficiency coplanar RF antennas for quantum sensing applications. Single and double ring coplanar RF antennas were designed with -37 dB experimental return loss at 2.87 GHz, the zero-field splitting frequency of the negatively charged NV defect in diamond. The efficiency of both antennas was demonstrated in magnetic field sensing experiments with NV color centers in diamond. An RF amplifier was not needed, and the 0 dB output of a standard RF signal generator was adequate to run the ODMR experiments due to the high efficiency of the RF antennas. Amplifier ; Radio frequency ; Optoelectronics ; Materials science ; Computer science ; Telecommunications ; Bandwidth (computing) Diamond and Carbon-based Materials Research ; Advanced Fiber Laser Technologies ; Mechanical and Optical Resonators
Authors: Brian C. Searle | Ariana E. Shannon | Damien B. Wilburn
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-01-03)
Field: Chemistry — Spectroscopy

Scribe: next-generation library searching for DDA experiments ABSTRACT Spectrum library searching is a powerful alternative to database searching for data dependent acquisition experiments, but has been historically limited to identifying previously observed peptides in libraries. Here we present Scribe, a new library search engine designed to leverage deep learning fragmentation prediction software such as Prosit. Rather than relying on highly curated DDA libraries, this approach predicts fragmentation and retention times for every peptide in a FASTA database. Scribe embeds Percolator for FDR correction and an interference tolerant label-free quantification integrator to enable an end-to-end proteomics workflow. By leveraging expected relative fragmentation and retention time values, we find that library searching with Scribe can outperform traditional database searching tools, both in terms of sensitivity and quantitative precision. Scribe and its graphical interface are easy to use, freely accessible, and fully open source. Computer science ; Workflow ; Leverage (statistics) ; Python (programming language) ; Fragmentation (computing) ; Integrator ; Open source ; Software ; Information retrieval ; Data mining ; Database ; Artificial intelligence ; Operating system Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Machine Learning in Bioinformatics
Authors: Alexander Klein | Suresh K. Vasa | Rasmus Linser
Source: Journal of Biomolecular NMR (article, 2023-11-09)
Field: Chemistry — Spectroscopy

5D solid-state NMR spectroscopy for facilitated resonance assignment <sup>1</sup>H-detected solid-state NMR spectroscopy has been becoming increasingly popular for the characterization of protein structure, dynamics, and function. Recently, we showed that higher-dimensionality solid-state NMR spectroscopy can aid resonance assignments in large micro-crystalline protein targets to combat ambiguity (Klein et al., Proc. Natl. Acad. Sci. U.S.A. 2022). However, assignments represent both, a time-limiting factor and one of the major practical disadvantages within solid-state NMR studies compared to other structural-biology techniques from a very general perspective. Here, we show that 5D solid-state NMR spectroscopy is not only justified for high-molecular-weight targets but will also be a realistic and practicable method to streamline resonance assignment in small to medium-sized protein targets, which such methodology might not have been expected to be of advantage for. Using a combination of non-uniform sampling and the signal separating algorithm for spectral reconstruction on a deuterated and proton back-exchanged micro-crystalline protein at fast magic-angle spinning, direct amide-to-amide correlations in five dimensions are obtained with competitive sensitivity compatible with common hardware and measurement time commitments. The self-sufficient backbone walks enable efficient assignment with very high confidence and can be combined with higher-dimensionality sidechain-to-backbone correlations from protonated preparations into minimal sets of experiments to be acquired for simultaneous backbone and sidechain assignment. The strategies present themselves as potent alternatives for efficient assignment compared to the traditional assignment approaches in 3D, avoiding user misassignments derived from ambiguity or loss of overview and facilitating automation. This will ease future access to NMR-based characterization for the typical solid-state NMR targets at fast MAS. Chemistry ; Nuclear magnetic resonance spectroscopy ; Solid-state nuclear magnetic resonance ; Spectroscopy ; Nuclear magnetic resonance ; Resonance (particle physics) ; Solid-state ; Nuclear magnetic resonance crystallography ; Chemical physics ; Fluorine-19 NMR ; Physical chemistry ; Atomic physics ; Stereochemistry ; Physics ; Quantum mechanics Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Solid-state spectroscopy and crystallography
Authors: Katarina Domijan
Source: Chemometrics and Intelligent Laboratory Systems (article, 2023-08-23)
Field: Chemistry — Analytical Chemistry

What is to be gained by ensemble models in analysis of spectroscopic data? An empirical study was carried out to compare different implementations of ensemble models aimed at improving prediction in spectroscopic data. A wide range of candidate models were fitted to benchmark datasets from regression and classification settings. A statistical analysis using linear mixed model was carried out on prediction performance criteria resulting from model fits over random splits of the data. The results showed that the ensemble classifiers were able to consistently outperform candidate models in our application. Computer science Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Fault Detection and Control Systems
Authors: Yao Liu | Jianfang Xiong | Fu Qiao | Lele Xu | Zhen Xu
Source: Journal of the Science of Food and Agriculture (article, 2023-10-30)
Field: Chemistry — Analytical Chemistry

Detection of paralytic shellfish toxins by near‐infrared spectroscopy based on a near‐Bayesian <scp>SVM</scp> classifier with unequal misclassification costs Compared with the traditional support vector machines (SVMs) and the NBSVM, the u-NBSVM model achieved better detection performance. The results of this study indicate that NIRS technology combined with the u-NBSVM model can be used for rapid and non-destructive PST detection in mussels. © 2023 Society of Chemical Industry. Saxitoxin ; Paralytic shellfish poisoning ; Shellfish ; Support vector machine ; Contamination ; Shellfish poisoning ; Environmental science ; Artificial intelligence ; Computer science ; Fishery ; Biology ; Toxin ; Ecology ; Microbiology Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Irina Novoselova | Константин Петров | Karina Kalugyan
Source: E3S Web of Conferences (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Organizational and technological approaches to assessing the safety of buildings affected by emergencies This article is devoted to the problem of assessing the safety of buildings affected by natural disasters and man-made accidents. The work describes stages of assessing the safety of buildings affected by natural disasters and man-made accidents; proposes technical and organizational measures for improving the quality of the assessment of technical condition and safety of capital construction projects; reviews main directions for solving the problem of timely organization of the process of assessing the technical condition and safety of buildings affected by natural and man-made emergencies. Risk analysis (engineering) ; Quality (philosophy) ; Natural disaster ; Work (physics) ; Process (computing) ; Natural (archaeology) ; Construction engineering ; Engineering ; Business ; Architectural engineering ; Forensic engineering ; Computer science ; Transport engineering ; Geography Structural mechanics and materials ; Construction Management and Sustainability ; Advanced Energy Technologies and Civil Engineering Innovations
Authors: Joshua Moskowitz | Betsy Jean Yakes
Source: Journal of Regulatory Science (article, 2023-04-11)
Field: Chemistry — Analytical Chemistry

Portable Spectroscopy for Food Safety and Adulteration Screening In this review we discuss various applications of portable vibrational spectroscopy in food adulteration analyses and authentication confirmation. These applications generally involve the adulteration of a food product with materials which may be of lesser monetary value and may also be detrimental to human health. Portable spectroscopic testing for food authentication opens potential for rapid and on-site analyses of food products at various stages in the food production chain. These portable techniques also require the development of data analysis methods for each individual application, which will also be discussed in this review. Specific food safety applications for portable spectroscopy to be discussed include adulteration detection and evaluation of authenticity. Adulteration detection examples focus on the commonly adulterated milk powder and spice commodities, as well as the potential for component substitution (e.g., artificial sweeteners). For authentication, examples from marine oil dietary supplements, olive oils, honeys, coffees, and grains are presented along with examples of speciation (e.g. fish) and growth conditions (bell peppers). Authentication (law) ; Food science ; Food safety ; Olive oil ; Biochemical engineering ; Edible oil ; Food processing ; Food products ; Fish <Actinopterygii> ; Biotechnology ; Nanotechnology ; Environmental science ; Computer science ; Chemistry ; Materials science ; Engineering ; Biology ; Computer security ; Fishery Spectroscopy and Chemometric Analyses ; Identification and Quantification in Food ; Advanced Chemical Sensor Technologies
Authors: Maryam Shirmohammad | Michael Short | Haishan Zeng
Source: Biosensors (article, 2023-11-09)
Field: Chemistry — Spectroscopy

Collision Enhanced Raman Scattering (CERS): An Ultra-High Efficient Raman Enhancement Technique for Hollow Core Photonic Crystal Fiber Based Raman Spectroscopy Gas Analyzer Raman enhancement techniques are essential for gas analysis to increase the detection sensitivity of a Raman spectroscopy system. We have developed an efficient Raman enhancement technique called the collision-enhanced Raman scattering (CERS), where the active Raman gas as the analyte is mixed with a buffer gas inside the hollow-core photonic-crystal fiber (HCPCF) of a fiber-enhanced Raman spectroscopy (FERS) system. This results in an enhanced Raman signal from the analyte gas. In this study, we first showed that the intensity of the 587 cm<sup>-1</sup> stimulated Raman scattering (SRS) peak of H<sub>2</sub> confined in an HCPCF is enhanced by as much as five orders of magnitude by mixing with a buffer gas such as helium or N<sub>2</sub>. Secondly, we showed that the magnitudes of Raman enhancement depend on the type of buffer gas, with helium being more efficient compared to N<sub>2</sub>. This makes helium a favorable buffer gas for CERS. Thirdly, we applied CERS for Raman measurements of propene, a metabolically interesting volatile organic compound (VOC) with an association to lung cancer. CERS resulted in a substantial enhancement of propene Raman peaks. In conclusion, the CERS we developed is a simple and efficient Raman-enhancing mechanism for improving gas analysis. It has great potential for application in breath analysis for lung cancer detection. Raman spectroscopy ; Raman scattering ; Materials science ; Coherent anti-Stokes Raman spectroscopy ; Analytical Chemistry (journal) ; Chemistry ; Optics ; Chromatography Spectroscopy and Laser Applications ; Advanced Chemical Sensor Technologies ; Photonic Crystal and Fiber Optics
Authors: Zhemin Zhang | Jin-Zhong Zhang | Xiangyu Ye | Keai Ma | Haihang Li
Source: Polymers (article, 2023-02-27)
Field: Materials Science — Polymers and Plastics

Correlation Analysis and Prediction Model of Thermal Protection Performance of Aramid 1414 Fabric The thermal protection performance of fire suit is vital to the safety of firefighters. Using certain physical properties of fabrics to evaluate their thermal protection performance speeds up the process. This work aims to develop a TPP value prediction model that can be easily applied. Five properties of three types of Aramid 1414 made of the same material were tested, and the relationships between the physical properties of Aramid 1414 and its thermal protection performance (TPP value) were investigated. The results showed that the TPP value of the fabric had a positive correlation with grammage and air gap, and a negative correlation with the underfill factor. A stepwise regression analysis was used to solve the collinearity issue between the independent variables. Finally, a model for predicting TPP value by air gap and underfill factor was developed. The method adopted in this work reduced the number of independent variables in the prediction model, which is conducive to the application of the model. Aramid ; Collinearity ; Materials science ; Work (physics) ; Regression analysis ; Composite material ; Computer science ; Environmental science ; Mathematics ; Statistics ; Mechanical engineering ; Engineering ; Machine learning Textile materials and evaluations ; Occupational Health and Performance ; Thermoregulation and physiological responses
Authors: Peter A. Crozier | Adrià Marcos Morales | Matan Leibovich | Sreyas Mohan | Piyush Haluai | Mai Tan | Joshua Vincent | Advait Gilankar | Yifan Wang | Carlos Fernandez‐Granda
Source: Microscopy and Microanalysis (article, 2023-07-22)
Field: Materials Science — Surfaces, Coatings and Films

The Impact of Artificial Intelligence on <i>In Situ</i> Electron Microscopy Journal Article The Impact of Artificial Intelligence on In Situ Electron Microscopy Get access Peter A Crozier, Peter A Crozier School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Corresponding author: crozier@asu.edu Search for other works by this author on: Oxford Academic Google Scholar Adrià Marcos Morales, Adrià Marcos Morales Courant Institute of Mathematical Sciences, New York University, New York, NY, USA Search for other works by this author on: Oxford Academic Google Scholar Matan Leibovich, Matan Leibovich Courant Institute of Mathematical Sciences, New York University, New York, NY, USA Search for other works by this author on: Oxford Academic Google Scholar Sreyas Mohan, Sreyas Mohan Courant Institute of Mathematical Sciences, New York University, New York, NY, USA Search for other works by this author on: Oxford Academic Google Scholar Piyush Haluai, Piyush Haluai School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Search for other works by this author on: Oxford Academic Google Scholar Mai Tan, Mai Tan School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Search for other works by this author on: Oxford Academic Google Scholar Joshua Vincent, Joshua Vincent School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Search for other works by this author on: Oxford Academic Google Scholar Advait Gilankar, Advait Gilankar School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Search for other works by this author on: Oxford Academic Google Scholar Yifan Wang, Yifan Wang School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA Search for other works by this author on: Oxford Academic Google Scholar Carlos Fernandez-Granda Carlos Fernandez-Granda Courant Institute of Mathematical Sciences, New York University, New York, NY, USA Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 1595–1596, https://doi.org/10.1093/micmic/ozad067.1105 Published: 22 July 2023 State (computer science) ; Tempe ; Energy (signal processing) ; Library science ; Engineering physics ; Art history ; Engineering ; Physics ; Computer science ; Art ; Chemistry ; Algorithm Electron and X-Ray Spectroscopy Techniques ; Machine Learning in Materials Science ; Advanced Electron Microscopy Techniques and Applications
Authors: Seinn Moh Moh | Naoaki Kurisawa | Kiyotake Suenaga | Hisashi Kato‐Noguchi
Source: Plants (article, 2023-04-15)
Field: Materials Science — Biomaterials

Allelopathic Potential of Marsdenia tenacissima (Roxb.) Moon against Four Test Plants and the Biological Activity of Its Allelopathic Novel Compound, 8-Dehydroxy-11β-O-Acetyl-12β-O-Tigloyl-17β-Marsdenin Plant parts and extracts that are rich in bioactive substances with allelopathic potential can be explored as a possible alternative to herbicides for natural weed control in sustainable agriculture. In the present study, we investigated the allelopathic potential of <i>Marsdenia tenacissima</i> leaves and its active substances. Aqueous methanol extracts of <i>M. tenacissima</i> showed significant inhibitory activities against the growth of lettuce (<i>Lactuca sativa</i> L.), alfalfa (<i>Medicago sativa</i> L.), timothy (<i>Phleum pratense</i> L.), and barnyard grass (<i>Echinochloa crusgalli</i> (L.) Beauv.). The extracts were purified through various chromatography steps, and one active substance was isolated and determined by spectral data to be a novel compound, assigned as steroidal glycoside 3 (8-dehydroxy-11<i>β</i>-<i>O</i>-acetyl-12<i>β</i>-<i>O</i>-tigloyl-17<i>β</i>-marsdenin). Steroidal glycoside 3 significantly inhibited the seedling growth of cress at a concentration of 0.03 mM. The concentrations needed for 50% growth inhibition of the cress shoots and roots were 0.25 and 0.03 mM, respectively. These results suggest that steroidal glycoside 3 may be responsible for the allelopathy of <i>M. tenacissima</i> leaves. Allelopathy ; Lactuca ; Glycoside ; Weed ; Shoot ; Seedling ; Botany ; Medicago sativa ; Echinochloa ; Bioassay ; Biology ; Echinochloa crus-galli ; Chemistry ; Germination Phytochemistry and Bioactive Compounds ; Cynara cardunculus studies ; Allelopathy and phytotoxic interactions
Authors: Plácido L. Vidal | Joaquim de Moura | Jorge Novo | Marcos Ortega
Source: Medical & Biological Engineering & Computing (article, 2023-01-24)
Field: Chemistry — Analytical Chemistry

Multivendor fully automatic uncertainty management approaches for the intuitive representation of DME fluid accumulations in OCT images Diabetes represents one of the main causes of blindness in developed countries, caused by fluid accumulations in the retinal layers. The clinical literature defines the different types of diabetic macular edema (DME) as cystoid macular edema (CME), diffuse retinal thickening (DRT), and serous retinal detachment (SRD), each with its own clinical relevance. These fluid accumulations do not present defined borders that facilitate segmentational approaches (specially the DRT type, usually not taken into account by the state of the art for this reason) so a diffuse paradigm is used for its detection and visualization. In this paper, we propose three novel approaches for the representation and characterization of these types of DME. A baseline proposal, using a convolutional neural network as backbone, another based on transfer learning from a general domain, and a third approach exploiting information of regions without a defined label. Overall, our baseline proposal obtained an AUC of 0.9583 ± 0.0093, the approach pretrained with a general-domain dataset an AUC of 0.9603 ± 0.0087, and the approach pretrained in the domain taking advantage of uncertainty, an AUC of 0.9619 ± 0.0073. Human physiology ; Representation (politics) ; Computer science ; Artificial intelligence ; Computer vision ; Medicine ; Internal medicine Spectroscopy and Chemometric Analyses ; Industrial Vision Systems and Defect Detection ; Image Processing Techniques and Applications
Authors: Charles Prouveur | Matthieu Haefelé | Tobias Kenter | Nils Voss
Source:  (article, 2023-06-26)
Field: Materials Science — Electronic, Optical and Magnetic Materials

FPGA Acceleration for HPC Supercapacitor Simulations In the search of more energy efficient computing devices that could be assembled to build future exascale systems, this study proposes a chip to chip comparison between a CPU, a GPU and a FPGA, as well as a scalability study on multiple FPGAs from two of the available vendors. The application considered here has been extracted from a production code in material science. This allows for the benchmarking of different implementations to be performed on a production test case and not just theoretical ones. The core algorithm is a matrix free conjugate gradient that computes the total electrostatic energy with an Ewald summation at each iteration. Computer science ; Field-programmable gate array ; Scalability ; Benchmarking ; Parallel computing ; Code (set theory) ; Acceleration ; Computational science ; Conjugate gradient method ; Implementation ; System on a chip ; Energy (signal processing) ; Efficient energy use ; Chip ; Computer architecture ; Embedded system ; Algorithm ; Set (abstract data type) Supercapacitor Materials and Fabrication ; Parallel Computing and Optimization Techniques ; Low-power high-performance VLSI design