jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Damien de Mijolla | Jonathan Holdship | S. Viti | Johannes Heyl
Source: The Astrophysical Journal (article, 2024-01-30)
Field: Chemistry — Spectroscopy

Disentangling Multiple Emitting Components in Molecular Observations with Nonnegative Matrix Factorization Abstract Molecular emission from the galactic and extragalactic interstellar medium (ISM) is often used to determine the physical conditions of the dense gas. However, even from spatially resolved regions, the observed molecules do not necessarily arise from a single component. Disentangling multiple gas components is often a degenerate problem in radiative transfer studies. In this paper, we investigate the use of the nonnegative matrix factorization (NMF) approach as a means to recover gas components from a set of blended line intensity maps of molecular transitions that may trace different physical conditions. We run a series of experiments on synthetic data sets designed to replicate conditions in two very different environments: galactic pre-stellar cores and the ISM in high-redshift galaxies. We find that the NMF algorithm often recovers the multiple components resembling those used in the data-generating process, provided that the different components have similar column densities. When NMF fails to recover all the individual components it does however group together the most similarly emitting ones. We further found that initialization and regularisation are key factors in the efficiency of the NMF algorithm. Physics ; Factorization ; Matrix (chemical analysis) ; Astrophysics ; Algorithm Spectroscopy and Laser Applications ; Atmospheric Ozone and Climate ; Astrophysics and Star Formation Studies
Authors: Yoondam Seo | Inseon Kang | Hyeonjeong Lee | Jiin Hwang | Soo Heon Kwak | Min‐Kyu Oh | Hyunbeom Lee | Hophil Min
Source: Analytical and Bioanalytical Chemistry (article, 2024-10-18)
Field: Chemistry — Spectroscopy

Simple and robust high-throughput serum proteomics workflow with low-microflow LC–MS/MS Clinical proteomics has substantially advanced in identifying and quantifying proteins from biofluids, such as blood, contributing to the discovery of biomarkers. The throughput and reproducibility of serum proteomics for large-scale clinical sample analyses require improvements. High-throughput analysis typically relies on automated equipment, which can be costly and has limited accessibility. In this study, we present a rapid, high-throughput workflow low-microflow LC-MS/MS method without automation. This workflow was optimized to minimize the preparation time and costs by omitting the depletion and desalting steps. The developed method was applied to data-independent acquisition (DIA) analysis of 235 samples, and it consistently yielded approximately 6000 peptides and 600 protein groups, including 33 FDA-approved biomarkers. Our results demonstrate that an 18-min DIA high-throughput workflow, assessed through intermittently collected quality control samples, ensures reproducibility and stability even with 2 µL of serum. It was successfully used to analyze serum samples from patients with diabetes having chronic kidney disease (CKD), and could identify five dysregulated proteins across various CKD stages. Workflow ; Proteomics ; Throughput ; Biomarker discovery ; Reproducibility ; Quantitative proteomics ; Computer science ; Chromatography ; Chemistry ; Database Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Paul Schütze | Aenne Abel | Florian Burkart | Luís Silva | Hannes Dinter | Kevin Dojan | A. Herkert | S. Jaster-Merz | Max Kellermeier | Willi Kuropka | Frank Mayet | Sara Ruiz Daza | Simon Spannagel | Thomas Vinatier | Håkan Wennlöf
Source: Frontiers in Physics (article, 2024-11-05)
Field: Materials Science — Surfaces, Coatings and Films

electronCT - an imaging technique using very-high energy electrons The electronCT technique is an imaging method based on the multiple Coulomb scattering of relativistic electrons and has potential applications in medical and industrial imaging. It utilizes a pencil beam of electrons in the very high energy electron (VHEE, 50–250 MeV) range and a single detection layer for the determination of the beam profile. The technique constitutes a projectional, two-dimensional imaging method and thus also qualifies for the tomographic reconstruction of samples. Given the simplicity of the technical setup and its location behind the sample, the electronCT technique has potential synergies with VHEE radiotherapy, making use of the same electron source for both treatment and diagnostics and thus being a candidate for in situ imaging and patient localization. At the same time, several technical challenges arise from the measurement technique when applied for the imaging of living beings. Measurements performed at the ARES linear particle accelerator at an electron energy of 155 MeV using a mouse phantom and a Timepix3 silicon pixel detector assembly demonstrate the feasibility of this technique. Both projectional and tomographic reconstructions are presented and the potential and limits of the technology are discussed. Electron ; Materials science ; Energy (signal processing) ; Physics ; Nuclear physics ; Quantum mechanics Electron and X-Ray Spectroscopy Techniques ; Advanced X-ray and CT Imaging ; Nuclear Physics and Applications
Authors: Assil Halimi | Yifeng Che | Koroush Shirvan
Source:  (preprint, 2024-07-30)
Field: Materials Science — Materials Chemistry

Design and Full Core Fuel Performance Assessment of High Burnup Cores for 4-Loop PWRs Increasing the fuel discharge burnup of current light water reactors (LWRs) promises reductions in fuel cycle and/or operations costs. By assuming a constant core power density, the economic gain is enabled by better fuel utilization and/or increased capacity factor. In this effort to investigate greater than 62 MWd/kgU maximum rod average burnup for 110+ kW/l core power density, two core designs have been developed for a standard 17x17, 193 fuel assemblies pressurized water reactor (PWR). The levelized unit cost methodology is employed to evaluate the operation and maintenance and capital costs of the fuel cycle and examine the economic viability of both core design pathways. Core design and optimization are performed using the commercial STUDSVIK code package. Fuel performance analysis is realized in full core configuration via auditing FRAPCON4.1 and the high-fidelity code BISON. To provide a realistic assessment, the core design process takes into consideration best practices in current PWR core design. It features acceptable performance in terms of various core design constraints on maximum allowable peaking and boron concentration. Gadolinia (Gd2O3) is used as a burnable poison with a maximum of 9 wt% concentration while feeding 89 or 77 fuel assemblies in a 3-batch refueling scheme. Full core fuel performance simulation that allows for characterization of relevant fuel temperatures, plenum pressures, stresses, and strains is performed with respect to two bounding burnup levels. Such performance is potentially licensable for the 18-month high burnup core (&amp;lt;68 MWd/kgU peak pin) while it is more challenging for the 24-month high burnup core design pathway (&amp;lt;75 MWd/kgU peak pin). Maximum rod plenum pressure is identified to be the most limiting fuel performance parameter. While the scope of the present study focuses on the steady state plus overpower conditions, the acceptability of the new discharge burnup has to be further assessed by considering uncertainties and impact under accident scenarios in the future. Burnup ; Nuclear engineering ; Pressurized water reactor ; Core (optical fiber) ; Environmental science ; Materials science ; Process engineering ; Engineering Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Nuclear Engineering Thermal-Hydraulics
Authors: Mikidadi S. Gurisha | Atumain A. Makoba | Hellen E. Kiyengo | P.V. Kanaka Rao
Source: Physical Science International Journal (article, 2024-06-25)
Field: Materials Science — Materials Chemistry

Determination of Natural Radioactivity Levels and Radiation Hazards from the Soil of Tin Mining in Kyerwa District, Tanzania Gamma spectrometry was used to determine the activity concentrations of the natural radionuclides 226Ra, 232Th, and 40K in soil samples from the Tin mining in Kyerwa District, Tanzania. The study findings revealed that the mean activity concentrations of 226Ra, 232Th, and 40K were 90.68, 65.45, and 630.95 Bq/kg, respectively. These values were all greater than the average global activity concentrations for 226Ra, 232Th, and 40K which are 32 Bq/kg, 45 Bq/kg, and 420 Bq/kg, respectively. Assessments of the radiological risks associated with these naturally occurring radionuclides were done. In this case, the radium equivalent activity (Raeq), external hazard index (Hex), internal hazard index (Hin), and radioactivity level index (Iγ) were calculated. The results show that the mean values of Raeq, Hex, Hin, and Iγ were 230.6 Bq/kg, 0.628, 0.861, and 0.831, respectively. These results were below the global criteria levels for Raeq, Hex, Hin, and Iγ, which are 370 Bq/kg, 1, 1, and 2, respectively. Estimates for the absorbed dose rate in the air (DR), the annual effective dose equivalent (AEDE), and the annual gonadal equivalent dose (AGED) were also made. The findings revealed that the corresponding mean values for DR, AEDE, and AGED were 106.8 nGy/h, 1.07 mSv/y, and 744.4 μSvy-1. The mean values exceeded the global average value of 57 nGy/h for DR, 0.07 mSv/y for AEDE, and 2984 Sv/y for AGED. Therefore, Tin mining activities in the Kyerwa District could endanger the mining community from natural radioactive sources. In this study, therefore, we recommend performing a periodic inspection of the mining areas, monitoring the mining workers, and determining the level of activity and concentrations of different radionuclides in the mining area. Tanzania ; Natural radioactivity ; Natural (archaeology) ; Environmental science ; Tin ; Natural hazard ; Geography ; Archaeology ; Materials science ; Environmental planning ; Radionuclide ; Metallurgy ; Physics ; Nuclear physics ; Meteorology Graphite, nuclear technology, radiation studies ; Nuclear and radioactivity studies ; Radioactivity and Radon Measurements
Authors: Eric P. Kraybill | David Chen | Saadat Hasan Khan | Praveen Kalra
Source: JMIR Perioperative Medicine (article, 2024-12-02)
Field: Materials Science — Materials Chemistry

Reducing Greenhouse Gas Emissions and Modifying Nitrous Oxide Delivery at Stanford: Observational, Pilot Intervention Study Converting N<sub>2</sub>O delivery from centralized storage to point-of-care E-cylinders dramatically reduced waste and expense with no detriment to patient care. Our results provide strong evidence for analyzing N<sub>2</sub>O storage in health care systems that rely on centralized storage, and consideration of E-cylinder implementation to reduce emissions. The reduction in N<sub>2</sub>O waste will help meet SHC's goal of reducing scope 1 and 2 emissions by 50% before 2030. Preprint ; Nitrous oxide ; Greenhouse gas ; Environmental science ; Chemistry ; Computer science ; Geology ; World Wide Web Catalytic Processes in Materials Science ; Ammonia Synthesis and Nitrogen Reduction
Authors: Elvin R. Cabrera | Robert Schrader | T.G. Walker | Arthur Laganowsky | David H. Russell | Brian H. Clowers
Source: International Journal of Mass Spectrometry (article, 2024-01-09)
Field: Chemistry — Spectroscopy

Nonlinear frequency modulation for Fourier transform ion mobility mass spectrometry improves experimental efficiency Chemistry ; Sawtooth wave ; Mass spectrometry ; Ion-mobility spectrometry ; Fourier transform ion cyclotron resonance ; Ion ; Fourier transform ; Frequency modulation ; Modulation (music) ; SIGNAL (programming language) ; Analytical Chemistry (journal) ; Computational physics ; Physics ; Radio frequency ; Acoustics Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Metabolomics and Mass Spectrometry Studies
Authors: Е. С. Прокудина | Е. А. Сенокосова | Л. В. Антонова | R. А. Mukhamadiyarov | Vladislav A. Koshelev | E. O. Krivkina | Е. А. Великанова | N. А. Kochergin
Source: Siberian Journal of Clinical and Experimental Medicine (article, 2024-01-15)
Field: Materials Science — Biomaterials

Morphological features of biological and tissue-engineered vascular patches remodeling: results of tests on a sheep model One of the ways to reconstruct the arterial wall is endarterectomy with a vascular patch. The use of vascular wall prostheses made from existing materials can lead to complications with the need for reoperation. The search for new materials for the manufacture of vascular patches that have optimal compatibility with the vessel wall is still relevant. Aim: To study the dynamics and compare the morphological features of remodeling of tissue-engineered vascular patches from silk fibroin (SF) and biological xenopericardium (XP) flaps implanted into the wall of the sheep carotid artery. Material and Methods. Matrices from a 15% SF solution (n = 2) were prepared by electrospinning. For comparison, bovine pericardial flaps were used (n = 2). Vascular patches were implanted into the wall of the carotid artery in sheep for 2 and 6 months. A histological examination of explanted samples of vascular patches, scanning electron microscopy and confocal microscopy with specific immunofluorescent staining of the preparations were performed. Results. Based on the implanted SF-patch, neointima and neoadventitia were formed. After 2 months of implantation, the SFmatrix retained its structure; after 6 months, there were signs of moderate biodegradation of the material with the replacement of the vessel wall with its own tissue. There were no areas of calcification or massive inflammation. After 6 months, neointimal hyperplasia was detected in the projection of the implanted SF-patch. Based on the implanted XP-flap, neointima and neoadventitia were also formed. After 2 months, delamination of the implanted XP was revealed. After 6 months, neointimal hyperplasia was found in the projection of the XP-patch. Conclusion. Remodeling of the SF-patches and XP-flaps implanted into the wall of the sheep carotid artery followed the formation of a three-layer structure resembling the architecture of the vessel’s own wall, with signs of moderate biodegradation of the material. Neointimal hyperplasia is explained by insufficient compliance of the arterial wall and the patch and requires improvement in the composition of the implanted matrix. Neointima ; Vascular tissue ; Neointimal hyperplasia ; Calcification ; Common carotid artery ; Medicine ; Biomedical engineering ; Anatomy ; Pathology ; Carotid arteries ; Stent ; Restenosis ; Surgery ; Biology Electrospun Nanofibers in Biomedical Applications ; Silk-based biomaterials and applications ; Bone Tissue Engineering Materials
Authors: Xiaoyan Ye | Akihiro NAKATANI
Source: Mechanics of Materials (article, 2024-05-15)
Field: Materials Science — Biomaterials

Computational study of the influence of microstructure on fracture behavior near crack-tip field in nacre-like materials The small-scale failure process around a plane strain mode I crack in nacre-like materials is analyzed. The displacement increments of boundary nodes are specified by the analytical solutions based on the orthotropic linear elasticity to conduct an incremental finite element analysis. We set up a structural model composed of staggered arranged brittle aragonite tablets and cohesive zones within a process window surrounding the crack tip to investigate the toughness as well as the deformation mechanism in the fracture process zone. The results obtained by the parametric studies of different geometries and mechanical properties in the microstructure of the materials show that the aspect of failure in the near-tip fields can be categorized into four distinct fracture mechanisms. These mechanisms significantly affect the fracture toughness with differences of hundreds of times. We show a failure-mechanism map in which these fracture mechanisms can be divided into regions of geometry and mechanical properties in microstructure. Findings obtained in this study about the toughening mechanisms give us the useful knowledge to design novel materials with specific microstructures to control fracture mechanisms. Materials science ; Microstructure ; Composite material ; Fracture (geology) ; Field (mathematics) ; Structural engineering Calcium Carbonate Crystallization and Inhibition ; High-pressure geophysics and materials ; Rock Mechanics and Modeling
Authors: Zipora Lansky | Diede de Haan | Yuval Piven | Katya Rechav | Assaf Gal
Source: Advanced Science (article, 2024-09-06)
Field: Materials Science — Biomaterials

Hexagonal Patterns in Diatom Silica Form via a Directional Two‐Step Process Organisms are able to control material patterning down to the nanometer scale. This is exemplified by the intricate geometrical patterns of the silica cell wall of diatoms, a group of unicellular algae. Theoretical and modeling studies propose putative physical and chemical mechanisms to explain morphogenesis of diatom silica. Nevertheless, direct investigations of the underlying formation process are challenging because this process occurs within the confines of the living cell. Here, a method is developed for in situ 3D visualization of silica development in the diatom Stephanopyxis turris, using electron microscopy slice-and-view techniques. The formation of an isotropic hexagonal pattern made of nanoscale pores is documented. Surprisingly, these data reveal a directional process that starts with elongation of silica rods along one of the three equivalent orientations of the hexagonal lattice. Only as a secondary step, these rods are connected by crisscrossing bridges that give rise to the complete hexagonal pattern. These in situ observations combine two known properties of diatom silica, close packing of pores and branching of rods, to a unified process that yields isotropic patterns from an anisotropic background. Future research into diatom morphogenesis should focus on rod elongation and branching as the key for pattern formation. Diatom ; Rod ; Elongation ; Hexagonal crystal system ; Frustule ; Anisotropy ; Materials science ; Isotropy ; Nanoscopic scale ; Nanotechnology ; Nanometre ; Crystallography ; Morphogenesis ; Geometry ; Optics ; Chemistry ; Composite material ; Botany ; Physics ; Biology Diatoms and Algae Research ; Protist diversity and phylogeny ; Paleontology and Stratigraphy of Fossils
Authors: Sung‐Huan Yu | Shiau-Ching Chen | Pei‐Shan Wu | P.-S. Kuo | Ting-An Chen | Hsiang‐Ying Lee | Miao‐Hsia Lin
Source: Molecular & Cellular Proteomics (article, 2024-04-15)
Field: Chemistry — Spectroscopy

Quantification Quality Control Emerges as a Crucial Factor to Enhance Single-Cell Proteomics Data Analysis Mass spectrometry (MS)-based single-cell proteomics (SCP) provides us the opportunity to unbiasedly explore biological variability within cells without the limitation of antibody availability. This field is rapidly developed with the main focuses on instrument advancement, sample preparation refinement, and signal boosting methods; however, the optimal data processing and analysis are rarely investigated which holds an arduous challenge because of the high proportion of missing values and batch effect. Here, we introduced a quantification quality control to intensify the identification of differentially expressed proteins (DEPs) by considering both within and across SCP data. Combining quantification quality control with isobaric matching between runs (IMBR) and PSM-level normalization, an additional 12% and 19% of proteins and peptides, with more than 90% of proteins/peptides containing valid values, were quantified. Clearly, quantification quality control was able to reduce quantification variations and q-values with the more apparent cell type separations. In addition, we found that PSM-level normalization performed similar to other protein-level normalizations but kept the original data profiles without the additional requirement of data manipulation. In proof of concept of our refined pipeline, six uniquely identified DEPs exhibiting varied fold-changes and playing critical roles for melanoma and monocyte functionalities were selected for validation using immunoblotting. Five out of six validated DEPs showed an identical trend with the SCP dataset, emphasizing the feasibility of combining the IMBR, cell quality control, and PSM-level normalization in SCP analysis, which is beneficial for future SCP studies. Proteomics ; Computer science ; Computational biology ; Quality (philosophy) ; Chemistry ; Biology ; Biochemistry Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Ubiquitin and proteasome pathways
Authors: Borislav Bedzhev | Dilyan Dimitrov
Source: Environment Technology Resources Proceedings of the International Scientific and Practical Conference (article, 2024-06-22)
Field: Materials Science — Materials Chemistry

TWO GENERALIZATIONS OF SKEW-SYMMETRIC SEQUENCES WITH ODD LENGTHS The signals, exploited by the radar sensor networks and remote control systems, have to provide simultaneously high range resolution and ability to work stable in a hostile radio electronic environment. An effective approach for satisfying of these requirements is the frequent change of many different signals, which autocorrelation functions have small sidelobes. Accounting this situation in the paper the generalizations of the skew-symmetric sequences with odd lengths, which are phase manipulated signals, possessing high autocorrelation merit factor, are explored. As a result, two methods for synthesis of infinite families of phase manipulated signals with good autocorrelation properties are substantiated. Skew ; Mathematics ; Combinatorics ; Computer science ; Telecommunications Quasicrystal Structures and Properties ; Finite Group Theory Research