jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: C. M. Greenfield | C. Collins | Participants, Workshop
Source: arXiv (Cornell University) (preprint, 2023-03-20)
Field: Materials Science — Materials Chemistry

Report of the US ITER Research Program Research Needs Workshop The US ITER Research Program Basic Research Needs Workshop, held over the course of several months in 2022 with over 400 participants, sought to identify steps to be taken to both maximize the return of the US investment in ITER construction and operation and to ensure US research priorities on ITER strengthen the domestic program aimed at the development of a fusion pilot plant (FPP). Research program ; Investment (military) ; Basic research ; Engineering management ; Research development ; Engineering ; Computer science ; Systems engineering ; Aeronautics ; Political science ; Library science ; Physics Fusion materials and technologies ; Magnetic confinement fusion research ; Korean Peninsula Historical and Political Studies
Authors: Reta Birhanu Kitata | Marija Veličković | Zhangyang Xu | Rui Zhao | David Scholten | Rosalie Chu | Danny Orton | William Chrisler | Jeremy Mathews | Paul Piehowski | Tao Liu | Richard Smith | Huiping Liu | Clive Wasserfall | Chia‐Feng Tsai | Tujin Shi
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-16)
Field: Chemistry — Spectroscopy

Robust collection and processing for label-free single voxel proteomics With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of ∼900 and ∼4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 μm × 20 μm × 10 μm (close to single cells) and 200 μm × 200 μm × 10 μm (∼100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics. Voxel ; Proteome ; Proteomics ; Computer science ; Computational biology ; Chemistry ; Biology ; Artificial intelligence ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Advanced Biosensing Techniques and Applications
Authors: Andrew J. Sweatt | Cameron Griffiths | B. Bishal Paudel | Kevin A. Janes
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-07-11)
Field: Chemistry — Spectroscopy

Proteome-wide copy-number estimation from transcriptomics Protein copy numbers constrain systems-level properties of regulatory networks, but absolute proteomic data remain scarce compared to transcriptomics obtained by RNA sequencing. We addressed this persistent gap by relating mRNA to protein statistically using best-available data from quantitative proteomics-transcriptomics for 4366 genes in 369 cell lines. The approach starts with a central estimate of protein copy number and hierarchically appends mRNA-protein and mRNA-mRNA dependencies to define an optimal gene-specific model that links mRNAs to protein. For dozens of independent cell lines and primary prostate samples, these protein inferences from mRNA outmatch stringent null models, a count-based protein-abundance repository, and empirical protein-to-mRNA ratios. The optimal mRNA-to-protein relationships capture biological processes along with hundreds of known protein-protein interaction complexes, suggesting mechanistic relationships are embedded. We use the method to estimate viral-receptor abundances of CD55-CXADR from human heart transcriptomes and build 1489 systems-biology models of coxsackievirus B3 infection susceptibility. When applied to 796 RNA sequencing profiles of breast cancer from The Cancer Genome Atlas, inferred copy-number estimates collectively reclassify 26% of Luminal A and 29% of Luminal B tumors. Protein-based reassignments strongly involve a pharmacologic target for luminal breast cancer (CDK4) and an α-catenin that is often undetectable at the mRNA level (CTTNA2). Thus, by adopting a gene-centered perspective of mRNA-protein covariation across different biological contexts, we achieve accuracies comparable to the technical reproducibility limits of contemporary proteomics. The collection of gene-specific models is assembled as a web tool for users seeking mRNA-guided predictions of absolute protein abundance (http://janeslab.shinyapps.io/Pinferna). Biology ; Messenger RNA ; Proteomics ; Computational biology ; Proteome ; Transcriptome ; Gene ; Human Protein Atlas ; Copy-number variation ; Systems biology ; Gene expression ; Genetics ; Bioinformatics ; Genome ; Protein expression Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Gene expression and cancer classification
Authors: Stepan Lys
Source: Energy Engineering and Control Systems (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Analysis of Calculation Model for Primary Coolant Fission Products The sources of radioactive contamination of the primary coolant by fission products when the unit is operating at the rated power are as follows: defect fuel elements with gas leakiness and substantial damages, surface contamination of the outer surfaces of fuel claddings, superficial contamination of structural materials of fuel assemblies. Initially in the reactor operation (if there are no manufacturing defects in fuel elements), the contamination of the coolant by fission products is determined by the release into the reactor coolant circuit of fission fragments of Uranium-235 (due to their kinetic energy) that is present on the outer surfaces of fuel elements as contamination in their manufacturing. During normal operation of the reactor, the integrity of cladding may fail due to various processes of corrosion fatigue type. These processes result in, first of all, micro-fissures and then in large defects in the claddings, which is accompanied by an increase in the release of fission products from fuel elements into the primary coolant. Coolant ; Fuel element failure ; Nuclear engineering ; Fission products ; Fission ; Cladding (metalworking) ; Contamination ; Nuclear fission product ; Materials science ; Nuclear fuel ; Pressurized water reactor ; Nuclear reactor core ; Environmental science ; Waste management ; Metallurgy ; Nuclear physics ; Neutron ; Engineering ; Mechanical engineering Nuclear Materials and Properties ; Graphite, nuclear technology, radiation studies ; Nuclear reactor physics and engineering
Authors: Md Tanvir Emrose | Emily L. Payne | Chenglong You | Georgios Veronis
Source: arXiv (Cornell University) (preprint, 2023-10-20)
Field: Materials Science — Materials Chemistry

Broadband switchable infrared absorbers using phase-change materials We introduce multilayer structures with the phase-change material Ge$_2$Sb$_2$Te$_5$ (GST) for use as broadband switchable absorbers in the infrared wavelength range. We optimize both the material composition and the layer thicknesses of the multilayer structures, in order to maximize the difference between the absorption for GST in its crystalline phase and the absorption for GST in its amorphous phase in the wavelength range of interest. We show that in the optimized structures near perfect absorption can be switched to very low absorption in a broad wavelength range by switching GST from its crystalline to its amorphous phase. Our optimized lithography-free structures have better performance than harder-to-fabricate three-dimensional structures. Our results could pave the way to a new class of broadband switchable absorbers and thermal sources in the infrared wavelength range. Materials science ; Amorphous solid ; Infrared ; Absorption (acoustics) ; Wavelength ; Broadband ; Optoelectronics ; Phase (matter) ; Optics ; Lithography ; Phase change ; Chemistry ; Engineering physics ; Physics ; Composite material ; Crystallography Phase-change materials and chalcogenides ; Transition Metal Oxide Nanomaterials ; solar cell performance optimization
Authors: Morten M. Smedskjær
Source: VBN Forskningsportal (Aalborg Universitet) (article, 2023-10-12)
Field: Materials Science — Materials Chemistry

Cracking the Code: Using Data Analysis to Engineer Stronger and Tougher Glasses:Invited Talk Cracking ; Code (set theory) ; Forensic engineering ; Computer science ; Engineering ; Materials science ; Programming language ; Composite material Material Selection and Properties ; Structural Analysis of Composite Materials ; Engineering and Material Science Research
Authors: Puoya Tabaghi | Michael Khanzadeh | Yusu Wang | Sivash Mirarab
Source: arXiv (Cornell University) (preprint, 2023-01-06)
Field: Chemistry — Analytical Chemistry

Principal Component Analysis in Space Forms Principal Component Analysis (PCA) is a workhorse of modern data science. While PCA assumes the data conforms to Euclidean geometry, for specific data types, such as hierarchical and cyclic data structures, other spaces are more appropriate. We study PCA in space forms; that is, those with constant curvatures. At a point on a Riemannian manifold, we can define a Riemannian affine subspace based on a set of tangent vectors. Finding the optimal low-dimensional affine subspace for given points in a space form amounts to dimensionality reduction. Our Space Form PCA (SFPCA) seeks the affine subspace that best represents a set of manifold-valued points with the minimum projection cost. We propose proper cost functions that enjoy two properties: (1) their optimal affine subspace is the solution to an eigenequation, and (2) optimal affine subspaces of different dimensions form a nested set. These properties provide advances over existing methods, which are mostly iterative algorithms with slow convergence and weaker theoretical guarantees. We evaluate the proposed SFPCA on real and simulated data in spherical and hyperbolic spaces. We show that it outperforms alternative methods in estimating true subspaces (in simulated data) with respect to convergence speed or accuracy, often both. Affine space ; Tangent space ; Mathematics ; Affine hull ; Affine transformation ; Subspace topology ; Pure mathematics ; Euclidean space ; Pseudo-Riemannian manifold ; Manifold (fluid mechanics) ; Linear subspace ; Riemannian manifold ; Curvature ; Mathematical analysis ; Ricci curvature ; Geometry Spectroscopy and Chemometric Analyses ; Face and Expression Recognition ; Mineral Processing and Grinding
Authors: Minh Thư Đỗ | Huyền Quyên Lê | Sĩ Thiện Lê
Source: Can Tho University Journal of Science (article, 2023-05-19)
Field: Materials Science — General Materials Science

Khảo sát các yếu tố chính ảnh hưởng đến quá trình tạo bột rau má bằng phương pháp sấy vi sóng sủi bọt Phương pháp sấy vi sóng sủi bọt được thực hiện để khảo sát ảnh hưởng của nồng độ chất tạo bọt (lòng trắng trứng) và chất ổn định (carboxymethyl cellulose - CMC) đến độ ổn định của lớp bọt rau má và ảnh hưởng của độ dày lớp bọt trải cùng với công suất vi sóng lên màu sắc bột rau má thành phẩm. Kết quả cho thấy hỗn hợp bọt đạt mức độ ổn định nhất khi tỷ lệ chất tạo bọt và chất ổn định bọt nằm trong một khoảng giá trị cụ thể mà ở đây là 15% lòng trắng trứng và 1,4% CMC (so với khối lượng mẫu); Màu sắc tối ưu của bọt đạt được ở độ dày bọt trải dày 4 mm trên đĩa thủy tinh và được mang đi sấy trong lò vi sóng với công suất 130 W. Kết quá thí nghiệm là cơ sở bước đầu cho việc tối ưu hóa các thông số trong quá trình tạo bột rau má bằng phương pháp sấy vi sóng sủi bọt. Chemistry ; Stereochemistry Material Properties and Applications
Authors: Yue Pan | Xusheng Wang | Chunyu Liu | Junmin Peng | Qian Li
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-10-06)
Field: Chemistry — Spectroscopy

Multimodal joint deconvolution and integrative signature selection in proteomics Abstract Deconvolution is an efficient approach for detecting cell-type-specific (cs) transcriptomic signals without cellular segmentation. However, this type of methods have not been extended to the proteomics research. Here we present a novel algorithm and tool to dissect bulk proteome by leveraging the information shared between transcriptome-proteome. Our tool first identifies potential cell marker proteins by integrating RNA and protein bulk expression profiles and then jointly quantifies the cell abundance in mixture proteomes without using a reference signature matrix, enabling the downstream analyses such as cs-protein Quantitative Trait Loci (cspQTL) mapping. This new method and the cspQTL analysis are implemented in the R package MIC-SQTL that also provides integrative visualization of bulk multimodal samples, available at https://bioconductor.org/packages/MICSQTL . Proteome ; Bioconductor ; Deconvolution ; Proteomics ; Computational biology ; Computer science ; Transcriptome ; Quantitative proteomics ; Biology ; Data mining ; Bioinformatics ; Gene expression ; Gene ; Genetics ; Algorithm Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Single-cell and spatial transcriptomics
Authors: Giulia Preti | Gianmarco De Francisci Morales | Francesco Bonchi
Source: arXiv (Cornell University) (preprint, 2023-06-05)
Field: Chemistry — Spectroscopy

Hyper-distance Oracles in Hypergraphs We study point-to-point distance estimation in hypergraphs, where the query is parameterized by a positive integer s, which defines the required level of overlap for two hyperedges to be considered adjacent. To answer s-distance queries, we first explore an oracle based on the line graph of the given hypergraph and discuss its limitations: the main one is that the line graph is typically orders of magnitude larger than the original hypergraph. We then introduce HypED, a landmark-based oracle with a predefined size, built directly on the hypergraph, thus avoiding constructing the line graph. Our framework allows to approximately answer vertex-to-vertex, vertex-to-hyperedge, and hyperedge-to-hyperedge s-distance queries for any value of s. A key observation at the basis of our framework is that, as s increases, the hypergraph becomes more fragmented. We show how this can be exploited to improve the placement of landmarks, by identifying the s-connected components of the hypergraph. For this task, we devise an efficient algorithm based on the union-find technique and a dynamic inverted index. We experimentally evaluate HypED on several real-world hypergraphs and prove its versatility in answering s-distance queries for different values of s. Our framework allows answering such queries in fractions of a millisecond, while allowing fine-grained control of the trade-off between index size and approximation error at creation time. Finally, we prove the usefulness of the s-distance oracle in two applications, namely, hypergraph-based recommendation and the approximation of the s-closeness centrality of vertices and hyper-edges in the context of protein-to-protein interactions. Hypergraph ; Oracle ; Parameterized complexity ; Vertex (graph theory) ; Computer science ; Graph ; Combinatorics ; Theoretical computer science ; Mathematics ; Algorithm Advanced Proteomics Techniques and Applications ; Graph Theory and Algorithms ; Gene expression and cancer classification
Authors: Zahra Sharbaf | Ignacio Ferreras | O. Lahav
Source: arXiv (Cornell University) (preprint, 2023-09-06)
Field: Chemistry — Analytical Chemistry

What drives the variance of galaxy spectra? We present a study aimed at understanding the physical phenomena underlying the formation and evolution of galaxies following a data-driven analysis of spectroscopic data based on the variance in a carefully selected sample. We apply Principal Component Analysis (PCA) independently to three subsets of continuum-subtracted optical spectra, segregated into their nebular emission activity as quiescent, star-forming, and Active Galactic Nuclei (AGN). We emphasize that the variance of the input data in this work only relates to the absorption lines in the photospheres of the stellar populations. The sample is taken from the Sloan Digital Sky Survey (SDSS) in the stellar velocity dispersion range 100-150 km/s, to minimise the ``blurring'' effect of the stellar motion. We restrict the analysis to the first three principal components (PCs), and find that PCA segregates the three types with the highest variance mapping SSP-equivalent age, along with an inextricable degeneracy with metallicity, even when all three PCs are included. Spectral fitting shows that stellar age dominates PC1, whereas PC2 and PC3 have a mixed dependence of age and metallicity. The trends support - independently of any model fitting - the hypothesis of an evolutionary sequence from star-formation to AGN to quiescence. As a further test of the consistency of the analysis, we apply the same methodology in different spectral windows, finding similar trends, but the variance is maximal in the blue wavelength range, roughly around the 4000A break. Astrophysics ; Physics ; Metallicity ; Galaxy ; Principal component analysis ; Sky ; Degeneracy (biology) ; Spectral line ; Star formation ; Astronomy ; Statistics ; Mathematics Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models
Authors: Majid Ghadiri | Mehrdad Farajzadeh Ahari | Mobin Marvi
Source: Research Square (preprint, 2023-12-04)
Field: Materials Science — Materials Chemistry

Auxetic Metamaterial Pre-twisted Helical Nanobeams: Vibrational Characteristics <title>Abstract</title> The current investigation pertains to the vibrational characteristics of an out of plane helical nanobeam composed of auxetic material. This study marks the first instance of such an analysis. The Frenet-triad is a mathematical tool utilized to account for the impact of curvature, allowing for the dynamic alteration of the coordinate system and the precise definition of the location vector. In order to examine this model, the governing equations are formulated utilizing Timoshenko's beam theory and Eringen's nonlocal elasticity theory, and applying Hamilton's principle. The generalized differential quadrature method (GDQM) is employed to solve the governing equations under various boundary conditions. The present study validates the precision and effectiveness of the existing model through a comparison between the outcomes obtained from the simplified approach and the benchmark results reported in the literature. The findings reveal a satisfactory level of conformity between the two sets of results. Ultimately, the numerical outcomes are derived with a focus on exploring the impact of various factors such as inclination angle, auxetic rib length, curvatures, tortuosity, and pre-twists on the helical nanobeam. The findings of this work may be used as a benchmark for further investigations. Auxetics ; Curvature ; Boundary value problem ; Metamaterial ; Mathematical analysis ; Quadrature (astronomy) ; Classical mechanics ; Physics ; Mathematics ; Geometry Nonlocal and gradient elasticity in micro/nano structures ; Cellular and Composite Structures ; Advanced Materials and Mechanics
Authors: Jon Bartholomew | Daniel Hutzschenreuter | Siniša Prugovečki | Cristian Zet
Source: ACTA IMEKO (article, 2023-03-31)
Field: Materials Science — Surfaces, Coatings and Films

Introductory notes for the Acta IMEKO first issue 2023, Special issue on metrology and digital transformation This is an editorial, hence no abstract. Metrology ; Transformation (genetics) ; Digital transformation ; Engineering ethics ; Computer science ; Engineering ; Physics ; Chemistry ; Optics ; World Wide Web Electron and X-Ray Spectroscopy Techniques ; Advancements in Photolithography Techniques
Authors: Xinqiang Ding
Source: arXiv (Cornell University) (preprint, 2023-10-31)
Field: Materials Science — Materials Chemistry

Bayesian Multistate Bennett Acceptance Ratio Methods The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating configurations sampled from thermodynamic states with a prior distribution, BayesMBAR computes a posterior distribution of free energies. Using the posterior distribution, we derive free energy estimations and compute their associated uncertainties. Notably, when a uniform prior distribution is used, BayesMBAR recovers the MBAR's result but provides more accurate uncertainty estimates. Additionally, when prior knowledge about free energies is available, BayesMBAR can incorporate this information into the estimation procedure by using non-uniform prior distributions. As an example, we show that, by incorporating the prior knowledge about the smoothness of free energy surfaces, BayesMBAR provides more accurate estimates than the MBAR method. Given MBAR's widespread use in free energy calculations, we anticipate BayesMBAR to be an essential tool in various applications of free energy calculations. Generalization ; Smoothness ; Bayesian probability ; Prior probability ; Energy (signal processing) ; Posterior probability ; Distribution (mathematics) ; Computer science ; Prior information ; Work (physics) ; Statistical physics ; Energy distribution ; Applied mathematics ; Mathematical optimization ; Algorithm ; Mathematics ; Statistics ; Physics ; Artificial intelligence ; Mathematical analysis ; Thermodynamics Machine Learning in Materials Science ; Spectroscopy and Quantum Chemical Studies ; Advanced Chemical Physics Studies
Authors: J. Erb | David Shrekenhamer | Timothy Sleasman | Thomas M. Antonsen | Steven M. Anlage
Source: arXiv (Cornell University) (preprint, 2023-08-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Control of the Scattering Properties of Complex Systems By Means of Tunable Metasurfaces We demonstrate the ability to control the scattering properties of a two-dimensional wave-chaotic microwave billiard through the use of tunable metasurfaces located on the interior walls of the billiard. The complex reflection coefficient of the metasurfaces can be varied by applying a DC voltage bias to varactor diodes on mushroom-shaped resonant patches, and this proves to be very effective at perturbing the eigenmodes of the cavity. Placing multiple metasurfaces inside the cavity allows us to engineer desired scattering conditions, such as coherent perfect absorption (CPA), by actively manipulating the poles and zeros of the scattering matrix through the application of multiple voltage biases. We demonstrate the ability to create on-demand CPA conditions at a specific frequency, and document the near-null of output power as a function of four independent parameters tuned through the CPA point. A remarkably low output-to-input power ratio of $\frac{P_{out}}{P_{in}} = 3.71 \times 10^{-8}$ is achieved near the CPA point at 8.54 GHz. Dynamical billiards ; Varicap ; Scattering ; Optics ; Physics ; Microwave ; Matrix (chemical analysis) ; Power (physics) ; Biasing ; Voltage ; Optoelectronics ; Materials science ; Capacitance ; Quantum mechanics Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Advanced Antenna and Metasurface Technologies