jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Jade K. Macdonald | Harrison Taylor | Mengjun Wang | Andrew DelaCourt | Christin Edge | David Lewin | Naoto Kubota | Naoto Fujiwara | Fahmida Rasha | Cesia A. Marquez | Atsushi Ono | Shiro Oka | Kazuaki Chayama | Sara Lewis | Bachir Taouli | Myron Schwartz | Maria Isabel Fiel | Richard R. Drake | Yujin Hoshida | Anand S. Mehta | Peggi M. Angel
Source: Journal of Proteome Research (article, 2024-07-09)
Field: Chemistry — Spectroscopy

The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma Hepatocellular carcinoma (HCC) mortality rates continue to increase faster than those of other cancer types due to high heterogeneity, which limits diagnosis and treatment. Pathological and molecular subtyping have identified that HCC tumors with poor outcomes are characterized by intratumoral collagenous accumulation. However, the translational and post-translational regulation of tumor collagen, which is critical to the outcome, remains largely unknown. Here, we investigate the spatial extracellular proteome to understand the differences associated with HCC tumors defined by Hoshida transcriptomic subtypes of poor outcome (Subtype 1; S1; <i>n</i> = 12) and better outcome (Subtype 3; S3; <i>n</i> = 24) that show differential stroma-regulated pathways. Collagen-targeted mass spectrometry imaging (MSI) with the same-tissue reference libraries, built from untargeted and targeted LC-MS/MS was used to spatially define the extracellular microenvironment from clinically-characterized, formalin-fixed, paraffin-embedded tissue sections. Collagen α-1(I) chain domains for discoidin-domain receptor and integrin binding showed distinctive spatial distribution within the tumor microenvironment. Hydroxylated proline (HYP)-containing peptides from the triple helical regions of fibrillar collagens distinguished S1 from S3 tumors. Exploratory machine learning on multiple peptides extracted from the tumor regions could distinguish S1 and S3 tumors (with an area under the receiver operating curve of ≥0.98; 95% confidence intervals between 0.976 and 1.00; and accuracies above 94%). An overall finding was that the extracellular microenvironment has a high potential to predict clinically relevant outcomes in HCC. Tumor microenvironment ; Hepatocellular carcinoma ; Stroma ; Extracellular ; Proteome ; Cancer research ; Discoidin domain ; Biology ; Extracellular matrix ; Pathology ; Chemistry ; Immunohistochemistry ; Medicine ; Bioinformatics ; Biochemistry ; Receptor ; Receptor tyrosine kinase Advanced Proteomics Techniques and Applications ; Cancer, Lipids, and Metabolism ; Cell Adhesion Molecules Research
Authors: Zhishuai Zheng | Zhedong Ge | Zhikang Tian | Xiaoxia Yang | Yucheng Zhou
Source: Journal of Real-Time Image Processing (article, 2024-08-01)
Field: Chemistry — Organic Chemistry

WoodGLNet: a multi-scale network integrating global and local information for real-time classification of wood images Scale (ratio) ; Artificial intelligence ; Computer science ; Pattern recognition (psychology) ; Computer vision ; Geography ; Cartography Wood and Agarwood Research ; Industrial Vision Systems and Defect Detection ; Remote Sensing and LiDAR Applications
Authors: Marcela Vieira da Costa | Ênio Tarso de Souza Costa | João Paulo Dianin de Oliveira | Geraldo Jânio Lima | Luiz Roberto Guimarães Guilherme | Geila Santos Carvalho | Mariene Helena Duarte | Jernimo Juvêncio Chivale | David C. Weindorf | Somsubhra Chakraborty | Bruno Teixeira Ribeiro
Source: Spectrochimica Acta Part B Atomic Spectroscopy (article, 2024-07-18)
Field: Chemistry — Analytical Chemistry

Assessment of coffee leaves nutritive value via portable X-ray fluorescence spectrometry and machine learning algorithms Mass spectrometry ; X-ray fluorescence ; Algorithm ; X-ray ; Analytical Chemistry (journal) ; Chemistry ; Fluorescence ; Value (mathematics) ; Computer science ; Chromatography ; Physics ; Machine learning ; Optics Spectroscopy and Chemometric Analyses ; Heavy Metals in Plants ; Coffee research and impacts
Authors: Jun Hu | Wennan Liu | Liang Yang | Haohao Lv | Chaohui Zhan | Peng Qiao
Source: Infrared Physics & Technology (article, 2024-04-25)
Field: Chemistry — Analytical Chemistry

Research on classification methods for rubber based on terahertz time-domain spectroscopy with data fusion strategy Terahertz radiation ; Spectroscopy ; Terahertz time-domain spectroscopy ; Terahertz spectroscopy and technology ; Materials science ; Fusion ; Sensor fusion ; Computer science ; Domain (mathematical analysis) ; Time domain ; Optics ; Remote sensing ; Artificial intelligence ; Optoelectronics ; Physics ; Computer vision ; Astronomy ; Mathematics ; Geology ; Mathematical analysis Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Advanced Chemical Sensor Technologies
Authors: Katsuhiko Ariga
Source: Micromachines (review, 2024-02-17)
Field: Chemistry — Organic Chemistry

Confined Space Nanoarchitectonics for Dynamic Functions and Molecular Machines Nanotechnology has advanced the techniques for elucidating phenomena at the atomic, molecular, and nano-level. As a post nanotechnology concept, nanoarchitectonics has emerged to create functional materials from unit structures. Consider the material function when nanoarchitectonics enables the design of materials whose internal structure is controlled at the nanometer level. Material function is determined by two elements. These are the functional unit that forms the core of the function and the environment (matrix) that surrounds it. This review paper discusses the nanoarchitectonics of confined space, which is a field for controlling functional materials and molecular machines. The first few sections introduce some of the various dynamic functions in confined spaces, considering molecular space, materials space, and biospace. In the latter two sections, examples of research on the behavior of molecular machines, such as molecular motors, in confined spaces are discussed. In particular, surface space and internal nanospace are taken up as typical examples of confined space. What these examples show is that not only the central functional unit, but also the surrounding spatial configuration is necessary for higher functional expression. Nanoarchitectonics will play important roles in the architecture of such a total system. Nanotechnology ; Space (punctuation) ; Function (biology) ; Molecular machine ; Computer science ; Materials science Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials ; Nanopore and Nanochannel Transport Studies
Authors: Souhir Bouzidi | Najah Rhimi | J. Dhahri | Zouhaier Aloui | Abdelaziz Bouazizi | K. Khirouni | Malek Gassoumi | J. Juraszek
Source: Journal of Materials Science Materials in Electronics (article, 2024-12-23)
Field: Materials Science — Materials Chemistry

Eu-doped Mg–Ni ferrites: a reliable strategy to enhance dielectric properties for high-frequency applications Materials science ; Spinel ; Ionic radius ; Dielectric ; Analytical Chemistry (journal) ; X-ray photoelectron spectroscopy ; Rietveld refinement ; Lattice constant ; Dielectric spectroscopy ; Crystallite ; Doping ; Scanning electron microscope ; Dielectric loss ; Ion ; Nuclear magnetic resonance ; Diffraction ; Crystal structure ; Crystallography ; Optics ; Optoelectronics ; Metallurgy ; Physical chemistry ; Electrochemistry ; Chemistry ; Composite material ; Electrode Magnetic Properties and Synthesis of Ferrites ; Electromagnetic wave absorption materials ; Multiferroics and related materials
Authors: Natalie Warren | Umar Yunusa | Arnav B. Singhal | Emily A. Sprague‐Klein
Source: Chemical Physics Reviews (article, 2024-02-05)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Facilitating excited-state plasmonics and photochemical reaction dynamics Continuously advancing technologies is crucial to tackling modern challenges such as efficient energy transfer, directing catalytic behavior, and better understanding of microscopic phenomena. At the heart of many of these problems is nanoscale chemistry. In previous decades, the scientific community has made significant progress in nanoscale structures and technologies, especially relating to their interactions with light. Plasmonic nanostructures have been extensively studied over the past decades because of their fascinating properties and vast technological applications. They can confine light into intense local electromagnetic fields, which has been exploited in the fields of spectroscopy, energy harvesting, optoelectronics, chemical sensing, and biomedicine. Recently, however, plasmonic nanostructures have shown great potential to trigger chemical transformations of proximal molecular species via hot carrier and thermally driven processes. In this review, we discuss the basic concepts governing nanoscale light–matter interactions, the immediate phenomena induced by them, and how we can use nanoscale light–matter interactions to our advantage with surface-enhanced spectroscopy techniques and chemical reactions in confined plasmonic environments. Excited state ; Plasmon ; Photochemistry ; Dynamics (music) ; Reaction dynamics ; Chemistry ; Materials science ; Physics ; Optoelectronics ; Atomic physics ; Molecule ; Organic chemistry Gold and Silver Nanoparticles Synthesis and Applications ; Plasmonic and Surface Plasmon Research ; Copper-based nanomaterials and applications
Authors: Leonarc Michelle Santos | Vince Angelo A. Chavez | Denny Lane B. Sombillo
Source: Journal of Physics G Nuclear and Particle Physics (article, 2024-11-06)
Field: Chemistry — Spectroscopy

Pole structure of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mrow> <mml:mi>P</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>ψ</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>N</mml:mi> </mml:mrow> </mml:msubsup> <mml:msup> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>4312</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> </mml:mrow> </mml:msup> </mml:math> via machine learning and uniformized S-matrix Abstract We probed the pole structure of the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi>P</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>ψ</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>N</mml:mi> </mml:mrow> </mml:msubsup> <mml:msup> <mml:mrow> <mml:mo stretchy="false">(</mml:mo> <mml:mn>4312</mml:mn> <mml:mo stretchy="false">)</mml:mo> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> </mml:mrow> </mml:msup> </mml:math> using a trained deep neural network. The training dataset was generated using uniformized independent S -matrix poles to ensure that the resulting interpretation is as model-independent as possible. To prevent possible ambiguity in the interpretation of the pole structure, we included the contribution from the off-diagonal elements of the S -matrix. Our trained model favors a possible three-pole structure of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msubsup> <mml:mrow> <mml:mi>P</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>ψ</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>N</mml:mi> </mml:mrow> </mml:msubsup> <mml:msup> <mml:mrow> <mml:mfenced close=")" open="("> <mml:mrow> <mml:mn>4312</mml:mn> </mml:mrow> </mml:mfenced> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> </mml:mrow> </mml:msup> </mml:math> signal, with one pole on each of the unphysical sheets. The two poles on two different Riemann sheets can be associated with a pole-shadow pair which is a characteristic of a true resonance. On the other hand, the last isolated pole is most likely associated with the coupled-channel effect in the meson–baryon system. The combined effect of these poles produced a peak below the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:msub> <mml:mrow> <mml:mi mathvariant="normal">Σ</mml:mi> </mml:mrow> <mml:mrow> <mml:mi>c</mml:mi> </mml:mrow> </mml:msub> <mml:mover accent="true"> <mml:mrow> <mml:mi>D</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>¯</mml:mo> </mml:mrow> </mml:mover> </mml:math> threshold which mimics the line shape of a hadronic molecule. Matrix (chemical analysis) ; Physics ; Computer science ; Materials science ; Composite material Mass Spectrometry Techniques and Applications ; Medical Imaging Techniques and Applications ; Chemical Thermodynamics and Molecular Structure
Authors: Zuhao Shi | Bin Liu | Yuanzheng Yue | Arramel Arramel | Neng Li
Source: Journal of the American Ceramic Society (article, 2024-01-31)
Field: Chemistry — Inorganic Chemistry

Unraveling medium‐range order and melting mechanism of ZIF‐4 under high temperature Abstract Glass formation in zeolitic imidazolate frameworks (ZIFs) has garnered significant attention in the field of metal–organic frameworks (MOFs) in recent years. Numerous works have been conducted to investigate the microscopic mechanisms involved in the melting–quenching process of ZIFs. Understanding the density variations that occur during the melting process of ZIFs is crucial for comprehending the origins of glass formation. However, conducting large‐scale simulations has been challenging due to limitations in computational resources. In this work, we used deep‐learning methods to accurately construct a potential function that describes the atomic‐scale melting behavior of ZIF‐4. The results revealed the spatial heterogeneity associated with the formation of low‐density phases during the melting process of ZIF‐4. This work discusses the advantages and limitations of applying deep‐learning simulation methods to complex structures like ZIFs, providing valuable insights for the development of machine‐learning approaches in designing MOF glasses. Melting temperature ; Mechanism (biology) ; Atmospheric temperature range ; Materials science ; Range (aeronautics) ; Order (exchange) ; Chemistry ; Chemical engineering ; Mineralogy ; Thermodynamics ; Composite material ; Physics ; Business Metal-Organic Frameworks: Synthesis and Applications ; Crystallography and molecular interactions ; X-ray Diffraction in Crystallography
Authors: Monika Sobiech
Source: International Journal of Molecular Sciences (review, 2024-11-30)
Field: Chemistry — Analytical Chemistry

Computer-Assisted Strategies as a Tool for Designing Green Monomer-Based Molecularly Imprinted Materials Molecularly imprinted polymers (MIPs) are defined as artificial receptors due to their selectivity and specificity. Their advantageous properties compared to biological alternatives have sparked interest among scientists, as detailed in numerous review papers. Currently, there is significant attention on adhering to the principles of green chemistry and environmental protection. In this context, MIP research groups have focused on developing eco-friendly procedures. The application of "greener" monomers and reagents, along with the utilization of computational methodologies for design and property analysis, are two activities that align with the green chemistry principles for molecularly imprinted technology. This review discusses the application of computational methodologies in the preparation of MIPs based on eco-friendly non-acrylic/vinylic monomers and precursors, such as alkoxysilanes, ionic liquids, deep eutectic solvents, bio-based molecules-specifically saccharides, and biomolecules like proteins. It provides a brief introduction to MIP materials, the green aspects of MIP production, and the application of computational simulations. Following this, brief descriptions of the studied monomers, molecular simulation studies of green monomer-based MIPs, and computational strategies are presented. Finally, conclusions and an outlook on the future directions of computational analysis in the production of green imprinted materials are pointed out. To the best of my knowledge, this work is the first to combine these two aspects of MIP green chemistry principles. Molecularly imprinted polymer ; Molecular imprinting ; Monomer ; Nanotechnology ; Chemistry ; Materials science ; Computer science ; Combinatorial chemistry ; Organic chemistry ; Selectivity ; Polymer ; Catalysis Analytical chemistry methods development ; Analytical Chemistry and Chromatography ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Zhen Zhang | Shiya Chen | Feng Zheng | Vladimir Antropov | Yang Sun | Kai‐Ming Ho
Source: Journal of the American Chemical Society (article, 2024-11-20)
Field: Materials Science — Materials Chemistry

Accelerated Exploration of Empty Material Compositional Space: Mg–Fe–B Ternary Metal Borides Borides are a family of materials with valuable properties for various applications. Their diverse structures and compositions, yet disparity in the constituent chemical elements for the known compounds, give elemental substitutions for prototypes great potential for material discovery. To explore uncharted material compositional space, we develop a workflow that joins high-throughput crystal structure prediction and automated diffraction pattern matching to discover new compounds with significant prediction and synthesis hurdles. Utilizing the workflow, we explore the empty Mg-Fe-B ternary compositional space, previously uncharted largely due to the immiscibility of Mg and Fe, as a paradigm. A total of 275 ternary boride prototypes are classified, using which we predict 23 (158) stable and metastable ternary phases within 50 (200) meV/atom above the convex hull. We identify Gd<sub>2</sub>(FeB)<sub>7</sub>-type Mg<sub>2</sub>Fe<sub>7</sub>B<sub>7</sub> and ZrCo<sub>3</sub>B<sub>2</sub>-type MgFe<sub>3</sub>B<sub>2</sub> to match previously unsolved experimental powder X-ray diffraction (PXRD) patterns. The discovered Mg<sub>2</sub>Fe<sub>7</sub>B<sub>7</sub> and related channeled structures feature mismatched Mg and (FeB) sublattice periods, for which we conduct structural analyses with respect to the PXRD. They are predicted to exhibit exceptionally fast superionic transport of Mg and outstanding electrochemical performance, which serve as post-Li-ion battery candidate electrode materials. This result opens a new avenue for borides' potential applications as electrode materials and fast ionic conductors. This work also portrays the map and landscape of ternary metal borides with similar chemical environments. With high efficiency, the prototype- and PXRD-assisted crystal structure prediction workflow opens a new avenue for exploring various material compositional spaces across the periodic table. Ternary operation ; Boride ; Metastability ; Chemistry ; Space (punctuation) ; Workflow ; Crystallography ; Boron ; Atom (system on chip) ; Inorganic chemistry ; Computer science ; Database ; Parallel computing Boron and Carbon Nanomaterials Research ; Advanced materials and composites ; Machine Learning in Materials Science
Authors: Pernilla Helmer | Jonas Björk | Johanna Rosén
Source: Inorganic Chemistry (article, 2024-08-26)
Field: Materials Science — Materials Chemistry

Computational Screening of Chalcogen-Terminated Inherent Multilayer MXenes and M<sub>2</sub>AX Precursors Sulfur-terminated single sheet (ss-)MXene was recently achieved by delamination of multilayered van der Waals bonded (vdW)-MXenes Nb<sub>2</sub>CS<sub>2</sub> and Ta<sub>2</sub>CS<sub>2</sub> synthesized through solid-state synthesis, rather than via the traditional way of selectively etching A-layers from the corresponding MAX phase. Inspired by this, we perform a computational screening study of vdW-MXenes M<sub>2</sub>CCh<sub>2</sub> isotypical to Nb<sub>2</sub>CS<sub>2</sub> and Ta<sub>2</sub>CS<sub>2</sub>, with M = Sc, Y, Ti, Zr, Hf, V, Nb, Ta, Mo, or W and Ch = S, Se, or Te. The thermodynamic stability of each vdW-MXene M<sub>2</sub>CCh<sub>2</sub> is assessed, and the dynamical stability of both vdW- and ss-MXene is considered through phonon dispersions. We predict seven stable vdW-MXenes, out of which four have not been reported previously, and one, V<sub>2</sub>CSe<sub>2</sub>, incorporates a new transition metal element into this family of materials. Electronic properties are presented for the vdW- and ss-forms of the stable vdW-MXenes, suggesting that the materials are either metallic, semimetallic, or semiconducting. In previous experimental reports the vdW-MXene Nb<sub>2</sub>CS<sub>2</sub> is synthesized by manipulation of the corresponding M<sub>2</sub>AX phase Nb<sub>2</sub>SC. Therefore, we also evaluate the thermodynamic stability of the corresponding M<sub>2</sub>AX phases, identifying 15 potentially stable phases. Six of these are experimentally reported, leaving nine new M<sub>2</sub>AX phases for future experimental investigation. MXenes ; van der Waals force ; Chalcogen ; Chemistry ; MAX phases ; Chemical stability ; Metal ; Phase (matter) ; Chemical physics ; Transition metal ; Crystallography ; Nanotechnology ; Molecule ; Materials science ; Organic chemistry MXene and MAX Phase Materials ; 2D Materials and Applications ; Ferroelectric and Negative Capacitance Devices
Authors: Yuya Oaki | Kosuke Sato
Source: RSC Applied Polymers (article, 2024-11-19)
Field: Materials Science — Polymers and Plastics

Amorphous conjugated polymer networks as an emerging class of polymer nanostructures This Perspective focuses on the unique polymerization processes, structures, and properties of amorphous conjugated polymer networks (CPNs) derived from simultaneous and random copolymerization of multiple conjugated monomers. Conjugated system ; Polymer ; Amorphous solid ; Nanostructure ; Materials science ; Nanotechnology ; Polymer science ; Chemistry ; Composite material ; Organic chemistry Conducting polymers and applications ; Advanced Polymer Synthesis and Characterization ; Dendrimers and Hyperbranched Polymers
Authors: Timo Sommer | Cian Clarke | Max García‐Melchor
Source: Chemical Science (review, 2024-11-28)
Field: Materials Science — Materials Chemistry

Beyond chemical structures: lessons and guiding principles for the next generation of molecular databases Databases of molecules and materials are indispensable for advancing chemical research, especially when enriched with electronic structure information from quantum chemistry methods like density functional theory. In this perspective, we review and analyze the current landscape of materials and molecular databases containing quantum chemical data. Our analysis reveals that the materials community has significantly benefited from data platforms such as the Materials Project, which seamlessly integrate chemical structures, electronic structure data, and open-source software. Conversely, quantum chemical data for molecular systems remains largely fragmented across individual datasets, lacking the comprehensive framework of a unified database. We distilled insights from these existing data resources into seven guiding principles termed QUANTUM, which build upon the foundational FAIR principles of data sharing (Findable, Accessible, Interoperable, and Reusable). These principles are aimed at advancing the development of molecular databases into robust, integrated data platforms. We conclude with an outlook on both short- and long-term objectives, guided by these QUANTUM principles, to foster future advancements in molecular quantum databases and enhance their utility for the research community. Interoperability ; Computer science ; Data science ; Database ; Quantum chemical ; Perspective (graphical) ; Data sharing ; Nanotechnology ; Chemistry ; World Wide Web ; Materials science ; Molecule Machine Learning in Materials Science ; Scientific Computing and Data Management ; Research Data Management Practices