jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Shameena Beegum | R. Pandiselvam | S. V. Ramesh | Shivaji Hausrao Thube | Thava Prakasa Pandian | Anandu Chandra Khanashyam | M. R. Manikantan | K. B. Hebbar
Source: Quality Assurance and Safety of Crops & Foods (article, 2022-04-28)
Field: Chemistry — Inorganic Chemistry

A critical appraisal on the antimicrobial, oral protective, and anti-diabetic functions of coconut and its derivatives The coconut palm is aptly described as the “tree of life” because of its myriad of uses and diversified value added products. Coconut and its derivatives are considered to be an emerging functional food. It is also called a “miracle food”. In recent years, there have been conflicting reports regarding the consumption of coconut oil and its health benefits. In this backdrop, our article systematically analyses the antimicrobial, oral protective, and anti-diabetic effects of coconut products in light of the recent scientific literature. Numerous scientific reports have highlighted that the coconut oil has antimicrobial properties improving oral hygiene. Although its anti-obesity and hypoglycemic effects are backed by emerging scientific literature, many questions remain unanswered. In general, consumption of coconut oil has many beneficial effects; nevertheless, long-term clinical trials are warranted. Indeed, the exploration of coconut phytochemicals, clinical trials, and epidemiological studies unleash the true therapeutic prospects of coconut and its derivatives. At this juncture, we suggest shifting our research focus from the fatty acid composition of coconut oil towards characterization of other phytochemicals such as polyphenols, phytosterols, etc., conduct of clinical trials and epidemiological studies to unleash the true potential of coconut products. Coconut oil ; Antimicrobial ; Biotechnology ; Cocos nucifera ; Medicine ; Clinical trial ; Food science ; Traditional medicine ; Toxicology ; Biology ; Pathology ; Botany Coconut Research and Applications ; Natural Products and Biological Research ; Phytochemicals and Antioxidant Activities
Authors: P. Hao | Ziwei Dai | V. Laheri | F.A. Gilabert
Source: International Journal of Plasticity (article, 2022-10-28)
Field: Materials Science — Polymers and Plastics

A unified amorphous–crystalline viscoplastic hardening law for non-isothermal modelling of thermoplastics and thermosets Materials science ; Viscoplasticity ; Thermosetting polymer ; Constitutive equation ; Amorphous solid ; Hardening (computing) ; Isothermal process ; Composite material ; Softening ; Thermodynamics ; Finite element method ; Crystallography Polymer crystallization and properties ; Mechanical Behavior of Composites ; Polymer Nanocomposites and Properties
Authors: Alexandru B. Georgescu | Andrew J. Millis | James M. Rondinelli
Source: Physical review. B./Physical review. B (article, 2022-06-29)
Field: Materials Science — Materials Chemistry

Trigonal symmetry breaking and its electronic effects in the two-dimensional dihalides <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>M</mml:mi><mml:msub><mml:mi>X</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math> and trihalides <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>M</mml:mi><mml:msub><mml:mi>X</mml:mi><mml:mn>3</mml:mn></mml:msub></mml:mrow></mml:math> We study the consequences of the approximately trigonal (${D}_{3d}$) point symmetry of the transition metal ($M$) site in two-dimensional van der Waals ${MX}_{2}$ dihalides and ${MX}_{3}$ trihalides. The trigonal symmetry leads to a 2-2-1 orbital splitting of the transition metal $d$ shell, which is best represented by $d$ orbitals that describe the trigonal rather than ${O}_{h}$ symmetry. The ligand-ligand bond length differences (rather than metal-ligand) take the role of a Jahn-Teller-like mode and in combination with interlayer distances and dimensionality effects tune the crystal field splittings and bandwidths. These effects, in turn, are amplified by electronic correlation effects---leading to crystal field splittings of the order of 0.1--1 eV between the singlet and the lowest orbital doublet---as opposed to the often assumed degenerate $3\phantom{\rule{0.16em}{0ex}}{t}_{2g}$ states. Our calculations explain why most of the materials in this family are insulating, and why these considerations have to be taken into account in realistic models of them. Further, orbital order coupled to various lower symmetry lattice modes may lift the remaining orbital degeneracies, and we explain how these may support unique electronic states using ${\mathrm{ZrI}}_{2}$ and ${\mathrm{CuCl}}_{2}$ as examples, and offer a brief overview of possible electronic configurations in this class of materials. By building and analyzing Wannier models adapted to the appropriate symmetry we examine how the interplay among trigonal symmetry, electronic correlation effects, and $p\text{\ensuremath{-}}d$ orbital charge transfer leads to insulating, orbitally polarized magnetic and/or orbital-selective Mott states, and we provide a simple framework and numerical tool for others. Our paper establishes a rigorous framework to understand, control, and tune the electronic states in low-dimensional correlated halides. Our analysis shows that trigonal symmetry and its breaking is a key feature of the two-dimensional halides that needs to be accounted for in search of novel electronic states in materials ranging from ${\mathrm{CrI}}_{3}$ to $\ensuremath{\alpha}\text{\ensuremath{-}}{\mathrm{RuCl}}_{3}$. Ligand field theory ; Physics ; Atomic orbital ; Singlet state ; Crystallography ; Atomic physics ; Condensed matter physics ; Chemistry ; Quantum mechanics ; Ion ; Electron ; Excited state 2D Materials and Applications ; Iron-based superconductors research ; Inorganic Chemistry and Materials
Authors: Vincenzo Barone | Cristina Puzzarini
Source: Annual Review of Physical Chemistry (review, 2022-11-22)
Field: Chemistry — Spectroscopy

Gas-Phase Computational Spectroscopy: The Challenge of the Molecular Bricks of Life Gas-phase molecular spectroscopy is a natural playground for accurate quantum-chemical computations. However, the molecular bricks of life (e.g., DNA bases or amino acids) are challenging systems because of the unfavorable scaling of quantum-chemical models with the molecular size (active electrons) and/or the presence of large-amplitude internal motions. From the theoretical point of view, both aspects prevent the brute-force use of very accurate but very expensive state-of-the-art quantum-chemical methodologies. From the experimental point of view, both features lead to congested gas-phase spectra, whose assignment and interpretation are not at all straightforward. Based on these premises, this review focuses on the current status and perspectives of the fully a priori prediction of the spectral signatures of medium-sized molecules (containing up to two dozen atoms) in the gas phase with special reference to rotational and vibrational spectroscopies of some representative molecular bricks of life. Scaling ; Spectroscopy ; Molecule ; Chemical physics ; Phase (matter) ; Quantum ; Physics ; Chemistry ; Quantum mechanics ; Geometry ; Mathematics Molecular Spectroscopy and Structure ; Advanced Chemical Physics Studies ; Spectroscopy and Laser Applications
Authors: Nicole Strittmatter | Jennifer Moss | Alan Race | Daniel Sutton | Jaime Rodriguez Canales | Stephanie Ling | Edmond Wong | Joanne Wilson | Aaron Smith | Colin Howes | Josephine Bunch | Simon T. Barry | Richard J. A. Goodwin | Marianne Ashford
Source: Theranostics (article, 2022-01-01)
Field: Chemistry — Spectroscopy

Multi-modal molecular imaging maps the correlation between tumor microenvironments and nanomedicine distribution Gaining insight into the heterogeneity of nanoparticle drug distribution within tumors would improve both design and clinical translation of nanomedicines. There is little data showing the spatio-temporal behavior of nanomedicines in tissues as current methods are not able to provide a comprehensive view of the nanomedicine distribution, released drug or its effects in the context of a complex tissue microenvironment. Methods: A new experimental approach which integrates the molecular imaging and bioanalytical technologies MSI and IMC was developed to determine the biodistribution of total drug and drug metabolite delivered via PLA-PEG nanoparticles and to overlay this with imaging of the nanomedicine in the context of detailed tumor microenvironment markers. This was used to assess the nanomedicine AZD2811 in animals bearing three different pre-clinical PDX tumors. Results: This new approach delivered new insights into the nanoparticle/drug biodistribution. Mass spectrometry imaging was able to differentiate the tumor distribution of co-dosed deuterated non-nanoparticle-formulated free drug alongside the nanoparticle-formulated drug by directly visualizing both delivery approaches within the same animal or tissue. While the IV delivered free drug was uniformly distributed, the nanomedicine delivered drug was heterogeneous. By staining for multiple biomarkers of the tumor microenvironment on the same tumor sections using imaging mass cytometry, co-registering and integrating data from both imaging modalities it was possible to determine the features in regions with highest nanomedicine distribution. Nanomedicine delivered drug was associated with regions higher in macrophages, as well as more stromal regions of the tumor. Such a comparison of complementary molecular data allows delineation of drug abundance in individual cell types and in stroma. Conclusions: This multi-modal imaging solution offers researchers a better understanding of drug and nanocarrier distribution in complex tissues and enables data-driven drug carrier design. Nanomedicine ; Biodistribution ; Mass cytometry ; Context (archaeology) ; Drug delivery ; Distribution (mathematics) ; Tumor microenvironment ; Nanotechnology ; Biomedical engineering ; Chemistry ; Cancer research ; Nanoparticle ; Medicine ; Materials science ; Tumor cells ; Biology Mass Spectrometry Techniques and Applications ; Nanoparticle-Based Drug Delivery ; Inhalation and Respiratory Drug Delivery
Authors: Leon E. Niezen | Peter J. Schoenmakers | Bob W.J. Pirok
Source: Analytica Chimica Acta (article, 2022-02-18)
Field: Chemistry — Analytical Chemistry

Critical comparison of background correction algorithms used in chromatography The objective of the present work was to make a quantitative and critical comparison of a number of drift and noise-removal algorithms, which were proven useful by other researchers, but which had never been compared on an equal basis. To make a rigorous and fair comparison, a data generation tool is developed in this work, which utilizes a library of experimental backgrounds, as well as peak shapes obtained from curve fitting on experimental data. Several different distribution functions are used, such as the log-normal, bi-Gaussian, exponentially convoluted Gaussian, exponentially modified Gaussian and modified Pearson VII distributions. The tool was used to create a set of hybrid (part experimental, part simulated) data, in which the background and all peak profiles and areas are known. This large data set (500 chromatograms) was analysed using seven different drift-correction and five different noise-removal algorithms (35 combinations). Root-mean square errors and absolute errors in peak area were determined and it was shown that in most cases the combination of sparsity-assisted signal smoothing and asymmetrically reweighted penalized least-squares resulted in the smallest errors for relatively low-noise signals. However, for noisier signals the combination of sparsity-assisted signal smoothing and a local minimum value approach to background correction resulted in lower absolute errors in peak area. The performance of correction algorithms was studied as a function of the density and coverage of peaks in the chromatogram, shape of the background signal, and noise levels. The developed data-generation tool is published along with this article, so as to allow similar studies with other simulated data sets and possibly other algorithms. The rigorous assessment of correction algorithms in this work may facilitate further automation of data-analysis workflows. Smoothing ; Algorithm ; Noise (video) ; Gaussian ; Data set ; Gaussian noise ; SIGNAL (programming language) ; Statistics ; Chemistry ; Mathematics ; Artificial intelligence ; Computer science Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models ; Analytical Chemistry and Chromatography
Authors: Mingli Chen | Meng Wang
Source: Atomic Spectroscopy (article, 2022-06-30)
Field: Materials Science — Surfaces, Coatings and Films

ICP-MS-Based Methodology In Metallomics: Towards Single Particle Analysis, Single Cell Analysis, And Spatial Metallomics As an emerging interdisciplinary science, metallomics aims to integrate research fields related to metals and metalloids in biological systems from a systematic perspective. Inductively coupled plasma mass spectrometry (ICP-MS) is considered one of the most versatile tools for metallomics research. This review presents a brief overview of ICP-MS and describes recent advances in ICP-MS instrumentation. Then, ICP-MS-based methods and applications are discussed, focusing on single particle analysis, single cell analysis, and spatial metallomics. With the rapid developments in instrumentation and methodology, ICP-MS-based methodologies will evolve further and play a dominant role in metallomics research. Chemistry ; Particle (ecology) Electron and X-Ray Spectroscopy Techniques ; Ion-surface interactions and analysis ; Analytical chemistry methods development
Authors: Amelia C. Y. Liu | Espen Drath Bøjesen | Rico F. Tabor | Stephen Mudie | Alessio Zaccone | Peter Harrowell | Timothy C. Petersen
Source: Science Advances (article, 2022-03-18)
Field: Materials Science — Materials Chemistry

Local symmetry predictors of mechanical stability in glasses The mechanical properties of crystals are controlled by the translational symmetry of their structures. But for glasses with a disordered structure, the link between the symmetry of local particle arrangements and stability is not well established. In this contribution, we provide experimental verification that the centrosymmetry of nearest-neighbor polyhedra in a glass strongly correlates with the local mechanical stability. We examine the distribution of local stability and local centrosymmetry in a glass during aging and deformation using microbeam x-ray scattering. These measurements reveal the underlying relationship between particle-level structure and larger-scale behavior and demonstrate that spatially connected, coordinated local transformations to lower symmetry structures are fundamental to these phenomena. While glassy structures lack obvious global symmetry breaking, local structural symmetry is a critical factor in predicting stability. Local symmetry ; Symmetry (geometry) ; Stability (learning theory) ; Polyhedron ; Materials science ; Symmetry breaking ; Microbeam ; Deformation (meteorology) ; Particle (ecology) ; Local structure ; Condensed matter physics ; Chemical physics ; Statistical physics ; Physics ; Optics ; Composite material ; Mathematics ; Geometry ; Quantum mechanics ; Computer science Material Dynamics and Properties ; Glass properties and applications ; Metallic Glasses and Amorphous Alloys
Authors: Shawn J. Rice | Chandra P. Belani
Source: PROTEOMICS (article, 2022-06-16)
Field: Chemistry — Spectroscopy

Optimizing data‐independent acquisition (DIA) spectral library workflows for plasma proteomics studies Traditional data-independent acquisition (DIA) workflows employ off-column fractionation with data-dependent acquisition (DDA) to generate spectral libraries for data extraction. Recent advances have led to the establishment of library-independent approaches for DIA analyses. The selection of a DIA workflow may affect the outcome of plasma proteomics studies. Here, we establish a gas-phase fractionation (GPF) workflow to create DIA libraries for DIA with parallel accumulation and serial fragmentation (diaPASEF). This workflow along with three other workflows, fractionated DDA libraries, fractionated DIA libraries, and predicted spectra libraries, were evaluated on 20 plasma samples from nonsmall cell lung cancer patients with low or high levels of IL-6. We sought to optimize protein identification and total experiment time. The novel GPF workflow for diaPASEF outperformed the traditional ddaPASEF workflow in the number of identified and quantified proteins. A library-independent workflow based on predicted spectra identified and quantified the most proteins in our experiment at the cost of computational power. Overall, the choice of DIA library workflow seemed to have a limited effect on the overall outcome of a plasma proteomics experiment, but it can affect the number of proteins identified and the total experiment time. Workflow ; Proteomics ; Computer science ; Identification (biology) ; Proteome ; Computational biology ; Bioinformatics ; Chemistry ; Database ; Biology Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Ajay Bhandari | Kartikey Jaiswal | Anup Singh | Wenbo Zhan
Source: Cancers (article, 2022-08-29)
Field: Materials Science — Biomaterials

Convection-Enhanced Delivery of Antiangiogenic Drugs and Liposomal Cytotoxic Drugs to Heterogeneous Brain Tumor for Combination Therapy Although convection-enhanced delivery can successfully bypass the blood-brain barrier, its clinical performance remains disappointing. This is primarily attributed to the heterogeneous intratumoral environment, particularly the tumor microvasculature. This study investigates the combined convection-enhanced delivery of antiangiogenic drugs and liposomal cytotoxic drugs in a heterogeneous brain tumor environment using a transport-based mathematical model. The patient-specific 3D brain tumor geometry and the tumor's heterogeneous tissue properties, including microvascular density, porosity and cell density, are extracted from dynamic contrast-enhanced magnetic resonance imaging data. Results show that antiangiogenic drugs can effectively reduce the tumor microvascular density. This change in tissue structure would inhibit the fluid loss from the blood to prevent drug concentration from dilution, and also reduce the drug loss by blood drainage. The comparisons between different dosing regimens demonstrate that the co-infusion of liposomal cytotoxic drugs and antiangiogenic drugs has the advantages of homogenizing drug distribution, increasing drug accumulation, and enlarging the volume where tumor cells can be effectively killed. The delivery outcomes are susceptible to the location of the infusion site. This combination treatment can be improved by infusing drugs at higher microvascular density sites. In contrast, infusion at a site with high cell density would lower the treatment effectiveness of the whole brain tumor. Results obtained from this study can deepen the understanding of this combination therapy and provide a reference for treatment design and optimization that can further improve survival and patient quality of life. Drug delivery ; Medicine ; Liposome ; Brain tumor ; Drug ; Pharmacology ; Distribution (mathematics) ; Pharmacokinetics ; Cytotoxic T cell ; Cancer research ; Biomedical engineering ; Pathology ; Materials science ; Chemistry ; Nanotechnology Nanoparticle-Based Drug Delivery ; Glioma Diagnosis and Treatment ; Mathematical Biology Tumor Growth
Authors: Ali. A. Salem | Kwan Yiew Lau | Zulkurnain Abdul‐Malek | Nabil Mohammed | Abdullah M. Al‐Shaalan | Abdullrahman A. Al-Shamma’a | Hassan M. Hussein Farh
Source: Polymers (article, 2022-02-14)
Field: Materials Science — Materials Chemistry

Polymeric Insulator Conditions Estimation by Using Leakage Current Characteristics Based on Simulation and Experimental Investigation The current work contributes an estimate of the time-frequency characteristics of a leakage current in assessing the health condition of a polluted polymeric insulator. A 33 kV polymer insulator string was subjected to a series of laboratory tests under a range of environmental conditions, including pollution, wetting rate (WR), non-soluble deposit density (NSDD), and non-uniform distribution pollution (F<sub>T/B</sub>). The temporal and frequency features of the leakage current were then extracted and used as assessment indicators for insulator conditions based on laboratory test findings. Two indices were generated from the leakage current waveform in the time domain: the curve slope index (F<sub>1</sub>), which is determined by measuring the inclination of the curve between two successive time peaks of the leakage current, and the crest factor indicator (F<sub>2</sub>). The frequency domain of the leakage current signal was used to calculate the other two indices. These are the odd harmonic indicators derived from the odd frequency harmonics of the leakage current up to the 9th component (F<sub>3</sub>) and the 5th to 3rd harmonics ratio (F<sub>4</sub>). The findings showed that the suggested indicators were capable of evaluating insulator conditions. Finally, the confusion matrix for the experimental and prediction results obtained with the proposed indices was used to assess which indicator performed the best. Therefore, the analysis suggests an alternative and effective method for estimating the health condition of a polluted insulator through leakage current characteristics obtained in the time and frequency domains. Insulator (electricity) ; Harmonics ; Waveform ; Leakage (economics) ; Materials science ; Frequency domain ; Time domain ; Acoustics ; Environmental science ; Mathematics ; Composite material ; Computer science ; Electrical engineering ; Physics ; Engineering ; Voltage High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Infrastructure Maintenance and Monitoring
Authors: Kenneth Weke | Sachin Kote | Jakub Faktor | Sofian Al Shboul | Naomi Uwugiaren | Paul M. Brennan | David R. Goodlett | Ted R. Hupp | Irena Đapić
Source: Analytica Chimica Acta (article, 2022-03-11)
Field: Chemistry — Spectroscopy

DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues Developments in quantitative proteomics and data-independent acquisition (DIA) methodology is enabling quantification of proteins in biological samples. Currently, there are a few reports on DIA mass spectrometry (MS) approaches for proteome analysis of formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, to facilitate detection and quantification of immune- and glioblastoma (GBM)-relevant proteins from FFPE patient materials, we established a simple and precise DIA-MS workflow. We first evaluated different lysis buffers for their efficiency in protein extractions from FFPE GBM tissues. Our results showed that more than 1700 proteins were detected and over 1400 proteins were quantified from GBM FFPE tissue microdissections. GBM-relevant proteins (e.g., GFAP, FN1, VIM, and MBP) were quantified with high precision (median coefficient of variation <12%). In addition, immune-related proteins (e.g., ILF2, MIF, and CD38) were consistently detected and quantified. The strategy holds great potential for routinizing protein quantification in FFPE tissue samples. Proteome ; Chemistry ; Proteomics ; Quantitative proteomics ; Lysis ; Mass spectrometry ; Molecular biology ; Computational biology ; Chromatography ; Biochemistry ; Biology ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications