jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Kenneth R. Olson | Kasey J. Clear | Tsuyoshi Takata | Yan Gao | Zhilin Ma | Ella Pfaff | Anthony Travlos | Jennifer Luu | Katherine J. Wilson | Zachary Joseph | Ian T Kyle | Stephen M. Kasko | Prentiss Jones | Jon M. Fukuto | Ming Xian | Gang Wu | Karl D. Straub
Source: Antioxidants (article, 2024-05-20)
Field: Chemistry — Organic Chemistry

Reaction Mechanisms of H2S Oxidation by Naphthoquinones 1,4-naphthoquinones (NQs) catalytically oxidize H<sub>2</sub>S to per- and polysufides and sulfoxides, reduce oxygen to superoxide and hydrogen peroxide, and can form NQ-SH adducts through Michael addition. Here, we measured oxygen consumption and used sulfur-specific fluorophores, liquid chromatography tandem mass spectrometry (LC-MS/MS), and UV-Vis spectrometry to examine H<sub>2</sub>S oxidation by NQs with various substituent groups. In general, the order of H<sub>2</sub>S oxidization was DCNQ ~ juglone > 1,4-NQ > plumbagin >DMNQ ~ 2-MNQ > menadione, although this order varied somewhat depending on the experimental conditions. DMNQ does not form adducts with GSH or cysteine (Cys), yet it readily oxidizes H<sub>2</sub>S to polysulfides and sulfoxides. This suggests that H<sub>2</sub>S oxidation occurs at the carbonyl moiety and not at the quinoid 2 or 3 carbons, although the latter cannot be ruled out. We found little evidence from oxygen consumption studies or LC-MS/MS that NQs directly oxidize H<sub>2</sub>S<sub>2-4</sub>, and we propose that apparent reactions of NQs with inorganic polysulfides are due to H<sub>2</sub>S impurities in the polysulfides or an equilibrium between H<sub>2</sub>S and H<sub>2</sub>S<sub>n</sub>. Collectively, NQ oxidation of H<sub>2</sub>S forms a variety of products that include hydropersulfides, hydropolysulfides, sulfenylpolysulfides, sulfite, and thiosulfate, and some of these reactions may proceed until an insoluble S<sub>8</sub> colloid is formed. Chemistry ; Menadione ; Plumbagin ; Hydrogen peroxide ; Sulfite ; Juglone ; Adduct ; Oxygen ; Moiety ; Medicinal chemistry ; Organic chemistry ; Combinatorial chemistry Free Radicals and Antioxidants ; Organic Chemistry Cycloaddition Reactions ; Sulfur-Based Synthesis Techniques
Authors: Renan Tosin | Mário Cunha | Filipe Monteiro-Silva | Filipe Neves dos Santos | Teresa Barroso | Rui C. Martins
Source: Frontiers in Plant Science (article, 2024-02-15)
Field: Chemistry — Analytical Chemistry

Bi-directional hyperspectral reconstruction of cherry tomato: diagnosis of internal tissues maturation stage and composition The proposed approach for inner tomato tissue spectral inference is highly reliable, provides early indications and is easy to operate. This study highlights the potential of Vis-NIR devices in precision fruit maturation assessment, surpassing conventional labour-intensive techniques in cost-effectiveness and efficiency. The implications of this advancement extend to various agronomic and food chain applications, promising substantial improvements in monitoring and enhancing fruit quality. Hyperspectral imaging ; Lycopene ; Principal component analysis ; Partial least squares regression ; Pulp (tooth) ; Correlation coefficient ; Mathematics ; Coefficient of determination ; Horticulture ; Chlorophyll ; Biological system ; Computer science ; Chemistry ; Food science ; Artificial intelligence ; Biology ; Carotenoid ; Statistics ; Medicine ; Pathology Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Remote Sensing in Agriculture
Authors: Flavia Guarracino | Massimiliano Fraldi | Nicola M. Pugno
Source: Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences (article, 2024-08-12)
Field: Materials Science — Materials Chemistry

Local-to-non-local transition laws for stiffness-tuneable monoatomic chains preserving springs mass Recently, non-local configurations have been proposed by adding beyond nearest neighbour couplings among elements in lattices to obtain roton-like dispersion relations and phase and group velocities with opposite signs. Even though the introduction of non-local elastic links in metamaterials has unlocked unprecedented possibilities, literature models and prototypes seem neither to provide criteria to compare local and non-local lattices nor to discuss any related rules governing the transition between the two configurations. A physically reasonable principle that monoatomic one-dimensional chains must obey to pass from single- to multi-connected systems is here proposed through a mass conservation law for elastic springs thereby introducing a suitable real dimensionless parameter [Formula: see text] to tune stiffness distribution. Therefore, the dispersion relations as a function of [Formula: see text] and of the <i>degree of non-locality</i> [Formula: see text] are derived analytically, demonstrating that the proposed principle can be rather interpreted as a general mechanical consistency condition to preserve proper dynamics, involving the spring-to-bead mass ratio. Finally, after discussing qualitative results and deriving some useful inequalities, numerical simulations and two-dimensional FFTs are performed for some paradigmatic examples to highlight key dynamics features exhibited by chains with finite length as the parameters [Formula: see text] and [Formula: see text] vary.This article is part of the theme issue 'Current developments in elastic and acoustic metamaterials science (Part 2)'. Dimensionless quantity ; Monatomic gas ; Stiffness ; Dispersion (optics) ; Phase transition ; Statistical physics ; Dispersion relation ; Metamaterial ; Physics ; Classical mechanics ; Theoretical physics ; Mechanics ; Condensed matter physics ; Quantum mechanics Nonlocal and gradient elasticity in micro/nano structures ; Advanced Materials and Mechanics ; Mechanical and Optical Resonators
Authors: Marco Bernet | Léa Deillon | Markus Bambach�
Source: Journal of Materials Research and Technology (article, 2024-07-01)
Field: Materials Science — Ceramics and Composites

Exploring co-processing strategies for multi-material spark plasma sintering of pure Cu with AlSi10Mg by master sintering curves Manufacturing complex multi-material metallic components without assembly operations is currently being explored using novel additive manufacturing techniques. For materials combinations that are difficult to process via melting-based processes, multi-material spark plasma sintering (SPS) appears as a promising alternative. However, due to different sintering kinetics, materials with very different melting points might have to be co-sintered at non-optimal conditions. In this work, the potential to improve the co-sinterability of dissimilar materials, namely pure copper and AlSi10Mg, is evaluated by altering the sintering kinetics of copper using different particle size distributions (PSD). Using the master sintering curve (MSC) approach, the densification behaviour of spherical pure copper powder during SPS is evaluated systematically to study the influence of PSD, uniaxial applied pressure, and isothermal holding temperature. An intermediate-sized monomodal and close-to-optimal bimodal PSD are compared for processing at lower sintering temperatures. It was observed that, compared to an intermediate monomodal PSD, a near-optimal bimodal powder mixture yields fully dense Cu–AlSi10Mg components at lower temperature and shorter process times. Therefore, the use of a bimodal mixture enables multi-material sintering, offers energy and cost savings to produce multi-material components, and improves compatibility between materials with very different melting points. Spark plasma sintering ; Materials science ; Sintering ; Isothermal process ; Copper ; Melting point ; Metallurgy ; Composite material ; Thermodynamics Advanced ceramic materials synthesis ; Advanced materials and composites ; Aluminum Alloys Composites Properties
Authors: József Kántor | Gusztáv Fekete | Attila Gergely
Source: Polymers (article, 2024-09-17)
Field: Materials Science — Surfaces, Coatings and Films

Oil Sorption Properties of Centrifugally Spun Polyisobutylene-Based Thermoplastic Elastomer Microfibers Fiber-based sorbent materials are an essential part of containing oil spills, thus preventing ecological damage. Poly(styrene-<i>b</i>-isobutylene-<i>b</i>-styrene) thermoplastic elastomer fibers were successfully produced by centrifugal spinning. Scanning electron microscopy revealed that the fibers were bead free and smooth-surfaced, with an average fiber diameter of 5.9 ± 2.3 μm. Contact angle measurements proved the highly hydrophobic (water contact angle of 126.8 ± 6.4°) and highly oleophilic nature of the fiber mat. The sorption and retention capacities of the fiber mat were tested for various oils and benchmarked against polypropylene as the industry standard and polystyrene, which is widely used in the literature. The oil uptake of the fiber mat showed a strong correlation with the viscosity of the oil, resulting in sorption capacities of 10.1 ± 0.8 g/g for sunflower oil, 19.9 ± 2.1 g/g for motor oil, and 23.8 ± 1.8 g/g for gear oil. Oil-water separation tests were also conducted, resulting in ~100% oil removal. The thermoplastic elastomer fiber mat outperformed the industry standard; however, the polystyrene fiber mat demonstrated the best oil sorption performance. Materials science ; Composite material ; Sorption ; Thermoplastic elastomer ; Fiber ; Elastomer ; Polypropylene ; Contact angle ; Polystyrene ; Sorbent ; Thermoplastic ; Natural rubber ; Copolymer ; Polymer ; Adsorption ; Chemistry ; Organic chemistry Surface Modification and Superhydrophobicity ; Electrospun Nanofibers in Biomedical Applications ; Advanced Sensor and Energy Harvesting Materials
Authors: Yuya Matsubara | Ryo Okabe | Ren Masayama | Nozomi Morishita Watanabe | Hiroshi Umakoshi | Kento Kasahara | Nobuyuki Matubayasi
Source: The Journal of Chemical Physics (preprint, 2024-07-10)
Field: Chemistry — Electrochemistry

A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation We propose a theoretical approach to estimate the permeability coefficients of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of our approach involves reformulating the returning probability (RP) theory, a rigorous bimolecular reaction theory, to describe permeation phenomena. This reformulation relies on the parallelism between permeation and bimolecular reaction processes. In the present method, the permeability coefficient is represented in terms of the thermodynamic and kinetic quantities for the reactive (R) phase that exists within the inner region of a membrane. One can evaluate these quantities using multiple MD trajectories starting from phase R. We apply the RP theory to the permeation of ethanol and methylamine at different concentrations (infinitely dilute and 1 mol % conditions of permeants). Under the 1 mol% condition, the present method yields a larger permeability coefficient for ethanol (0.12 ± 0.01 cm s-1) than for methylamine (0.069 ± 0.006 cm s-1), while the values of the permeability coefficient are satisfactorily close to those obtained from the brute-force MD simulations (0.18 ± 0.03 and 0.052 ± 0.005 cm s-1 for ethanol and methylamine, respectively). Moreover, upon analyzing the thermodynamic and kinetic contributions to the permeability, we clarify that a higher concentration dependency of permeability for ethanol, as compared to methylamine, arises from the sensitive nature of ethanol's free-energy barrier within the inner region of the membrane against ethanol concentration. Molecular dynamics ; Permeability (electromagnetism) ; Dynamics (music) ; Statistical physics ; Computer science ; Membrane ; Biochemical engineering ; Chemistry ; Engineering ; Physics ; Computational chemistry Electrochemical Analysis and Applications
Authors: Osmo Anttalainen | Markus Karjalainen | Elie Lattouf | Oliver Hecht | Paula Vanninen | Hanna Hakulinen | Tapio Kotiaho | C. L. Paul Thomas | Gary A. Eiceman
Source: Analytical Chemistry (article, 2024-06-10)
Field: Chemistry — Spectroscopy

Time-Resolved Ion Mobility Spectrometry with a Stop Flow Confined Volume Reaction Region An ion source concept is described where the sample flow is stopped in a confined volume of an ion mobility spectrometer creating time-dependent patterns of ion patterns of signal intensities for ions from mixtures of volatile organic compounds and improved signal-to-noise rate compared to conventional unidirectional drift gas flow. Hydrated protons from a corona discharge were introduced continuously into the confined volume with the sample in air at ambient pressure, and product ions were extracted continuously using an electric field for subsequent mobility analysis. Ion signal intensities for protonated monomers and proton bound dimers were measured and computationally extracted using mobilities from mobility spectra and exhibited distinct times of appearance over 30 s or more after sample injection. Models, and experimental findings with a ternary mixture, suggest that the separation of vapors as ions over time was consistent with differences in the reaction rate for reactions between primary ions from hydrated protons and constituents and from cross-reactions that follow the initial step of ionization. The findings suggest that the concept of stopped flow, introduced here for the first time, may provide a method for the temporal separation of atmospheric pressure ions. This separation relies on ion kinetics and does not require chromatographic technology. Chemistry ; Ion ; Analytical Chemistry (journal) ; Ion-mobility spectrometry ; Ionization ; Mass spectrometry ; Volumetric flow rate ; Corona discharge ; Proton ; Atmospheric pressure ; Volume (thermodynamics) ; Electrode ; Chromatography ; Physical chemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Chemical Sensor Technologies ; Analytical Chemistry and Chromatography
Authors: Emily Carney | Forough Ghasem Zadeh Moslabeh | Sooyeon Kang | Bruce A. Bunnell | Moo‐Yeal Lee | Neda Habibi
Source: Heliyon (article, 2024-06-25)
Field: Materials Science — Biomaterials

Self-assembling peptides induced by eyes absent enzyme to boost the efficacy of doxorubicin therapy in drug-resistant breast cancer cells Enzyme-induced self-assembly (EISA) is a recently developed nanotechnology technique in which small molecules are induced by cellular enzymes self-assembling into nanostructures inside cancer cells. This technique can boost the efficacy of chemotherapy drugs by avoiding drug efflux, inhibiting the cells' DNA repair mechanisms, and targeting the mitochondria. In this work, we study the self-assembly of a short peptide and its fluorescence analogue induced by Eyes absent (EYA) tyrosine phosphatases to boost the efficacy of doxorubicin (DOX) therapy in drug-resistant types of breast cancer cells, MDA-MB-231 and MCF-7. The peptides Fmoc-FF-YP and NBD-FF-YP were synthesized with the solid-phase peptide synthesis (SPPS) method and analyzed with HPLC and MALDI-TOF. Dynamic light scattering was used to determine the size distribution of peptides exposed to the EYA enzyme <i>in vitro</i>. The presence of EYA enzymes in breast cancer cells was confirmed using the western blotting assay. The intracellular location of the peptide self-assembly was studied by imaging fluorescence NBD-tagged peptides. The efficacy of the peptide alone and with DOX was determined against MCF-7 and MDA-MB-231 using MTT and LIVE-DEAD assays. Nucleus and cytoplasm F-actin (Phalloidin) staining was used to determine cell morphology changes in response to the combination therapy of peptides/DOX. At an optimal concentration, the peptides are not toxic to the cells; however, they boost the efficacy of DOX against drug-resistant breast cancer cells. We used state-of-the-art computer-aided techniques to predict the molecular structure of peptides and their interactions with EYA. This study demonstrates an approach for incorporating non-cytotoxic components into DOX combination therapy, thereby avoiding increased systemic burden or adverse effects. Doxorubicin ; Breast cancer ; Cancer therapy ; Drug ; Medicine ; Cancer ; Pharmacology ; Chemotherapy ; Cancer research ; Internal medicine Supramolecular Self-Assembly in Materials ; Glycosylation and Glycoproteins Research ; Chemical Synthesis and Analysis
Authors: Weejarin Paphussaro | Sittiruk Roytrakul | Narumon Phaonakrop | Wannapol Buthasane | Anudep Rungsipipat | Theerawat Tharasanit | Gunnaporn Suriyaphol
Source: BMC Veterinary Research (article, 2024-06-29)
Field: Chemistry — Spectroscopy

Analysis of serum peptidome profiles of non-metastatic and metastatic feline mammary carcinoma using liquid chromatography-tandem mass spectrometry The presence of both pro- and anti-proliferative proteins was observed, potentially indicating a distinctive characteristic of NmFMC. Conversely, proteins associated with poor prognosis and metastasis were noted in the mFMC group. Liquid chromatography–mass spectrometry ; Mass spectrometry ; Mammary carcinoma ; Tandem mass spectrometry ; Chromatography ; Chemistry ; Carcinoma ; Medicine ; Pathology Advanced Proteomics Techniques and Applications ; Peptidase Inhibition and Analysis ; Genomics and Phylogenetic Studies
Authors: Ana Luíza Seidinger | Felipe Luz Torres Silva | Mayara Ferreira Euzébio | Anna Krieger | João Meidânis | Junier Marrero-Gutiérrez | Thais Maria Santos Bezerra | Luciano de Souza Queiróz | Alex Silva | Iva Loureiro Hoffmann | Camila Maia Martin Daiggi | Hélder Tedeschi | Marcos N. Eberlin | Lívia S. Eberlin | José Andrés Yunes | Andréia M. Porcari | Izilda Aparecida Cardinalli
Source: Biomedicines (article, 2024-11-13)
Field: Chemistry — Spectroscopy

Tumor-Promoted Changes in Pediatric Brain Histology Can Be Distinguished from Normal Parenchyma by Desorption Electrospray Ionization Mass Spectrometry Imaging <b>Background:</b> Central nervous system (CNS) tumors are the second most frequent type of neoplasm in childhood and adolescence, after leukemia. Despite the incorporation of molecular classification and improvement of protocols combining chemotherapy, surgery, and radiotherapy, CNS tumors are still the most lethal neoplasm in this age group. Mass spectrometry imaging (MSI) is a powerful tool to map the distribution of molecular species in tissue sections. Among MSI techniques, desorption electrospray ionization (DESI-MSI) has been demonstrated to enable reliable agreement with the pathological evaluation of different adult cancer types, along with an acceptable time scale for intraoperative use. <b>Methods:</b> In the present work, we aimed to investigate the chemical profile obtained by DESI-MSI as an intraoperative surgical management tool by profiling 162 pediatric brain biopsies and reporting the results according to the histopathology and molecular profile of the tumors. <b>Results:</b> The 2D chemical images obtained by DESI-MSI allowed us to distinguish tumor-transformed tissue from non-tumor tissue with an accuracy of 96.8% in the training set and 94.3% in the validation set after statistical modeling of our data using Lasso. In addition, high-grade and low-grade tumors also displayed a distinct chemical profile when analyzed by DESI-MSI. We also provided evidence that the chemical profile of brain tumors obtained by DESI-MSI correlates with methylation-based molecular classes and specific immunophenotypes found in brain biopsies. <b>Conclusions:</b> The results presented herein support the incorporation of DESI-MSI analysis as an intraoperative assistive tool in prospective clinical trials for pediatric brain tumors management in the near future. Mass spectrometry imaging ; Mass spectrometry ; Parenchyma ; Chemistry ; Electrospray ionization ; Desorption electrospray ionization ; Histology ; Pathology ; Medicine ; Ionization ; Chromatography ; Chemical ionization Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Advanced Proteomics Techniques and Applications
Authors: Jeppe Kjærgaard Larsen | Ben Stocks | John Henderson | Daniel P. Andersson | Jesper Bäckdahl | Daniel Eriksson-Hogling | Jacob V. Stidsen | Kei Sakamoto | Kurt Højlund | Mikael Rydén | Juleen R. Zierath | Anna Krook | Atul S. Deshmukh
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-02-07)
Field: Chemistry — Spectroscopy

Personalized Molecular Signatures of Insulin Resistance and Type 2 Diabetes Abstract Highlights Advanced proteomics analysis reveals personalized signatures of insulin resistance Fasting muscle proteome and phosphoproteome predicts whole-body insulin sensitivity Insulin-stimulated phosphoproteome reveals selective insulin resistance signatures Phosphoproteome and proteome atlas explains sex-specific muscle metabolism Graphical Abstract Insulin resistance is a hallmark of type 2 diabetes, which is a highly heterogeneous disease with diverse pathology. Understanding the molecular signatures of insulin resistance and its association with individual phenotypic traits is crucial for advancing precision medicine in type 2 diabetes. Utilizing cutting-edge proteomics technology, we mapped the proteome and phosphoproteome of skeletal muscle from &gt;120 men and women with normal glucose tolerance or type 2 diabetes, with varying degrees of insulin sensitivity. Leveraging deep in vivo phenotyping, we reveal that fasting proteome and phosphoproteome signatures strongly predict insulin sensitivity. Furthermore, the insulin-stimulated phosphoproteome revealed both dysregulated and preserved signaling nodes - even in individuals with severe insulin resistance. While substantial sex-specific differences in the proteome and phosphoproteome were identified, molecular signatures of insulin resistance remained largely similar between men and women. These findings underscore the need for precision medicine approaches in type 2 diabetes care, acknowledging disease heterogeneity. Insulin resistance ; Proteome ; Type 2 diabetes ; Proteomics ; Insulin ; Diabetes mellitus ; Biology ; Bioinformatics ; Skeletal muscle ; Insulin receptor ; Computational biology ; Endocrinology ; Internal medicine ; Medicine ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Metabolism, Diabetes, and Cancer ; Adipose Tissue and Metabolism