jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yuanjiao Yang | Shan Wu | Yunlong Chen | Huangxian Ju
Source: Chemical Science (review, 2023-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Surface-enhanced Raman scattering sensing for detection and mapping of key cellular biomarkers Cellular biomarkers mainly contain proteins, nucleic acids, glycans and many small molecules including small biomolecule metabolites, reactive oxygen species and other cellular chemical entities. The detection and mapping of the key cellular biomarkers can effectively help us to understand important cellular mechanisms associated with physiological and pathological processes, which greatly promote the development of clinical diagnosis and disease treatment. Surface-enhanced Raman scattering (SERS) possesses high sensitivity and is free from the influence of strong self-fluorescence in living systems as well as the photobleaching of the dyes. It exhibits rich and narrow chemical fingerprint spectra for multiplexed detection, and has become a powerful tool to detect and map cellular biomarkers. In this review, we present an overview of recent advances in the detection and mapping of different classes of cellular biomarkers based on SERS sensing. These advances fully confirm that the SERS-based sensors and sensing methods have great potential for the exploration of biological mechanisms and clinical applications. Additionally, we also discuss the limitations of present research and the future developments of the SERS technology in this field. Key (lock) ; Raman scattering ; Nanotechnology ; Computer science ; Computational biology ; Materials science ; Raman spectroscopy ; Physics ; Biology ; Optics Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Biosensors and Analytical Detection
Authors: Xumei Ouyang | Yu Liu | Ke Zheng | Zhiqing Pang | Shaojun Peng
Source: Asian Journal of Pharmaceutical Sciences (article, 2023-12-29)
Field: Materials Science — Biomaterials

Recent advances in zwitterionic nanoscale drug delivery systems to overcome biological barriers Nanoscale drug delivery systems (nDDS) have been employed widely in enhancing the therapeutic efficacy of drugs against diseases with reduced side effects. Although several nDDS have been successfully approved for clinical use up to now, biological barriers between the administration site and the target site hinder the wider clinical adoption of nDDS in disease treatment. Polyethylene glycol (PEG)-modification (or PEGylation) has been regarded as the gold standard for stabilising nDDS in complex biological environment. However, the accelerated blood clearance (ABC) of PEGylated nDDS after repeated injections becomes great challenges for their clinical applications. Zwitterionic polymer, a novel family of anti-fouling materials, have evolved as an alternative to PEG due to their super-hydrophilicity and biocompatibility. Zwitterionic nDDS could avoid the generation of ABC phenomenon and exhibit longer blood circulation time than the PEGylated analogues. More impressively, zwitterionic nDDS have recently been shown to overcome multiple biological barriers such as nonspecific organ distribution, pressure gradients, impermeable cell membranes and lysosomal degradation without the need of any complex chemical modifications. The realization of overcoming multiple biological barriers by zwitterionic nDDS may simplify the current overly complex design of nDDS, which could facilitate their better clinical translation. Herein, we summarise the recent progress of zwitterionic nDDS at overcoming various biological barriers and analyse their underlying mechanisms. Finally, prospects and challenges are introduced to guide the rational design of zwitterionic nDDS for disease treatment. PEGylation ; Nanotechnology ; Drug delivery ; Biochemical engineering ; Polyethylene glycol ; Chemistry ; Materials science ; Engineering Nanoparticle-Based Drug Delivery ; Polymer Surface Interaction Studies ; Dendrimers and Hyperbranched Polymers
Authors: Jaime A. Martins | Daniela Rodrigues | Ana M. Cavaco | M. D. Carlos Antunes | Rui Guerra
Source: Postharvest Biology and Technology (article, 2023-02-13)
Field: Chemistry — Analytical Chemistry

Estimation of soluble solids content and fruit temperature in 'Rocha' pear using Vis-NIR spectroscopy and the SpectraNet–32 deep learning architecture Spectra-based methods are becoming increasingly important in Precision Agriculture as they offer non-destructive, quick tools for measuring the quality of produce. This study introduces a novel approach for estimating the soluble solids content (SSC) of ‘Rocha’ pears using the SpectraNet–32 deep learning architecture, which operates on 1D fruit spectra in the visible to near-infrared region (Vis-NIRS). This method was also able to estimate fruit temperatures, which improved the SSC prediction performance. The dataset consisted of 3300 spectra from 1650 ‘Rocha’ pears collected from local markets over several weeks during the 2010 and 2011 seasons, which had varying edaphoclimatic conditions. Two types of partial least squares (PLS) feature selection methods, under various configurations, were applied to the input spectra to identify the most significant wavelengths for training SpectraNet–32. The model’s robustness was also compared to a similar state-of-the-art deep learning architecture, DeepSpectra, as well as four other classical machine learning algorithms: PLS, multiple linear regression (MLR), support vector machine (SVM), and multi-layer perceptron (MLP). In total, 23 different experimental method configurations were assessed, with 150 neural networks each. SpectraNet–32 consistently outperformed other methods in several metrics. On average, it was 6.1% better than PLS in terms of the root mean square error of prediction (RMSEP, 1.08 vs. 1.15%), 7.7% better in prediction gain (PG, 1.67 vs. 1.55), 3.6% better in the coefficient of determination (R2, 0.58 vs. 0.56) and 5.8% better in the coefficient of variation (CV%, 8.35 vs. 8.86). PEAR ; Spectroscopy ; Botany ; Chemistry ; Horticulture ; Food science ; Biology ; Physics Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Advanced Chemical Sensor Technologies
Authors: Sascha Knecht | H. Christian Eberl | Norbert Kreisz | Ukamaka Juliet Ugwu | Tatiana Starikova | Bernhard Küster | Stephanie Wilhelm
Source: Molecular & Cellular Proteomics (review, 2023-08-18)
Field: Chemistry — Spectroscopy

An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science. Proteomics ; Computational biology ; Mass spectrometry ; Computer science ; Proteome ; Data science ; Chemistry ; Biochemical engineering ; Bioinformatics ; Biology ; Biochemistry ; Chromatography ; Engineering Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Nele Pien | Hubert Krzyslak | S. Shastry Kallaje | Joeri Van Meerssche | Diego Mantovani | Catharina De Schauwer | Peter Dubruel | Sandra Van Vlierberghe | Cristian Pablo Pennisi
Source: Applied Materials Today (review, 2023-02-10)
Field: Materials Science — Biomaterials

Tissue engineering of skeletal muscle, tendons and nerves: A review of manufacturing strategies to meet structural and functional requirements Additive manufacturing technologies have become at the forefront in tissue engineering, enabling the fabrication of complex tissues with intricate geometries that were not feasible using conventional manufacturing techniques. Due to the rapid progress in this field, it has become difficult not only to choose the most appropriate method, but also the optimal material, biological model (i.e., cells and bioactive compounds), and processing technique to fulfill the macro- and microstructural architecture and functions of biological tissues. The aim of this review is to describe recent advances in tissue engineering fabrication methods, from established electrospinning to emerging additive manufacturing technologies, with particular emphasis on tissues that exhibit hierarchically organized anisotropic architecture (skeletal muscle, tendons, and peripheral nerves). One of the current challenges is that the designs are usually dictated by the constraints imposed by the methods, rather than by criteria based on mechanical and biological requirements. Therefore, the review focuses on describing how the anatomical structure and function of muscles, tendons, and nerves should serve as the basis for an efficient three-dimensional design that considers both micro and macro aspects of the tissue. In addition, the individual factors that influence the fabrication strategy are discussed and related to the mechanical and biological properties of the three tissue types. The review highlights the advantages and limitations of each fabrication strategy and provides an overview of critical aspects relevant to future research strategies in this area. Macro ; Tissue engineering ; Computer science ; Fabrication ; Function (biology) ; Nanotechnology ; Biochemical engineering ; Engineering ; Materials science ; Biomedical engineering ; Biology ; Medicine Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; 3D Printing in Biomedical Research
Authors: Jacob C.M. Low | Alan J. Wright | Friederike Hesse | Jianbo Cao | Kevin M. Brindle
Source: Progress in Nuclear Magnetic Resonance Spectroscopy (review, 2023-02-10)
Field: Chemistry — Spectroscopy

Metabolic imaging with deuterium labeled substrates Deuterium metabolic imaging (DMI) is an emerging clinically-applicable technique for the non-invasive investigation of tissue metabolism. The generally short T<sub>1</sub> values of <sup>2</sup>H-labeled metabolites in vivo can compensate for the relatively low sensitivity of detection by allowing rapid signal acquisition in the absence of significant signal saturation. Studies with deuterated substrates, including [6,6'-<sup>2</sup>H<sub>2</sub>]glucose, [<sup>2</sup>H<sub>3</sub>]acetate, [<sup>2</sup>H<sub>9</sub>]choline and [2,3-<sup>2</sup>H<sub>2</sub>]fumarate have demonstrated the considerable potential of DMI for imaging tissue metabolism and cell death in vivo. The technique is evaluated here in comparison with established metabolic imaging techniques, including PET measurements of 2-deoxy-2-[<sup>18</sup>F]fluoro-d-glucose (FDG) uptake and <sup>13</sup>C MR imaging of the metabolism of hyperpolarized <sup>13</sup>C-labeled substrates. Chemistry ; In vivo ; Metabolism ; Metabolic pathway ; Choline ; Preclinical imaging ; Hyperpolarization (physics) ; Carbohydrate metabolism ; Cellular metabolism ; Nuclear magnetic resonance ; Biochemistry ; Nuclear magnetic resonance spectroscopy ; Biology ; Stereochemistry Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; Atomic and Subatomic Physics Research
Authors: Lennart Schada von Borzyskowski | Helena Schulz-Mirbach | Mauricio Troncoso Castellanos | Francesca Severi | Paul A. Gómez-Coronado | Nicole Paczia | Timo Glatter | Arren Bar‐Even | Steffen N. Lindner | Tobias J. Erb
Source: Metabolic Engineering (article, 2023-01-30)
Field: Materials Science — Biomaterials

Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol Ethylene glycol (EG) is a promising next generation feedstock for bioprocesses. It is a key component of the ubiquitous plastic polyethylene terephthalate (PET) and other polyester fibers and plastics, used in antifreeze formulations, and can also be generated by electrochemical conversion of syngas, which makes EG a key compound in a circular bioeconomy. The majority of biotechnologically relevant bacteria assimilate EG via the glycerate pathway, a wasteful metabolic route that releases CO<sub>2</sub> and requires reducing equivalents as well as ATP. In contrast, the recently characterized β-hydroxyaspartate cycle (BHAC) provides a more efficient, carbon-conserving route for C2 assimilation. Here we aimed at overcoming the natural limitations of EG metabolism in the industrially relevant strain Pseudomonas putida KT2440 by replacing the native glycerate pathway with the BHAC. We first prototyped the core reaction sequence of the BHAC in Escherichia coli before establishing the complete four-enzyme BHAC in Pseudomonas putida. Directed evolution on EG resulted in an improved strain that exhibits 35% faster growth and 20% increased biomass yield compared to a recently reported P. putida strain that was evolved to grow on EG via the glycerate pathway. Genome sequencing and proteomics highlight plastic adaptations of the genetic and metabolic networks in response to the introduction of the BHAC into P. putida and identify key mutations for its further integration during evolution. Taken together, our study shows that the BHAC can be utilized as 'plug-and-play' module for the metabolic engineering of two important microbial platform organisms, paving the way for multiple applications for a more efficient and carbon-conserving upcycling of EG in the future. Pseudomonas putida ; Ethylene glycol ; Ethylene ; Chemistry ; Monomer ; Biochemistry ; Organic chemistry ; Enzyme ; Catalysis biodegradable polymer synthesis and properties ; Enzyme Catalysis and Immobilization ; Microbial Metabolic Engineering and Bioproduction
Authors: Feng‐Hui Gong | Yun‐Long Tang | Yujia Wang | Yuting Chen | Bo Wu | Lixin Yang | Yin‐Lian Zhu | Xiuliang Ma
Source: Nature Communications (article, 2023-06-08)
Field: Materials Science — Materials Chemistry

Absence of critical thickness for polar skyrmions with breaking the Kittel’s law The period of polar domain (d) in ferroics was commonly believed to scale with corresponding film thicknesses (h), following the classical Kittel's law of d ∝ [Formula: see text]. Here, we have not only observed that this relationship fails in the case of polar skyrmions, where the period shrinks nearly to a constant value, or even experiences a slight increase, but also discovered that skyrmions have further persisted in [(PbTiO<sub>3</sub>)<sub>2</sub>/(SrTiO<sub>3</sub>)<sub>2</sub>]<sub>10</sub> ultrathin superlattices. Both experimental and theoretical results indicate that the skyrmion periods (d) and PbTiO<sub>3</sub> layer thicknesses in superlattice (h) obey the hyperbolic function of d = Ah + [Formula: see text] other than previous believed, simple square root law. Phase-field analysis indicates that the relationship originates from the different energy competitions of the superlattices with PbTiO<sub>3</sub> layer thicknesses. This work exemplified the critical size problems faced by nanoscale ferroelectric device designing in the post-Moore era. Skyrmion ; Ferroelectricity ; Polar ; Superlattice ; Condensed matter physics ; Phase (matter) ; Physics ; Materials science ; Algorithm ; Computer science ; Quantum mechanics Ferroelectric and Piezoelectric Materials ; Multiferroics and related materials ; Acoustic Wave Resonator Technologies
Authors: Tagyedeen H. Shoaib | Nihal Abdelmoniem | Rua M. Mukhtar | Amal Th. Alqhtani | Abdullah L. Alalawi | Razan Alawaji | Mashael S. Althubyani | Shaimaa G. A. Mohamed | Gamal A. Mohamed | Sabrin R. M. Ibrahim | Hazem G. A. Hussein | Abdulrahim A. Alzain
Source: Molecules (article, 2023-09-16)
Field: Chemistry — Organic Chemistry

Molecular Docking and Molecular Dynamics Studies Reveal the Anticancer Potential of Medicinal-Plant-Derived Lignans as MDM2-P53 Interaction Inhibitors The interaction between the tumor suppressor protein p53 and its negative regulator, the MDM2 oncogenic protein, has gained significant attention in cancer drug discovery. In this study, 120 lignans reported from Ferula sinkiangensis and <i>Justicia procumbens</i> were assessed for docking simulations on the active pocket of the MDM2 crystal structure bound to Nutlin-3a. The docking analysis identified nine compounds with higher docking scores than the co-crystallized reference. Subsequent AMDET profiling revealed satisfactory pharmacokinetic and safety parameters for these natural products. Three compounds, namely, justin A, 6-hydroxy justicidin A, and 6'-hydroxy justicidin B, were selected for further investigation due to their strong binding affinities of -7.526 kcal/mol, -7.438 kcal/mol, and -7.240 kcal/mol, respectively, which surpassed the binding affinity of the reference inhibitor Nutlin-3a (-6.830 kcal/mol). To assess the stability and reliability of the binding of the candidate hits, a molecular dynamics simulation was performed over a duration of 100 ns. Remarkably, the thorough analysis demonstrated that all the hits exhibited stable molecular dynamics profiles. Based on their effective binding to MDM2, favorable pharmacokinetic properties, and molecular dynamics behavior, these compounds represent a promising starting point for further refinement. Nevertheless, it is essential to synthesize the suggested compounds and evaluate their activity through in vitro and in vivo experiments. Molecular dynamics ; Chemistry ; Mdm2 ; Computational biology ; Docking (animal) ; Biology ; Biochemistry ; Computational chemistry ; Medicine ; Apoptosis Synthesis and biological activity ; Cancer therapeutics and mechanisms ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Murtadha Almousawi | Shaohua Xie | Daekun Kim | Kailong Ye | Xing Zhang | Jeremia Loukusa | Lu Ma | Steven N. Ehrlich | Laurène Tétard | Fudong Liu
Source: Environmental Science & Technology (article, 2023-12-22)
Field: Materials Science — Materials Chemistry

Hydroxyls on CeO<sub>2</sub> Support Promoting CuO/CeO<sub>2</sub> Catalyst for Efficient CO Oxidation and NO Reduction by CO Transition metal catalysts, such as copper oxide, are more attractive alternatives to noble metal catalysts for emission control due to their higher abundance, lower cost, and excellent catalytic activity. In this study, we report the preparation and application of a novel CuO/CeO<sub>2</sub> catalyst using a hydroxyl-rich Ce(OH)<sub><i>x</i></sub> support for CO oxidation and NO reduction by CO. Compared to the catalyst prepared from a regular CeO<sub>2</sub> support, the new CuO/CeO<sub>2</sub> catalyst prepared from the OH-rich Ce(OH)<sub><i>x</i></sub> (CuO/CeO<sub>2</sub>-OH) showed significantly higher catalytic activity under different testing conditions. The effect of OH species in the CeO<sub>2</sub> support on the catalytic performance and physicochemical properties of the CuO/CeO<sub>2</sub> catalyst was characterized in detail. It is demonstrated that the abundant OH species enhanced the CuO<sub><i>x</i></sub> dispersion on CeO<sub>2</sub>, increased the CuO<sub><i>x</i></sub>-CeO<sub>2</sub> interfaces and surface defects, promoted the oxygen activation and mobility, and boosted the NO adsorption and dissociation on CuO/CeO<sub>2</sub>-OH, thus contributing to its superior catalytic activity for both CO oxidation and NO reduction by CO. These results suggest that the OH-rich Ce(OH)<sub><i>x</i></sub> is a superior support for the preparation of highly efficient metal catalysts for different applications. Catalysis ; Oxide ; Chemistry ; Metal ; Redox ; Adsorption ; Transition metal ; Inorganic chemistry ; Dissociation (chemistry) ; Copper ; Dispersion (optics) ; Selective catalytic reduction ; Oxygen ; Chemical engineering ; Physical chemistry ; Organic chemistry Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Copper-based nanomaterials and applications
Authors: Mahfoozur Rahman | Obaid Afzal | Shehla Nasar Mir Najib Ullah | Mohammad Y. Alshahrani | Ali G. Alkhathami | Abdulmalik Saleh Alfawaz Altamimi | Salem Salman Almujri | Waleed Hassan Almalki | Eman Shorog | Manal A. Alossaimi | Ashok Kumar Mandal | Alhamyani abdulrahman | Ankit Sahoo
Source: ACS Omega (article, 2023-12-13)
Field: Materials Science — Biomaterials

Nanomedicine-Based Drug-Targeting in Breast Cancer: Pharmacokinetics, Clinical Progress, and Challenges Breast cancer (BC) is a malignant neoplasm that begins in the breast tissue. After skin cancer, BC is the second most common type of cancer in women. At the end of 2040, the number of newly diagnosed BC cases is projected to increase by over 40%, reaching approximately 3 million worldwide annually. The hormonal and chemotherapeutic approaches based on conventional formulations have inappropriate therapeutic effects and suboptimal pharmacokinetic responses with nonspecific targeting actions. To overcome such issues, the use of nanomedicines, including liposomes, nanoparticles, micelles, hybrid nanoparticles, etc., has gained wider attention in the treatment of BC. Smaller dimensional nanomedicine (especially 50-200 nm) exhibited improved in vivo effectiveness, such as better tissue penetration and more effective tumor suppression through enhanced retention and permeation, as well as active targeting of the drug. Additionally, nanotechnology, which further extended and developed theranostic nanomedicine by incorporating diagnostic and imaging agents in one platform, has been applied to BC. Furthermore, hybrid and theranostic nanomedicine has also been explored for gene delivery as anticancer therapeutics in BC. Moreover, the nanocarriers' size, shape, surface charge, chemical compositions, and surface area play an important role in the nanocarriers' stability, cellular absorption, cytotoxicity, cellular uptake, and toxicity. Additionally, nanomedicine clinical translation for managing BC remains a slow process. However, a few cases are being used clinically, and their progress with the current challenges is addressed in this Review. Therefore, this Review extensively discusses recent advancements in nanomedicine and its clinical challenges in BC. Nanomedicine ; Nanocarriers ; Medicine ; Breast cancer ; Drug delivery ; Drug ; Pharmacology ; Cancer ; Pharmacokinetics ; Nanotechnology ; Cancer research ; Nanoparticle ; Internal medicine ; Materials science Nanoparticle-Based Drug Delivery ; RNA Interference and Gene Delivery ; Nanoplatforms for cancer theranostics
Authors: Ao Huang | Jiang Huang | Hui‐Ying Luo | Zhi‐Wang Luo | Pu Wang | Ping Wang | Yan Guan | He‐Lou Xie
Source: Journal of Materials Chemistry C (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Circularly polarized organic room temperature phosphorescence activated by liquid crystalline polymer networks Circularly polarized organic room temperature phosphorescence (CPRTP) with g max = +0.098 was activated by the rigid environment of an in situ cross-linked liquid crystalline polymer network. Phosphorescence ; Materials science ; Polymer ; Liquid crystalline ; Polymer network ; Photochemistry ; Optics ; Fluorescence ; Composite material ; Chemistry Luminescence and Fluorescent Materials ; Organic Light-Emitting Diodes Research ; Synthesis and Properties of Aromatic Compounds