jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Anuar Makhmut | Di Qin | Sonja Fritzsche | Jose Nimo | Janett König | Fabian Coscia
Source: Cell Systems (article, 2023-10-30)
Field: Chemistry — Spectroscopy

A framework for ultra-low-input spatial tissue proteomics Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell function and heterogeneity in (patho)physiology. However, optimized workflows that preserve morphological information for phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected tissue are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low-input archival material. Benchmarking in murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions. Applied to human tonsil, we profiled 146 microregions including T and B lymphocyte niches and quantified cell-type-specific markers, cytokines, and transcription factors. These data also highlighted proteome dynamics within activated germinal centers, illuminating sites undergoing B cell proliferation and somatic hypermutation. This approach has broad implications in biomedicine, including early disease profiling and drug target and biomarker discovery. A record of this paper's transparent peer review process is included in the supplemental information. Proteomics ; Proteome ; Biology ; Computational biology ; Bioinformatics ; Cell biology ; Genetics Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Cell Image Analysis Techniques
Authors: G. D. A. Wood | D. D. Khalyavin | D. A. Mayoh | Juba Bouaziz | A. E. Hall | S. J. R. Holt | Fabio Orlandi | Pascal Manuel | Stefan Blügel | J. B. Staunton | O. A. Petrenko | M. R. Lees | G. Balakrishnan
Source: Physical review. B./Physical review. B (article, 2023-05-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Double-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>Q</mml:mi></mml:math> ground state with topological charge stripes in the centrosymmetric skyrmion candidate <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mi>GdRu</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi>Si</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math> ${\mathrm{GdRu}}_{2}{\mathrm{Si}}_{2}$ is a centrosymmetric magnet in which a skyrmion lattice has recently been discovered. Here, we investigate the magnetic structure of the zero-field ground state using neutron diffraction on single crystal and polycrystalline ${^{160}\mathrm{GdRu}}_{2}{\mathrm{Si}}_{2}$. In addition to observing the principal propagation vectors ${\mathbf{q}}_{1}$ and ${\mathbf{q}}_{2}$, we discover higher-order magnetic satellites, notably ${\mathbf{q}}_{1}+2{\mathbf{q}}_{2}$. The appearance of these satellites is explained within the framework of a double-$Q$ constant-moment solution. Using powder diffraction, we implement a quantitative refinement of this model. This structure, which contains vortexlike motifs, is shown to have a one-dimensional topological charge density. Physics ; Skyrmion ; Charge (physics) ; Ground state ; Topological quantum number ; Neutron diffraction ; Topology (electrical circuits) ; Lattice (music) ; Diffraction ; Magnetic moment ; Lattice constant ; Crystallography ; Condensed matter physics ; Particle physics ; Atomic physics ; Quantum mechanics ; Combinatorics ; Chemistry ; Mathematics Magnetic and transport properties of perovskites and related materials ; Advanced Condensed Matter Physics ; Rare-earth and actinide compounds
Authors: Johannes Hartl | Florian Kurth | Kai Kappert | David Horst | Michael Mülleder | Gunther Hartmann | Markus Ralser
Source: EMBO Molecular Medicine (article, 2023-03-20)
Field: Chemistry — Spectroscopy

Quantitative protein biomarker panels: a path to improved clinical practice through proteomics The utilisation of protein biomarker panels, rather than individual protein biomarkers, offers a more comprehensive representation of human physiology. It thus has the potential to improve diagnosis, prognosis and the differentiation of responders from nonresponders in the context of precision medicine. Although several proteomic techniques exist for measuring biomarker panels, the integration of proteomics into clinical practice has been limited. In this Commentary, we highlight the significance of quantitative protein biomarker panels in clinical medicine and outline the challenges that must be addressed in order to identify the most promising panels and implement them in clinical routines to realise their medical potential. Furthermore, we argue that the absolute quantification of protein panels through targeted mass spectrometric assays remains the most promising technology for translating proteomics into routine clinical applications due to its high flexibility, low sample costs, independence from affinity reagents and low entry barriers for its integration into existing laboratory workflows. Proteomics ; Biomarker ; Context (archaeology) ; Quantitative proteomics ; Flexibility (engineering) ; Computational biology ; Workflow ; Biomarker discovery ; Computer science ; Bioinformatics ; Data science ; Medicine ; Biology Advanced Proteomics Techniques and Applications ; Biosensors and Analytical Detection ; Advanced Biosensing Techniques and Applications
Authors: Carlos Marcuello | Brigitte Chabbert | Françoise Berzin | Nicolas Bercu | Michaël Molinari | Véronique Aguié‐Béghin
Source: Materials (article, 2023-03-18)
Field: Materials Science — Polymers and Plastics

Influence of Surface Chemistry of Fiber and Lignocellulosic Materials on Adhesion Properties with Polybutylene Succinate at Nanoscale The production of bio-based composites with enhanced characteristics constitutes a strategic action to minimize the use of fossil fuel resources. The mechanical performances of these materials are related to the specific properties of their components, as well as to the quality of the interface between the matrix and the fibers. In a previous research study, it was shown that the polarity of the matrix played a key role in the mechanisms of fiber breakage during processing, as well as on the final properties of the composite. However, some key questions remained unanswered, and new investigations were necessary to improve the knowledge of the interactions between a lignocellulosic material and a polar matrix. In this work, for the first time, atomic force microscopy based on force spectroscopy measurements was carried out using functionalized tips to characterize the intermolecular interactions at the single molecule level, taking place between poly(butylene succinate) and four different plant fibers. The efficiency of the tip functionalization was checked out by scanning electron microscopy and energy-dispersive X-ray spectroscopy, whereas the fibers chemistry was characterized by Fourier-transform infrared spectroscopy. Larger interactions at the nanoscale level were found between the matrix and hypolignified fibers compared to lignified ones, as in control experiments on single lignocellulosic polymer films. These results could significantly aid in the design of the most appropriate composite composition depending on its final use. Materials science ; Fiber ; Composite number ; Chemical engineering ; Polymer ; Composite material ; Fourier transform infrared spectroscopy ; Scanning electron microscope ; Spectroscopy ; Nanoscopic scale ; Surface modification ; Matrix (chemical analysis) ; Nanofiber ; Nanotechnology Natural Fiber Reinforced Composites ; Tree Root and Stability Studies ; Plant Surface Properties and Treatments
Authors: Qian Chen | Chunyan Fang | Fan Xia | Qiyue Wang | Fangyuan Li | Daishun Ling
Source: Acta Pharmaceutica Sinica B (article, 2023-09-03)
Field: Materials Science — Materials Chemistry

Metal nanoparticles for cancer therapy: Precision targeting of DNA damage Cancer, a complex and heterogeneous disease, arises from genomic instability. Currently, DNA damage-based cancer treatments, including radiotherapy and chemotherapy, are employed in clinical practice. However, the efficacy and safety of these therapies are constrained by various factors, limiting their ability to meet current clinical demands. Metal nanoparticles present promising avenues for enhancing each critical aspect of DNA damage-based cancer therapy. Their customizable physicochemical properties enable the development of targeted and personalized treatment platforms. In this review, we delve into the design principles and optimization strategies of metal nanoparticles. We shed light on the limitations of DNA damage-based therapy while highlighting the diverse strategies made possible by metal nanoparticles. These encompass targeted drug delivery, inhibition of DNA repair mechanisms, induction of cell death, and the cascading immune response. Moreover, we explore the pivotal role of physicochemical factors such as nanoparticle size, stimuli-responsiveness, and surface modification in shaping metal nanoparticle platforms. Finally, we present insights into the challenges and future directions of metal nanoparticles in advancing DNA damage-based cancer therapy, paving the way for novel treatment paradigms. Radiation therapy ; Nanotechnology ; Cancer therapy ; DNA damage ; Cancer treatment ; Limiting ; Cancer ; Genome instability ; Nanoparticle ; DNA ; Materials science ; Medicine ; Chemistry ; Engineering Nanoparticles: synthesis and applications ; Nanoparticle-Based Drug Delivery ; Advanced biosensing and bioanalysis techniques
Authors: Nadhem Missaoui | Amani Chrouda | Hamza Kahri | Andrew J. Gross | Mohammad Rezaei Ardani | Ai Ling Pang | Mohsen Ahmadipour
Source: Separation and Purification Technology (article, 2023-04-02)
Field: Chemistry — Inorganic Chemistry

PEG-templated synthesis of ultramicroporous n-ZIF-67 nanoparticles with high selectivity for the adsorption and uptake of CO2 over CH4 and N2 Adsorption ; Zeolitic imidazolate framework ; Thermogravimetric analysis ; Metal-organic framework ; Chemical engineering ; Langmuir adsorption model ; Chemistry ; Nanoparticle ; Desorption ; Physisorption ; Specific surface area ; Polyethylene glycol ; Materials science ; Organic chemistry ; Nanotechnology Metal-Organic Frameworks: Synthesis and Applications ; Carbon Dioxide Capture Technologies ; Covalent Organic Framework Applications
Authors: David E. Salazar Marcano | Nada D. Savić | Shorok A. M. Abdelhameed | Francisco de Azambuja | Tatjana N. Parac‐Vogt
Source: JACS Au (review, 2023-02-13)
Field: Materials Science — Materials Chemistry

Exploring the Reactivity of Polyoxometalates toward Proteins: From Interactions to Mechanistic Insights The latest advances in the study of the reactivity of metal-oxo clusters toward proteins showcase how fundamental insights obtained so far open new opportunities in biotechnology and medicine. In this Perspective, these studies are discussed through the lens of the reactivity of a family of soluble anionic metal-oxo nanoclusters known as polyoxometalates (POMs). POMs act as catalysts in a wide range of reactions with several different types of biomolecules and have promising therapeutic applications due to their antiviral, antibacterial, and antitumor activities. However, the lack of a detailed understanding of the mechanisms behind biochemically relevant reactions-particularly with complex biological systems such as proteins-still hinders further developments. Hence, in this Perspective, special attention is given to reactions of POMs with peptides and proteins showcasing a molecular-level understanding of the reaction mechanism. In doing so, we aim to highlight both existing limitations and promising directions of future research on the reactivity of metal-oxo clusters toward proteins and beyond. Reactivity (psychology) ; Chemistry ; Psychology ; Computational biology ; Biology ; Medicine Polyoxometalates: Synthesis and Applications ; Chemical Synthesis and Reactions ; biodegradable polymer synthesis and properties
Authors: Arnau Call | Giorgio Capocasa | Andrea Palone | Laia Vicens | Eric Aparicio | Najoua Choukairi Afailal | Nikos Siakavaras | Maria Eugènia López Saló | Massimo Bietti | Miguel Costas
Source: Journal of the American Chemical Society (article, 2023-08-04)
Field: Chemistry — Organic Chemistry

Highly Enantioselective Catalytic Lactonization at Nonactivated Primary and Secondary <i>γ</i>-C–H Bonds Chiral oxygenated aliphatic moieties are recurrent in biological and pharmaceutically relevant molecules and constitute one of the most versatile types of functionalities for further elaboration. Herein we report a protocol for straightforward and general access to chiral <i>γ</i>-lactones via enantioselective oxidation of strong nonactivated primary and secondary C(<i>sp<sup>3</sup></i>)-H bonds in readily available carboxylic acids. The key enabling aspect is the use of robust sterically encumbered manganese catalysts that provide outstanding enantioselectivities (up to >99.9%) and yields (up to 96%) employing hydrogen peroxide as the oxidant. The resulting <i>γ</i>-lactones are of immediate interest for the preparation of <i>inter alia</i> natural products and recyclable polymeric materials. Chemistry ; Enantioselective synthesis ; Primary (astronomy) ; Catalysis ; Stereochemistry ; Organic chemistry Catalytic C–H Functionalization Methods ; Asymmetric Hydrogenation and Catalysis ; Synthesis and Catalytic Reactions
Authors: Hao Wang | Fei Xu | Zhencai Zhang | Mi Feng | Ming Jiang | Suojiang Zhang
Source: RSC Sustainability (article, 2023-01-01)
Field: Materials Science — Biomaterials

Bio-based polycarbonates: progress and prospects The review covers the advancements in bio-based polycarbonates with regards to their raw materials, polymerization techniques, and modification strategies. Raw material ; Process engineering ; Polymerization ; Materials science ; Environmental science ; Biochemical engineering ; Polymer science ; Nanotechnology ; Computer science ; Engineering ; Polymer ; Chemistry ; Composite material ; Organic chemistry biodegradable polymer synthesis and properties ; Lignin and Wood Chemistry ; Catalysis for Biomass Conversion
Authors: Shikha Gulati | Arikta Baul | Anoushka Amar | Rachit Wadhwa | Sanjay Kumar | Rajender S. Varma
Source: Nanomaterials (review, 2023-01-30)
Field: Materials Science — Materials Chemistry

Eco-Friendly and Sustainable Pathways to Photoluminescent Carbon Quantum Dots (CQDs) Carbon quantum dots (CQDs), a new family of photoluminescent 0D NPs, have recently received a lot of attention. They have enormous future potential due to their unique properties, which include low toxicity, high conductivity, and biocompatibility and accordingly can be used as a feasible replacement for conventional materials deployed in various optoelectronic, biomedical, and energy applications. The most recent trends and advancements in the synthesizing and setup of photoluminescent CQDs using environmentally friendly methods are thoroughly discussed in this review. The eco-friendly synthetic processes are emphasized, with a focus on biomass-derived precursors. Modification possibilities for creating newer physicochemical properties among different CQDs are also presented, along with a brief conceptual overview. The extensive amount of writings on them found in the literature explains their exceptional competence in a variety of fields, making these nanomaterials promising alternatives for real-world applications. Furthermore, the benefits, drawbacks, and opportunities for CQDs are discussed, with an emphasis on their future prospects in this emerging research field. Nanotechnology ; Environmentally friendly ; Photoluminescence ; Materials science ; Carbon quantum dots ; Nanomaterials ; Biochemical engineering ; Computer science ; Biocompatibility ; Quantum dot ; Engineering ; Optoelectronics Carbon and Quantum Dots Applications ; Nanocluster Synthesis and Applications ; Quantum Dots Synthesis And Properties
Authors: Satyadip Paul | Mani Gupta | Kaushik Dey | Ashok Kumar Mahato | Saikat Bag | Arun Torris | E. Bhoje Gowd | Hasnain Sajid | Matthew A. Addicoat | Supratim Datta | Rahul Banerjee
Source: Chemical Science (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Hierarchical covalent organic framework-foam for multi-enzyme tandem catalysis Covalent organic frameworks (COFs) are ideal host matrices for biomolecule immobilization and biocatalysis due to their high porosity, various functionalities, and structural robustness. However, the porosity of COFs is limited to the micropore dimension, which restricts the immobilization of enzymes with large volumes and obstructs substrate flow during enzyme catalysis. A hierarchical 3D nanostructure possessing micro-, meso-, and macroporosity could be a beneficial host matrix for such enzyme catalysis. In this study, we employed an <i>in situ</i> CO<sub>2</sub> gas effervescence technique to induce disordered macropores in the ordered 2D COF nanostructure, synthesizing hierarchical TpAzo COF-foam. The resulting TpAzo foam matrix facilitates the immobilization of multiple enzymes with higher immobilization efficiency (approximately 1.5 to 4-fold) than the COF. The immobilized cellulolytic enzymes, namely β-glucosidase (BGL), cellobiohydrolase (CBH), and endoglucanase (EG), remain active inside the TpAzo foam. The immobilized BGL exhibited activity in organic solvents and stability at room temperature (25 °C). The enzyme-immobilized TpAzo foam exhibited significant activity towards the hydrolysis of <i>p</i>-nitrophenyl-β-d-glucopyranoside (BGL@TpAzo-foam: <i>K</i><sub>m</sub> and <i>V</i><sub>max</sub> = 23.5 ± 3.5 mM and 497.7 ± 28.0 μM min<sup>-1</sup>) and carboxymethylcellulose (CBH@TpAzo-foam: <i>K</i><sub>m</sub> and <i>V</i><sub>max</sub> = 18.3 ± 4.0 mg mL<sup>-1</sup> and 85.2 ± 9.6 μM min<sup>-1</sup> and EG@TpAzo-foam: <i>K</i><sub>m</sub> and <i>V</i><sub>max</sub> = 13.2 ± 2.0 mg mL<sup>-1</sup> and 102.2 ± 7.1 μM min<sup>-1</sup>). Subsequently, the multi-enzyme immobilized TpAzo foams were utilized to perform a one-pot tandem conversion from carboxymethylcellulose (CMC) to glucose with high recyclability (10 cycles). This work opens up the possibility of synthesizing enzymes immobilized in TpAzo foam for tandem catalysis. Tandem ; Covalent bond ; Covalent organic framework ; Catalysis ; Chemistry ; Enzyme ; Organic synthesis ; Chemical engineering ; Combinatorial chemistry ; Materials science ; Organic chemistry ; Nanotechnology ; Composite material ; Engineering Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Luminescence and Fluorescent Materials
Authors: Tongchang Fang | Liwei Wang | Miaomiao Wu | Xiaotian Qi | Chao Liu
Source: Angewandte Chemie International Edition (article, 2023-12-08)
Field: Chemistry — Organic Chemistry

Diborodichloromethane as Versatile Reagent for Chemodivergent Synthesis of <i>gem</i>‐Diborylalkanes The development of boron reagents is crucial for synthetic chemistry. Herein, we present a scalable and practical synthesis of diborodichloromethane (DBDCM) through the reaction of trichloromethyllithium with bis(pinacolato)diboron (B<sub>2</sub> pin<sub>2</sub> ). The resulting DBDCM reagent serves as a basic synthetic unit for the construction of various structurally diverse gem-diborylalkanes through controllable C-Cl functionalizations. Moreover, we have developed consecutive tetra-functionalizations of DBDCM for the construction of diverse tertiary and quaternary carbon containing molecules. The use of isotopically enriched <sup>13</sup> C-chloroform and <sup>10</sup> B<sub>2</sub> pin<sub>2</sub> enables the synthesis of isotopically enriched <sup>13</sup> C-DBDCM and <sup>10</sup> B-DBDCM reagents, which are beneficial for the convenient synthesis of carbon-13 and boron-10 molecules. Reagent ; Combinatorial chemistry ; Computer science ; Chemistry ; Organic chemistry Organoboron and organosilicon chemistry ; Chemical Synthesis and Analysis ; Organophosphorus compounds synthesis
Authors: Eirini Myrovali | Kyrillos Papadopoulos | Georgia Charalampous | Paraskevi Kesapidou | G. Vourlias | Th. Kehagias | M. Angelakeris | Ulf Wiedwald
Source: ACS Omega (article, 2023-03-30)
Field: Materials Science — Biomaterials

Toward the Separation of Different Heating Mechanisms in Magnetic Particle Hyperthermia Magnetic particle hyperthermia (MPH) is a promising method for cancer treatment using magnetic nanoparticles (MNPs), which are subjected to an alternating magnetic field for local heating to the therapeutic range of 41-45 °C. In this window, the malignant regions (i.e., cancer cells) undergo a severe thermal shock while healthy tissues sustain this thermal regime with significantly milder side effects. Since the heating efficiency is directly associated with nanoparticle size, MNPs should acquire the appropriate size to maximize heating together with minimum toxicity. Herein, we report on facile synthetic controls to synthesize MNPs by an aqueous precipitation method, whereby tuning the pH values of the solution (9.0-13.5) results in a wide range of average MNP diameters from 16 to 76 nm. With respect to their size, the structural and magnetic properties of the MNPs are evaluated by adjusting the most important parameters, i.e. the MNP surrounding medium (water/agarose), the MNP concentration (1-4 mg mL<sup>-1</sup>), and the field amplitude (20-50 mT) and frequency (103, 375, 765 kHz). Consequently, the maximum heating efficiency is determined for each MNP size and set of parameters, outlining the optimum MNPs for MPH treatment. In this way, we can address the different heat generation mechanisms (Brownian, Néel, and hysteresis losses) to different sizes and separate Brownian and hysteresis losses for optimized sizes by studying the heat generation as a function of the medium viscosity. Finally, MNPs immobilized into agarose solution are studied under low-field MPH treatment to find the optimum conditions for clinical applications. Magnetic nanoparticles ; Particle size ; Magnetic hyperthermia ; Materials science ; Nanoparticle ; Agarose ; Viscosity ; Magnetic separation ; Aqueous solution ; Precipitation ; Magnetic field ; Hysteresis ; Range (aeronautics) ; Chemical engineering ; Nuclear magnetic resonance ; Nanotechnology ; Chemistry ; Chromatography ; Composite material ; Condensed matter physics ; Physical chemistry ; Physics Nanoparticle-Based Drug Delivery ; Characterization and Applications of Magnetic Nanoparticles ; Microfluidic and Bio-sensing Technologies