jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Franz F. Dressler | Johannes Brägelmann | Markus Reischl | Sven Perner
Source: Molecular & Cellular Proteomics (article, 2022-07-16)
Field: Chemistry — Spectroscopy

Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure Several algorithms for the normalization of proteomic data are currently available, each based on a priori assumptions. Among these is the extent to which differential expression (DE) can be present in the dataset. This factor is usually unknown in explorative biomarker screens. Simultaneously, the increasing depth of proteomic analyses often requires the selection of subsets with a high probability of being DE to obtain meaningful results in downstream bioinformatical analyses. Based on the relationship of technical variation and (true) biological DE of an unknown share of proteins, we propose the "Normics" algorithm: Proteins are ranked based on their expression level-corrected variance and the mean correlation with all other proteins. The latter serves as a novel indicator of the non-DE likelihood of a protein in a given dataset. Subsequent normalization is based on a subset of non-DE proteins only. No a priori information such as batch, clinical, or replicate group is necessary. Simulation data demonstrated robust and superior performance across a wide range of stochastically chosen parameters. Five publicly available spike-in and biologically variant datasets were reliably and quantitively accurately normalized by Normics with improved performance compared to standard variance stabilization as well as median, quantile, and LOESS normalizations. In complex biological datasets Normics correctly determined proteins as being DE that had been cross-validated by an independent transcriptome analysis of the same samples. In both complex datasets Normics identified the most DE proteins. We demonstrate that combining variance analysis and data-inherent correlation structure to identify non-DE proteins improves data normalization. Standard normalization algorithms can be consolidated against high shares of (one-sided) biological regulation. The statistical power of downstream analyses can be increased by focusing on Normics-selected subsets of high DE likelihood. Normalization (sociology) ; Replicate ; Computer science ; A priori and a posteriori ; Variance (accounting) ; Correlation ; Data mining ; Quantile ; Database normalization ; Computational biology ; Pattern recognition (psychology) ; Statistics ; Artificial intelligence ; Mathematics ; Biology Advanced Proteomics Techniques and Applications ; Gene expression and cancer classification ; Bioinformatics and Genomic Networks
Authors: Laila A. Jaragh-Alhadad | Haider Behbehani | Sadashiva S. Karnik
Source: Drug Delivery (article, 2022-08-26)
Field: Materials Science — Biomaterials

Cancer targeted drug delivery using active low-density lipoprotein nanoparticles encapsulated pyrimidines heterocyclic anticancer agents as microtubule inhibitors Recently, nanomedicine had the potential to increase the delivery of active compounds to specific cell sites. Nano-LDL particles are recognized as an excellent active nano-platform for cancer-targeted delivery. Loading of therapeutic agents into nano-LDL particles achieved by surface loading, core loading, and apolipoprotein-B100 interaction. Therefore, loading nano-LDL particles' core with pyrimidine heterocyclic anticancer agents will increase cancer cytotoxic activity targeting tubulin protein. First, by mimicking the native LDL particle's metabolic pathway, and second the agent's chemical functional groups like the native amino acids cytosine and thymine structures will not be recognized as a foreign entity from the cell's immune system. Nano-LDL particles will internalize through LDL-receptors endocytosis and transport the anticancer agent into the middle of the cancer cell, reducing its side effects on other healthy cells. Generally, the data revealed that pyrimidine heterocyclic anticancer agents' size is at the nano level. Agents' morphological examination showed nanofibers, thin sheets, clusters, and rod-like structures. LDL particles' size became bigger after loading with pyrimidine heterocyclic anticancer agents and ranged between 121.6 and 1045 nm. Then, particles were tested for their cytotoxicity against breast (MDA468) and prostate (DU145) cancer cell lines as surrogate models with dose-response study 10, 5, 1 µM. The IC<sub>50</sub> values of the agents against DU145 and MDA468 possessed cell growth inhibition even at the 1 µM concentration ranges of 3.88 ± 1.05 µM and 3.39 ± 0.97 µM, respectively. In sum, nano-LDL particles proved their efficiency as active drug delivery vehicles to target tubulin in cancer cells. Drug ; Cancer ; Drug delivery ; Targeted drug delivery ; Pharmacology ; Nanoparticle ; Materials science ; Nanotechnology ; Cancer research ; Medicine ; Internal medicine Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Graphene and Nanomaterials Applications
Authors: Kai Liu | Jinwen Guo | Yingdong Li | Jinguang Chen | Pingli Li
Source: Membranes (article, 2022-08-24)
Field: Materials Science — Materials Chemistry

High-Flux Ultrafiltration Membranes Combining Artificial Water Channels and Covalent Organic Frameworks Artificial water channels (AWCs) have been well investigated, and the imidazole-quartet water channel is one of the representative channels. In this work, covalent organic frameworks (COFs) composite membranes were fabricated through assembling COF layers and imidazole-quartet water channel. The membranes were synthesized by interfacial polymerization and self-assembly process, using polyacrylonitrile (PAN) ultrafiltration substrates with artificial water channels (HC6H) as modifiers. Effective combination of COF layers and imidazole-quartet water channels provide the membrane with excellent performance. The as-prepared membrane exhibits a water permeance above 271.7 L·m−2·h−1·bar−1, and high rejection rate (>99.5%) for CR. The results indicated that the composite structure based on AWCs and COFs may provide a new idea for the development of high-performance membranes for dye separation. Ultrafiltration (renal) ; Polyacrylonitrile ; Membrane ; Permeance ; Materials science ; Imidazole ; Chemical engineering ; Covalent bond ; Polymer chemistry ; Nanotechnology ; Chemistry ; Chromatography ; Composite material ; Polymer ; Organic chemistry ; Engineering Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation Technologies
Authors: Oluwaseyi Shofolawe-Bakare | Judith U. de Mel | Sushil K. Mishra | Mehjabeen Hossain | Christine M. Hamadani | Mercedes C. Pride | Gaya S. Dasanayake | Wake Monroe | Eric W. Roth | Eden E. L. Tanner | Robert J. Doerksen | Adam E. Smith | Thomas A. Werfel
Source: Macromolecular Bioscience (article, 2022-09-20)
Field: Materials Science — Biomaterials

ROS‐Responsive Glycopolymeric Nanoparticles for Enhanced Drug Delivery to Macrophages Macrophages play a diverse, key role in many pathologies, including inflammatory diseases, cardiovascular diseases, and cancer. However, many therapeutic strategies targeting macrophages suffer from systemic off-target toxicity resulting in notoriously narrow therapeutic windows. To address this shortcoming, the development of poly(propylene sulfide)-b-poly(methacrylamidoglucopyranose) [PPS-b-PMAG] diblock copolymer-based nanoparticles (PMAG NPs) capable of targeting macrophages and releasing drug in the presence of reactive oxygen species (ROS) is reported. PMAG NPs have desirable physicochemical properties for systemic drug delivery, including slightly negative surface charge, ≈100 nm diameter, and hemo-compatibility. Additionally, due to the presence of PPS in the NP core, PMAG NPs release drug cargo preferentially in the presence of ROS. Importantly, PMAG NPs display high cytocompatibility and are taken up by macrophages in cell culture at a rate ≈18-fold higher than PEGMA NPs-NPs composed of PPS-b-poly(oligoethylene glycol methacrylate). Computational studies indicate that PMAG NPs likely bind with glucose transporters such as GLUT 1/3 on the macrophage cell surface to facilitate high levels of internalization. Collectively, this study introduces glycopolymeric NPs that are uniquely capable of both receptor-ligand targeting to macrophages and ROS-dependent drug release and that can be useful in many immunotherapeutic settings. Drug delivery ; Nanoparticle ; Chemistry ; Drug ; Drug carrier ; Nanotechnology ; Pharmacology ; Materials science ; Medicine ; Organic chemistry Nanoparticle-Based Drug Delivery ; Graphene and Nanomaterials Applications ; Curcumin's Biomedical Applications
Authors: Xiang Gao | Meiling Wen | Yang Liu | Tian Hou | Bin Niu | Meiwen An
Source: Polymers (article, 2022-11-19)
Field: Materials Science — Biomaterials

Synthesis and Characterization of PU/PLCL/CMCS Electrospun Scaffolds for Skin Tissue Engineering As tissue regeneration material, electrospun fibers can mimic the microscale and nanoscale structure of the natural extracellular matrix (ECM), which provides a basis for cell growth and achieves organic integration with surrounding tissues. At present, the challenge for researchers is to develop a bionic scaffold for the regeneration of the wound area. In this paper, polyurethane (PU) is a working basis for the subsequent construction of tissue-engineered skin. poly(L-lactide-co-caprolactone) (PLCL)/carboxymethyl chitosan (CMCS) composite fibers were prepared via electrospinning and cross-linked by glutaraldehyde. The effect of CMCS content on the surface morphology, mechanical properties, hydrophilicity, swelling degree, and cytocompatibility were explored, aiming to assess the possibility of composite scaffolds for tissue engineering applications. The results showed that randomly arranged electrospun fibers presented a smooth surface. All scaffolds exhibited sufficient tensile strength (5.30-5.60 MPa), Young's modulus (2.62-4.29 MPa), and swelling degree for wound treatment. The addition of CMCS improved the hydrophilicity and cytocompatibility of the scaffolds. Electrospinning ; Materials science ; Ultimate tensile strength ; Scaffold ; Glutaraldehyde ; Composite number ; Regeneration (biology) ; Polyurethane ; Swelling ; Tissue engineering ; Microscale chemistry ; Caprolactone ; Biomedical engineering ; Composite material ; Chemistry ; Polymer ; Copolymer Electrospun Nanofibers in Biomedical Applications ; Silk-based biomaterials and applications ; biodegradable polymer synthesis and properties
Authors: Daksh Singh Davas | Srashti Bhardwaj | Raju Sen | Dinesh Kumar Gopalakrishnan | Janakiram Vaitla
Source: Advanced Synthesis & Catalysis (article, 2022-08-02)
Field: Chemistry — Organic Chemistry

Synthesis of Olefins by Formal Carbene Coupling Abstract In this review, the coupling of two carbene precursors for the synthesis of alkenes is surveyed. The key to selective carbene coupling is the difference in the rate of carbene generation between the two carbene precursors. This strategy requires judicious selection between two carbene precursors as well as fine‐tuning of reaction conditions to obtain the desired chemo‐ and stereoselectivity. These couplings were carried out in the presence and absence of a metal catalyst. The present review describes inter‐ and intramolecular coupling of diazo compounds and cross‐coupling between diazo and non‐diazo compounds. magnified image Carbene ; Diazo ; Chemistry ; Intramolecular force ; Stereoselectivity ; Coupling (piping) ; Transition metal carbene complex ; Combinatorial chemistry ; Catalysis ; Cyclopropanation ; Photochemistry ; Organic chemistry ; Materials science Cyclopropane Reaction Mechanisms ; Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions
Authors: Shigeyoshi Inoue | Rebecca L. Melen | Sjoerd Harder
Source: European Journal of Inorganic Chemistry (article, 2022-08-10)
Field: Chemistry — Inorganic Chemistry

Main Group Catalysis Abstract Main group compounds have drawn much attention due to their potential applications in bond activation and catalysis. The development in the field of main group catalysis has deepened our understanding both experimentally and theoretically, allowing rational design of main group compounds to fine‐tune their reactivity and related catalytic applications. With diverse ongoing research in this area, new classes of more environmentally friendly, cheap, and abundant main group catalysts are being discovered to serve as transition metal mimics. The Guest Editors briefly introduce the field of main group catalysis and the research in this collection. Chemistry ; Catalysis ; Group (periodic table) ; Reactivity (psychology) ; Nanotechnology ; Environmentally friendly ; Combinatorial chemistry ; Organic chemistry Asymmetric Hydrogenation and Catalysis ; Organoboron and organosilicon chemistry ; Catalytic Cross-Coupling Reactions
Authors: Fan Yang | Ji Feng | Jinxing Chen | Zuyang Ye | Jihua Chen | Dale K. Hensley | Yadong Yin
Source: Nano Research (article, 2022-01-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Engineering surface strain for site-selective island growth of Au on anisotropic Au nanostructures Controlled growth of islands on plasmonic metal nanoparticles represents a novel strategy in creating unique morphologies that are difficult to achieve by conventional colloidal synthesis processes, where the nanoparticle morphologies are typically determined by the preferential development of certain crystal facets. This work exploits an effective surface-engineering strategy for site-selective island growth of Au on anisotropic Au nanostructures. Selective ligand modification is first employed to direct the site-selective deposition of a thin transition layer of a secondary metal, e.g., Pd, which has a considerable lattice mismatch with Au. The selective deposition of Pd on the original seeds produces a high contrast in the surface strain that guides the subsequent site-selective growth of Au islands. This strategy proves effective in not only inducing the island growth of Au on Au nanostructures but also manipulating the location of grown islands. By taking advantage of the iodide-assisted oxidative ripening process and the surface strain profile on Au nanostructures, we further demonstrate the precise control of the islands’ number, coverage, and wetting degree, allowing fine-tuning of nanoparticles’ optical properties. Nanostructure ; Materials science ; Nanotechnology ; Ostwald ripening ; Nanoparticle ; Surface engineering ; Island growth ; Wetting layer ; Chemical engineering ; Layer (electronics) ; Epitaxy Gold and Silver Nanoparticles Synthesis and Applications ; Quantum Dots Synthesis And Properties ; Copper-based nanomaterials and applications
Authors: Pau Nadal Rodríguez | Ouldouz Ghashghaei | Andrea Bagán | Carmen Escolano | Rodolfo Lavilla
Source: Biomedicines (review, 2022-06-23)
Field: Chemistry — Organic Chemistry

Heterocycle-Based Multicomponent Reactions in Drug Discovery: From Hit Finding to Rational Design In the context of the structural complexity necessary for a molecule to selectively display a therapeutical action and the requirements for suitable pharmacokinetics, a robust synthetic approach is essential. Typically, thousands of relatively similar compounds should be prepared along the drug discovery process. In this respect, heterocycle-based multicomponent reactions offer advantages over traditional stepwise sequences in terms of synthetic economy, as well as the fast access to chemsets to study the structure activity relationships, the fine tuning of properties, and the preparation of larger amounts for preclinical phases. In this account, we briefly summarize the scientific methodology backing the research line followed by the group. We comment on the main results, clustered according to the targets and, finally, in the conclusion section, we offer a general appraisal of the situation and some perspectives regarding future directions in academic and private research. Context (archaeology) ; Drug discovery ; Computer science ; Process (computing) ; Biochemical engineering ; Drug ; Rational design ; Combinatorial chemistry ; Data science ; Management science ; Risk analysis (engineering) ; Computational biology ; Pharmacology ; Nanotechnology ; Chemistry ; Business ; Medicine ; Engineering ; Biology ; Bioinformatics ; Materials science ; Programming language Click Chemistry and Applications ; Multicomponent Synthesis of Heterocycles ; Chemical Synthesis and Analysis
Authors: Modi Gu | Lorenzo Travaglini | Jonathan Hopkins | Daniel Ta | Antonio Lauto | Paweł Wagner | Klaudia Wagner | Erica Zeglio | Lilli Jephcott | David L. Officer | Damia Mawad
Source: Synthetic Metals (article, 2022-02-09)
Field: Materials Science — Polymers and Plastics

Molecular design of an electropolymerized copolymer with carboxylic and sulfonic acid functionalities Sulfonate ; PEDOT:PSS ; Sulfonic acid ; Copolymer ; Conjugated system ; Polymer chemistry ; Materials science ; Polymer ; Conductive polymer ; Electrolyte ; Aqueous solution ; Electrochemistry ; Pendant group ; Chemical engineering ; Chemistry ; Organic chemistry ; Electrode ; Sodium Conducting polymers and applications ; Advanced Sensor and Energy Harvesting Materials ; Electrochemical sensors and biosensors
Authors: Cora Pravda Bartus | Tímea Hegedűs | Gábor Kozma | Imre Szenti | Róbert Vajtai | Zoltán Kónya | Ákos Kukovecz
Source: Journal of Molecular Structure (article, 2022-03-19)
Field: Materials Science — Materials Chemistry

Exfoliation of black phosphorus in isopropanol-water cosolvents Chemistry ; Black phosphorus ; Exfoliation joint ; Phosphorus ; Environmental chemistry ; Organic chemistry ; Chemical engineering 2D Materials and Applications ; MXene and MAX Phase Materials ; Graphene research and applications
Authors: Juraj Jašík | Stanislav Valtera | Mykhailo Vaidulych | Muntaseer Bunian | Lei Yu | Avik Halder | Hana Tarábková | Martin Jindra | Ladislav Kavan | Otakar Frank | Stephan Bartling | Štefan Vajda
Source: Faraday Discussions (article, 2022-07-28)
Field: Materials Science — Materials Chemistry

Oxidative dehydrogenation of cyclohexene on atomically precise subnanometer Cu<sub>4−<i>n</i></sub>Pd<sub><i>n</i></sub> (0 ≤ <i>n</i> ≤ 4) tetramer clusters: the effect of cluster composition and support on performance The pronounced effects of the composition of four-atom monometallic Cu and Pd and bimetallic CuPd clusters and the support on the catalytic activity and selectivity in the oxidative dehydrogenation of cyclohexene are reported. The ultra-nanocrystalline diamond supported clusters are highly active and dominantly produce benzene; some of the mixed clusters also produce cyclohexadiene, which are all clusters with a much suppressed combustion channel. The also highly active TiO<sub>2</sub>-supported tetramers solely produce benzene, without any combustion to CO<sub>2</sub>. The selectivity of the zirconia-supported mixed CuPd clusters and the monometallic Cu cluster is entirely different; though they are less active in comparison to clusters with other supports, these clusters produce significant fractions of cyclohexadiene, with their selectivity towards cyclohexadiene gradually increasing with the increasing number of copper atoms in the cluster, reaching about 50% for Cu<sub>3</sub>Pd<sub>1</sub>. The zirconia-supported copper tetramer stands out from among all the other tetramers in this reaction, with a selectivity towards cyclohexadiene of 70%, which far exceeds those of all the other cluster-support combinations. The findings from this study indicate a positive effect of copper on the stability of the mixed tetramers and potential new ways of fine-tuning catalyst performance by controlling the composition of the active site and <i>via</i> cluster-support interactions in complex oxidative reactions under the suppression of the undesired combustion of the feed. Dehydrogenation ; Tetramer ; Cluster (spacecraft) ; Cyclohexene ; Crystallography ; Chemistry ; Chemical physics ; Oxidative phosphorylation ; Materials science ; Computational chemistry ; Nanotechnology ; Catalysis ; Organic chemistry ; Computer science Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Machine Learning in Materials Science
Authors: Mariia Ivanchenko | Alison L. Carroll | Andrea B. Brothers | Hao Jing
Source: Nanoscale Advances (article, 2022-11-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Facile aqueous synthesis of hollow dual plasmonic hetero-nanostructures with tunable optical responses through nanoscale Kirkendall effects Herein, we report the colloidal synthesis of hollow dual-plasmonic nanoparticles (NPs) using Au@Cu<sub>2</sub>O core-shell NPs as templates and exploiting the nanoscale Kirkendall effect. In our synthesis, we used organic compounds as a source of chalcogenide ions for an anion exchange reaction at elevated temperatures using polyvinylpyrrolidone (PVP) as a capping reagent to transform the solid Cu<sub>2</sub>O shell into a hollow copper chalcogenide shell. The resulting structures possess different features depending on the chalcogenide precursor employed. TEM images confirm the complete transformation of Au@Cu<sub>2</sub>O templates when 1,1-dimethyl-2-selenourea was added and the formation of hollow Au@Cu<sub>2-<i>x</i></sub> Se nanostructures. In contrast, residues of Cu<sub>2</sub>O attached to the Au core were present when thioacetamide was used for the synthesis of Au@Cu<sub>2-<i>x</i></sub> S with all other conditions kept the same. The divergence of architectures caused distinct optical properties of Au@Cu<sub>2-<i>x</i></sub> S and Au@Cu<sub>2-<i>x</i></sub> Se NPs. This synthetic approach is an effective pathway for maneuvering the size of interior voids by varying the concentration of chalcogenide ions in the reaction mixture. The insights gained from this work will enrich the synthetic toolbox at the nanoscale and guide us on the rational design of multicomponent plasmonic nanoparticles with precisely controlled hollow interiors and sophisticated geometries, further enhancing our capabilities to fine-tune the electronic, optical, compositional, and physicochemical properties. Kirkendall effect ; Plasmon ; Nanoscopic scale ; Nanostructure ; Materials science ; Nanotechnology ; Aqueous solution ; Chemical engineering ; Chemistry ; Optoelectronics ; Metallurgy ; Physical chemistry Gold and Silver Nanoparticles Synthesis and Applications ; Nanocluster Synthesis and Applications ; Copper-based nanomaterials and applications