jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tatjana Sajic | Rodolfo Ciuffa | Vera Lemos | Pan Xu | Valentina Leone | Chen Li | Evan G. Williams | Georgios Makris | Amir Banaei‐Esfahani | Mathias Heikenwälder | Kristina Schoonjans | Ruedi Aebersold
Source: Scientific Reports (article, 2019-05-06)
Field: Chemistry — Spectroscopy

A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model To-date, most proteomic studies aimed at discovering tissue-based cancer biomarkers have compared the quantity of selected proteins between case and control groups. However, proteins generally function in association with other proteins to form modules localized in particular subcellular compartments in specialized cell types and tissues. Sub-cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells. Here, we describe a strategy for tissue-biomarker detection based on a mitochondrial fold enrichment (mtFE) score, which is sensitive to protein abundance changes as well as changes in subcellular distribution between mitochondria and cytosol. The mtFE score integrates protein abundance data from total cellular lysates and mitochondria-enriched fractions, and provides novel information for the classification of cancer samples that is not necessarily apparent from conventional abundance measurements alone. We apply this new strategy to a panel of wild-type and mutant mice with a liver-specific gene deletion of Liver receptor homolog 1 (Lrh-1<sup>hep-/-</sup>), with both lines containing control individuals as well as individuals with liver cancer induced by diethylnitrosamine (DEN). Lrh-1 gene deletion attenuates cancer cell metabolism in hepatocytes through mitochondrial glutamine processing. We show that proteome changes based on mtFE scores outperform protein abundance measurements in discriminating DEN-induced liver cancer from healthy liver tissue, and are uniquely robust against genetic perturbation. We validate the capacity of selected proteins with informative mtFE scores to indicate hepatic malignant changes in two independent mouse models of hepatocellular carcinoma (HCC), thus demonstrating the robustness of this new approach to biomarker research. Overall, the method provides a novel, sensitive approach to cancer biomarker discovery that considers contextual information of tested proteins. Proteome ; Biology ; Liver cancer ; Mitochondrion ; Proteomics ; Human Protein Atlas ; Subcellular localization ; Hepatocellular carcinoma ; Gene ; Gene expression profiling ; Cancer ; Biomarker ; Cancer cell ; Computational biology ; Gene expression ; Cancer research ; Bioinformatics ; Cell biology ; Biochemistry ; Genetics ; Protein expression Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mitochondrial Function and Pathology
Authors: Dong Joon Youn | Jingfa Li | Sara Livazović | Yabin Sun | Shuyu Sun
Source: Polymers (article, 2019-09-02)
Field: Materials Science — Materials Chemistry

Controlling Factors of Degassing in Crosslinked Polyethylene Insulated Cables Here, we analyze the degassing process of a byproduct (methane) formed during the peroxide-induced crosslinking of polyethylene. A diffusion model based on Fick's law is used to obtain the controlling factors of degassing in a crosslinked polyethylene (XLPE) insulated power cable (132 kV with 18 mm of insulation). We quantitatively analyze different scenarios of the diffusion of methane through the XLPE insulation and two semiconductor layers under various in situ degassing conditions. The analyzed degassing conditions include heat transfer and its effect on the diffusion properties, the different transport and boundary conditions due to the free spaces within the cable conductor, and the nonuniform distribution of methane concentrations within the insulation layers. Our simulation results clearly demonstrate that the free spaces between the copper strands in the cable conductor significantly affect the degassing efficiency. However, the temperature-diffusion coupling has a relatively minor effect on the overall degassing efficiency due to the rapid temperature increase of the polymer layers during the initial stages of degassing. Moreover, we find that the nonuniform distribution of methane in the initial stages also plays an important role in degassing in the cable, but this effect varies significantly during the degassing process. Polyethylene ; Materials science ; Diffusion ; Methane ; Composite material ; Conductor ; Gaseous diffusion ; Coupling (piping) ; Electrode ; Chemistry ; Thermodynamics High voltage insulation and dielectric phenomena ; Thermal Analysis in Power Transmission ; Advanced Battery Technologies Research
Authors: Vivian Soares | Ana Flávia Moraes | Janaína dos Santos | Marina Carla Grando | Cleuzir da Luz | Gustavo Lopes Colpani | Luciano Luiz Silva | Márcio Antônio Fiori | Josiane Maria Muneron de Mello
Source: Materials Research (article, 2019-01-01)
Field: Chemistry — Organic Chemistry

Obtaining of Fe3O4@C Core-Shell Nanoparticles as an Adsorbent of Tetracycline in Aqueous Solutions Tetracycline is used to treat various diseases in animals and humans, so its high use causes this substance to be frequently found in effluents and in potable water reservoirs, causing serious problems for human health and the environment. Many processes are applied and evaluated in an attempt to removal tetracycline found in environment, such as adsorption. The application of iron-carbon nanoparticles with core-shell structure (Fe 3 O 4 @C) as adsorbent, can be an alternative to removal of these contaminants. In the present study Fe 3 O 4 @C nanoparticles were synthesized and used to adsorb tetracycline in aqueous solutions. The core-shell characterization was performed using X-ray diffraction techniques, infrared spectroscopy, surface area, chemical analysis and morphology, and adsorption capacity through isotherms. The results indicated that Fe 3 O 4 @C nanoparticles presented good tetracycline removal capability, 73.3%, when applied an initial concentration of antibiotic of the 30 mg L -1 and 0.5 g of adsorbent. Aqueous solution ; Adsorption ; Shell (structure) ; Nanoparticle ; Chemistry ; Core (optical fiber) ; Tetracycline ; Chemical engineering ; Materials science ; Nuclear chemistry ; Nanotechnology ; Organic chemistry ; Composite material ; Biochemistry ; Antibiotics ; Engineering Nanomaterials for catalytic reactions ; Adsorption and biosorption for pollutant removal ; Nanoparticle-Based Drug Delivery
Authors: Hawraa Kassem Hami | Ruba Fahmi Abbas | Ala'a Abdull wahid Jasim | Diffaf Abdul abass | Marwa A. Abed | Asma A. Maryoosh
Source: Egyptian Journal of Chemistry (article, 2019-06-26)
Field: Chemistry — Organic Chemistry

Kinetics study of Removal Doxycycline drug from aqueous solution using Aluminum Oxide surface The batch adsorption of doxycycline from aqueous solution using aluminum oxide under different experimental conditions was investigated in this study. The effect of initial concentration, sample volume, contact time and pH ‎ have been reported. A comparison of kinetic models applied to the adsorption of doxycycline on the adsorbents was evaluated for the pseudo first-order, the pseudo-second-order, Elovich, Fractional power and intra particle diffusion kinetic models were utilized to the adsorption data in respect of investigating the kinetic process; kinetic data were best fitted to the pseudo-second-order model validated by normalized standard deviation (NSD), average relative error (ARE) and chi-square test (Chi-X2). The result suggested that the intra particle diffusion was one of the rate-limiting steps. Adsorption ; Diffusion ; Aqueous solution ; Kinetics ; Particle size ; Particle (ecology) ; Chemistry ; Doxycycline ; Kinetic energy ; Dissolution ; Materials science ; Thermodynamics ; Chromatography ; Analytical Chemistry (journal) ; Physical chemistry ; Physics Nanomaterials for catalytic reactions ; Analytical chemistry methods development ; Analytical Chemistry and Chromatography
Authors: Nastaran Mozaffari | Seyed Alireza Hajiseyed Mirzahosseini | Amir Hossein Sari | Leila Fekri Aval
Source: Journal of theoretical and applied physics (article, 2019-12-17)
Field: Materials Science — Materials Chemistry

Investigation of carbon monoxide gas adsorption on the Al2O3/Pd(NO3)2/zeolite composite film Abstract In this study, Al 2 O 3 /Pd(NO 3 ) 2 /zeolite composite films have been fabricated by roll coating method and characterized by X-ray diffraction, energy-dispersive X-ray spectroscopy and field emission scanning electron microscopy. The gas adsorption was tested in an experimental setup by a continuous gas analyzer KIMO KIGAZ 210 at constant temperature and pressure (32 °C and 1.5 bar) and as a function of reaction time (s). The inlet CO gas concentration was 150 mg L −1 , and the saturation level of CO gas concentration was 5 mg L −1 . The maximum adsorption capacity ( q max ) and maximum adsorption efficiency (%) were calculated as 111.16 mg g −1 and 97%, respectively. Pseudo-first-order, pseudo-second-order, and intra-particle diffusion models were investigated to kinetic study of CO adsorption on Al 2 O 3 /Pd(NO 3 ) 2 /zeolite adsorbents. Results indicated that CO adsorption follows the pseudo-second-order model well according to regression coefficient value ( R 2 = 0.98), and the value of pseudo-second-order rate constant of adsorption was obtained as 2 × 10 −5 g mg −1 s −1 . According to the intra-particle diffusion model, adsorption is affected by only one process. So, adsorption of CO by Al 2 O 3 /Pd(NO 3 ) 2 /zeolite adsorbent indicated an effective adsorption by obtained results. Adsorption ; Zeolite ; Materials science ; Analytical Chemistry (journal) ; Carbon monoxide ; Diffusion ; Saturation (graph theory) ; Activation energy ; Particle size ; Scanning electron microscope ; Chemistry ; Catalysis ; Physical chemistry ; Chromatography ; Composite material ; Thermodynamics ; Organic chemistry Catalytic Processes in Materials Science ; Gas Sensing Nanomaterials and Sensors ; ZnO doping and properties
Authors: Katarzyna Michocka | Katarzyna Staszak | Daniela Gwiazdowska | Daria Wieczorek
Source: Molecules (article, 2019-11-05)
Field: Chemistry — Organic Chemistry

Synthesis, Surface and Antimicrobial Activity of New Lactose-Based Surfactants This work presents a synthesis method for new surfactants based on lactose. The compounds obtained belong to the homologous series of O-β-D-Galactopyranosyl-(1→4)-<i>N</i>-alkyl-(3-sulfopropyl)-D-glucosamine hydrochloride, containing 12 and 14 carbon atoms in the alkyl chain, and they may serve as an example of cationic surfactants. The newly synthesized compounds exhibit good surface properties, low value of CMC (Critical Micelle Concentration) and good wetting properties. These surfactants' ability to produce foam is considerably higher than in the commercial surfactants. Moreover, antibacterial and fungistatic activity was carried out by well diffusion assay against the selected bacteria (Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa), yeasts (Candida albicans) and filamentous fungi (Fusarium graminearum, F. avenaceum, F. oxysporum, F. culmorum, F. equiseti, Alternaria alternata and Botrytis cinerea). It was shown that the resulting quaternary salts significantly inhibit the growth of tested microorganisms. Antibacterial and fungistatic activity of the surfactant compounds varied depending on the species of bacteria or fungi. The results of antimicrobial activity of new lactose derivatives indicate that the compounds exhibit larger or similar antagonistic activity against tested bacteria and fungi than typical cationic surfactant cetylpyridinium chloride. Fusarium oxysporum ; Critical micelle concentration ; Chemistry ; Antimicrobial ; Botrytis cinerea ; Pulmonary surfactant ; Bacteria ; Antibacterial activity ; Cetylpyridinium chloride ; Bacillus subtilis ; Cationic polymerization ; Organic chemistry ; Microbiology ; Nuclear chemistry ; Micelle ; Biochemistry ; Biology ; Botany Surfactants and Colloidal Systems ; Environmental Chemistry and Analysis ; Antimicrobial agents and applications
Authors: Frédéric A. Perras | Marek Pruski
Source: The Journal of Chemical Physics (article, 2019-07-18)
Field: Chemistry — Spectroscopy

Linear-scaling <i>ab initio</i> simulations of spin diffusion in rotating solids We investigated the utility of locally restricting the basis sets involved in low-order correlations in Liouville space (LCL) calculations of spin diffusion. Using well-known classical models of spin diffusion, we describe a rationale for selecting the optimal basis set for such calculations. We then show that the use of these locally restricted basis sets provides the same computational accuracy as the full LCL set while reducing the computational time by several orders of magnitude. Speeding up the calculations also enables us to use higher maximum spin orders and increase the computational accuracy. Furthermore, unlike exact and full LCL calculations, locally restricted LCL calculations scale linearly with the system size and should thus enable the ab initio study of spin diffusion in spin systems containing several thousand spins. Spins ; Spin (aerodynamics) ; Statistical physics ; Basis (linear algebra) ; Scaling ; Basis set ; Diffusion ; Ab initio ; Spin diffusion ; Linear scale ; Ab initio quantum chemistry methods ; Physics ; Set (abstract data type) ; Space (punctuation) ; Mathematics ; Quantum mechanics ; Computer science ; Condensed matter physics ; Density functional theory ; Molecule ; Thermodynamics ; Geometry Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Physics of Superconductivity and Magnetism
Authors: P. L. de Andrés | Javier Sánchez-Montero | Álvaro Ridruejo
Source: Scientific Reports (article, 2019-08-20)
Field: Materials Science — Metals and Alloys

Hydrogen in α-iron: role of phonons in the diffusion of interstitials at high temperature Ab-initio Density Functional Theory has been used to compute phonons for interstitial hydrogen in α-iron. In the harmonic approximation, these phonons yield Helmholtz's free energy as a function of temperature, which can be used to obtain diffusion barriers from an Arrhenius plot. By comparing with the experimental database compiled by Kiuchi and McLellan, we show that the role of phonons is crucial to understand the diffusion of interstitial hydrogen at T > 300 K. The computed specific heat for Fe<sub>16</sub>H and Fe behaves quite differently due to the appearance of optical modes and could be used to calibrate the amount of interstitials in the iron matrix. Phonon ; Diffusion ; Arrhenius plot ; Hydrogen ; Yield (engineering) ; Ab initio ; Density functional theory ; Materials science ; Condensed matter physics ; Activation energy ; Helmholtz free energy ; Arrhenius equation ; Thermodynamics ; Chemistry ; Physics ; Physical chemistry ; Computational chemistry ; Quantum mechanics Hydrogen embrittlement and corrosion behaviors in metals ; Nuclear Materials and Properties ; Microstructure and Mechanical Properties of Steels
Authors: Vincent Guérineau | Gautier Vilmart | Nelly Dorval | Aurélie Julian-Jankowiak
Source: Corrosion Science (article, 2019-10-15)
Field: Materials Science — Ceramics and Composites

Comparison of ZrB2-SiC, HfB2-SiC and HfB2-SiC-Y2O3 oxidation mechanisms in air using LIF of BO2(g) Materials science ; Volatilisation ; Ceramic ; Phase (matter) ; Analytical Chemistry (journal) ; Chemical engineering ; Composite material ; Chemistry ; Environmental chemistry ; Organic chemistry Advanced ceramic materials synthesis ; Advanced materials and composites ; Nuclear materials and radiation effects
Authors: A. Díaz | J.M. Alegre | I.I. Cuesta | Zhiliang Zhang
Source: International Journal of Mechanical Sciences (article, 2019-09-18)
Field: Materials Science — Metals and Alloys

Numerical study of hydrogen influence on void growth at low triaxialities considering transient effects Hydrogen ; Materials science ; Void (composites) ; Softening ; Necking ; Strain rate ; Plasticity ; Hardening (computing) ; Composite material ; Hydrogen embrittlement ; Mechanics ; Chemistry ; Physics Hydrogen embrittlement and corrosion behaviors in metals ; Microstructure and mechanical properties ; Corrosion Behavior and Inhibition
Authors: Hezam Fares | Yasser Hussein | Yasser Hussein Eissa Mohammed | Anup Kempaiah | Shaukath Ara Khanum
Source: Journal of Applied Pharmaceutical Science (article, 2019-07-01)
Field: Chemistry — Organic Chemistry

Synthesis, in silico study and in vitro anti-microbial evaluation of some new N-benzoyl-N'-[2-(4-chloro-phenoxy)-acetyl]-hydrazides analogs In bacterial resistance duty, the prompt increase against existent anti-microbial drugs is a challenging universal health problem. Bacteria represent a highly significant threat globally to healthcare-associated infections, also responsible for the majority of hospital infections, which leads to an increase in the mortality and burden of worldwide healthcare duty. In this investigation, we reported the synthesis novel substitutes of phenoxy hydrazide analogs (6a-f) and have been screened for in vitro anti-bacterial and anti-fungal activities to determine the inhibition zone by using the paper disk agar diffusion technique and broth dilution to evaluate the minimum inhibitory concentration values. The structure-activity relationship suggest that among the series (6a-f), compounds (6e) with two chloro groups and (6f) with four fluoro groups showed good inhibition against pathogenic microbes. Furthermore, these results were also confirmed by the in silico study. Based on this studies, there are a scopes of developing compounds (6e) and (6f) into potent anti-microbial drugs in the near future. In silico ; In vitro ; Chemistry ; Stereochemistry ; Combinatorial chemistry ; Biochemistry ; Gene Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Multicomponent Synthesis of Heterocycles
Authors: Insung Han | Xianghui Xiao | Haiping Sun | Ashwin J. Shahani
Source: Acta Crystallographica Section A Foundations and Advances (article, 2019-02-06)
Field: Materials Science — Materials Chemistry

A side-by-side comparison of the solidification dynamics of quasicrystalline and approximant phases in the Al–Co–Ni system Quasicrystals and their approximants have triggered widespread interest due to the challenge of solving their complex crystal structures as well as their possibly exceptional properties. The structural motifs of approximants are similar to those of the corresponding quasicrystals, but to what extent are their crystallization pathways the same? Unfortunately, there have been very few in situ experimental investigations to answer this question. Here, by leveraging the high penetrating power of hard X-rays, synchrotron-based X-ray tomography was conducted in order to capture the nucleation and growth of a decagonal quasicrystal and its related approximant. The combination of data-driven computational analysis with new thermodynamic databases allowed the characterization, with high precision, of the constitutional and kinetic driving forces for crystallization. The experimental results prove that the growth of both crystals from a liquid is dominated by first-order kinetics. Nevertheless, and somewhat surprisingly, significant differences were observed in their rates of nucleation and growth. The reasons for such divergent behaviours are discussed in light of contemporary theories of intermetallic crystallization. Quasicrystal ; Nucleation ; Intermetallic ; Crystallization ; Materials science ; Crystal growth ; Synchrotron ; Kinetic energy ; Crystallography ; Thermodynamics ; Physics ; Chemistry ; Metallurgy ; Optics ; Classical mechanics Quasicrystal Structures and Properties ; X-ray Diffraction in Crystallography ; Mineralogy and Gemology Studies
Authors: Qi Qi | Chunhui Liu | Lintao Liu | Qingyi Meng | Shuhua Wei | Anjie Ming | Jing Zhang | Yanrong Wang | Lidong Wu | Xiaoli Zhu | Feng Wei | Yan Jiang
Source: Micromachines (article, 2019-04-27)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Fabrication, Characterization, and Application of Large-Scale Uniformly Hybrid Nanoparticle-Enhanced Raman Spectroscopy Substrates Surface-enhanced Raman spectroscopy (SERS) substrates with high sensitivity and reproducibility are highly desirable for high precision and even molecular-level detection applications. Here, large-scale uniformly hybrid nanoparticle-enhanced Raman spectroscopy (NERS) substrates with high reproducibility and controllability were developed. Using oxygen plasma treatment, large-area and uniformly rough polystyrene sphere (URPS) arrays in conjunction with 20 nm Au films (AuURPS) were fabricated for SERS substrates. Au nanoparticles and clusters covered the surface of the URPS arrays, and this increased the Raman signal. In the detection of malachite green (MG), the fabricated NERS substrates have high reproducibility and sensitivity. The enhancement factor (EF) of Au nanoparticles and clusters was simulated by finite-difference time-domain (FDTD) simulations and the EF was more than 10<sup>4</sup>. The measured EF of our developed substrate was more than 10<sup>8</sup> with a relative standard deviation as low as 6.64%-13.84% over 15 points on the substrate. The minimum limit for the MG molecules reached 50 ng/mL. Moreover, the Raman signal had a good linear relationship with the logarithmic concentration of MG, as it ranged from 50 ng/mL to 5 μg/mL. The NERS substrates proposed in this work may serve as a promising detection scheme in chemical and biological fields. Raman spectroscopy ; Fabrication ; Characterization (materials science) ; Nanoparticle ; Materials science ; Nanotechnology ; Nanoscopic scale ; Scale (ratio) ; Chemical engineering ; Engineering ; Optics ; Physics Gold and Silver Nanoparticles Synthesis and Applications ; Spectroscopy Techniques in Biomedical and Chemical Research ; Quantum Dots Synthesis And Properties
Authors: Martyn Kelly
Source: Metabarcoding and Metagenomics (article, 2019-12-18)
Field: Materials Science — Biomaterials

Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation: lessons from the UK diatom metabarcoding exercise Development of effective metabarcoding-based tools for ecological assessment requires more than just detailed knowledge of ecology and molecular genetics. There is also a need to understand the context within which they will be used, and for the organisation that uses it to understand the techniques involved and, more especially, how the data that are produced differs from that generated by traditional ecological methods. Lessons learnt during the development of a metabarcoding tool for phytobenthos in the UK are set out in this paper. This attempted to develop a molecular “mirror” of the existing light microscopy-based approach to ecological assessment. Although this conservative approach does not exploit the full potential of metabarcoding data, it does mean that benchmarks exist against which performance and data can be judged. However, the pace of developments within molecular ecology means that regulators will need to find ways of incorporating new scientific insights whilst, at the same time, ensuring a stable regulatory regime. Installation of a metabarcoding technique within a regulatory organisation, in other words, is more than a transaction in which one approach is switched for another. A deeper transformation of the organisation is required. Pace ; Ecology ; Context (archaeology) ; Exploit ; Set (abstract data type) ; Data science ; Molecular ecology ; Computer science ; Biology ; Geography ; Sociology ; Computer security Diatoms and Algae Research ; Environmental DNA in Biodiversity Studies ; Microbial Community Ecology and Physiology