jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Rachit Bansal | Zehra Elgundi | Sophia C. Goodchild | Andrew Care | Megan S. Lord | Alison Rodger | Anwar Sunna
Source: Nanomaterials (article, 2020-05-30)
Field: Materials Science — Biomaterials

The Effect of Oligomerization on A Solid-Binding Peptide Binding to Silica-Based Materials The bifunctional linker-protein G (LPG) fusion protein comprises a peptide (linker) sequence and a truncated form of Streptococcus strain G148 protein G (protein G). The linker represents a multimeric solid-binding peptide (SBP) comprising 4 × 21-amino acid sequence repeats that display high binding affinity towards silica-based materials. In this study, several truncated derivatives were investigated to determine the effect of the SBP oligomerization on the silica binding function of LPG (for the sake of clarity, LPG will be referred from here on as 4 × LPG). Various biophysical characterization techniques were used to quantify and compare the truncated derivatives against 4 × LPG and protein G without linker (PG). The derivative containing two sequence repeats (2 × LPG) showed minimal binding to silica, while the truncated derivative with only a single sequence (1 × LPG) displayed no binding. The derivative containing three sequence repeats (3 × LPG) was able to bind to silica with a binding affinity of K<sub>D</sub> = 53.23 ± 4.5 nM, which is 1.5 times lower than that obtained for 4 × LPG under similar experimental conditions. Circular dichroism (CD) spectroscopy and fluorescence spectroscopy studies indicated that the SBP degree of oligomerization has only a small effect on the secondary structure (the linker unravels the beginning of the protein G sequence) and chemical stability of the parent protein G. However, based on quartz crystal microbalance with dissipation monitoring (QCM-D), oligomerization is an important parameter for a strong and stable binding to silica. The replacement of three sequence repeats by a (GGGGS)<sub>12</sub> glycine-rich spacer indicated that the overall length rather than the SBP oligomerization mediated the effective binding to silica. Linker ; Circular dichroism ; Peptide ; Sequence (biology) ; Bifunctional ; Chemistry ; Binding site ; Peptide sequence ; Stereochemistry ; Biophysics ; Crystallography ; Biochemistry ; Biology Diatoms and Algae Research ; Biochemical and Structural Characterization ; Advanced biosensing and bioanalysis techniques
Authors: Xia Jiang | Genyun Tang | Jie Yang | Jiacheng Ding | Hongwei Lin | Xiaoliang Xiang
Source: RSC Advances (article, 2020-01-01)
Field: Chemistry — Organic Chemistry

Synthesis of some new acylhydrazone compounds containing the 1,2,4-triazole structure and their neuritogenic activities in Neuro-2a cells In the present study, a novel series of acylhydrazone compounds (A0-A10) with the structure of 1,2,4-triazole have been designed and synthesized. In addition, all the synthesized compounds have been evaluated for neuritogenic activity in mouse neuroblastoma (Neuro-2a) cells. Notably, we found that one of these 11 acylhydrazone compounds, compound A5 (2-(4-amino-5-(pyridin-4-yl)-4<i>H</i>-1,2,4-triazol-3-ylthio)-<i>N</i>'-(2-hydroxybenzylidene)-acetohydrazide) displays excellent neuritogenic activity. Moreover, our present study revealed that compound A5 had the ability to induce neurite outgrowth through the PI3K/Akt and MEK-ERK signaling pathway in Neuro-2a cells. These findings suggest that compound A5 might exert neuritogenic effects and thus may be useful for the treatment of neural repair and regeneration. Chemistry ; Combinatorial chemistry ; 1,2,4-Triazole ; Stereochemistry ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Synthesis of Tetrazole Derivatives
Authors: Justyna Odrobińska | Magdalena Skonieczna | Dorota Neugebauer
Source: Pharmaceutics (article, 2020-12-03)
Field: Chemistry — Organic Chemistry

PEG Graft Polymer Carriers of Antioxidants: In Vitro Evaluation for Transdermal Delivery The in vitro biochemical evaluation of the applicability of polymers carrying active substances (micelles and conjugates) was carried out. Previously designed amphiphilic graft copolymers with retinol or 4-<i>n</i>-butylresorcinol functionalized polymethacrylate backbone and poly(ethylene glycol) (PEG) side chains that included Janus-type heterografted copolymers containing both PEG and poly(ε-caprolactone) (PCL) side chains were applied as micellar carriers. The polymer self-assemblies were convenient to encapsulate arbutin (ARB) as the selected active substances. Moreover, the conjugates of PEG graft copolymers with ferulic acid (FA) or lipoic acid (LA) were also investigated. The permeability of released active substances through a membrane mimicking skin was evaluated by conducting transdermal tests in Franz diffusion cells. The biological response to new carriers with active substances was tested across cell lines, including normal human dermal fibroblasts (NHDF), human epidermal keratinocyte (HaCaT), as well as cancer melanoma (Me45) and metastatic human melanoma (451-Lu), for comparison. These polymer systems were safe and non-cytotoxic at the tested concentrations for healthy skin cell lines according to the MTT test. Cytometric evaluation of cell cycles as well as cell death defined by Annexin-V apoptosis assays and senescence tests showed no significant changes under action of the delivery systems, as compared to the control cells. In vitro tests confirmed the biochemical potential of these antioxidant carriers as beneficial components in cosmetic products, especially applied in the form of masks and eye pads. HaCaT ; Chemistry ; Transdermal ; PEG ratio ; In vitro ; Biochemistry ; Pharmacology ; Medicine Advanced Polymer Synthesis and Characterization ; Advancements in Transdermal Drug Delivery ; Photochromic and Fluorescence Chemistry
Authors: Kadda Argoub | Benkouider ALİ MUSTAPHA | Yahiaoui Ahmed | Toubal KHALED | Djebar Hadji
Source: International Journal of Thermodynamics (article, 2020-02-29)
Field: Chemistry — Organic Chemistry

Enthalpy of Formation Modeling Using Third Order Group Contribution Technics and Calculation by DFT Method. Recently, with the development of calculators and numerical tools, quantum computations to explore the electronic, structural and dynamic properties of matter without resorting to experimental knowledge have seen increasing development. Thus, it is possible to perform ab-initio calculations with increasing precision and for increasingly larger systems. In the scientific literature, papers using ab-initio quantum computation for the prediction of formation enthalpies is more and more numerous. The aim of this paper is to develop a theoretical method to calculate standard enthalpy of formation in gas stat for organic compounds using group contribution technics (third-order group contribution method). For the establishment of this method, 750 molecules are used. In parallel with group contribution methods, this paper presents another approach to calculate gas-state formation enthalpies based on DFT method. The calculation involved 30 molecules with at least one ring from C3 to C13. Finally, DFT and group contribution results are compared. Standard enthalpy of formation ; Computation ; Enthalpy ; Ab initio ; Standard enthalpy change of formation ; Thermodynamics ; Molecule ; Group (periodic table) ; Computer science ; Ab initio quantum chemistry methods ; Computational chemistry ; Statistical physics ; Chemistry ; Physics ; Quantum mechanics ; Algorithm Chemical Thermodynamics and Molecular Structure ; thermodynamics and calorimetric analyses ; Phase Equilibria and Thermodynamics
Authors: Sergio Pablo‐García | Moises Álvarez‐Moreno | Núria López
Source: International Journal of Quantum Chemistry (article, 2020-07-09)
Field: Materials Science — Materials Chemistry

Turning chemistry into information for heterogeneous catalysis Abstract The growing generation of data and their wide availability has led to the development of tools to produce, analyze, and store this information. Computational chemistry studies, especially catalytic applications, often yield a vast amount of chemical information that can be analyzed and stored using these tools. In this manuscript, we present a framework that automatically performs a fully automated procedure consisting of the transfer of an adsorbate from a known metal slab to a new metal slab with similar packing. Our method generates the new geometry and also performs the required calculations and analysis to finally upload the processed data to an online database (ioChem‐BD). Two different implementations have been built, one to relocate minimum energy point structures and the second to transfer transition states. Our framework shows good performance for the minimum point location and a decent performance for the transition state identification. Most of the failures occurred during the transition state searches and needed additional steps to fully complete the process. Further improvements of our framework are required to increase the performance of both implementations. These results point to the avoidhuman path as a feasible solution for studies on very large systems that require a significant amount of human resources and, in consequence, are prone to human errors. Implementation ; Computer science ; Upload ; Process (computing) ; Point (geometry) ; Path (computing) ; Identification (biology) ; Chemistry ; Software engineering ; Mathematics Machine Learning in Materials Science ; Catalysis and Oxidation Reactions ; Catalysis and Hydrodesulfurization Studies
Authors: Saeedeh Mohammadi | Mohammad Esmailpour | Mina Mohammadi
Source: Research Square (Research Square) (preprint, 2020-05-15)
Field: Materials Science — Materials Chemistry

Chloroquine drug and Graphene complex for treatment of COVID-19 Abstract This paper is a new step in helping the treatment of coronavirus by improving the performance of chloroquine drug. For this purpose, we propose a complex of chloroquine drug with graphene nanoribbon (GNR) scheme. We compute the structural and electrical properties and absorption of chloroquine (C18H26ClN3) and GNR complex using the density functional theory (DFT) method. By creating a drug and GNR complex, the density of states of electrons increases and the energy gap decreases compared to the chloroquine. Also, using absorption calculations and spectrums such as infrared and UV-Vis spectra, we showed that GNR is a suitable structure for creating chloroquine drug complex. Our results show that the dipole moment, global softness and electrophilicity for the drug complex increases compared to the non-complex state. Our calculations can be useful for increasing performance and reducing the side effects of chloroquine, and thus can be effective in treating coronavirus. Chloroquine ; Drug ; Density functional theory ; Graphene ; Absorption (acoustics) ; Microgrid ; Dipole ; Materials science ; Chemistry ; Computational chemistry ; Pharmacology ; Physics ; Nanotechnology ; Medicine ; Malaria ; Quantum mechanics ; Immunology Dielectric properties of ceramics ; Graphene and Nanomaterials Applications ; Vitamin C and Antioxidants Research
Authors: Benjamin D. Knapp | Lillian Zhu | Kerwyn Casey Huang
Source: PLoS Biology (article, 2020-11-06)
Field: Chemistry — Physical and Theoretical Chemistry

SiCTeC: An inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging Single-cell imaging, combined with recent advances in image analysis and microfluidic technologies, have enabled fundamental discoveries of cellular responses to chemical perturbations that are often obscured by traditional liquid-culture experiments. Temperature is an environmental variable well known to impact growth and to elicit specific stress responses at extreme values; it is often used as a genetic tool to interrogate essential genes. However, the dynamic effects of temperature shifts have remained mostly unstudied at the single-cell level, due largely to engineering challenges related to sample stability, heatsink considerations, and temperature measurement and feedback. Additionally, the few commercially available temperature-control platforms are costly. Here, we report an inexpensive (<$110) and modular Single-Cell Temperature Controller (SiCTeC) device for microbial imaging-based on straightforward modifications of the typical slide-sample-coverslip approach to microbial imaging-that controls temperature using a ring-shaped Peltier module and microcontroller feedback. Through stable and precise (±0.15°C) temperature control, SiCTeC achieves reproducible and fast (1-2 min) temperature transitions with programmable waveforms between room temperature and 45°C with an air objective. At the device's maximum temperature of 89°C, SiCTeC revealed that Escherichia coli cells progressively shrink and lose cellular contents. During oscillations between 30°C and 37°C, cells rapidly adapted their response to temperature upshifts. Furthermore, SiCTeC enabled the discovery of rapid morphological changes and enhanced sensitivity to substrate stiffness during upshifts to nonpermissive temperatures in temperature-sensitive mutants of cell-wall synthesis enzymes. Overall, the simplicity and affordability of SiCTeC empowers future studies of the temperature dependence of single-cell physiology. Temperature control ; Microfluidics ; Modular design ; Materials science ; Nanotechnology ; Thermoelectric cooling ; Single-cell analysis ; Biology ; Biological system ; Heat sink ; Thermoelectric effect ; Cell ; Computer science ; Biochemistry ; Mechanical engineering thermodynamics and calorimetric analyses ; Gene Regulatory Network Analysis ; Viral Infectious Diseases and Gene Expression in Insects
Authors: Hidayat Hidayat
Source: International journal of science engineering and information technology (article, 2020-12-18)
Field: Materials Science — Materials Chemistry

Analysis Of Load Variations On ST 60 Steel Using Vickers Method The use of metal in the industrial world, especially ST60 Steel, is a very vital need, this can be seen from the increasing number of machine or equipment components or construction parts made of steel. Hardness is one of the mechanical properties that is often used as a guide in selecting materials for an equipment component. To find out the hardness price of a material, various testing methods can be used, including the Vickers method, which is tested by applying a force to the indented diamond pyramid against the material for which the hardness value is determined. The amount of hardness value is determined by the magnitude of the loading force divided by the area of indentation. In this study, what was investigated was the effect of force on the hardness of the Vickers method. The results showed that the load variation had little effect on the results of the Vickers hardness value, especially for high loads (100 Kgf). The average hardness value for the mild steel being tested is 163 HV and 168 HV, the highest hardness value is 174 HV and the lowest hardness value is 156 HV, so that a tolerance of ± 10 HV commonly used in the Vickers test is sufficient.Keywords: Hardness, ST 60 Steel , Loading Variations, Vickers Test Vickers hardness test ; Materials science ; Indentation ; Indentation hardness ; Hardness ; Composite material ; Diamond ; Knoop hardness test ; Metallurgy ; Microstructure Material Selection and Properties ; Engineering Structural Analysis Methods ; Metal Forming Simulation Techniques
Authors: Rong‐Jun Xie
Source: Journal of the Ceramic Society of Japan (article, 2020-09-30)
Field: Materials Science — Materials Chemistry

Development of sialon phosphors and their applications to solid-state lighting InGaN-LED-driven solid-state lighting [i.e., white light-emitting diodes (wLEDs)] is now penetrating to our daily life and replacing traditional lighting sources rapidly owing to its energy-saving, high efficiency and environment friendly. Phosphors play key roles in improving the color rendition/gamut, luminous efficiency and lifetime of wLEDs, but the traditional ones for lamps usually do not meet the requirements for wLEDs. This triggers the search for new phosphors that can be excited by blue- or near ultraviolet LEDs. Sialon-based nitride phosphors are emerged as a new family of luminescent materials, superior to oxide or sulfide counterparts in terms of high conversion efficiency, small Stokes shift, excellent chemical and thermal stability. In this mini review, nitride phosphors will be introduced, including their classification, photoluminescence properties, structure-property relations, and applications in general illumination and backlighting. Phosphor ; Luminous efficacy ; Materials science ; Backlight ; Sialon ; Optoelectronics ; Light-emitting diode ; Solid-state lighting ; Gamut ; Photoluminescence ; Nitride ; Luminous flux ; Luminescence ; Diode ; Optics ; Nanotechnology ; Layer (electronics) ; Composite material ; Ceramic ; Liquid-crystal display Luminescence Properties of Advanced Materials ; Luminescence and Fluorescent Materials ; Ammonia Synthesis and Nitrogen Reduction
Authors: Rustam Rustam | Agus Yodi Gunawan | Made Tri Ari Penia Kresnowati
Source: Acta Polytechnica (article, 2020-11-16)
Field: Chemistry — Analytical Chemistry

ARTIFICIAL NEURAL NETWORK APPROACH FOR THE IDENTIFICATION OF CLOVE BUDS ORIGIN BASED ON METABOLITES COMPOSITION This paper examines the use of an artificial neural network approach in identifying the origin of clove buds based on metabolites composition. Generally, large data sets are critical for an accurate identification. Machine learning with large data sets lead to a precise identification based on origins. However, clove buds uses small data sets due to the lack of metabolites composition and their high cost of extraction. The results show that backpropagation and resilient propagation with one and two hidden layers identifies the clove buds origin accurately. The backpropagation with one hidden layer offers 99.91% and 99.47% for training and testing data sets, respectively. The resilient propagation with two hidden layers offers 99.96% and 97.89% accuracy for training and testing data sets, respectively. Backpropagation ; Artificial neural network ; Identification (biology) ; Computer science ; Artificial intelligence ; Composition (language) ; Pattern recognition (psychology) ; Training set ; Layer (electronics) ; Machine learning ; Data mining ; Biology ; Chemistry ; Botany Spectroscopy and Chemometric Analyses
Authors: Bandar R. Alsehli
Source: Egyptian Journal of Chemistry (article, 2020-10-31)
Field: Chemistry — Analytical Chemistry

Evaluation and Comparison between a Conventional Acid Digestion Method and a Microwave Digestion System for Heavy Metals Determination in Mentha Samples by ICP-MS. Mentha is the most common plant species grown in Saudi Arabia's Madinah city. Locally, the two popular types of mint are commercially called (Hasawi or Habaq) and (Mograbi). Both species are used in herbal teas, alone or as spice mixtures for many foods to offer aroma and flavour. In this research Hasawi mint samples were collected from three different locations and digested by two methods (acid digestion method and a microwave digestion system). Then, they were analysed for their metal contents by ICP-MS. The results from both digestion methods revealed that the following 10 metals were presented: V, Cr, Mn, Co, Ni, Cu, Zn, As, Cd and Pb. The microwave digestion system was the best for all studied heavy metals in term of sample preparation procedures, linearity (≥ 0.999), recovery (97%- 101%, n=2) and precision (R.S.D% ≈ 1-2 %, n=2). Mint samples from first location contained 7 metals within the permissible limit while the remaining three metals (Cr, Cu and Zn) had higher levels. The second location contained 9 metals within the permissible limit but only one metal (Cu) had a higher level. The third location contained 6 metals within the permissible limit while it had 4 metals (Cr, Ni, Cu, Cd) with higher level. All locations contained As, Cd and Pb within permissible limit except the third location which had a cadmium amount of (0.6 mg/kg) while the cadmium permissible level is (0.3 mg/kg). Some farmers use composts (from inorganic sources), fertilizers and plant nutrients in relatively large amounts that are rich in some metals and this might explain some of the higher value of metals in the mint. Moreover, contamination from industrial activities nearby mint farms might also be expected. Cadmium ; Microwave digestion ; Detection limit ; Chemistry ; Digestion (alchemy) ; Metal ; Heavy metals ; Zinc ; Environmental chemistry ; Chromatography Heavy Metals in Plants ; Heavy metals in environment ; Geochemistry and Geologic Mapping
Authors: Ying Wu | Yuvixza Lizarme-Salas | Yun Cheuk Leung | Luke Hunter | Junming Ho
Source: Australian Journal of Chemistry (article, 2020-05-13)
Field: Chemistry — Spectroscopy

Predicting Octanol–Water Partition Coefficients of Fluorinated Drug-Like Molecules: A Combined Experimental and Theoretical Study In this paper, a dataset of 11 fluorinated compounds containing a variety of functional groups (amides, esters, indoles, and ethers) as well as mono, gem-difluoro, erythro-difluoro, and threo-difluoro patterns were synthesised and their octanol–water partition coefficients (log P) were measured using a shake-flask method. The resulting data was used to assess the performance of several popular empirical fragment-based methods as well as quantum chemical implicit solvent models (SMD and SM12). Overall, the empirical miLOGP, ALOGPS, and ALOGP methods performed the best with a mean absolute deviation (MAD) of ~0.25 log units, while the best performing implicit solvent model SMD has a slightly higher MAD of 0.36 log units. Based on the present work and previous studies, the miLOGP and ALOGP empirical methods are recommended for fast and moderately accurate prediction of log P for neutral organic solutes. Chemistry ; Partition coefficient ; Octanol ; Solvent ; Quantum chemistry ; Molecule ; Computational chemistry ; Absolute deviation ; Partition (number theory) ; Ionic liquid ; Organic chemistry ; Supramolecular chemistry ; Mathematics ; Catalysis ; Statistics Analytical Chemistry and Chromatography ; Computational Drug Discovery Methods ; Metabolomics and Mass Spectrometry Studies
Authors: Bakhodur Abdusatorov | Alexey I. Salimon | Yekaterina D. Bedoshvili | Yelena V. Likhoshway | Alexander M. Korsunsky
Source: Sensors and Actuators A Physical (article, 2020-08-26)
Field: Materials Science — Biomaterials

FEM exploration of the potential of silica diatom frustules for vibrational MEMS applications Frustule ; Finite element method ; Diatom ; Microelectromechanical systems ; Materials science ; Natural frequency ; Vibration ; Stiffness ; Range (aeronautics) ; Acoustics ; Composite material ; Nanotechnology ; Structural engineering ; Physics ; Engineering ; Geology Diatoms and Algae Research ; Planetary Science and Exploration ; Protist diversity and phylogeny