jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yating Pan | Xinyi Liao | Lili Yang | Chunlei Zhang | Jue Wang | Peiyong Zheng | Guanzhen Yu | Haiyan Song
Source: Frontiers in Pharmacology (article, 2022-06-30)
Field: Materials Science — Biomaterials

Extract of Marsdenia tenacissima (Roxb.) Moon [Apocynaceae] Suppresses Hepatocellular Carcinoma by Inhibiting Angiogenesis The extract of <i>Marsdenia</i> <i>tenacissima</i> (Roxb.) Moon [Apocynaceae] (MTE) has shown a significant anti-cancer effect on hepatocellular carcinoma (HCC), but its mechanism remains unclear. In this study, we used transcriptomics methods to investigate the underlying mechanism of MTE against HCC. Both MHCC97H and HepG2 cell lines were treated with MTE. The cell viability and migration were measured using the cell counting kit-8 assay and transwell assay. RNA-sequencing was used to identify differentially expressed genes (DEGs) between HepG2 cells treated with and without MTE. The expression levels of selected DEGs-vascular endothelial growth factor-A (VEGFA), platelet-derived growth factor receptor-β (PDGFRB), and von Willebrand factor (VWF)-were verified by RT-PCR and Western blot. The effect of conditioned medium from HCC cells with MTE treatment (CM-MTE) on blood vessels was observed by tube formation assay of HUVECs and chick chorioallantoic membrane (CAM) assay. A mouse model of HCC patient-derived tumor xenograft (PDX) was established and treated with MTE. The effect of MTE on the growth and angiogenesis of HCC-PDX was analyzed. The results demonstrated that MTE inhibited the viability and migration of HCC cells. RNA-seq showed that MTE treatment downregulated multiple genes associated with metabolism and angiogenesis. The expression levels of VEGFA, VWF, PDGFB, and PDGFRB in HCC cells were significantly suppressed by MTE. Meanwhile, MTE effectively inhibited the tube-forming capability of HUVECs and the angiogenesis of chick CAM. <i>In vivo</i> experiments revealed that the extract reduced tumor volume, inhibited the proliferation of HCC cells, and expanded the necrotic area of the tumor. Immunohistochemical results showed that the expression levels of CD31, PDGFB, VEGF, VWF, and PDGFRB in the HCC-PDX tumor tissues were all downregulated by MTE in a dose-dependent manner. Taken together, MTE could inhibit angiogenesis by repressing the expression of VEGF, VWF, PDGF, and PDGFRB in HCC cells, a mechanism that may enable MTE to counter HCC development. Apocynaceae ; Hepatocellular carcinoma ; Angiogenesis ; Traditional medicine ; Hepatic carcinoma ; Pharmacology ; Medicine ; Cancer research Phytochemistry and Bioactive Compounds ; Magnolia and Illicium research ; Angiogenesis and VEGF in Cancer
Authors: Aline M. Thomas | Ethan Yang | Matthew D. Smith | Chengyan Chu | Peter A. Calabresi | Kristine Glunde | Peter C.M. van Zijl | Jeff W. M. Bulte
Source: Journal of Neuroinflammation (article, 2022-06-03)
Field: Materials Science — Materials Chemistry

CEST MRI and MALDI imaging reveal metabolic alterations in the cervical lymph nodes of EAE mice Taken together, we demonstrate the utility of CEST MRI signal changes in superficial cervical LNs as a complementary imaging biomarker for monitoring disease activity in MS. CEST MRI biomarkers corresponded to disease activity, correlated with immune activation (surface markers, antigen-stimulated proliferation), and correlated with LN metabolite levels. Multiple sclerosis ; Experimental autoimmune encephalomyelitis ; Magnetic resonance imaging ; Medicine ; Immune system ; Pathology ; Mass spectrometry imaging ; Encephalomyelitis ; Myelin ; Chemistry ; Central nervous system ; Immunology ; Internal medicine ; Radiology Lanthanide and Transition Metal Complexes ; MRI in cancer diagnosis ; Electron Spin Resonance Studies
Authors: Jana Sonnenschein | Mario Hermes | Stefan Höving | Norbert Kockmann | Kerstin Wohlgemuth
Source: Computers & Chemical Engineering (article, 2022-10-05)
Field: Materials Science — Materials Chemistry

Population balance modeling of unstirred cooling crystallization on an integrated belt filter Crystallization ; Balance (ability) ; Filter (signal processing) ; Population ; Materials science ; Environmental science ; Control theory (sociology) ; Process engineering ; Engineering ; Computer science ; Chemical engineering ; Artificial intelligence ; Electrical engineering ; Biology Crystallization and Solubility Studies ; Freezing and Crystallization Processes ; Coagulation and Flocculation Studies
Authors: Cheng‐tao Su | Bin Li | Hai Yin | Ji‐ping Zou | Feng Zhang | Yande Liu
Source: Journal of Spectroscopy (article, 2022-12-03)
Field: Chemistry — Analytical Chemistry

Identification of Damage in Pear Using Hyperspectral Imaging Technology Crown pears are an important economic crop, but their quality and economy are seriously affected by the different levels of damage. To improve the overall quality of crown pears, sorting of crown pears with different levels of damage is required. However, there are some shortcomings in the traditional detection methods, such as low efficiency and large error. Therefore, the hyperspectral technology was used to discriminate between sound and 3 different levels of damage (defined as level I, II, and III damage, respectively) of crown pears in this study. To improve the discriminatory accuracy of the model, absorbance (A) spectra and Kubelka–Munk (K-M) spectra were added to reflectance (R) spectra. The three spectra were pretreated; then, the partial least squares discriminant analysis (PLS-DA) model and the support vector machine (SVM) model were established to discriminate the crown pears with different levels of damage. The results of the discriminant model show that the discrimination accuracy of the SVM based on R, A, and K-M spectra is higher than that of PLS-DA of them; the A-RAW-SVM model has the best discrimination performance with an overall discrimination accuracy of 100% for the test and 98.98% for calibration sets, respectively. Finally, the spectra were selected by the competitive adaptive reweighted sampling (CARS) and the uninformative variables elimination (UVE) to obtain the characteristic wavelengths, and the SVM models were built based on the filtered R, A, and K-M. Their discrimination results show that the A-RAW-CARS-SVM model has the best discrimination ability, and the discrimination accuracies of the test and calibration sets of the model are 96.88% and 100%, respectively. The results show that the best discrimination of different levels of damage of crown pears is the SVM model based on a spectra. This study provides a theoretical basis and experimental basis for detecting the damage of crown pears using hyperspectral. Hyperspectral imaging ; Support vector machine ; Linear discriminant analysis ; Artificial intelligence ; Pattern recognition (psychology) ; PEAR ; Calibration ; Partial least squares regression ; Mathematics ; Sorting ; Computer science ; Statistics ; Biological system ; Algorithm ; Biology Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Essential Oils and Antimicrobial Activity
Authors: Felix Dionisius | Jos Istiyanto | Danardono Agus Sumarsono | Gatot Prayogo | Ario Sunar Baskoro | Mohammad Malawat
Source: International Journal of Automotive and Mechanical Engineering (article, 2022-03-24)
Field: Materials Science — Materials Chemistry

Modeling of Crashworthiness Criteria based on Variation of Hole as Crush Initiator in Thin-Walled Square Crashworthiness is the ability to protect its occupant by absorbing the energy of impact during a collision. A crush initiator is one way to increase crashworthiness criteria at collision. The most widely applied crush initiator applications are holes, wall thickness reduction, grooves, notch, bead and corrugated. This study discussed making a functional model from the crashworthiness criteria which is known by CFE and SEA. Variable used variations of the crush initiator in the form of circular holes with different rotation angles and diameters. The rotation angle referred to in this study was 2 holes which are rotated based on the midpoint of the hole distance to the radial axis of the hole. The crush initiator was placed in a square column at each side with steel material. Besides, the wall thickness variable was added which can increase the energy absorption during a collision. The method used numerical simulation and experimental dynamic loading. The numerical simulation used the explicit finite element method by using ESI PAM-Crash. Both methods used the drop test model by using impact transferability. Impact transferability was rigid which was used to transfer impact loading during impact conditions. Experimental was used to validate the function model which was obtained through the least square method with sampling from numerical simulations. The results showed the same patterns produced by the functional and experimental models using the Taguchi method (L9) with 3 runs. The maximum of this pattern is 23% for CFE and 17% for SEA. Meanwhile, the average error of the S/N ratio shows 8.77% for CFE and 2.16% for SEA. This model function could be used by a crashworthy designer to estimate the value of CFE and SEA. Crashworthiness ; Collision ; Structural engineering ; Finite element method ; Materials science ; Square (algebra) ; Rotation (mathematics) ; Mechanics ; Engineering ; Geometry ; Computer science ; Mathematics ; Physics High-Velocity Impact and Material Behavior ; Cellular and Composite Structures ; Transportation Safety and Impact Analysis
Authors: Jinjia Feng | Zhen Wang | Yaliang Li | Bolin Ding | Zhewei Wei | Hongteng Xu
Source: Proceedings of the 31st ACM International Conference on Information &amp; Knowledge Management (article, 2022-10-16)
Field: Materials Science — Materials Chemistry

MGMAE Masked autoencoder (MAE), as an effective self-supervised learner for computer vision and natural language processing, has been recently applied to molecule representation learning. In this paper, we identify two issues in applying MAE to pre-train Transformer-based models on molecular graphs that existing works have ignored. (1) As only atoms are abstracted as tokens and then reconstructed, the chemical bonds are not decided in the decoded molecule, making molecules with different arrangements of the same atoms indistinguishable. (2) Although a high mask ratio that corresponds to a challenging reconstruction task has been proved beneficial in the vision domain, it cannot be trivially leveraged on molecular graphs as there is less redundancy of information in graph data. To resolve these issues, we propose a novel framework, Molecular Graph Mask AutoEncoder (MGMAE). As the first step in MGMAE, we transform each molecular graph into a heterogeneous atom-bond graph to fully use the bond attributes and design unidirectional position encoding for such graphs. Then we propose a hybrid masking mechanism that exploits the complementary nature between atoms' attributive and spatial features. Meanwhile, we compensate for the mask embedding by a dynamic aggregation representation that exploits the correlations between topologically adjacent tokens. As a result, MGMAE can reconstruct the masked atoms, the masked bonds, and the relative distance among atoms simultaneously, with a high mask ratio. We compare MGMAE with the state-of-the-art methods on various molecular benchmarks and show the competitiveness of MGMAE in both regression and classification tasks. Computer science ; Molecular graph ; Autoencoder ; Embedding ; Exploit ; Theoretical computer science ; Graph embedding ; Graph ; Artificial intelligence ; Subspace topology ; Pattern recognition (psychology) ; Algorithm ; Deep learning Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Advanced Graph Neural Networks
Authors: Fernando Gomes de Souza | Thaís Nogueira Barradas | Vinicius Freitas Caetano | Angela Becerra
Source: Brazilian Journal of Experimental Design Data Analysis and Inferential Statistics (article, 2022-05-18)
Field: Materials Science — Polymers and Plastics

Nanoparticles improving polyaniline electrical conductivity: A meta-analysis study Polyaniline is a conductive polymer that attracts the attention of many researchers around the world. The history of this polymer begins in 1862 when Letheby first reported this material. Since then, a myriad of studies has been conducted onthis material, and new works continue to investigate the potential of this material. Polyaniline has been improved with the help of Nanotechnology. The use of nanofillers has been seen as a quick and economical way to modify materials, drivinginnovations based on new physical and chemical properties from the conductive polymer materials and nanoparticles joining. Several works address the use of different nanoparticles, which leads to the practical impossibility of sifting through all this information. Thus, this work proposes to systematically collect data in the literature and investigate which nanoparticles can increase the electrical conductivity of Polyaniline (PAni). The results obtained demonstrate that among the possiblenanofillers, graphene and carbon nanotubes have great prominence. Furthermore, the results of the meta-analysis prove that PAni's conductivity increases when this polymer is modified with the aforementioned nanofillers. Polyaniline ; Conductive polymer ; Materials science ; Carbon nanotube ; Nanoparticle ; Nanotechnology ; Conductivity ; Polymer ; Graphene ; Electrical conductor ; Polyaniline nanofibers ; Carbon Nanoparticles ; Composite material ; Chemistry Conducting polymers and applications ; Electrochemical sensors and biosensors
Authors: Seham Alzahrani | Hiba Ali | Eman Hillal Althubaiti | M. M. Ahmed
Source: Indian Journal of Pharmaceutical Sciences (article, 2022-01-01)
Field: Materials Science — Materials Chemistry

Green Synthesis of Gold Nanoparticles, Silver Nanoparticles and Gold-Silver Alloy Nanoparticles Using Ziziphus spina-christi Leaf Extracts and Antibacterial Activity against Multidrug-Resistant Bacteria Multidrug-resistant bacteria continue to pose the greatest threat to public health. Metallic nanoparticles are one of the more promising strategies for combating antibiotic resistance. This research aims to determine the effect of gold and silver nanoparticles and gold-silver alloy nanoparticles as antibacterial agents. On the other hand, biogenic synthesized gold and silver nanoparticles using Ziziphus spina-christi leaf extract and preparation of gold-silver alloy nanoparticles for treatment of multidrug-resistant bacteria were studied. The formation of nanoparticles was characterized using ultraviolet-visible spectrophotometer, fourier transforms infrared spectroscopy, X-ray diffraction and transmission electron microscopy. Antibacterial activity of the biosynthesized gold nanoparticles, silver nanoparticles and gold-silver alloy nanoparticles was studied against Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii and Enterococcus faecalis. In the present study, the minimum inhibitory concentration ranged from 61.33 to 64 μg/ml and the minimum bactericidal concentration of the silver nanoparticles ranged from 85.33 to 93.33 μg/ml against multidrug-resistant strains. Synthesized gold nanoparticles had no inhibition zone, indicating that silver nanoparticles have no negative effect on multidrug-resistant bacteria. Minimum inhibitory concentration of gold nanoparticles was in high concentration against multidrug-resistant strain was not bactericidal. The highest minimum inhibitory concentration of gold nanoparticles was 114 μg/ml. Finally, the minimum inhibitory concentration ranged from 53.33 to 62 μg/ml and the minimum bactericidal concentration of the gold-silver alloy nanoparticles ranged from 77.33 to 93.33 μg/ml against multidrug-resistant strains. These results indicate that gold-silver alloy nanoparticles showed higher antimicrobial ability when compared to silver nanoparticles and gold nanoparticles alone. Finally, the synthesized nanoparticles could be used as an alternative antimicrobial agent against multidrug-resistant bacteria, according to our findings. Silver nanoparticle ; Colloidal gold ; Minimum bactericidal concentration ; Enterococcus faecalis ; Nanoparticle ; Nuclear chemistry ; Minimum inhibitory concentration ; Multiple drug resistance ; Acinetobacter baumannii ; Chemistry ; Antibacterial activity ; Bacteria ; Materials science ; Escherichia coli ; Antimicrobial ; Pseudomonas aeruginosa ; Nanotechnology ; Antibiotics ; Biology ; Biochemistry ; Organic chemistry Nanoparticles: synthesis and applications
Authors: Samuel J. Avis | Jack R. Panter | Halim Kusumaatmaja
Source: The Journal of Chemical Physics (article, 2022-09-27)
Field: Materials Science — Materials Chemistry

A robust and memory-efficient transition state search method for complex energy landscapes Locating transition states is crucial for investigating transition mechanisms in wide-ranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom, on-the-fly adaptive remeshing and coarse-graining, and energy landscapes that are locally flat or discontinuous. To resolve these challenges, we introduce a new double-ended method, the Binary-Image Transition State Search (BITSS). It uses just two states that converge to the transition state, resulting in a fast, flexible, and memory-efficient method. We also show that it is more robust compared to existing bracketing methods that use only two states. We demonstrate its versatility by applying BITSS to three very different classes of problems: Lennard-Jones clusters, shell buckling, and multiphase phase-field models. Bracketing (phenomenology) ; Granularity ; Statistical physics ; Computer science ; Binary number ; Phase transition ; State (computer science) ; Degrees of freedom (physics and chemistry) ; Algorithm ; Theoretical computer science ; Physics ; Mathematics ; Quantum mechanics Machine Learning in Materials Science ; Block Copolymer Self-Assembly ; Protein Structure and Dynamics
Authors: Intan Sue Liana Abdul Hamid | Khi Khim Beh | Mohammad Faiz Mohamed Omar | Khairu Anuar Mohamad Zain | Nuha Abd Rhaffor | Sofiyah Sal Hamid | Asrulnizam Abd Manaf
Source: Micromachines (article, 2022-01-01)
Field: Materials Science — Surfaces, Coatings and Films

Three-Dimensional Soft Material Micropatterning via Grayscale Photolithography for Improved Hydrophobicity of Polydimethylsiloxane (PDMS) In this present work, we aim to improve the hydrophobicity of a polydimethylsiloxane (PDMS) surface. Various heights of 3D PDMS micropillars were fabricated via grayscale photolithography, and improved wettability was investigated. Two approaches of PDMS replication were demonstrated, both using a single master mold to obtain the micropillar arrays. The different heights of fabricated PDMS micropillars were characterized by scanning electron microscopy (SEM) and a surface profiler. The surface hydrophobicity was characterized by measuring the water contact angles. The fabrication of PDMS micropillar arrays was shown to be effective in modifying the contact angles of pure water droplets with the highest 157.3-degree water contact angle achieved by implementing a single mask grayscale lithography technique. Polydimethylsiloxane ; Materials science ; Contact angle ; Soft lithography ; Photolithography ; Micropatterning ; PDMS stamp ; Wetting ; Fabrication ; Scanning electron microscope ; Mold ; Nanotechnology ; Grayscale ; Composite material ; Optics Surface Modification and Superhydrophobicity ; Advanced Sensor and Energy Harvesting Materials ; Nanomaterials and Printing Technologies
Authors: Xiaofan Zhai | Wei Cao | Yimeng Zhang | Peng Ju | Juna Chen | Jizhou Duan | Chengjun Sun
Source: Frontiers in Microbiology (article, 2022-03-18)
Field: Materials Science — Materials Chemistry

Study on the Bacterial Communities of the Biofilms on Titanium, Aluminum, and Copper Alloys at 5,772 m Undersea in Yap Trench Biofilms formed on metal surfaces strongly affect metallic instruments serving in marine environments. However, due to sampling difficulty, less has been known about the bacterial communities of the biofilm on metallic surfaces in hadal environments, so the failure process of these deep-sea metallic instruments influenced by microbial communities could be hardly predicted. In this research, seven alloys, including titanium, aluminum, and copper alloys, were exposed in Yap Trench hadal environment for 1 year. Thus, the communities of the biofilms formed on metallic surfaces at 5,772 m undersea in Yap Trench were initially reported in previous studies. Then, 16S rRNA gene sequencing was performed to visualize the <i>in situ</i> bacterial communities of the biofilms formed on titanium, aluminum, and copper alloys at 5,772 m undersea in Yap Trench. It was found that Proteobacteria was the dominant phylum in all samples, but distinct genera were discovered on various alloys. The titanium alloy provided a suitable substrate for a mutualistic symbiotic biofilm with abundant bacterial richness. Aluminum alloys without copper components showed the least bacterial richness and formed a cold-adapted and oligotrophic-adapted biofilm containing the genera <i>Sulfurimonas</i> and <i>PS1 Clade</i>, while copper-present alloys showed relatively high bacterial richness with copper-resistant or even copper-utilizing biofilms constituting the genera <i>Stenotrophomonas</i>, <i>Burkholderia-Caballeronia-Paraburkholderia</i>, and <i>Achromobacter</i> on the surfaces. Furthermore, among all the element components contained in alloys investigated in this research, copper element showed the strongest influences on the composition and function of microbial communities in the biofilms formed on various metallic surfaces. Biofilm ; Copper ; Titanium ; Aluminium ; Materials science ; Bacteria ; Metallurgy ; Biology ; Paleontology Corrosion Behavior and Inhibition ; Marine Biology and Environmental Chemistry ; Metal Extraction and Bioleaching
Authors: Mukundan Ragavan | Marc McLeod | Anna Rushin | Matthew E. Merritt
Source: Frontiers in Physiology (article, 2022-02-07)
Field: Chemistry — Spectroscopy

Detecting de novo Hepatic Ketogenesis Using Hyperpolarized [2-13C] Pyruvate The role of ketones in metabolic health has progressed over the past two decades, moving from what was perceived as a simple byproduct of fatty acid oxidation to a central player in a multiplicity of disease states. Previous work with hyperpolarized (HP) <sup>13</sup>C has shown that ketone production can be detected when using precursors that labeled acetyl-CoA at the C1 position, often in tissues that are not normally recognized as ketogenic. Here, we assay metabolism of HP [2-<sup>13</sup>C]pyruvate in the perfused mouse liver, a classic metabolic testbed where nutritional conditions can be precisely controlled. Livers perfused with long-chain fatty acids or the medium-chain fatty acid octanoate showed no evidence of ketogenesis in the <sup>13</sup>C spectrum. In contrast, addition of dichloroacetate, a potent inhibitor of pyruvate dehydrogenase kinase, resulted in significant production of both acetoacetate and 3-hydroxybutyrate from the pyruvate precursor. This result indicates that ketones are readily produced from carbohydrates, but only in the case where pyruvate dehydrogenase activity is upregulated. Ketogenesis ; Ketone bodies ; Pyruvate dehydrogenase complex ; Gluconeogenesis ; Pyruvate dehydrogenase kinase ; Pyruvate decarboxylation ; Chemistry ; Biochemistry ; Citric acid cycle ; Metabolism ; Beta oxidation ; Fatty acid ; Glycolysis ; Pyruvate kinase ; Enzyme Advanced NMR Techniques and Applications ; Diet and metabolism studies ; Diet, Metabolism, and Disease