jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Benedict Terkula Iber | Donald Torsabo | Che Engku Noramalina Che Engku Chik | Fachrul Wahab | Siti Rozaimah Sheikh Abdullah | Hassimi Abu Hassan | Nor Azman Kasan
Source: Heliyon (article, 2023-02-21)
Field: Materials Science — Biomaterials

A study on the effects of interfering with the conventional sequential protocol for chemical isolation and characterization of chitosan from biowaste of giant freshwater prawn Macrobrachium rosenbergii Unless better measures are put in place to address the environmental and social impacts emanating from the huge waste generated from sea food processing industries; 'tragedy of the commons' is inevitable. Needless to re-emphasise the enormous contributions of aquaculture as the perfect substitute to capture fisheries which has been proven unsustainable. Be that as it may, the huge amount of bio-waste produced could be transformed into useful products such as chitin and chitosan with far reaching applications. Chitin and chitosan have been consistently processed from many sources following the traditional chemical sequence of Demineralization (DM), Deproteinization (DP), Decolouration (DC) and Deacetylation (DA). In this study, this method was re-ordered, resulting to 4 sequences of chemical processes. HCl, NaOH, ethanol (97%) and NaOH (50%) were used for DM, DP, DC and DA respectively. The results of this study showed that better chitin (23.99 ± 0.61%) and chitosan (15.17 ± 1.69%) yields were obtained from sequence four (SQ4) following the order of DC-DM-DP-DA. In addition, physicochemical properties such as DDA (80.67 ± 2.52%) and solubility (66.43 ± 2.61%) were significantly higher (p ≤ 0.05) in SQ4 thereby making the obtained product suitable for use as coagulant and flocculant in wastewater treatment. Results of FTIR, XRD and SEM of the study proved that the resultant product exhibited the characteristic nature of chitosan with porous and fibril nature. In the analysis of the physical properties of chitosan obtained from bio-waste of <i>Macrobrachium</i> <i>rosenbergii</i>, the high Carr's index (CI) and low bulk as well as tapped densities were an indication that the chitosan produced in this study had poor flowability and compressibility, thereby making it unfit for application in pharmaceutical industries. Chitosan ; Chitin ; Demineralization ; Chemistry ; Macrobrachium rosenbergii ; Pulp and paper industry ; Food science ; Nuclear chemistry ; Biotechnology ; Chemical engineering ; Prawn ; Materials science ; Fishery ; Biology ; Organic chemistry ; Composite material ; Engineering Nanocomposite Films for Food Packaging ; Aquaculture Nutrition and Growth ; Aquatic life and conservation
Authors: Dehao Hou | Wenjun Ma | Lingyan Hu | Yushui Huang | Yunjun Yu | Xiaofeng Wan | Xiaolong Wu | Xi Li
Source: Atmosphere (article, 2023-09-13)
Field: Materials Science — Materials Chemistry

Modeling of Nonlinear SOEC Parameter System Based on Data-Driven Method Based on the basic nonlinear parameter system of the solid oxide electrolysis cell, the data-driven method was used for system identification. The basic model of the solid oxide electrolysis cell was accomplished in Simulink and experiments were performed under a diversified input/output operating environment. The experimental results of the solid oxide electrolysis cell basic parameter system generated 15 datasets. The system identification process involved the utilization of these datasets with the application of nonlinear autoregressive-exogenous models. Initially, data identification came from the Matlab mechanism model. Then, the nonlinear autoregressive-exogenous structures were estimated and selected exploratively through an individual operating condition. In terms of fitness, we conclude that the solid oxide electrolysis cell parameter system cannot be satisfied by a solitary autoregressive-exogenous model for all datasets. Nevertheless, the nonlinear autoregressive-exogenous model utilized S-type nonlinearities to fit a total of 2 validation datasets and 15 estimated datasets. The obtained results were compared with the basic parameter system of a solid oxide electrolysis cell, and the nonlinear autoregressive-exogenous projected output demonstrated an accuracy of over 93% across diverse operational circumstances—regardless of whether there was noise interference. This result has positive significance for the future use of the solid oxide electrolysis cell to achieve the dual carbon goal in China. Autoregressive model ; Nonlinear system ; Nonlinear autoregressive exogenous model ; Electrolytic process ; Electrolysis ; MATLAB ; Biological system ; Identification (biology) ; Computer science ; STAR model ; System identification ; Electrolytic cell ; Control theory (sociology) ; Noise (video) ; Econometrics ; Mathematics ; Data modeling ; Chemistry ; Physics ; Time series ; Artificial intelligence ; Autoregressive integrated moving average ; Machine learning Advancements in Solid Oxide Fuel Cells ; Molten salt chemistry and electrochemical processes ; Fuel Cells and Related Materials
Authors: Natalia Berdzik | Hanna Koenig | Lucyna Mrówczyńska | Damian Nowak | Beata Jasiewicz | Tomasz Pospieszny
Source: The Journal of Organic Chemistry (article, 2023-12-07)
Field: Chemistry — Organic Chemistry

Synthesis and Hemolytic Activity of Bile Acid-Indole Bioconjugates Linked by Triazole New formyl and acetyl derivatives of bile acid propargyl esters and their bioconjugates with modified gramine molecules have been obtained using the click chemistry method to study their hemolytic potency. The structures of all compounds were confirmed by spectral (<sup>1</sup>H- and <sup>13</sup>C NMR and FT-IR) analysis and mass spectrometry (ESI-MS) as well as PM5 semiempirical methods. According to the results, the structural modification of formyl and acetyl bile acid derivatives, leading to the formation of new propargyl esters and indole bioconjugates, reduces their hemolytic activity. According to molecular docking studies, the tested ligands are highly likely to exhibit a similar affinity, as native ligands, for the active sites of specific protein domains (PDB IDs: 2Q85 and 5V5Z). The obtained results may be helpful for the development of selective bile acid bioconjugates as effective antibacterial, antifungal, or antioxidant agents. Chemistry ; Click chemistry ; Indole test ; Bile acid ; Combinatorial chemistry ; Docking (animal) ; Stereochemistry ; Biochemistry Click Chemistry and Applications ; Monoclonal and Polyclonal Antibodies Research ; HIV/AIDS drug development and treatment
Authors: Frank Hirschmann | Hender López | Felix Roosen‐Runge | Tilo Seydel | Frank Schreiber | Martin Oettel
Source: The Journal of Chemical Physics (article, 2023-02-27)
Field: Materials Science — Materials Chemistry

Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm. Globular protein ; Bovine serum albumin ; Molecule ; SPHERES ; Chemistry ; Brownian motion ; Chemical physics ; Statistical physics ; Physics ; Materials science ; Biological system ; Crystallography ; Chromatography Material Dynamics and Properties ; Protein Structure and Dynamics ; Blood properties and coagulation
Authors: Colin L. Welsh | Abigail E. Conklin | Lalima K. Madan
Source: Biology (article, 2023-10-26)
Field: Materials Science — Materials Chemistry

Crystal Structures Reveal Hidden Domain Mechanics in Protein Kinase A (PKA) Cyclic-AMP-dependent protein kinase A (PKA) is a critical enzyme involved in various signaling pathways that plays a crucial role in regulating cellular processes including metabolism, gene transcription, cell proliferation, and differentiation. In this study, the mechanisms of allostery in PKA were investigated by analyzing the vast repertoire of crystal structures available in the RCSB database. From existing structures of murine and human PKA, we elucidated the conformational ensembles and protein dynamics that are altered in a ligand-dependent manner. Distance metrics to analyze conformations of the G-loop were proposed to delineate different states of PKA and were compared to existing structural metrics. Furthermore, ligand-dependent flexibility was investigated through normalized B'-factors to better understand the inherent dynamics in PKA. The presented study provides a contemporary approach to traditional methods in engaging the use of crystal structures for understanding protein dynamics. Importantly, our studies provide a deeper understanding into the conformational ensemble of PKA as the enzyme progresses through its catalytic cycle. These studies provide insights into kinase regulation that can be applied to both PKA individually and protein kinases as a class. Protein kinase A ; Biology ; Allosteric regulation ; Kinase ; Protein dynamics ; Computational biology ; Protein kinase domain ; Protein structure ; Structural biology ; Cell biology ; Biochemistry ; Biophysics ; Enzyme ; Gene Enzyme Structure and Function ; Protein Kinase Regulation and GTPase Signaling ; Computational Drug Discovery Methods
Authors: Peijun Song | Jun Xu | Xinjie Liu | Zhi Zhang | Xinglong Rao | Ricardo P. Martinho | Qingjia Bao | Chaoyang Liu
Source: Journal of Magnetic Resonance (article, 2023-12-23)
Field: Chemistry — Spectroscopy

Stationary wavelet denoising of solid-state NMR spectra using multiple similar measurements Spectral line ; Noise reduction ; Wavelet ; Noise (video) ; Algorithm ; Signal-to-noise ratio (imaging) ; SIGNAL (programming language) ; Chemistry ; Nuclear magnetic resonance ; Analytical Chemistry (journal) ; Mathematics ; Computational physics ; Pattern recognition (psychology) ; Artificial intelligence ; Computer science ; Physics ; Statistics Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Advanced MRI Techniques and Applications
Authors: Edi Topić | Pavla Šenjug | Dario Barišić | Ivor Lončarić | Damir Pajić | Mirta Rubčić
Source: Crystal Growth & Design (article, 2023-05-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Structure-Related Evolution of Magnetic Order in Anisidinium Tetrachlorocuprates(II) Tetrachlorocuprate(II) hybrids of the three anisidine isomers (<i>ortho</i>-, <i>meta</i>-, and <i>para</i>-, or 2-, 3-, and 4-methoxyaniline, respectively) were prepared and studied in the solid state via X-ray diffraction and magnetization measurements. Depending on the position of the methoxy group of the organic cation, and subsequently, the overall cation geometry, a layered, defective layered, and the structure comprising discrete tetrachlorocuprate(II) units were obtained for the <i>para</i>-, <i>meta</i>-, and <i>ortho</i>-anisidinium hybrids, respectively. In the case of layered and defective layered structures, this affords quasi-2D-layered magnets, demonstrating a complex interplay of strong and weak magnetic interactions that lead to the long-range ferromagnetic (FM) order. In the case of the structure with discrete CuCl<sub>4</sub><sup>2-</sup> ions, a peculiar antiferromagnetic (AFM) behavior was revealed. The structural and electronic origins of magnetism are discussed in detail. To supplement it, the method for calculation of dimensionality of the inorganic framework as a function of interaction length was developed. The same was used to discriminate between <i>n</i>-dimensional and "almost" <i>n</i>-dimensional frameworks, to estimate the organic cation geometry limits for layered halometallates, and to provide additional reasoning behind the observed relation between cation geometry and framework dimensionality, as well as their relation to differences in magnetic behavior. Ferromagnetism ; Antiferromagnetism ; Magnetism ; Chemistry ; Magnetization ; Ion ; Condensed matter physics ; Crystallography ; Curse of dimensionality ; Materials science ; Chemical physics ; Physics ; Mathematics ; Magnetic field ; Organic chemistry ; Quantum mechanics Magnetism in coordination complexes ; Crystal Structures and Properties ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Paula Fernández-Gómez | Carmen Pérez de la Lastra | Carlota Tosat‐Bitrián | Jesús Alejandro Bueso de Barrio | Sebastián A. Thompson | Begoña Sot | Gorka Salas | Álvaro Somoza | Ana Espinosa | Milagros Castellanos | Valle Palomo
Source: Frontiers in Bioengineering and Biotechnology (review, 2023-07-21)
Field: Materials Science — Materials Chemistry

Nanomedical research and development in Spain: improving the treatment of diseases from the nanoscale The new and unique possibilities that nanomaterials offer have greatly impacted biomedicine, from the treatment and diagnosis of diseases, to the specific and optimized delivery of therapeutic agents. Technological advances in the synthesis, characterization, standardization, and therapeutic performance of nanoparticles have enabled the approval of several nanomedicines and novel applications. Discoveries continue to rise exponentially in all disease areas, from cancer to neurodegenerative diseases. In Spain, there is a substantial net of researchers involved in the development of nanodiagnostics and nanomedicines. In this review, we summarize the state of the art of nanotechnology, focusing on nanoparticles, for the treatment of diseases in Spain (2017-2022), and give a perspective on the future trends and direction that nanomedicine research is taking. Nanoscopic scale ; Nanotechnology ; Materials science Nanoparticles: synthesis and applications ; Nanotechnology research and applications
Authors: Haiming Yi | Lei Hou | Yuhong Jin | Nasser A. Saeed | Kandil, Ali | Duan, Hao
Source: arXiv (Cornell University) (preprint, 2023-12-13)
Field: Chemistry — Analytical Chemistry

Time Series Diffusion Method: A Denoising Diffusion Probabilistic Model for Vibration Signal Generation Diffusion models have demonstrated powerful data generation capabilities in various research fields such as image generation. However, in the field of vibration signal generation, the criteria for evaluating the quality of the generated signal are different from that of image generation and there is a fundamental difference between them. At present, there is no research on the ability of diffusion model to generate vibration signal. In this paper, a Time Series Diffusion Method (TSDM) is proposed for vibration signal generation, leveraging the foundational principles of diffusion models. The TSDM uses an improved U-net architecture with attention block, ResBlock and TimeEmbedding to effectively segment and extract features from one-dimensional time series data. It operates based on forward diffusion and reverse denoising processes for time-series generation. Experimental validation is conducted using single-frequency, multi-frequency datasets, and bearing fault datasets. The results show that TSDM can accurately generate the single-frequency and multi-frequency features in the time series and retain the basic frequency features for the diffusion generation results of the bearing fault series. It is also found that the original DDPM could not generate high quality vibration signals, but the improved U-net in TSDM, which applied the combination of attention block and ResBlock, could effectively improve the quality of vibration signal generation. Finally, TSDM is applied to the small sample fault diagnosis of three public bearing fault datasets, and the results show that the accuracy of small sample fault diagnosis of the three datasets is improved by 32.380%, 18.355% and 9.298% at most, respectively. Series (stratigraphy) ; Computer science ; Diffusion ; Fault (geology) ; Noise reduction ; Bearing (navigation) ; SIGNAL (programming language) ; Probabilistic logic ; Vibration ; Sample (material) ; Time series ; Noise (video) ; Algorithm ; Pattern recognition (psychology) ; Artificial intelligence ; Data mining ; Machine learning ; Acoustics Spectroscopy and Chemometric Analyses ; Infrared Thermography in Medicine ; Machine Fault Diagnosis Techniques
Authors: Zheng‐Hua He | Yaoyao Huang | Guang‐Fu Ji | Jun Chen | Qiang Wu
Source: International Journal of Molecular Sciences (article, 2023-08-08)
Field: Materials Science — Materials Chemistry

The Structure Properties of Carbon Materials Formed in 2,4,6-Triamino-1,3,5-Trinitrobenzene Detonation: A Theoretical Insight for Nucleation of Diamond-like Carbon The structure and properties of nano-carbon materials formed in explosives detonation are always a challenge, not only for the designing and manufacturing of these materials but also for clearly understanding the detonation performance of explosives. Herein, we study the dynamic evolution process of condensed-phase carbon involved in 2,4,6-Triamino-1,3,5-trinitrobenzene (TATB) detonation using the quantum-based molecular dynamics method. Various carbon structures such as, graphene-like, diamond-like, and "diaphite", are obtained under different pressures. The transition from a C sp<sup>2</sup>- to a sp<sup>3</sup>-hybrid, driven by the conversion of a hexatomic to a non-hexatomic ring, is detected under high pressure. A tightly bound nucleation mechanism for diamond-like carbon dominated by a graphene-like carbon layer is uncovered. The graphene-like layer is readily constructed at the early stage, which would connect with surrounding carbon atoms or fragments to form the tetrahedral structure, with a high fraction of sp<sup>3</sup>-hybridized carbon. After that, the deformed carbon layers further coalesce with each other by bonding between carbon atoms within the five-member ring, to form the diamond-like nucleus. The complex "diaphite" configuration is detected during the diamond-like carbon nucleation, which illustrates that the nucleation and growth of detonation nano-diamond would accompany the intergrowth of graphene-like layers. Graphene ; Carbide-derived carbon ; Detonation ; Carbon fibers ; Nucleation ; Diamond ; Materials science ; Molecular dynamics ; Chemical physics ; TATB ; Nanotechnology ; Chemical engineering ; Explosive material ; Crystallography ; Chemistry ; Carbon nanofiber ; Composite material ; Computational chemistry ; Composite number ; Organic chemistry ; Carbon nanotube Diamond and Carbon-based Materials Research ; Energetic Materials and Combustion ; Graphene research and applications
Authors: Xunxun Wu | Xintong Yang | Zhiyun Cheng | Suyun Li | Xiaokun Li | Haiyun Zhang | Yong Diao
Source: Molecules (article, 2023-06-26)
Field: Chemistry — Analytical Chemistry

Identification of Gentian-Related Species Based on Two-Dimensional Correlation Spectroscopy (2D-COS) Combined with Residual Neural Network (ResNet) Gentian is a traditional Chinese herb with heat-clearing, damp-drying, inflammation-alleviating and digestion-promoting effects, which is widely used in clinical practice. However, there are many species of gentian. According to the pharmacopoeia, Gentiana manshurica Kitag, Gentiana scabra Bge, Gentiana triflora Pall and Gentianarigescens Franch are included. Therefore, accurately identifying the species of gentian is important in clinical use. In recent years, with the advantages of low cost, convenience, fast analysis and high sensitivity, infrared spectroscopy (IR) has been extensively used in herbal identification. Unlike one-dimensional spectroscopy, a two-dimensional correlation spectrum (2D-COS) can improve the resolution of the spectrum and better highlight the details that are difficult to detect. In addition, the residual neural network (ResNet) is an important breakthrough in convolutional neural networks (CNNs) for significant advantages related to image recognition. Herein, we propose a new method for identifying gentian-related species using 2D-COS combined with ResNet. A total of 173 gentian samples from seven different species are collected in this study. In order to eliminate a large amount of redundant information and improve the efficiency of machine learning, the extracted feature band method was used to optimize the model. Four feature bands were selected from the infrared spectrum, namely 3500-3000 cm<sup>-1</sup>, 3000-2750 cm<sup>-1</sup>, 1750-1100 cm<sup>-1</sup> and 1100-400 cm<sup>-1</sup>, respectively. The one-dimensional spectral data were converted into synchronous 2D-COS images, asynchronous 2D-COS images, and integrative 2D-COS images using Matlab (R2022a). The identification strategy for these three 2D-COS images was based on ResNet, which analyzes 2D-COS images based on single feature bands and full bands as well as fused feature bands. According to the results, (1) compared with the other two 2D-COS images, synchronous 2D-COS images are more suitable for the ResNet model, and (2) after extracting a single feature band 1750-1100 cm<sup>-1</sup> to optimize ResNet, the model has the best convergence performance, the accuracy of training, test and external validation is 1 and the loss value is only 0.155. In summary, 2D-COS combined with ResNet is an effective and accurate method to identify gentian-related species. Gentiana ; Residual ; Residual neural network ; Convolutional neural network ; Pattern recognition (psychology) ; Artificial intelligence ; Biological system ; Chemistry ; Computer science ; Botany ; Biology ; Algorithm Spectroscopy and Chemometric Analyses ; Phytochemistry and Biological Activities ; Traditional Chinese Medicine Analysis