jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Shiqi Chen | Curtis W. Peterson | J. A. Parker | Stuart A. Rice | Andrew L. Ferguson | Norbert F. Scherer
Source: Research Square (preprint, 2020-10-02)
Field: Chemistry — Spectroscopy

Data-Driven Reaction Coordinate Discovery in Overdamped and non-Conservative Systems: Application to Optical Matter Structural Isomerization Abstract Powerful technique as it is to study the collective fluctuations and structural transitions in under-damped conservative systems, normal mode analysis cannot be applied to the optical matter (OM) system, an overdamped system subject to non-conservative forces, which consists of (nano-)particle constituents in solution that can self-organize into ordered arrays bound by electrodynamic interactions. We propose a data-driven approach based on principal component analysis (PCA) of deviations from a reference structure to determine the soft collective modes of non-conservative overdamped systems, such as OM structures, and harmonic linear discriminant analysis (HLDA) of time trajectories to estimate the reaction coordinate for structural transitions, which is demonstrated for structural isomerization of a six-particle OM system. The reaction coordinate we discover is in accord with committor analysis and the identified mechanism is in agreement with experiment. The PCA-HLDA approach to data-driven discovery of reaction coordinates aids in the understanding of non-conservative and overdamped systems. Isomerization ; Reaction coordinate ; Statistical physics ; Chemistry ; Computer science ; Physics ; Computational chemistry ; Catalysis Mass Spectrometry Techniques and Applications ; Computational Drug Discovery Methods ; Machine Learning in Materials Science
Authors: Federico Uliana | Matej Vizovišek | Laura Acquasaliente | Rodolfo Ciuffa | Andrea Fossati | Fabian Frommelt | Matthias Gstaiger | Vincenzo De Filippis | Ulrich auf dem Keller | Ruedi Aebersold
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-07-21)
Field: Chemistry — Spectroscopy

Mapping specificity, entropy, allosteric changes and substrates in blood proteases by a high-throughput protease screen Abstract Proteases are among the largest protein families in eukaryotic phylae with more than 500 genetically encoded proteases in humans. By cleaving a wide range of target proteins, proteases are critical regulators of a vast number of biochemical processes including apoptosis and blood coagulation. Over the last 20 years, knowledge of proteases has been drastically expanded by the development of proteomic approaches to identify and quantify proteases and their substrates. In spite of their merits, some of these methods are laborious, not scalable or incompatible with native environments. Consequentially, a large number of proteases remain poorly characterized. Here, we introduce a simple proteomic method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter and their analysis in a mass spectrometer. The method is significantly faster, cheaper, technically less demanding, easily multiplexed and produces accurate protease fingerprints in near-native conditions. By using the blood cascade proteases as a case study we obtained protease substrate profiles of unprecedented depth that can be reliably used to map specificity, entropy and allosteric changes of the protease and to design fluorescent probes and predict physiological substrates. The native protease characterization method is comparable in performance, but largely exceeds the throughput of current alternatives. Proteases ; Protease ; Biology ; Computational biology ; Biochemistry ; Enzyme Advanced Proteomics Techniques and Applications ; Protease and Inhibitor Mechanisms ; Enzyme Production and Characterization
Authors: Hediye Şule Aycan
Source: Turkiye Kimya Dernegi Dergisi Kisim C Kimya Egitimi (article, 2020-03-27)
Field: Chemistry — Physical and Theoretical Chemistry

Çağdaş Kimyanın Kökleri Bu çalışmada, 2018 Lise Kimya Programı 9. Sınıf ünitelerinden Kimya Bilimi Ünitesinin "Simyadan Kimyaya" konusunun anlatılmasında yararlı olabilecek bazı bilgiler üzerinde tartışılmıştır. Simya, basit metallerin soy metallere dönüştürülmesi süreçlerini kapsar. Bu da genellikle doğada bol bulunan bakır ve kurşunun Filozof Taşı yardımıyla altın ve gümüşe dönüştürülmesi demektir. Simya, ayrıca hastalıklar için çare olacak evrensel bir deva olan yaşam iksiri ile ölümsüzlüğü sağlayacak özel bir ilacı arama çabasıdır. Simyacılar sadece maddi değişimlerle ilgilenmemişlerdir. Onların paslı bir metali altın ya da gümüşe dönüştürme arzuları, aslında kötü insanların da ruhlarını temizleyerek iyi insan haline dönüşmeleriyle özdeşleştirilmiştir. Simyacıların ölümsüzlük olarak niteledikleri, bedenden çok ruhun ölümsüz olmasıdır. Onlar, her şeyin ve herkesin en iyi olmasını isteyen mükemmeliyetçilerdir. Bu bilgilerle, kimya dersini alan lise öğrencilerinin kimyanın bilim öncesi hali olan simya hakkında bilgilendirilmesi, kimya tarihi ve geçirdiği aşamalar bakımından önemlidir. Physics ; Molecular biology ; Humanities ; Theology ; Philosophy ; Biology Various Chemistry Research Topics
Authors: Aneta Gądek-Moszczak | Mariusz TWORZYDŁO | Paulina Romańska
Source: Metal ... (article, 2020-01-01)
Field: Materials Science — Polymers and Plastics

Spatial fiber orientation analysis Paper presents an analysis of 3D images of the composite with a polyamide (PA) matrix reinforced by short glass fibres. The aim of the study was the assessment of the orientation of the fibres. The algorithm used for analysis is based on describing ellipsoids on the detected objects for its orientation assessment. Three subsamples of 3D images were cropped from three different part of the original sample. Each subsample shows the visible difference in the fibre orientation. The detection of the fibres and the analysis of the direction were performed using open source software ImageJ. Analysis of obtained results shown that the ellipsoid method is sensitive to the differences in the fibre orientation and may deliver valuable information for structure description. Orientation (vector space) ; Computer science ; Geometry ; Mathematics Textile materials and evaluations ; 3D Shape Modeling and Analysis
Authors: Shih-Yi Hsu
Source: Digital Commons - University of South Florida (University of South Florida) (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Transcriptome Studies on the Toxicity of Silica Nanoparticles Nanotechnology enables more precise harmony in health condition via reducing the dosage amount, improving the delivery of hydrophobic drugs, more specific targeting to the cancerous sites, and so on. Nevertheless, issues regarding the toxicity of nanotechnology have begun to call for attention several decades later after the innovation of nanotechnology. Tools about risk management of nanotechnology have been developed, but recently not much evidence recognizes the toxicity of nanoparticles (NPs) except for some animal studies, which demonstrated organ damage after the exposure to NPs. Toxicogenomic approach refers to the method utilizing gene expression to evaluate the chemical toxicity. Databases as Gene Expression Omnibus and Database for Annotation, Visualization, and Integrated Discovery are useful platform to provide information about genomic and genetic pathway. After comparing groups at 4 hours and 24 hours, our study reveals the toxicity of silicon dioxide (SiO2) NPs to human aortic endothelial cells (HAECs) is affected by their morphology, and via regulation of different amounts of genes. Cytotoxicity is also related to materials as SiO2 and poly-amido-amine. More analyses with SiO2 NPs cultured with mouse macrophages and lung cancer cells, A549 cells, indicates the size as the attribute of silica nanotoxicity. Smaller SiO2 particles appear to be more toxic in medium concentration. Among all these three cells (HAECs, mouse macrophages, and A549 cells), tumor necrosis factor (TNF) signaling pathway is the most highly up-regulated pathway. Therefore, the expression of TNF signaling pathway highlights the sub cellular mechanism of toxicity resulted from silica NPs regardless of the morphology or the size of the particles, and the cell types. Transcriptome ; Toxicity ; Nanoparticle ; Computer science ; Nanotoxicology ; Chemistry ; Computational biology ; Biology ; Nanotechnology ; Materials science ; Biochemistry ; Gene ; Gene expression Nanoparticles: synthesis and applications ; Microplastics and Plastic Pollution
Authors: Nida Tabassum Khan | Samiullah Khan
Source: ACTA SCIENTIFIC MICROBIOLOGY (article, 2020-11-30)
Field: Materials Science — Materials Chemistry

Nanotoxicology - An Emerging Discipline Evolving from Nanoparticle Risk Assessment Nanotoxicology ; Nanotechnology ; Nanoparticle ; Risk assessment ; Risk analysis (engineering) ; Computer science ; Business ; Materials science ; Computer security Nanoparticles: synthesis and applications
Authors: Rajesh Kumar Verma - | Pushpender Kumar Gangwar - | Atul Kumar Pandey - | Vishalakshi Singh -
Source: International Journal on Science and Technology (article, 2020-12-19)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Utility of Magnetic Materials in Modern Energy Conversion Systems Magnetic materials play a huge role in making energy conversion devices work better. You see them everywhere—transformers, electric machines, power converters. Things like permeability, coercivity, remanence, and saturation really matter for how these devices perform. People use soft magnetic alloys, ferrites, and rare-earth permanent magnets to boost efficiency and cut down on energy losses in all sorts of electromagnetic systems. This paper dives into why magnetic materials matter so much for energy conversion. It covers topics like how electromagnetic energy moves, what causes hysteresis, how core losses happen, and why magnetic anisotropy is important. You’ll also see how these materials come into play in wind energy systems, solar inverters, and electric vehicles. Plus, there’s a section on newer stuff—like nanostructured magnetic materials and high-frequency soft magnetic composites. These high-frequency composites really help devices run better and waste less energy. Magnet ; Energy transformation ; Work (physics) ; Magnetic energy ; Magnetic core ; Energy conversion efficiency ; Electric power ; Electric energy ; Mechanical energy Magnetic Properties and Applications ; Magnetic Properties of Alloys ; Innovative Energy Harvesting Technologies
Authors: M. Tayseer | A. El‐Zein | M. Talaat
Source: The Egyptian International Journal of Engineering Sciences and Technology (article, 2020-08-01)
Field: Materials Science — Materials Chemistry

Voltage Variations and Composite Solid Insulation Effects on Electrical Tree Propagation Based on Finite Element Method This paper investigates the effect of the voltage variations and the change of solid insulation material on the initiation and propagation of Electrical Tree (ET) through solid dielectrics based on the application of Finite Element Method (FEM) approach using the environmental domain of [COMSOL Multiphysics 𝟓. 𝟑𝒂] program as an innovative way to be used in the complicated study of Electrical Treeing Phenomenon (ETP). This research provides an innovative solution to suppress the initiation point of ET and suppress its growth rates using a composite solid insulation material of Poly – Vinyl Chloride (PVC) and Cross – Linked Polyethylene (XLPE) regardless to the mechanical features of this composition. In this research, the study cases are conducted for High Voltage (HV) and Extra High Voltage (EHV) power system networks as the effect of ETP is to be observed clearly. Simulation model is used in this research to imitate the proposed hyperbolic needle – plane system. Case studies are compared between each others to validate the results Electrical treeing ; Multiphysics ; Finite element method ; Materials science ; Voltage ; Composite material ; Polyethylene ; High voltage ; Composite number ; Partial discharge ; Dielectric ; Mechanical engineering ; Electronic engineering ; Structural engineering ; Engineering ; Electrical engineering ; Optoelectronics High voltage insulation and dielectric phenomena ; Thermal Analysis in Power Transmission ; Lightning and Electromagnetic Phenomena
Authors: Youngjo Kim | Yoshiaki Kawajiri | Ronald W. Rousseau | Martha A. Grover
Source: ChemRxiv (preprint, 2020-09-28)
Field: Materials Science — Materials Chemistry

Modeling of Nucleation, Growth, Dissolution, and Disappearance of Paracetamol in Ethanol Solution for Unseeded Batch Cooling Crystallization with Temperature-Cycling Strategy A population balance model (PBM) is developed for unseeded batch crystallization, with temperature-cycling strategies to control the crystal size distribution. The model is able to predict the evolution of crystal size distributions of crystallizing paracetamol from ethanol solutions considering the characteristics of primary nucleation, secondary nucleation, growth, dissolution, and disappearance of crystals. Process analytical technology (PAT) tools were employed to collect solute concentration data and crystal size distribution data. This model employs a boundary condition to describe the disappearance of crystals in temperature-cycling strategies where the temperature is increased and decreased repeatedly. As a result, the obtained model can describe the evolution of crystal size distribution when repetition of cooling and heating is carried out. Moreover, this model can be applied to investigate phenomena that are challenging to explain with experimental data alone, thereby we can gain insight and optimize the operation of the process. Nucleation ; Crystallization ; Dissolution ; Crystal growth ; Materials science ; Crystal (programming language) ; Temperature cycling ; Thermodynamics ; Chemical engineering ; Chemistry ; Thermal ; Computer science ; Physical chemistry ; Physics Crystallization and Solubility Studies ; Freezing and Crystallization Processes
Authors: Gabriela Phillips | Heather A. Vincent | Lela Lackey | Nathaniel J. Moorman | Silvia B. V. Ramos | Amanda Solem | Alain Laederach | Anthony M. Mustoe | Kevin M. Weeks | Benjamin Ziehr | Meredith Corley
Source: UNC Libraries (article, 2020-04-22)
Field: Materials Science — Biomaterials

An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression Protein and mRNA expression are in most cases poorly correlated, which suggests that the posttranscriptional regulatory program of a cell is an important component of gene expression. This regulatory network is still poorly understood, including how RNA structure quantitatively contributes to translational control. We present here a series of structural and functional experiments that together allow us to derive a quantitative, structure-dependent model of translation that accurately predicts translation efficiency in reporter assays and primary human tissue for a complex and medically important protein, α-1-antitrypsin. Our model demonstrates the importance of accurate, experimentally derived RNA structural models partnered with Kozak sequence information to explain protein expression and suggests a strategy by which α-1-antitrypsin expression may be increased in diseased individuals. RNA ; Expression (computer science) ; Computational biology ; Protein expression ; Cell biology ; Biology ; Computer science ; Genetics ; Gene ; Programming language Silk-based biomaterials and applications ; Protease and Inhibitor Mechanisms ; Signaling Pathways in Disease
Authors: Rosa Gómez | Eugènia Martí | Daniel von Schiller | Susana Bernal | Rubén del Campo | Giulia Gionchetta | Clara Mendoza‐Lera | Daniele Nizzoli | Chris Robinson | Anna M. Romaní | Annamaria Zoppini
Source: Figshare (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

3. Water Physicochemistry in IRES Environmental science Thermal and Kinetic Analysis ; Water Quality Monitoring and Analysis ; Analytical chemistry methods development
Authors: Joanne Watson | Jean‐Marc Schwartz | Chiara Francavilla
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-08-25)
Field: Chemistry — Spectroscopy

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites 1 Abstract Mass spectrometry-based quantitative phosphoproteomics has become an essential approach in the study of cellular processes such as signaling. Commonly used methods to analyze phosphoproteomics datasets depend on generic, gene-centric annotations such as Gene Ontology terms which do not account for the function of a protein in a particular phosphorylation state. Analysis of phosphoproteomics data is hampered by a lack of phosphorylated site-specific annotations. We propose a method that combines shotgun phosphoproteomics data, protein-protein interactions, and functional annotations into a heterogeneous multilayer network. Phosphorylation sites are associated to potential functions using a random walk on heterogeneous network (RWHN) algorithm. We validated our approach against a model of the MAPK/ERK pathway and functional annotations from PhosphoSite Plus and were able to associate differentially regulated sites on the same proteins to their previously described specific functions. We further tested the algorithm on three previously published datasets and were able to reproduce their experimentally validated conclusions and to associate phosphorylation sites with known functions based on their regulatory patterns. Our approach provides a refinement of commonly used analysis methods and accurately predicts context-specific functions for sites with similar phosphorylation profiles. For table of contents only We confirm that the eTOC figure contains original material drawn by the authors. Phosphoproteomics ; Phosphorylation ; Computational biology ; Gene ontology ; Computer science ; Context (archaeology) ; Phosphopeptide ; Function (biology) ; Biology ; Protein phosphorylation ; Gene ; Gene expression ; Genetics ; Protein kinase A Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Gene expression and cancer classification
Authors: Krishna Chaitanya Patchava | Mohammed Benaïssa | Shuzhi Sam Ge
Source:  (article, 2020-07-01)
Field: Chemistry — Analytical Chemistry

Hilbert Huang Transformation with filtering as a pre-treatment method for the quantitative study of glucose in near infrared spectra In this paper, a novel pre-treatment technique Hilbert Huang Transformation with filtering (HHTF) that is coupling of the Hilbert Huang Transformation and the digital filtering is proposed for the measurement of glucose from near infrared spectroscopy. HHTF comprises of the Empirical Mode Decomposition (EMD) and the Hilbert Spectral Analysis. In Hilbert spectral analysis, Butterworth filtering was used to eliminate the noise present in the Intrinsic Mode Functions (IMFs). The traditional Partial Least squares Regression (PLSR) has been used as the regression method. The proposed HHTF with the PLSR method has been assessed to determine the concentration of glucose from near infrared spectra of two distinct compositions that are prepared by mixing triacetin, urea and glucose in a phosphate buffer solution (PBS) and another composition of glucose and human serum albumin in a PBS. The efficiency of the proposed method has been compared with the standard normal variate and the 1<sup>st</sup> derivative preprocessing methods and is shown to outperform both. Hilbert–Huang transform ; Partial least squares regression ; Mathematics ; Transformation (genetics) ; Chemistry ; Principal component regression ; Preprocessor ; Biological system ; Analytical Chemistry (journal) ; Regression analysis ; Artificial intelligence ; Computer science ; Statistics ; Chromatography ; White noise ; Biochemistry Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Fault Detection and Control Systems
Authors: 谷藤 幹子
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2020-11-13)
Field: Materials Science — Materials Chemistry

材料データプラットフォームシステムの設計と構築 マテリアル・インフォマティクスの進展に伴って,物質探索や材料の性能予測を可能とするデータ駆動型プラットフォームや,予測アプリケーションの需要が高まっている.この背景には,急伸する国家間のデータ覇権の動き,ビックデータとAI技術の急伸,インターネット通信網の大容量・高速化という主に3つの研究環境の変化がある.また実験装置の高度化に伴う高解像度のデータ処理や,IoT化によるデータ転送や蓄積技術,そして蓄積データを機械判読化し,その場で解析を行うアプリケーションの研究開発も取り組まれている.NIMSは.20年以上の運用の歴史を持つ無機材料・有機材料のデータベースMatNaviを通してデータ蓄積のノウハウを持ち,データの蓄積や利用について先導的立ち位置にあった.そのためマテリアルインテグレーション<sup>1</sup><sup>)</sup>やマテリアルズインフォマティクスの各研究プロジェクトにおいては,データ科学を使って情報の収集と分類を行い,そこから帰納的に結果を導き出して新しい知識体系を構築する成果が生まれると共に,データの生成(つくる)から活用(つかう)までの一気通貫のデータ基盤システム(データプラットフォーム)<sup>2</sup><sup>)</sup>の構築の重要性を認識していた.本プロジェクトは,これらの経験と成果に立脚し,第4期中長期計画(1.1.7情報統合型物質・材料研究領域)における研究開発『データ科学,計算科学,理論,実験を計算機上で融合させ,材料の開発時間を飛躍的に短くする統合型材料開発システムの構築を目指す』材料データプラットフォームを構築することとし,2017年度に5年事業として着手した. Computer science Machine Learning in Materials Science ; Diverse Musicological Studies ; Advanced Materials Characterization Techniques
Authors: Asmanik Asmanik | Happy Nursyam | Maheno Sri Widodo | Arning Wilujeng Ekawati | Putut Har Riyadi | Muhamad Amin
Source: Russian Journal of Agricultural and Socio-Economic Sciences (article, 2020-07-29)
Field: Chemistry — Analytical Chemistry

IN SILICO ANALYSIS AND OVARY FATTY ACID COMPOSITION OF COBIA FISH (RACHYCENTRON CANADUM) There has been not much information available related to the diet formulation for female Cobia (Rachycentron canadum) fish. This study characterized ovary fatty acid composition of female Cobia in their different gonad maturation stages and predicted the mechanism of HUFA (DHA/docosahexaenoic acid, EPA/eicosapentaenoic acid, and AA/arachidonic acid) in supporting gonad maturation through an in silico analysis. Fish samples consisted of three (3) categories: (1) prospective broodstocksimmature (initial development); (2) prospective broodstocksmaturing (middle development); and (3) broodstocksmature (advanced development). The in silico analysis was done through a molecular docking between ligand (DHA, EPA, and AA) and receptors Lpl, Fatp, Fabp, and Mttp. Our findings showed that fatty acids tended to increase along with the development of the ovary. The highest fatty acids for group 1 was C16:0>C18:1n9c>DHA, for group 2 was C18:1n9c>C16:0>DHA, and for group 3 was DHA>C16:0>C18:1n9c. DHA increased significantly during gonad maturation and the vice versa happened to EPA, while AA increased significantly at the end of gonad maturation. This affected, among others, the ratio of DHA/EPA and DHA/AA-DHA/EPA ration increased along with gonad maturation, while the opposite happened for DHA/AA ratio. The results of the in silico analysis showed that DHA had the smallest binding affinity for docking with Lpl, Fatp, and Fapb compared to EPA and AA. This means that DHA was predicted to have a strong binding with receptors during the oocyte lipidation. DHA also had the smallest binding affinity for docking with Mttp compared to EPA and AA. This means that DHA was predicted to have a strong binding with receptors in Vtg lipidation compared to EPA and AA. Fishery ; In silico ; Fish <Actinopterygii> ; Biology ; Chemistry ; Zoology ; Biochemistry Dye analysis and toxicity