jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ornella Bimaï | Ipsita A. Banerjee | Inna Rozman Grinberg | Ping Huang | Lucas Hultgren | Simon Ekström | Daniel Lundin | Britt‐Marie Sjöberg | Derek T. Logan
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-06-20)
Field: Chemistry — Inorganic Chemistry

Activity modulation in anaerobic ribonucleotide reductases: nucleotide binding to the ATP-cone allosterically mediates substrate binding to the active site Abstract A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding ATP or dATP it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerization and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri . The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it can not be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation. Allosteric regulation ; Binding site ; Nucleotide ; Ribonucleotide ; Substrate (aquarium) ; Biochemistry ; Chemistry ; Active site ; Enzyme ; Biology Metal-Catalyzed Oxygenation Mechanisms ; ATP Synthase and ATPases Research ; Enzyme Structure and Function
Authors: Wen-Liang Hwang | Shih-Shuo Tung
Source: Electronics (article, 2023-09-12)
Field: Materials Science — Materials Chemistry

Analysis of Function Approximation and Stability of General DNNs in Directed Acyclic Graphs Using Un-Rectifying Analysis A general lack of understanding pertaining to deep feedforward neural networks (DNNs) can be attributed partly to a lack of tools with which to analyze the composition of non-linear functions, and partly to a lack of mathematical models applicable to the diversity of DNN architectures. In this study, we analyze DNNs using directed acyclic graphs (DAGs) under a number of basic assumptions pertaining to activation functions, non-linear transformations, and DNN architectures. DNNs that satisfy these assumptions are referred to as general DNNs. Our construction of an analytic graph was based on an axiomatic method in which DAGs are built from the bottom–up through the application of atomic operations to basic elements in accordance with regulatory rules. This approach allowed us to derive the properties of general DNNs via mathematical induction. We demonstrate that the proposed analysis method enables the derivation of some properties that hold true for all general DNNs, namely that DNNs “divide up” the input space, “conquer” each partition using a simple approximating function, and “sparsify” the weight coefficients to enhance robustness against input perturbations. This analysis provides a systematic approach with which to gain theoretical insights into a wide range of complex DNN architectures. Directed acyclic graph ; Computer science ; Robustness (evolution) ; Deep neural networks ; Axiom ; Theoretical computer science ; Directed graph ; Artificial neural network ; Algorithm ; Mathematics ; Artificial intelligence Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Software Engineering Research
Authors: Jelita Asian | Nunik Destria Arianti | Ariefin Ariefin | Muhamad Muslih
Source: IAES International Journal of Artificial Intelligence (article, 2023-11-30)
Field: Chemistry — Analytical Chemistry

Comparison of feature extraction and auto-preprocessing for chili pepper (Capsicum Frutescens) quality classification using machine learning &lt;span lang="EN-US"&gt;The low-cost camera for machine vision, such as a webcam, still has a problem with resolution noise. Therefore, it is important to learn strategies to reduce noise from low-cost camera images so that they can be widely used for grading machines in the future. This paper aims to compare three feature extraction methods with auto-preprocessing to classify chili pepper &lt;/span&gt;&lt;em&gt;&lt;span lang="EN-US"&gt;(Capsicum Frutescens)&lt;/span&gt;&lt;/em&gt;&lt;span lang="EN-US"&gt; quality using a machine learning algorithm. Three extraction methods were used, including the color feature, oriented FAST and rotated BRIEF (ORB), and the combination color feature and ORB. A total of 525 image data for quality chili pepper were collected using the webcam. The auto-preprocessing strategy to classify chili peppers can improve the performance of machine-learning algorithms for all data generated by the feature extractor. The performance of the chili paper quality classification model with auto-preprocessing of the variable color feature can improve the performance of machine learning algorithms by up to 64.21%. The performance improvement of the classification model using the ORB feature variable and the auto-preprocessing of up to 4.41%. The performance improvement of the classification model using machine learning algorithms is 11.27% when using the combination color feature and ORB feature and auto-preprocessing.&lt;/span&gt; Chili pepper ; Computer science ; Pattern recognition (psychology) ; Artificial intelligence ; Feature extraction ; Preprocessor ; Pepper Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Smart Agriculture and AI
Authors: Abdul Rafay | Muzzamil Aziz | Amjad Zia | Abdul R. Asif
Source: Journal of Personalized Medicine (article, 2023-05-02)
Field: Chemistry — Spectroscopy

Automated Retrieval of Heterogeneous Proteomic Data for Machine Learning Proteomics instrumentation and the corresponding bioinformatics tools have evolved at a rapid pace in the last 20 years, whereas the exploitation of deep learning techniques in proteomics is on the horizon. The ability to revisit proteomics raw data, in particular, could be a valuable resource for machine learning applications seeking new insight into protein expression and functions of previously acquired data from different instruments under various lab conditions. We map publicly available proteomics repositories (such as ProteomeXchange) and relevant publications to extract MS/MS data to form one large database that contains the patient history and mass spectrometric data acquired for the patient sample. The extracted mapped dataset should enable the research to overcome the issues attached to the dispersions of proteomics data on the internet, which makes it difficult to apply emerging new bioinformatics tools and deep learning algorithms. The workflow proposed in this study enables a linked large dataset of heart-related proteomics data, which could be easily and efficiently applied to machine learning and deep learning algorithms for futuristic predictions of heart diseases and modeling. Data scraping and crawling offer a powerful tool to harvest and prepare the training and test datasets; however, the authors advocate caution because of ethical and legal issues, as well as the need to ensure the quality and accuracy of the data that are being collected. Proteomics ; Computer science ; Workflow ; Artificial intelligence ; Machine learning ; Raw data ; Resource (disambiguation) ; Deep learning ; Data science ; The Internet ; Data mining ; Database ; World Wide Web Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Machine Learning in Bioinformatics
Authors: Mariana Pop | Ioana-Monica Sas-Boca | Florin Popa
Source: Preprints.org (preprint, 2023-09-20)
Field: Materials Science — Materials Chemistry

Aspects Regarding the Influence of Hot Deformation on the Mechanical and Structural Properties of 42CrMo4 steel The aim of the paper is to analyze the experimental results of the influence of elevated temperatures and strain rate on the mechanical and structural properties of steel 42CrMo4. The experiments were based on uniaxial tension and compression tests at high temperatures between 700 °C and 1000 °C and strain rates range 0.0018 - 0.1 s-1. The influence of temperature and strain rate on yield stress, strain to fracture, hardness, structural changes, and fracture characteristics were analyzed. Due to the dynamic recrystallization phenomenon present during the hot tensile tests, an increase in the flow stress is observed at the beginning of the deformation, after which it decreases until the fracture. By increasing the deformation temperature from 700 °C to 1000 °C, the tensile stress decreases significantly for all strain rates. The increase in the strain rate leads to the increase in the tensile stress. In compression tests by increasing the strain rate, the true strain is slightly increasing, but this depends on the temperature. The non-uniformity of deformations obtained at different values of the strain rate and temperature were also analyzed. Analysis by scanning electron microscopy showed the ductile behavior of the material. The degree of damage of the material caused by the presence of cavities increases by increasing the deformation temperature. Materials science ; Strain rate ; Ultimate tensile strength ; Flow stress ; Composite material ; Deformation (meteorology) ; Slow strain rate testing ; Compression (physics) ; Strain (injury) ; Fracture (geology) ; Tensile testing ; Stress (linguistics) ; Tension (geology) ; Scanning electron microscope High-Velocity Impact and Material Behavior ; Metallurgy and Material Forming ; Metal Alloys Wear and Properties
Authors: Helen Abd Alhassan Mahmood | Rulla Sabah | Nisreen Kais Abood
Source: Indonesian Journal of Chemistry (article, 2023-12-06)
Field: Chemistry — Analytical Chemistry

Spectrophotometric Determination of Amoxicillin Using New Organic Reagent &lt;i&gt;via&lt;/i&gt; Different Analytical Methods New and simple spectrophotometric method was applied for amoxicillin determination by oxidative coupling with an organic reagent 1-(4-aminophenyl)-3-(5-(4-nitrophenyl)-furan-2-yl)-yl)-prop-2-en-1-one (H) to form an orange colored dye with λmax of 490 nm. The molecular structure of the new compound H was characterized using spectral analysis including 1H-NMR, FTIR, Mass spectroscopy, and UV-visible. The concentration range of oxidative coupling obeyed Beer's law was 2–50 μg/mL, the correlation coefficient was 0.9995, molar absorptivity was 0.63 × 104 L/mol cm, and the detection limit was 0.189 μg/mL. The concentration range of flow injection obeyed Beer's law was 1–150 μg/mL, the correlation coefficient was 0.9994, molar absorptivity was 0.295 × 104 L/mol cm, and the detection limit was 0.407 μg/mL. The proposed method was successfully applied in pharmaceutical formulation for amoxicillin determination. The results showed that amoxicillin could be reacted with a new compound H in the alkaline medium in the presence of oxidative agent NaIO4 and automated by flow injection analysis. The proposed methods have the advantage of simple, fast, very sensitive, good precision and accuracy. The suggested technique was effectively used to estimate amoxicillin in both its pure form and pharmaceutical formulations. Chemistry ; Molar absorptivity ; Detection limit ; Reagent ; Correlation coefficient ; Spectrophotometry ; Amoxicillin ; Oxidative coupling of methane ; Chromatography ; Analytical Chemistry (journal) ; Flow injection analysis ; Proton NMR ; Nuclear chemistry ; Organic chemistry ; Catalysis Analytical Methods in Pharmaceuticals ; Electrochemical sensors and biosensors ; Antibiotics Pharmacokinetics and Efficacy
Authors: Ying Wei | Ziwei Chen
Source: Applied Sciences (article, 2023-09-28)
Field: Materials Science — Materials Chemistry

New Insights on Environmentally Friendly Materials In recent years, the world has been confronting a growing planet-wide crisis due to uncontrolled population growth and rapid industrialization [...] Environmentally friendly ; Industrialisation ; Planet ; Business ; Natural resource economics ; Economics ; Ecology ; Market economy Magnesium Oxide Properties and Applications ; Concrete and Cement Materials Research
Authors: Nemanja Koljančić | Ivan Špánik
Source: Water (article, 2023-12-20)
Field: Chemistry — Analytical Chemistry

Investigative Approaches for Pollutants in Water: Aligning with Water Framework Directive Maximum Allowable Concentrations In the wake of rapid advancements in the pharmaceutical, food, and agricultural industries, the environment faces an increasing influx of diverse compounds, both intentionally and unintentionally released. These compounds fall into two categories: persistent and emerging pollutants. Persistent pollutants, characterized by their resistance to degradation and potential to accumulate in the environment, pose serious ecological threats. The Water Framework Directive (WFD) plays a pivotal role in monitoring and regulating these substances. This review discusses various contemporary analytical approaches to determine problematic substances, including benzo(a)pyrene, cypermethrin, dichlorvos, heptachlor, and heptachlor epoxide, aligning with the priorities outlined in the 2013 WFD classification. This review focuses on diverse water sampling methods, sample preparation techniques, and analytical methods, encompassing chromatographic, spectroscopic, and electrochemical approaches, with the primary goal of achieving the requirement laid on analytical methods used for the determination of maximum allowable concentrations defined in the WFD. Chromatographic methods, utilizing diverse mass spectrometers, have achieved detection limits as low as 10−6 μg/L, while modern electroanalytical techniques reach levels as low as 10−13 μg/L, reflecting an ongoing collective effort to enhance monitoring and safeguard the health of aquatic ecosystems. From sampling methods, large-volume sampling and passive sampling devices have been shown to be a cost-effective and modern solution, addressing limitations in traditional sampling methods, even if both of them face important pros and cons in terms of quantitative analysis. Water Framework Directive ; Environmental science ; Pollutant ; Sampling (signal processing) ; Biochemical engineering ; Aquatic ecosystem ; Heptachlor ; Environmental chemistry ; Water quality ; Environmental engineering ; Computer science ; Pesticide ; Chemistry ; Engineering ; Ecology ; Dieldrin Analytical chemistry methods development ; Pharmaceutical and Antibiotic Environmental Impacts ; Water Quality Monitoring and Analysis
Authors: Mehmet Emin Ergün | İsmail Özlüsoylu
Source: Turkish Journal of Forestry | Türkiye Ormancılık Dergisi (article, 2023-03-29)
Field: Materials Science — Polymers and Plastics

Guar sakızı ilaveli kitosan bazlı tutkalların bazı özelliklerinin belirlenmesi Ahşap sektöründe kullanılan tutkalların büyük bir bölümü fosil yakıt temelli olup özellikle içerisindeki formaldehit nedeniyle çevre ve insan sağlığı açısından riskler oluşturmaktadır. Bu olumsuz durumu azaltmak amacıyla son yıllarda formaldehit emisyonunu azaltmaya yönelik farklı yöntemler üzerine araştırmalar yapılmaktadır. Bu araştırmalar içerisinde biyo bazlı tutkal kullanımı sağlık açısından sahip olduğu olumlu özellikler nedeniyle ilgi görmektedir. Bu çalışmada, doğal polimerlerden kitosan ve guar sakızı kullanılarak üretilen bağlayıcının ahşap tutkalı olarak kullanılabilme potansiyeli araştırılmıştır. Bu amaçla kitosan bazlı tutkalın içerisine 4 farklı oranda (%0.06, %0.2, %1 ve %2) guar sakızı ilave edilmiştir. Elde edilen tutkalın viskozitesi ölçülerek, farklı orandaki guar sakızı ilavesinin bağ kuvveti üzerindeki etkisi belirlenmiştir. Ayrıca kitosan bazlı tutkalların odun ile etkileşimini incelemek amacıyla Fourier transform kızılötesi spektroskopisi (FTIR) analizi yapılmıştır. Guar sakızı ilaveli kitosan bazlı tutkalın viskozitesi 1380 CP ile 5264 CP arasında bulunmuştur. %0.2 oranında guar sakızı ilave edilmiş kitosan bazlı tutkalın bağ kuvvet değerinin, guar sakızı ilave edilmeyen gruba göre %88 oranında iyileştiği tespit edilmiştir. Guar sakızı ilaveli kitosan bazlı tutkalın özellikle çevreci yapısı ile olumlu özelliklere sahip olduğu ve farklı alanlarda kullanılabileceği sonucuna varılmıştır. Guar ; Molecular biology ; Physics ; Biology ; Food science Natural Fiber Reinforced Composites ; Electrospun Nanofibers in Biomedical Applications ; biodegradable polymer synthesis and properties
Authors: Princess Tiffany D. Mendoza | Charles R. Hurburgh | Dirk E. Maier | Paul R. Armstrong
Source: Applied Engineering in Agriculture (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

NIR Spectral Imaging for Animal Feed Quality and Safety Highlights Hyperspectral imaging can be a tool to address animal feed safety and quality issues. Various papers on hyperspectral imaging have emerged for grain and animal feed applications. More studies need to be done to use this technology in the field and in commercial scale. Abstract. The increasing need for safe and quality animal-derived food products and the limitations of slow and destructive traditional screening methods have driven the development of fast, accurate, and reliable testing methods for evaluation of animal feed safety and quality parameters. One of the methods being applied recently is near-infrared hyperspectral imaging (NIR HSI), an analytical technique that provides chemical and spatial information for the sample. It has been applied to various food and agricultural products and is gaining acceptance for commercial use in the food industry. This paper presents research progress with respect to applications of NIR HSI for safety and quality evaluation of animal feed ingredients, specifically in screening illegal adulteration and contamination of feed materials, detecting biological contamination and damage, measuring constituent concentrations and other quality properties, and evaluating feed processing parameters. Major results, multivariate analysis and hyperspectral image processing algorithms used, and limitations of the different studies being reviewed were highlighted. With its potential uses and applications on animal feed, NIR HSI is a promising breakthrough in the feed industry. Keywords: Animal feed, Feed safety, Feed quality, Hyperspectral imaging, NIR spectroscopy. Hyperspectral imaging ; Food safety ; Quality (philosophy) ; Animal feed ; Biochemical engineering ; Biotechnology ; Computer science ; Animal food ; Food quality ; Environmental science ; Agricultural engineering ; Artificial intelligence ; Engineering ; Biology ; Food science Spectroscopy and Chemometric Analyses
Authors: C. Muthuselvi | Meenakshi Sundaram Geetha | Nagarajan Mala
Source: Asian Journal of Applied Sciences (article, 2023-01-15)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Crystal Growth, Vibrational, Optical and Antimicrobial Activity Properties of N-(4-Hydroxyphenyl) Acetamide Nitrate Crystal Background and Objective: The commonly used medicines of N-(4-hydroxyphenyl) acetamide can help to treat pain and reduce high temperature.It belongs to the classes of analgesic and antipyretic drugs.In this study, the effect of nitric acid on the N-(4-hydroxyphenyl) acetamide crystals obtained from the aqueous ethanol solutions using the slow evaporation method was examined.Materials and Methods: Raw materials of N-(4-hydroxyphenyl) acetamide, nitric acid, ethanol and distilled water were used for this crystallization.The 4-HPAN crystals had been grown with high transparency using the slow evaporation method.The pure crystalline nature was characterized using ultraviolet-visible-near infrared, FT-IR and FT-Raman spectra, powder X-ray diffraction and scanning electron microscopy.Results: Crystallization of 4-HPA in the presence of nitric acid may permit the alteration of crystal shape by solution growth technique.The molecular structure obtained using Chem3D software was connected through the O-H…O hydrogen bond.The FT-IR and FT-Raman spectra confirmed the presence of the functional groups in the synthesized material.Using ultravioletvisible-near infrared spectral analysis, the optical quality of the grown crystal was studied and showed that the crystal has 100% transmittance with the lower cut-off wavelength of 305 nm.The plate-like morphology was confirmed by the scanning electron microscopy.The compound inhibits the growth of certainly tested microorganisms at high concentrations except for Escherichia coli. Conclusion:The synthesized N-(4-hydroxyphenyl) acetamide nitrate crystal has good crystallinity, functional group vibrations, high transparency in the visible region, plate like morphology with increasing oxygen and nitrogen composition and high inhibition against certain bacteria except Escherichia coli. Acetamide ; Antimicrobial ; Nitrate ; Crystal (programming language) ; Nuclear chemistry ; Chemistry ; Materials science ; Organic chemistry ; Computer science Nonlinear Optical Materials Research ; Crystallization and Solubility Studies ; Synthesis and biological activity
Authors: Kotomi Taniguchi | Prasanta Gorai | Jonathan C. Tan
Source: arXiv (Cornell University) (preprint, 2023-03-28)
Field: Chemistry — Spectroscopy

Carbon-Chain Chemistry in the Interstellar Medium The presence of carbon-chain molecules in the interstellar medium (ISM) has been known since the early 1970s and $&gt;130$ such species have been identified to date, making up $\sim 43$% of the total of detected ISM molecules. They are prevalent not only in star-forming regions in our Galaxy but also in other galaxies. These molecules provide important information on physical conditions, gas dynamics, and evolutionary stages of star-forming regions. Larger species of polycyclic aromatic hydrocarbons (PAHs) and fullerenes (C$_{60}$ and C$_{70}$), which may be related to the formation of the carbon-chain molecules, have been detected in circumstellar envelopes around carbon-rich Asymptotic Giant Branch (AGB) stars and planetary nebulae, while PAHs are also known to be a widespread component of the ISM in most galaxies. Recently, two line survey projects toward Taurus Molecular Cloud-1 with large single-dish telescopes have detected many new carbon-chain species, including molecules containing benzene rings. These new findings raise fresh questions about carbon-bearing species in the Universe. This article reviews various aspects of carbon-chain molecules, including observational studies, chemical simulations, quantum calculations, and laboratory experiments, and discusses open questions and how future facilities may answer them. Interstellar medium ; Carbon chain ; Astrobiology ; Chemistry ; Chain (unit) ; Carbon fibers ; Polymer science ; Physics ; Astrophysics ; Astronomy ; Materials science ; Organic chemistry ; Galaxy Molecular Spectroscopy and Structure ; Astrophysics and Star Formation Studies ; Advanced Chemical Physics Studies