scholarly journals Numerical Modeling of Chemical Compounds’ Fate and Kinetics in Living Organisms: An Inverse Numerical Method for Rate Estimation from Concentration

2018 ◽  
Author(s):  
Kovacs Emoke Dalma ◽  
Kovacs Melinda Haydee
Keyword(s):  
Numerical Modeling ◽  
Numerical Method ◽  
Chemical Compounds ◽  
Rate Estimation ◽  
Living Organisms

scholarly journals Recognition of Pharmacological Bi-Heterocyclic Compounds by Using Terahertz Time Domain Spectroscopy and Chemometrics

Sensors ◽  
2019 ◽  
Vol 19 (15) ◽  
pp. 3349 ◽  
Author(s):  
Maciej Roman Nowak ◽  
Rafał Zdunek ◽  
Edward Pliński ◽  
Piotr Świątek ◽  
Małgorzata Strzelecka ◽  
...  
Keyword(s):  
Heterocyclic Compounds ◽  
Chemical Compounds ◽  
Functional System ◽  
Support Vector ◽  
Optimal Parameters ◽  
Terahertz Time Domain Spectroscopy ◽  
Kernel Support Vector Machine ◽  
Inflammatory Drugs ◽  
Living Organisms

In this study, we presented the concept and implementation of a fully functional system for the recognition of bi-heterocyclic compounds. We have conducted research into the application of machine learning methods to correctly recognize compounds based on THz spectra, and we have described the process of selecting optimal parameters for the kernel support vector machine (KSVM) with an additional `unknown’ class. The chemical compounds used in the study contain a target molecule, used in pharmacy to combat inflammatory states formed in living organisms. Ready-made medical products with similar properties are commonly referred to as non-steroidal anti-inflammatory drugs (NSAIDs) once authorised on the pharmaceutical market. It was crucial to clearly determine whether the tested sample is a chemical compound known to researchers or is a completely new structure which should be additionally tested using other spectrometric methods. Our approach allows us to achieve 100% accuracy of the classification of the tested chemical compounds in the time of several milliseconds counted for 30 samples of the test set. It fits perfectly into the concept of rapid recognition of bi-heterocyclic compounds without the need to analyse the percentage composition of compound components, assuming that the sample is classified in a known group. The method allows us to minimize testing costs and significant reduction of the time of analysis.

scholarly journals The Radioprotective Effect of Procaine and Procaine-Derived Product Gerovital H3 in Lymphocytes from Young and Aged Individuals

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Anca Ungurianu ◽  
Denisa Margina ◽  
Claudia Borsa ◽  
Cristina Ionescu ◽  
Gudrun von Scheven ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Chemical Compounds ◽  
Dna Strand Breaks ◽  
Peripheral Blood Mononuclear ◽  
Strand Breaks ◽  
Young Subjects ◽  
Living Organisms ◽  
Dna Strand

Ionizing radiation induces genomic instability in living organisms, and several studies reported an ageing-dependent radiosensitivity. Chemical compounds, such as scavengers, radioprotectors, and modifiers, contribute to reducing the radiation-associated toxicity. These compounds are often antioxidants, and therefore, in order to be effective, they must be present before or during exposure to radiation. However, not all antioxidants provide radioprotection. In this study, we investigated the effects of procaine and of a procaine-based product Gerovital H3 (GH3) on the formation of endogenous and X-ray-induced DNA strand breaks in peripheral blood mononuclear cells (PBMCs) isolated from young and elderly individuals. Interestingly, GH3 showed the strongest radioprotective effects in PBMCs from young subjects, while procaine reduced the endogenous amount of DNA strand breaks more pronounced in aged individuals. Both procaine and GH3 inhibited lipid peroxidation, but procaine was more effective in inhibiting mitochondria free radicals’ generation, while GH3 showed a higher antioxidant action on macrophage-induced low-density lipoprotein oxidation. Our findings provide new insights into the mechanisms underlying the distinct effects of procaine and GH3 on DNA damage.

Application of the Conservation Element and Solution Element Method in Numerical Modeling of Three-Dimensional Heat Conduction With Melting and/or Freezing

2004 ◽  
Vol 126 (6) ◽  
pp. 937-945 ◽  
Author(s):  
Anahita Ayasoufi ◽  
Theo G. Keith ◽  
Ramin K. Rahmani
Keyword(s):  
Numerical Modeling ◽  
Heat Conduction ◽  
Fluid Mechanics ◽  
Phase Change ◽  
Numerical Method ◽  
Analytical Solutions ◽  
Three Dimensional ◽  
Solution Element ◽  
Explicit Numerical Method ◽  
Element Method

The conservation element and solution element (CE/SE) method, an accurate and efficient explicit numerical method for resolving moving discontinuities in fluid mechanics problems, is used to solve three-dimensional phase-change problems. Several isothermal phase-change cases are studied and comparisons are made to existing analytical solutions. The CE/SE method is found to be accurate, robust, and efficient for the numerical modeling of phase-change problems.

scholarly journals How can SHAP values help to shape metabolic stability of chemical compounds?

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Agnieszka Wojtuch ◽  
Rafał Jankowski ◽  
Sabina Podlewska
Keyword(s):  
Web Service ◽  
Chemical Compounds ◽  
Structural Features ◽  
Metabolic Stability ◽  
Structural Modifications ◽  
Pharmacokinetic Properties ◽  
Biological Target ◽  
Future Drug ◽  
Living Organisms ◽  
Great Complexity

Abstract Background Computational methods support nowadays each stage of drug design campaigns. They assist not only in the process of identification of new active compounds towards particular biological target, but also help in the evaluation and optimization of their physicochemical and pharmacokinetic properties. Such features are not less important in terms of the possible turn of a compound into a future drug than its desired affinity profile towards considered proteins. In the study, we focus on metabolic stability, which determines the time that the compound can act in the organism and play its role as a drug. Due to great complexity of xenobiotic transformation pathways in the living organisms, evaluation and optimization of metabolic stability remains a big challenge. Results Here, we present a novel methodology for the evaluation and analysis of structural features influencing metabolic stability. To this end, we use a well-established explainability method called SHAP. We built several predictive models and analyse their predictions with the SHAP values to reveal how particular compound substructures influence the model’s prediction. The method can be widely applied by users thanks to the web service, which accompanies the article. It allows a detailed analysis of SHAP values obtained for compounds from the ChEMBL database, as well as their determination and analysis for any compound submitted by a user. Moreover, the service enables manual analysis of the possible structural modifications via the provision of analogous analysis for the most similar compound from the ChEMBL dataset. Conclusions To our knowledge, this is the first attempt to employ SHAP to reveal which substructural features are utilized by machine learning models when evaluating compound metabolic stability. The accompanying web service for metabolic stability evaluation can be of great help for medicinal chemists. Its significant usefulness is related not only to the possibility of assessing compound stability, but also to the provision of information about substructures influencing this parameter. It can assist in the design of new ligands with improved metabolic stability, helping in the detection of privileged and unfavourable chemical moieties during stability optimization. The tool is available at https://metstab-shap.matinf.uj.edu.pl/.

Dimension of Molecules of Compounds of Biogenic Elements

2019 ◽  
pp. 127-153
Keyword(s):  
Chemical Bond ◽  
Chemical Elements ◽  
Chemical Compounds ◽  
Building Blocks ◽  
Chemical Activity ◽  
Biogenic Elements ◽  
Higher Dimension ◽  
Complex Molecules ◽  
P Elements ◽  
Living Organisms

Chemical compounds of biogenic elements are considered (i.e., chemical elements present in living organisms and ensuring the successful functioning of their various organs and systems). Biogenic elements are divided into s-, p-, and d-elements, in which respectively are completed with s-, p-, and d-electronic orbitals. In each of these groups, the structure of compounds of biogenic elements is investigated, and the dimension of the corresponding molecules is determined. It is proved that s- and d-biogenic elements exhibit increased chemical activity (higher than the standard valence) due to participation in the formation of a chemical bond of electrons of the preceding level. This leads to the creation of complex molecules of higher dimension. The chemical compounds of biogenic p-elements, which are the building blocks for the formation of biomolecules (elements of life), will be specifically investigated in subsequent chapters.

Application of the Conservation Element and Solution Element Method in Numerical Modeling of Three-Dimensional Heat Conduction With Melting and/or Freezing

2003 ◽  
Author(s):  
Anahita Ayasoufi ◽  
Theo G. Keith
Keyword(s):  
Numerical Modeling ◽  
Heat Conduction ◽  
Fluid Mechanics ◽  
Phase Change ◽  
Numerical Method ◽  
Analytical Solutions ◽  
Three Dimensional ◽  
Solution Element ◽  
Explicit Numerical Method ◽  
Element Method

The conservation element and solution element (CE/SE) method, an accurate and efficient explicit numerical method for resolving moving discontinuities in fluid mechanics problems, is used to solve three-dimensional phase change problems. Several isothermal phase change cases are studied and comparisons are made to existing analytical solutions. The CE/SE method is found to be accurate, robust and efficient for the numerical modeling of phase change problems.

scholarly journals UJI AKTIVITAS ANTIOKSIDAN KARANG LUNAK (Nepthea sp.) DENGAN MENGGUNAKAN METODE DPPH (1,1-difenil-2-pikrilhidrazil)

PHARMACON ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 425
Author(s):  
Priski Langi ◽  
Adithya Yudistira ◽  
Karlah L.R Mansauda
Keyword(s):  
Antioxidant Activity ◽  
Secondary Metabolites ◽  
Soft Coral ◽  
Chemical Compounds ◽  
Soft Corals ◽  
Dpph Method ◽  
Experimental Laboratory ◽  
Living Organisms ◽  
Ethanol Extracts ◽  
Method Of Extraction

ABSTRACTSoft corals (Nepthea sp.) are soft corals that have the ability to be antibacterial and anticancer. These chemical compounds are the result of secondary metabolites of living organisms that are often known as natural products, which are generally in the form of terpenoids. This study aims to analyze the antioxidant activity of Nepthea sp. Soft Coral (Nepthea sp.) Samples were obtained from Bangka Island waters, Likupang. This research is an experimental laboratory with maceration as method of extraction. Testing of ethanol extracts of soft corals (Nepthea sp.) was using the DPPH method (1,1-diphenyl-2-picrylhydrazy) with concentrations of 25, 50, 75, 100, 125, 150 mg / L to analyze antioxidant activity using a spectrophotometer. The greatest antioxidant level is found in Nepthea sp. with a concentration of 150mg/L. The results of this study showed that the antioxidant levels of Nepthea sp. from Bangka waters have antioxidant activity and the higher of the concentration the higher the antioxidant levels produced.  Keywords: Activity, Antioxidants, DPPH, Nepthea sp. ABSTRAK Karang lunak (Nepthea sp.) adalah karang lunak yang mempunyai kemampuan sebagai antibakteria dan antikanker. Senyawa kimia tersebut merupakan hasil metabolit sekunder organisme hidup yang sering dikenal dengan natural producty yang umumnya berupa terpenoid. Penelitian ini bertujuan untuk menganalisis aktivitas antioksidan dari Nepthea sp. Sampel Karang Lunak (Nepthea sp.) diperoleh dari perairan Bangka, Likupang. Penelitian ini merupakan eksperimental laboratorium dengan metode ekstraksi maserasi pengujian terhadap ekstrak etanol karang lunak (Nepthea sp.) menggunakan metode DPPH (1,1-difenil-2-pikrilhidrazi) dengan kosentrasi 25, 50, 75, 100, 125, 150 mg/L untuk menganalisis aktivitas antioksidan dengan menggunakan spektrofotometer. Kadar antioksidan yang paling besar terdapat pada Nepthea sp. dengan konsentrasi 150mg/L. Hasil penelitian ini memperlihatkan kadar antioksidan Nepthea sp. di perairan Bangka mempunyai aktivitas antioksidan dan semakin tinggi konsentrasi semakin tinggi pula kadar antioksidan yang dihasilkan. Kadar antioksidan yang paling besar terdapat pada Nepthea sp. dengan konsentrasi 150 mg/L.Kata Kunci  : Aktivitas, Antioksidan, DPPH, Nepthea sp.

scholarly journals BIO-SUSTAINABLE PRACTICES FOR IMPROVING SOIL HEALTH INDEX

2021 ◽  
Vol 8 (9) ◽  
pp. 15-22
Author(s):  
Suruchi Malik ◽  
Anil Kanaujia
Keyword(s):  
Negative Impact ◽  
Anthropogenic Activities ◽  
Soil Health ◽  
Chemical Compounds ◽  
Contaminated Site ◽  
Management Technique ◽  
Health Index ◽  
Harmful Substances ◽  
Living Organisms ◽  
Day By Day

As the anthropogenic activities are increasing day by day, the environmental pollution has also been rising. The continuous disposal and improper treatment of domestic, industrial, and agricultural wastes is highly toxic and has emerged as a serious pollution threat which is jeopardizing the environment & human health. Soil contamination is referred to as the accumulation in the soil of persistent harmful substances, chemical compounds, radioactive wastes, salts, or pathogens that have a negative impact on biological systems. Bioremediation is a waste management technique that includes the use of living organisms to eradicate or neutralize pollutants from a contaminated site. Other processes use plants, earthworms and biochar to attenuate the toxicity of contaminants.

The Structure and Higher Dimension of Molecules s- and p-Elements

2018 ◽  
pp. 23-52
Keyword(s):  
Chemical Compounds ◽  
Chemical Activity ◽  
Higher Dimension ◽  
Vital Activity ◽  
P Elements ◽  
Living Organisms

There are considered chemical compounds in which s- and p-elements participate, i.e., elements in which electrons fill with the s- and p-orbitals of atoms. Many of these elements, showing increased chemical activity, play an important role in the vital activity of living organisms and are included in drugs for the treatment of living organisms. The structures of these compounds have been determined and classified, and the molecules of these compounds have been shown to have both rule of higher dimensionality (4, 5, 6, and more). This can be of significant importance for nanomedicine.

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