Готові списки джерел за темами / Compound enumeration

Зміст

  1. Статті в журналах
  2. Дисертації
  3. Книги
  4. Частини книг
  5. Тези доповідей конференцій

Добірка наукової літератури з теми "Compound enumeration"

Автор: Grafiati
Опубліковано: 7 грудня 2024

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Статті в журналах з теми "Compound enumeration"

1

Dagar, Komal, Shankar Gupta, Alamjot Singh та Vivek Asati. "In silico studies for the identification of potential thiazolidine-2,4-diones as α-amylase inhibitors". Pharmaspire 15, № 01 (2023): 48–53. http://dx.doi.org/10.56933/pharmaspire.2023.15109.

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Анотація:
Type 2 diabetes, which is characterized by hyperglycemia, is a chronic endocrine metabolic condition. α-amylase inhibitors may have a major therapeutic impact in type 2 diabetic mellitus. In the present study, virtual screening database preparation by R-group enumeration, virtual screening, docking study, and pharmacokinetics analysis was performed by taking α-amylase as a target. The results highlight the important binding features of novel thiazolidine-2,4-dione compounds as α-amylase inhibitors. An R-group enumeration study was performed for the generation of novel thiazolidine-2,4-dione derivatives (6250 compounds). These derivatives further proceed for virtual screening study using Lipinski rule of 5, highthroughput virtual screening, standard precision, and extra precision (XP) screening filters. Only the top 4 compounds were selected after the XP docking process. The molecular docking study of virtual screening hits showed that compound 1 showed a good binding score of −9.129 kcal/mole on α-amylase enzyme (Protein Data Bank ID-3BAY). The present study may be used for the further development of potential compounds against type 2 diabetes.
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2

Osaka, Ichie, Jeffrey M. Hills, Sarah L. Kieweg, Heather E. Shinogle, David S. Moore, and P. Scott Hefty. "An Automated Image-Based Method for Rapid Analysis of Chlamydia Infection as a Tool for Screening Antichlamydial Agents." Antimicrobial Agents and Chemotherapy 56, no. 8 (May 21, 2012): 4184–88. http://dx.doi.org/10.1128/aac.00427-12.

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ABSTRACTA major limitation in the identification of novel antichlamydial compounds is the paucity of effective methods for large-scale compound screening. The immunofluorescence assay is the preferred approach for accurate quantification of the intracellular growth ofChlamydia. In this study, an immunofluorescence image-based method (termed image-based automated chlamydial identification and enumeration [iBAChIE]) was customized for fully automated quantification ofChlamydiainfection using the freely available open-source image analysis software program CellProfiler and the complementary data exploration software program CellProfiler Analyst. The method yielded enumeration of different species and strains ofChlamydiahighly comparably to the conventional manual methods while drastically reducing the analysis time. The inhibitory capability of established antichlamydial activity was also evaluated. Overall, these data support that iBAChIE is a highly effective tool for automated quantification ofChlamydiainfection and assessment of antichlamydial activities of molecules. Furthermore, iBAChIE is expected to be amenable to high-throughput screening studies for inhibitory compounds and fluorescently labeled molecules to study host-pathogen interactions.
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3

Silverstein, J., T. F. Hess, N. Al Mutaari, and R. Brown. "Enumeration of Toxic Compound Degrading Bacteria in a Multi-Species Activated Sludge Biomass." Water Science and Technology 29, no. 7 (April 1, 1994): 309–16. http://dx.doi.org/10.2166/wst.1994.0357.

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A most probable number (MPN) method has been described for the enumeration of bacteria responsible for 2,4-dinitrophenol (DNP) degradation in activated sludge cultures. Because of the encapsulation of cells within the activated sludge floc, the method of pretreatment may be critical for producing a homogeneous distribution of bacteria to insure accurate dilution and enumeration. In these experiments, pretreatments using mechanical shear and incubation of cultures in EDTA have been tested. The combination of mechanical shearing in a high speed blender and incubation in a 0.5% EDTA solution resulted in significantly higher MPN values for DNP-degrading organisms growing in activated sludge in sequencing batch reactors (SBRs) which had been supplemented with glucose. Shearing of flocs and the combination of shearing and EDTA treatment produced the identical MPN values in both pure and activated sludge cultures grown only in DNP.
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4

Smith, Bryan J. K., Melissa A. Boothe, Brice A. Fiddler, Tania M. Lozano, Russel K. Rahi, and Mark J. Krzmarzick. "Enumeration of Organohalide Respirers in Municipal Wastewater Anaerobic Digesters." Microbiology Insights 8s2 (January 2015): MBI.S31445. http://dx.doi.org/10.4137/mbi.s31445.

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Organohalide contaminants such as triclosan and triclocarban have been well documented in municipal wastewater treatment plants (WWTPs), but the degradation of these contaminants is not well understood. One possible removal mechanism is organohalide respiration by which bacteria reduce the halogenated compound. The purpose of this study was to determine the abundance of organohalide-respiring bacteria in eight WWTP anaerobic digesters. The obligate organohalide respiring Dehalococcoides mccartyi was the most abundant and averaged 3.3 × 107 copies of 16S rRNA genes per gram, while the Dehalobacter was much lower at 2.6 × 104 copies of 16S rRNA genes per gram. The genus Sulfurospirillum spp. was also detected at 1.0 × 107 copies of 16S rRNA genes per gram. No other known or putatively organohalide-respiring strains in the Dehalococcoidaceae family were found to be present nor were the genera Desulfitobacterium or Desulfomonile.
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5

Feuston, Bradley, Subhas Chakravorty, John Conway, J. Culberson, Joseph Forbes, Bryan Kraker, Patricia Lennon, et al. "Web Enabling Technology for the Design, Enumeration, Optimization and Tracking of Compound Libraries." Current Topics in Medicinal Chemistry 5, no. 8 (August 1, 2005): 773–83. http://dx.doi.org/10.2174/1568026054637656.

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6

Hamdy, Rania, Bahgat Fayed, Ahmed Mostafa, Noura M. Abo Shama, Sara Hussein Mahmoud, Chetan Hasmukh Mehta, Yogendra Nayak, and Sameh S. M. Soliman. "Iterated Virtual Screening-Assisted Antiviral and Enzyme Inhibition Assays Reveal the Discovery of Novel Promising Anti-SARS-CoV-2 with Dual Activity." International Journal of Molecular Sciences 22, no. 16 (August 22, 2021): 9057. http://dx.doi.org/10.3390/ijms22169057.

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Анотація:
Unfortunately, COVID-19 is still a threat to humankind and has a dramatic impact on human health, social life, the world economy, and food security. With the limited number of suggested therapies under clinical trials, the discovery of novel therapeutic agents is essential. Here, a previously identified anti-SARS-CoV-2 compound named Compound 13 (1,2,5-Oxadiazole-3-carboximidic acid, 4,4′-(methylenediimino) bis,bis[[(2-hydroxyphenyl)methylene]hydrazide) was subjected to an iterated virtual screening against SARS-CoV-2 Mpro using a combination of Ligand Designer and PathFinder. PathFinder, a computational reaction enumeration tool, was used for the rapid generation of enumerated structures via default reaction library. Ligand designer was employed for the computerized lead optimization and selection of the best structural modification that resulted in a favorable ligand–protein complex. The obtained compounds that showed the best binding to Mpro were re-screened against TMPRSS2, leading to the identification of 20 shared compounds. The compounds were further visually inspected, which resulted in the identification of five shared compounds M1–5 with dual binding affinity. In vitro evaluation and enzyme inhibition assay indicated that M3, an analogue of Compound 13 afforded by replacing the phenolic moiety with pyridinyl, possesses an improved antiviral activity and safety. M3 displayed in vitro antiviral activity with IC50 0.016 µM and Mpro inhibition activity with IC50 0.013 µM, 7-fold more potent than the parent Compound 13 and potent than the antivirals drugs that are currently under clinical trials. Moreover, M3 showed potent activity against human TMPRSS2 and furin enzymes with IC50 0.05, and 0.08 µM, respectively. Molecular docking, WaterMap analysis, molecular dynamics simulation, and R-group analysis confirmed the superiority of the binding fit to M3 with the target enzymes. WaterMap analysis calculated the thermodynamic properties of the hydration site in the binding pocket that significantly affects the biological activity. Loading M3 on zinc oxide nanoparticles (ZnO NPs) increased the antiviral activity of the compound 1.5-fold, while maintaining a higher safety profile. In conclusion, lead optimized discovery following an iterated virtual screening in association with molecular docking and biological evaluation revealed a novel compound named M3 with promising dual activity against SARS-CoV-2. The compound deserves further investigation for potential clinical-based studies.
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7

Mat Ripen, Adiratna, Hamidah Ghani, Chai Teng Chear, Mei Yee Chiow, Sharifah Nurul Husna Syed Yahya, Asiah Kassim, and Saharuddin Bin Mohamad. "Whole exome sequencing identifies compound heterozygous variants of CR2 gene in monozygotic twin patients with common variable immunodeficiency." SAGE Open Medicine 8 (January 2020): 205031212092265. http://dx.doi.org/10.1177/2050312120922652.

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Objectives: A pair of female Malay monozygotic twins who presented with recurrent upper respiratory tract infections, hepatosplenomegaly, bronchiectasis and bicytopenia were recruited in this study. Both patients were suspected with primary immunodeficiency diseases. However, the definite diagnosis was not clear due to complex disease phenotypes. The objective of this study was to identify the causative gene mutation in these patients. Methods: Lymphocyte subset enumeration test and whole exome sequencing were performed. Results: We identified a compound heterozygous CR2 mutation (c.1916G>A and c.2012G>A) in both patients. These variants were then confirmed using Sanger sequencing. Conclusion: Whole exome sequencing analysis of the monozygotic twins revealed compound heterozygous missense mutations in CR2.
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8

Osaka, Ichie, and P. Scott Hefty. "Simple Resazurin-Based Microplate Assay for Measuring Chlamydia Infections." Antimicrobial Agents and Chemotherapy 57, no. 6 (March 18, 2013): 2838–40. http://dx.doi.org/10.1128/aac.00056-13.

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ABSTRACTThe conventional method for quantification ofChlamydiainfection using fluorescence microscopy typically involves time- and labor-intensive manual enumeration, which is not applicable for a large-scale analysis required for an inhibitory compound screen. In this study, an alamarBlue (resazurin) assay was adopted to measureChlamydiainfection by measuring the redox capability of infected host cells in a 96-well format. The assay provided measurements comparable to those of the conventional microscopy method while drastically reducing the time required for analysis.
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9

Meringer, Markus, and H. James Cleaves. "Exploring astrobiology using in silico molecular structure generation." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2109 (November 13, 2017): 20160344. http://dx.doi.org/10.1098/rsta.2016.0344.

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Анотація:
The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, ‘animate’ matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic ‘chemical space’. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of ‘chemical spaces’ beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems. This article is part of the themed issue ‘Reconceptualizing the origins of life’.
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10

Stachelska, Milena Alicja, Adam Ekielski, Piotr Karpiński, Tomasz Żelaziński, and Bartosz Kruszewski. "New Genetic Determinants for qPCR Identification and the Enumeration of Selected Lactic Acid Bacteria in Raw-Milk Cheese." Molecules 29, no. 7 (March 29, 2024): 1533. http://dx.doi.org/10.3390/molecules29071533.

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Анотація:
Lactic acid bacteria (LAB) play an important role in the ripening of cheeses and contribute to the development of the desired profile of aroma and flavor compounds. Therefore, it is very important to monitor the dynamics of bacterial proliferation in order to obtain an accurate and reliable number of their cells at each stage of cheese ripening. This work aimed to identify and conduct a quantitative assessment of the selected species of autochthonous lactic acid bacteria from raw cow’s milk cheese by the development of primers and probe pairs based on the uniqueness of the genetic determinants with which the target microorganisms can be identified. For that purpose, we applied real-time quantitative PCR (qPCR) protocols to quantify Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactococcus lactis subsp. cremoris cells in cheese directly after production and over three-month and six-month ripening periods. While L. lactis subsp. cremoris shows good acidification ability and the ability to produce antimicrobial compounds, L. delbrueckii subsp. bulgaricus has good proteolytic ability and produces exo-polysaccharides, and S. thermophilus takes part in the formation of the diacetyl flavor compound by metabolizing citrate to develop aroma, they all play an important role in the cheese ripening. The proposed qPCR protocols are very sensitive and reliable methods for a precise enumeration of L. delbrueckii subsp. bulgaricus, S. thermophilus, and L. lactis subsp. cremoris in cheese samples.
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Дисертації з теми "Compound enumeration"

1

Jira, Jindalertudomdee. "Chemical Compound Enumeration and Host-Pathogen Protein Interaction Prediction by Graph-Based Approaches." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/217198.

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2

Zhao, Yang. "Computational Methods for Analyzing Chemical Graphs and Biological Networks." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188864.

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3

Pikalyova, Regina. "Chémoinformatique des chimiothèques à codage ADN : design, génération in silico, gestion, analyse, et comparaison." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAF032.

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Cette thèse est dédiée à la génération de l'espace virtuel de 2.5K chimiothèques codées par ADN et à leur analyse chémoinformatique détaillée par structures et propriétés. Des méthodologies basées sur GTM permettant de comparer rapidement et de sélectionner les chimiothèques DEL optimales parmi des milliers de possibilités en fonction de la similarité structurelle ou par propriétés par rapport à une base de données de référence ont été développées. Le problème de l'énumération combinatoire des composés a été abordé en développant un modèle d’apprentissage profond capable de prédire la position d'un composé sur la GTM en se basant uniquement sur les réactifs associés et les réactions, en évitant l'énumération. Des modèles permettant de prédire la réactivité des réactifs et l'activité biologique des composés DEL ont été créés. Ces derniers couplés à la visualisation GTM, ont permis de rationaliser et de faciliter la sélection des réactifs pour la synthèse DEL et la priorisation des hits
This thesis is dedicated to the generation of the virtual space of 2.5K DNA-encoded libraries and its detailed structural and property chemoinformatic analysis. GTM-based methodologies allowing to quickly compare and select optimal DELs out of thousands of possible ones based on the structural or property similarity to a reference database were developed. The problem of combinatorial compound enumeration was addressed by developing a highly performant deep learning model capable of predicting the position of a compound on the GTM based solely on its building blocks and reactions, skipping compound enumeration. Machine learning models allowing to predict the reactivity of building blocks and activity of DEL compounds were created. The latter coupled with GTM visualization, allowed to rationalize and facilitate the reagent selection for DEL synthesis and hit prioritization
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4

Martinez, Jorge Matadamas. "AXEL : a framework to deal with ambiguity in three-noun compounds." Thesis, Brunel University, 2010. http://bura.brunel.ac.uk/handle/2438/4774.

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Cognitive Linguistics has been widely used to deal with the ambiguity generated by words in combination. Although this domain offers many solutions to address this challenge, not all of them can be implemented in a computational environment. The Dynamic Construal of Meaning framework is argued to have this ability because it describes an intrinsic degree of association of meanings, which in turn, can be translated into computational programs. A limitation towards a computational approach, however, has been the lack of syntactic parameters. This research argues that this limitation could be overcome with the aid of the Generative Lexicon Theory (GLT). Specifically, this dissertation formulated possible means to marry the GLT and Cognitive Linguistics in a novel rapprochement between the two. This bond between opposing theories provided the means to design a computational template (the AXEL System) by realising syntax and semantics at software levels. An instance of the AXEL system was created using a Design Research approach. Planned iterations were involved in the development to improve artefact performance. Such iterations boosted performance-improving, which accounted for the degree of association of meanings in three-noun compounds. This dissertation delivered three major contributions on the brink of a so-called turning point in Computational Linguistics (CL). First, the AXEL system was used to disclose hidden lexical patterns on ambiguity. These patterns are difficult, if not impossible, to be identified without automatic techniques. This research claimed that these patterns can assist audiences of linguists to review lexical knowledge on a software-based viewpoint. Following linguistic awareness, the second result advocated for the adoption of improved resources by decreasing electronic space of Sense Enumerative Lexicons (SELs). The AXEL system deployed the generation of “at the moment of use” interpretations, optimising the way the space is needed for lexical storage. Finally, this research introduced a subsystem of metrics to characterise an ambiguous degree of association of three-noun compounds enabling ranking methods. Weighing methods delivered mechanisms of classification of meanings towards Word Sense Disambiguation (WSD). Overall these results attempted to tackle difficulties in understanding studies of Lexical Semantics via software tools.
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Книги з теми "Compound enumeration"

1

Pólya, George. Combinatorial enumeration of groups, graphs, and chemical compounds. New York: Springer-Verlag, 1987.

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2

Read, ed. Combinatorial enumeration of groups: graphs and chemical compounds. Berlino: Springer, 1987.

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3

Pólya, George. Combinatorial enumeration of groups, graphs, and chemical compounds. New York: Springer-Verlag, 1987.

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4

Pólya, G., and R. C. Read. Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0.

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5

Polya, Georg. Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds. Island Press, 1987.

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6

Pólya, George. Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds. Springer, 2012.

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7

Pólya, George. Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds. Springer New York, 2011.

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Частини книг з теми "Compound enumeration"

1

Pikalyova, Regina, Tagir Akhmetshin, Dragos Horvath, and Alexandre Varnek. "Combinatorial Library Neural Network (CoLiNN) for Combinatorial Library Visualization Without Compound Enumeration." In Lecture Notes in Computer Science, 3–14. Cham: Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-72359-9_1.

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2

Fujita, Shinsaku. "Compounds with Rotatable Ligands." In Symmetry and Combinatorial Enumeration in Chemistry, 271–95. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76696-1_20.

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3

Pólya, G., and R. C. Read. "Chemical Compounds." In Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds, 58–74. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0_4.

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Fujita, Shinsaku. "Desymmetrization of Para-Achiral Compounds." In Symmetry and Combinatorial Enumeration in Chemistry, 135–45. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76696-1_11.

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Fujita, Shinsaku. "Compounds with Achiral Ligands Only." In Symmetry and Combinatorial Enumeration in Chemistry, 197–213. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76696-1_15.

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6

Fujita, Shinsaku. "Compounds with Achiral and Chiral Ligands." In Symmetry and Combinatorial Enumeration in Chemistry, 255–70. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76696-1_19.

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Pólya, G., and R. C. Read. "Introduction." In Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds, 1–9. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0_1.

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Pólya, G., and R. C. Read. "Groups." In Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds, 10–31. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0_2.

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Pólya, G., and R. C. Read. "Graphs." In Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds, 32–57. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0_3.

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10

Pólya, G., and R. C. Read. "Asymptotic Evaluation of the Number of Combinations." In Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds, 75–95. New York, NY: Springer New York, 1987. http://dx.doi.org/10.1007/978-1-4612-4664-0_5.

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Тези доповідей конференцій з теми "Compound enumeration"

1

Lu, Yitong, Anuruddha Bhattacharjee, Daniel Biediger, MinJun Kim, and Aaron T. Becker. "Enumeration of Polyominoes & Polycubes Composed of Magnetic Cubes." In 2021 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS). IEEE, 2021. http://dx.doi.org/10.1109/iros51168.2021.9636784.

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2

"Assessment of Formula-Based Structural Annotation of Humic Substances by Mild Chemical Derivatization and Mass Spectrometry." In Sixth International Conference on Humic Innovative Technologies "Humic Substances and Eco-Adaptive Technologies ”(HIT – 2021). Non-Commercial Partnership "Center for Biogenic Resources "Humus Sapiens" (NP CBR "Humus Sapiens"), 2021. http://dx.doi.org/10.36291/hit.2021.mikhnevich.002.

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Natural organic matter (NOM) plays an important role in the environment and its chemical properties and molecular composition reflect balance between mineralization and sequestration of organic carbon. Ultrahigh resolution mass spectrometry (e.g., FTICR MS) provides essential molecular information about NOM. However, NOM molecular heterogeneity prevents application of tandem MS experiments and direct structural information is ultimately missing leaving opportunities to only ambiguous formula-based annotation. The main aim of this work was to develop a chemical workflow to reliably examine the accuracy of several FTICR MS-derived structural indices with the focus on aromaticity and O-functional groups, which greatly impact compound properties. Four NOM samples of different origin (coal, oxidized lignin, river, and permafrost thaw) were brominated by NBS in acetonitrile for 24 hrs at RT. Carboxylic groups in all samples were determined by selective deuteromethylation using CD 3OD/SOCl2 reaction and by HATU amidation with 15N labeled glycine. Carbonyl groups were reduced by NaBD4. All parent and labeled mixtures were analyzed by ESI FTCR MS. Custom python scripts were developed to treat spectra and enumerate specific structural moieties in individual components. Obtained data was used to assess reliability of exact aromaticity indices (AI)1 and aromaticity equivalents (Xc) 2. Lignin- and coal-derived samples turned out to be the most sensitive to bromination which corroborated with the model phenolic structures. On contrary, permafrost thaw, which is enriched with labile species, was mostly resistant to bromination - 22% of molecular ions were brominated. Moreover, unlike oxidized riverine sample, coal NOM included polybrominated species, which implies that reaction efficiency depends on reactivity (i.e. substituents) of aromatic fragments. Samples were characterized by drastically different bromine distributions on van Krevelen diagrams, which correlated with the distribution of non-carboxylic oxygen atoms. Further, we compared AI and Xc aromaticity indices in terms of the proportion of correctly assigned aromatics. The data on brominated molecules were in good agreement with the AI values; however, apparently AI tends to overestimate the number of non-aromatics in the sample since it describe averaged aromaticity rather than the factual presence of aromatic ring. On the other hand, Xc perfectly recognized non-aromatics. In general, a higher proportion of correctly attributed aromatics was observed for the aromaticity equivalent Xc (up to 68%), which tends to find aromatic moieties in non-aromatic molecules assigned by AI. Still, we observed a number of aromatic- and condensed aromatic-assigned compounds, which were resistant to bromination or included lesser Br-atoms than the evaluated number of aromatic rings. Reaction with NaBD4 and enumeration of labeling series revealed the presence of carbonyl groups in these species, which in case of multiple reducing could be reliably assigned to quinone – condensed non-aromatic compounds. The approach may be of great importance in biogeochemical and medicinal studies of NOM. Acknowledgements. This work was supported by the Russian Science Foundation gran No 21-47-04405. References 1. Zherebker, A., Lechtenfeld, O. J., Sarycheva, A., Kostyukevich, Y., Kharybin, O., Fedoros, E. I. and Nikolaev, E. N. Anal. Chem., 2020, 92 (13), 9032-9038; 2. Yassine, M.M., Harir, M., Dabek-Zlotorzynska, E. and Schmitt-Kopplin, P. Rapid Commun. Mass Spectrom., 2014, 28, 2445-2454.
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Esmail, Essam L. "Nomographs for Enumeration of Clutching Sequences Associated With Epicyclic-Type Automatic Transmission Mechanisms." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-66409.

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A new methodology for the enumeration of feasible clutching sequences for a given epicyclic gear mechanism (EGM) is presented using the kinematic nomographs of epicyclic-type transmission mechanisms. From such nomographs, the kinematic characteristics of an epicyclic gear mechanism can be expressed in terms of the gear ratios of its gear pairs. From a single nomograph, the angular velocities for all of the coaxial links can be estimated and compared directly without specifying the exact size of each gear. In addition, the angular velocities can be arranged in a descending sequence without using complicated artificial intelligence or algorithmic techniques. Then, a procedure for the enumeration of feasible clutching sequences associated with a transmission mechanism composed of two or more fundamental gear entities (FGEs) is developed. The reliability of the methodology is established by applying it to two transmission gear trains for which solutions are either fully or partially available in the literature. In the process, an incomplete in the results reported in previous literature is brought to light. And the root cause of this incompleteness is explored. The present methodology is judged to be more efficient for enumeration of all feasible clutching sequences of an EGM.
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Narikawa, N., S. Fujimoto, N. Sasaki, and S. Azuma. "An Automated Layout Design System for Industrial Plant Piping." In ASME 1991 International Computers in Engineering Conference and Exposition. American Society of Mechanical Engineers, 1991. http://dx.doi.org/10.1115/cie1991-0001.

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Abstract This paper describes a new approach to an automated layout design system for industrial plant piping. The routing system, which is the main part of this layout system, is composed of three steps, according to the practical layout design process. By dividing the layout design into the optimal routing phase (Step 1, Step 2) and the arrangement phase (Step 3), it is possible to design without depending on the routing order, and with small computer memory storage capacities. The optimal route is obtained by using the routing algorithm and heuristic search, based on expert knowledge. The arrangements are made by applying the enumeration method, taking the strong and weak constraints into account.
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Yang, Ting-Li, and Fang-Hua Yao. "Topological Characteristics and Automatic Generation of Structural Synthesis of Planar Mechanisms Based on the Ordered Single-Opened-Chains." In ASME 1994 Design Technical Conferences collocated with the ASME 1994 International Computers in Engineering Conference and Exhibition and the ASME 1994 8th Annual Database Symposium. American Society of Mechanical Engineers, 1994. http://dx.doi.org/10.1115/detc1994-0180.

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Abstract This paper presents a new viewpoint about structural composition of planar kinematic chains: single-opened-chains, which is composed of binary links, are regarded as basic structural units of mechanisms. The constraint characteristics (the constraint factors, Δj) of single opened chains and the constraint characteristics (the coupled degree κ and the κ-algorithm) of mechanical networks are presented. Thus a kinematic chain with v independent loops is regarded to be composed of one basic link and v single-opened-chains in regular sequence. Based on the ordered single-opened-chains and the topological constraints characteristics of mechanisms, a powerful new method for structural synthesis of planar kinematic chains with plane and nonplane linear graphs has been developed. This permits the development of a highly efficient and completely automatic program for the computer-generated enumeration of structural types of mechanisms. The method is illustrated by applying to the case of kinematic chains with up to six independent loops on a personal computer. The ordered single-opened-chains and the topological characteristics are used for setting up a new unified model for structics, kinematics and dynamics of planar mechanisms.
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Horvath, Roman, and Veronika Stoffova. "PROJECT-BASED AND PROBLEM-BASED TEACHING PROGRAMMING." In eLSE 2021. ADL Romania, 2021. http://dx.doi.org/10.12753/2066-026x-21-068.

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The article reports on the methods and forms of teaching programming used by the authors during the COVID-19 coronavirus pandemic. It describes how the authors communicated and discussed with the learners, how they changed and adapted their full-time teaching to distance learning, how they managed to maintain and adapt the best practices from classical teaching programming, and how teaching aids were changed to practical distance learning. They also analyse the suitability of some methods for distance learning such as problem-based and project-based teaching programming; programming according to instructions; use of classic and interactive electronic textbooks; use of programming courses via the internet; computer game programming, and gamification of programming. The process of programming is highly creative. A good programmer must possess a range of skills that he uses and combines to solve diverse problems. The source code does not mean a strict write-down of an algorithm. The source code reflects the skilful and optimal use of all elements of the programming environment that the programmer uses. Those elements include (besides the flow-control structures, miscellaneous statements like assigning the value, subroutine call, doing various operations and likewise) standard (ordinal or primitive) and compound data types and data structures (records, sets, enumerations, classes and similar) of the programming language. The problem solved by the programmer is represented using different data structures defined in the default packages delivered within the standard installation. The process often puts the programmer in defining new data structures (classes) to better express the data needed for the final solution. Encapsulating the data into the suitable classes within the proper data model often noticeably simplifies the solution. Thus, one of the programmer's skills is the ability to transform the problem to the proper data elements (classes) or the proper data model. In other words: to create a valid data model.
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He, Guoxi, Yongtu Liang, Limin Fang, Qi Zheng, and Liying Sun. "Optimization of Planning and Scheduling of Refinery Product Based on Downstream Requirements." In 2016 11th International Pipeline Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/ipc2016-64150.

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The disconnect between the optimization systems of upstream production and downstream demand poses a legitimate problem for China’s refined oil industry in terms of overproduction waste. Established methods only partially model the refinery system and are unable to integrate detailed production plans or meet market demands. Therefore, the research on production scheduling optimization combined with the demand of downstream pipeline network has very real applications that not only reduce the consumption of human/material resources, but also increase economic efficiency. This paper aims to optimize the production scheduling of refined oil transportation based on the demand of downstream product pipelines by analyzing the relationships between crude oil supply, refinery facility capacities and refinery tanks storage. The new model will minimize the refined production surplus therefore minimizing refinery costs and wastage. This is done by implementing models custom designed to optimize the three subsystems of the overall process: oil product blending scheduling optimization, producing and processing equipment scheduling optimization, and mixed crude oil scheduling optimization. We first analyzed the relationship between all the production units from the crude oil to the distributional destinations of oil products. A mathematical model of the refinery production scheduling was then built with minimum total surplus inventory as the objective function. We assumed a known downstream demand and used a step by step model to optimize oil stocks. The oil blending plan, production scheduling, amount of crude oil, and refined oil mixing ratios were all derived from the model using three methods: a nonlinear method called Particle Swarm Optimization (PSO), the simplex method and the enumeration method. The evidence laid out in this paper verifies our models functionality and suggests that systems can be significantly optimized by using these methods which can provide solutions for industries with similar challenges. Optimization of the refinery’s overall production process is achieved by implementing models for each of the three distinguished subsystems: oil blending model, plant scheduling model, and the mixed crude oil refining model. The demand dictates the final production quantities. From those figures we are able to place constraining limits on the input crude oil. The refined oil production scheme is continuously enhanced by determining the amount of constituent feed on the production equipment according to the results of previous production cycle. After optimization, the minimum surplus inventory of the five oil components approach their lower limits that were calculated using our models. We compare the literature on scheduling optimization challenges both in China and abroad while providing a detailed discussion of the present situation of Chinese refineries. The interrelationships of production processes on each other are revealed by analyzing the system and breaking it down to three fundamental parts. Basing the final production predictions on the downstream demand, we are able to achieve a minimum refinery surplus inventory by utilizing a comprehensive refinery scheduling model composed of three sub-models.
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