D. Milenkovic, M. Zivanovic, M. Dekić, Marijana Stanojević Pirković, Jelena R. Đorović Jovanović
In the present manuscript, the cytotoxic activity of flavylium cation substituted at 4- position with phenyl (FC-4Ph) was tested to two cells lines (human colorectal carcinoma, HCT-116, and human fibroblast lung, MRC-5). In vitro cytotoxicity experiments were performed to elucidate the possible anticancer activity of tested substance. Investigated compound did not show cytotoxic effect on HCT-116 after 24 h, while after 72 h exerted significant effect. A significant selectivity towards colorectal carcinoma cells was observed. On the other hand, this compound did not show any effect on MRC-5 cell line. The molecular interactions between receptor tyrosine kinase (RTK) and title compound was examined. The crystal structure of investigated receptor RTK was downloaded from Protein Data Bank. The native bound ligand ((E)-[4-(3,5-difluorophenyl)-3H-pyrrolo[2,3-b]pyridin-3-ylidene](3- methoxyphenyl)methanol was extracted from receptor and binding pocket analysis was performed. Re-docking was carried out with the FC-4Ph in order to generate the same docking pose as found in co-crystallized form of receptor. The obtained results of revealed that investigated compound binds at the same binding pockets to RTK, as well as native bound ligand, by weak non-covalent interactions. The most prominent interactions are hydrogen bonds, π-alkyl, and π-π interactions. The preliminary results suggest that investigated compound showed good binding affinity against RTK, as evident from the free binding energy (ΔGbind in kJ/mol).
{"title":"CYTOTOXIC ACTIVITY AND MOLECULAR DOCKING STUDY OF 4- SUBSTITUTED FLAVYLIUM SALT","authors":"D. Milenkovic, M. Zivanovic, M. Dekić, Marijana Stanojević Pirković, Jelena R. Đorović Jovanović","doi":"10.46793/iccbi21.466m","DOIUrl":"https://doi.org/10.46793/iccbi21.466m","url":null,"abstract":"In the present manuscript, the cytotoxic activity of flavylium cation substituted at 4- position with phenyl (FC-4Ph) was tested to two cells lines (human colorectal carcinoma, HCT-116, and human fibroblast lung, MRC-5). In vitro cytotoxicity experiments were performed to elucidate the possible anticancer activity of tested substance. Investigated compound did not show cytotoxic effect on HCT-116 after 24 h, while after 72 h exerted significant effect. A significant selectivity towards colorectal carcinoma cells was observed. On the other hand, this compound did not show any effect on MRC-5 cell line. The molecular interactions between receptor tyrosine kinase (RTK) and title compound was examined. The crystal structure of investigated receptor RTK was downloaded from Protein Data Bank. The native bound ligand ((E)-[4-(3,5-difluorophenyl)-3H-pyrrolo[2,3-b]pyridin-3-ylidene](3- methoxyphenyl)methanol was extracted from receptor and binding pocket analysis was performed. Re-docking was carried out with the FC-4Ph in order to generate the same docking pose as found in co-crystallized form of receptor. The obtained results of revealed that investigated compound binds at the same binding pockets to RTK, as well as native bound ligand, by weak non-covalent interactions. The most prominent interactions are hydrogen bonds, π-alkyl, and π-π interactions. The preliminary results suggest that investigated compound showed good binding affinity against RTK, as evident from the free binding energy (ΔGbind in kJ/mol).","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77881737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Patient routing is a key tool for ensuring the availability and quality of cancer care, ensuring early detection of pathology and timely treatment. Mathematical and simulation modeling methods allow to predict the bottlenecks of patient flows and plan the optimal distribution of healthcare resources. Goal to optimize patients’ pathways for oncology care using the simulation modelling methods. Materials and methods Patient routing was presented in the logic of discrete events, the average resource utilization, the patient’s stay time were described, the bottlenecks of the system were determined. Simulation modeling methods were used to build the optimal organization of oncology care services in the region. Results The average waiting time at the pre-hospital stage was 10 days, the average hospitalization time for X-ray therapy was 24 bed days, the throughput of the X-ray therapy room was 6 patients per week, the average duration of the X-ray therapy session per patient was 10 minutes. With the help of simulation modeling methods, a multimodal system of oncodermatology care was created and put into practice, which allowed to reduce the patient’s waiting time for treatment to 0.7 days, increasing the throughput of the entire system.
患者路径是确保癌症治疗的可用性和质量，确保早期发现病理和及时治疗的关键工具。数学和仿真建模方法允许预测患者流的瓶颈并规划医疗资源的最佳分配。目的利用模拟建模方法优化肿瘤患者的治疗途径。材料与方法在离散事件逻辑中提出了患者路径，描述了系统的平均资源利用率和患者住院时间，确定了系统的瓶颈。采用仿真建模方法构建区域肿瘤护理服务的最优组织。结果院前阶段平均候诊时间为10 d, x线治疗平均住院时间为24床d, x线治疗室吞吐量为6例/周，x线治疗时间平均为10 min /例。利用仿真建模方法，建立了肿瘤皮肤科多模式护理系统并付诸实践，使患者的等待治疗时间减少到0.7天，提高了整个系统的吞吐量。
{"title":"THE SIMULATION MODELLING METHODS FOR ORGANIZATION OF THE ONCOLOGY PATIENTS ROUTING","authors":"J. Zuenkova, D. Kicha","doi":"10.46793/iccbi21.247z","DOIUrl":"https://doi.org/10.46793/iccbi21.247z","url":null,"abstract":"Patient routing is a key tool for ensuring the availability and quality of cancer care, ensuring early detection of pathology and timely treatment. Mathematical and simulation modeling methods allow to predict the bottlenecks of patient flows and plan the optimal distribution of healthcare resources. Goal to optimize patients’ pathways for oncology care using the simulation modelling methods. Materials and methods Patient routing was presented in the logic of discrete events, the average resource utilization, the patient’s stay time were described, the bottlenecks of the system were determined. Simulation modeling methods were used to build the optimal organization of oncology care services in the region. Results The average waiting time at the pre-hospital stage was 10 days, the average hospitalization time for X-ray therapy was 24 bed days, the throughput of the X-ray therapy room was 6 patients per week, the average duration of the X-ray therapy session per patient was 10 minutes. With the help of simulation modeling methods, a multimodal system of oncodermatology care was created and put into practice, which allowed to reduce the patient’s waiting time for treatment to 0.7 days, increasing the throughput of the entire system.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79775602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary phenol known for its pharmacological and nutritional properties, its structural features and mechanisms of oxidative action have not been completely elucidated. Clarification of the 5CQA structure was conducted by comparing the experimental and simulated IR, Raman, 1H-NMR, 13C-NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution. Excellent agreement between all experimental and simulated spectra indicates correct arrangement of the atoms in the 5CQA molecule. In addition, the most stable conformation in solution coincides with that predicted with sophisticated NMR experiments. The quantum mechanics–based test for overall free-radical scavenging activity was applied for the investigation of antioxidative capacity of 5CQA relative to trolox (6-hydroxy-2,5,7,8- tetramethylchroman-2-carboxylic acid, Tx) as a reference compound. Hydrogen atom transfer (HAT), radical adduct formation (RAF), sequential proton loss electron transfer (SPLET), and single electron transfer – proton transfer (SET-PT) reactions of 5CQA and Tx with HO· and CH3OO· radicals were examined in benzene, pentyl ethanoate, and basic aqueous solutions. In non-polar solvents 5CQA reacts with HO· via HAT and RAF mechanisms, whereas HAT is the only reaction pathway with CH3OO·. At physiological conditions 5CQA exists in the form of monoanion and dianion. Both anionic forms undergo only HAT mechanism with CH3OO·. With HO·, the anions conform to the HAT, RAF, SPLET, and SET-PT mechanisms. Because all reactions of dianion are diffusion controlled, its contribution to scavenging HO· is comparable to that of more abundant monoanion. The calculated rate constant for overall reaction of 5CQA with HO· is in perfect agreement with the corresponding experimental value. The order of reactivity toward selected free radicals is the same in nonpolar and polar solutions: in comparison to Tx, 5CQA is more reactive toward HO·, but less reactive toward CH3OO·. Very good agreement between the experimental and calculated results confirms the ability of contemporary density functionals to quantify subtle physico-chemical interactions.
虽然绿原酸(5- o -咖啡酰奎宁酸，5CQA)是一种以其药理和营养特性而闻名的膳食酚，但其结构特征和氧化作用机制尚未完全阐明。通过比较实验和模拟的红外光谱、拉曼光谱、1H-NMR、13C-NMR和紫外光谱，对5CQA的结构进行了澄清。为此，对5CQA进行了全面的构象分析，以揭示其在气态和溶液中最稳定的构象。实验光谱和模拟光谱之间的良好一致性表明了5CQA分子中原子的正确排列。此外，溶液中最稳定的构象与复杂的核磁共振实验预测的构象一致。采用基于量子力学的整体自由基清除能力测试，研究了5CQA相对于trolox(6-羟基-2,5,7,8-四甲基铬-2-羧酸，Tx)作为参比化合物的抗氧化能力。研究了5CQA和Tx与HO·和ch300·自由基的氢原子转移(HAT)、自由基加合物形成(RAF)、序向质子损失电子转移(SPLET)和单电子转移-质子转移(SET-PT)反应。在非极性溶剂中，5CQA通过HAT和RAF机制与HO·反应，而HAT是与ch300·的唯一反应途径。生理条件下，5CQA以阴离子和阴离子的形式存在。两种阴离子形式都只与ch300·发生HAT机制。对于HO·，阴离子符合HAT、RAF、SPLET和SET-PT机制。由于所有的反应都是由扩散控制的，所以它对清除HO·的贡献与更丰富的阴离子相当。计算得到的5CQA与HO·的总反应速率常数与实验值吻合较好。在非极性溶液和极性溶液中，5CQA对选定自由基的反应顺序相同:与Tx相比，5CQA对HO·的反应更强，而对ch300·的反应更弱。实验结果与计算结果非常吻合，证实了当代密度泛函量化细微物理化学相互作用的能力。
{"title":"CHLOROGENIC ACID – APPLICATION OF CONTEMPORARY DENSITY FUNCTIONALS TO A SINGLE MOLECULE","authors":"S. Marković, Jelena Tošović","doi":"10.46793/iccbi21.081m","DOIUrl":"https://doi.org/10.46793/iccbi21.081m","url":null,"abstract":"Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary phenol known for its pharmacological and nutritional properties, its structural features and mechanisms of oxidative action have not been completely elucidated. Clarification of the 5CQA structure was conducted by comparing the experimental and simulated IR, Raman, 1H-NMR, 13C-NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution. Excellent agreement between all experimental and simulated spectra indicates correct arrangement of the atoms in the 5CQA molecule. In addition, the most stable conformation in solution coincides with that predicted with sophisticated NMR experiments. The quantum mechanics–based test for overall free-radical scavenging activity was applied for the investigation of antioxidative capacity of 5CQA relative to trolox (6-hydroxy-2,5,7,8- tetramethylchroman-2-carboxylic acid, Tx) as a reference compound. Hydrogen atom transfer (HAT), radical adduct formation (RAF), sequential proton loss electron transfer (SPLET), and single electron transfer – proton transfer (SET-PT) reactions of 5CQA and Tx with HO· and CH3OO· radicals were examined in benzene, pentyl ethanoate, and basic aqueous solutions. In non-polar solvents 5CQA reacts with HO· via HAT and RAF mechanisms, whereas HAT is the only reaction pathway with CH3OO·. At physiological conditions 5CQA exists in the form of monoanion and dianion. Both anionic forms undergo only HAT mechanism with CH3OO·. With HO·, the anions conform to the HAT, RAF, SPLET, and SET-PT mechanisms. Because all reactions of dianion are diffusion controlled, its contribution to scavenging HO· is comparable to that of more abundant monoanion. The calculated rate constant for overall reaction of 5CQA with HO· is in perfect agreement with the corresponding experimental value. The order of reactivity toward selected free radicals is the same in nonpolar and polar solutions: in comparison to Tx, 5CQA is more reactive toward HO·, but less reactive toward CH3OO·. Very good agreement between the experimental and calculated results confirms the ability of contemporary density functionals to quantify subtle physico-chemical interactions.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75657212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Dimić, D. Milenkovic, Edina H. Avdović, G. Kaluđerović, Jasmina M. Dimitrić Marković
Novel biologically active compounds can be obtained by the structural modification of coumarins. In this contribution, five new derivatives of 4-hydroxycoumarin with tyramine, octopamine, norepinephrine, 3-methoxytyramine, and dopamine were obtained. Their structures were optimized based on the previously obtained crystal structure of the 4-hydroxycoumarin-dopamine derivative. The special emphasis was put on the effect of various substituents on the structure of obtained compounds and intramolecular interactions governing the stability. To investigate their possible antitumor activity, molecular docking and molecular dynamics simulations were performed with Carbonic anhydrase, a prognostic factor in several cancers, and compared to the native ligand, 5-acetamido-1,3,4-thiadiazole- 2-sulfonamide. The results have shown that all of the coumarin-neurotransmitter derivatives bind to the active pocket of protein with the binding energies higher than for the native ligand. The main contributions to the binding energies were discussed. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of gyration (Rg), as results of MD simulations, were used to predict the activity of compounds towards chosen protein. The highest MD binding energies were obtained for the derivatives with dopamine and 3-methoxytyramine, with the van der Waals interaction and hydrogen bonds being the most important contributors.
{"title":"MOLECULAR DOCKING AND MOLECULAR DYNAMICS STUDIES OF THE INTERACTION BETWEEN COUMARIN-NEUROTRANSMITTER DERIVATIVES AND CARBONIC ANHYDRASE IX","authors":"D. Dimić, D. Milenkovic, Edina H. Avdović, G. Kaluđerović, Jasmina M. Dimitrić Marković","doi":"10.46793/iccbi21.056d","DOIUrl":"https://doi.org/10.46793/iccbi21.056d","url":null,"abstract":"Novel biologically active compounds can be obtained by the structural modification of coumarins. In this contribution, five new derivatives of 4-hydroxycoumarin with tyramine, octopamine, norepinephrine, 3-methoxytyramine, and dopamine were obtained. Their structures were optimized based on the previously obtained crystal structure of the 4-hydroxycoumarin-dopamine derivative. The special emphasis was put on the effect of various substituents on the structure of obtained compounds and intramolecular interactions governing the stability. To investigate their possible antitumor activity, molecular docking and molecular dynamics simulations were performed with Carbonic anhydrase, a prognostic factor in several cancers, and compared to the native ligand, 5-acetamido-1,3,4-thiadiazole- 2-sulfonamide. The results have shown that all of the coumarin-neurotransmitter derivatives bind to the active pocket of protein with the binding energies higher than for the native ligand. The main contributions to the binding energies were discussed. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of gyration (Rg), as results of MD simulations, were used to predict the activity of compounds towards chosen protein. The highest MD binding energies were obtained for the derivatives with dopamine and 3-methoxytyramine, with the van der Waals interaction and hydrogen bonds being the most important contributors.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80795220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Milena Živković, D. Nikezic, T. Miladinović, D. Krstić
In this paper, the characteristics of phantoms from their origin to the latest species are considered. With the development of technique and technology, the characteristics of phantoms have also been improved, whose importance in monitoring human health is extremely important. The first species were adapted to certain nations and precisely constructed so that sizes such as the height and mass of the phantoms were appropriate and represented the real inhabitants of those areas, that is, the inhabitants of America and Japan. Later, female, children’s phantoms were formed, as well as phantoms of pregnant women in different stages of pregnancy. The latest generations of phantoms, voxel, and mesh phantoms, represent realistic presentations of the human body and are applied in dosimetry and radiation protection in different areas, as well as in different irradiation conditions. The International Commission on Radiation Protection – ICRP continuously studies data on radiation doses and effects and issues appropriate protection recommendations and promotes phantoms that represent the human body and organs of great importance for the occurrence of cancer.
{"title":"OVERVIEW OF PHANTOMS IN DOSIMETRY AND RADIATION PROTECTION","authors":"Milena Živković, D. Nikezic, T. Miladinović, D. Krstić","doi":"10.46793/iccbi21.141z","DOIUrl":"https://doi.org/10.46793/iccbi21.141z","url":null,"abstract":"In this paper, the characteristics of phantoms from their origin to the latest species are considered. With the development of technique and technology, the characteristics of phantoms have also been improved, whose importance in monitoring human health is extremely important. The first species were adapted to certain nations and precisely constructed so that sizes such as the height and mass of the phantoms were appropriate and represented the real inhabitants of those areas, that is, the inhabitants of America and Japan. Later, female, children’s phantoms were formed, as well as phantoms of pregnant women in different stages of pregnancy. The latest generations of phantoms, voxel, and mesh phantoms, represent realistic presentations of the human body and are applied in dosimetry and radiation protection in different areas, as well as in different irradiation conditions. The International Commission on Radiation Protection – ICRP continuously studies data on radiation doses and effects and issues appropriate protection recommendations and promotes phantoms that represent the human body and organs of great importance for the occurrence of cancer.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"75 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77387326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. Erceg, Gaja Brakus, D. Kojić, N. Vukić, V. Teofilović, Jelena Tanasić, I. Ristić
Chitosan based hydrogel was synthesized via free-radical polymerization in a two-step procedure, after modification of chitosan by acrylic acid. Dynamic swelling test was carried out in distilled water at room temperature. Swelling kinetics was modeling using the principle of assuming the equation for a swelling ratio-time empirical dependence. Using regression analysis in this way gives the possibility for simpler determination of swelling ratio-time empirical dependence, knowing the graph functions. Obtained hydrogel was used for preparation of new bilayer hydrogel system which has potential application in wound dressing systems and other fields where pH sensitivity and improved mechanical properties of biopolymers are required in framework of green, cost-effective process.
{"title":"DESCRIPTION OF CHITOSANE GRAFTED ACRYLIC ACID BASED HYDROGEL SWELLING KINETICS AND THEIR USE IN NEW DESIGNED SYSTEM","authors":"T. Erceg, Gaja Brakus, D. Kojić, N. Vukić, V. Teofilović, Jelena Tanasić, I. Ristić","doi":"10.46793/iccbi21.418e","DOIUrl":"https://doi.org/10.46793/iccbi21.418e","url":null,"abstract":"Chitosan based hydrogel was synthesized via free-radical polymerization in a two-step procedure, after modification of chitosan by acrylic acid. Dynamic swelling test was carried out in distilled water at room temperature. Swelling kinetics was modeling using the principle of assuming the equation for a swelling ratio-time empirical dependence. Using regression analysis in this way gives the possibility for simpler determination of swelling ratio-time empirical dependence, knowing the graph functions. Obtained hydrogel was used for preparation of new bilayer hydrogel system which has potential application in wound dressing systems and other fields where pH sensitivity and improved mechanical properties of biopolymers are required in framework of green, cost-effective process.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76967049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dario Balaban, Jelena Lubura, P. Kojić, J. Pavličević, Bojana Ikonić, O. Bera
Rubber vulcanization is kinetically a complex process, since it consists of two simultaneous reactions: curing and degradation. To determine reaction kinetics, it is necessary to determine a kinetic model which describes the process adequately. Proposed kinetic model has six adjustable parameters. In order to determine kinetic parameters of the proposed kinetic model, commercially available rubber gum was used. Oscillating disc rheometer was used to investigate experimental dependence of torque on time, at six temperatures in the range from 130 to 180 °C, with a step of 10 °C. Matlab application, built via App Designer feature, was developed in order to fit the experimental data to the proposed kinetic model. Developed Matlab application, consisting of two tabs, enables user to upload raw rheometer data, perform manual fitting or automatic fitting (manual or automatic estimation of initial values of adjustable parameters), test the effect of constant values of some kinetic parameters on the overall quality of fit, visualize the dependence of kinetic parameters on temperature and to determine the values of Arrhenius expression for curing and degradation process. Both fitting methods were proven to be efficient; overall determination coefficient and MAPE value for automatic and manual fitting methods were >0.99 and <1%, and >0.999 and <1%, respectively. Arrhenius parameters were also determined with high accuracy (R2>0.98). Developed application enables simple and efficient determination of kinetic parameters by means of different fitting methods, simultaneous fitting of data on all temperatures, and testing the effect of constant kinetic parameters values on fitting results
{"title":"DEVELOPING OF MATLAB APPLICATION FOR DETERMINING THE REACTION KINETICS OF RUBBER VULCANIZATION PROCESS","authors":"Dario Balaban, Jelena Lubura, P. Kojić, J. Pavličević, Bojana Ikonić, O. Bera","doi":"10.46793/iccbi21.101b","DOIUrl":"https://doi.org/10.46793/iccbi21.101b","url":null,"abstract":"Rubber vulcanization is kinetically a complex process, since it consists of two simultaneous reactions: curing and degradation. To determine reaction kinetics, it is necessary to determine a kinetic model which describes the process adequately. Proposed kinetic model has six adjustable parameters. In order to determine kinetic parameters of the proposed kinetic model, commercially available rubber gum was used. Oscillating disc rheometer was used to investigate experimental dependence of torque on time, at six temperatures in the range from 130 to 180 °C, with a step of 10 °C. Matlab application, built via App Designer feature, was developed in order to fit the experimental data to the proposed kinetic model. Developed Matlab application, consisting of two tabs, enables user to upload raw rheometer data, perform manual fitting or automatic fitting (manual or automatic estimation of initial values of adjustable parameters), test the effect of constant values of some kinetic parameters on the overall quality of fit, visualize the dependence of kinetic parameters on temperature and to determine the values of Arrhenius expression for curing and degradation process. Both fitting methods were proven to be efficient; overall determination coefficient and MAPE value for automatic and manual fitting methods were >0.99 and <1%, and >0.999 and <1%, respectively. Arrhenius parameters were also determined with high accuracy (R2>0.98). Developed application enables simple and efficient determination of kinetic parameters by means of different fitting methods, simultaneous fitting of data on all temperatures, and testing the effect of constant kinetic parameters values on fitting results","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78276944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Milošević, N. Di Trani, V. Simić, A. Grattoni, M. Kojic
In this work we present computational model for intraocular drug transport using coupled convective-diffusive equations. Model can simulate drug transport using either injection or by state of the art implant devices. We are using Navier-Stokes equation for fluid flow in vitreous humor, and composite smeared finite element (CSFE) for convection in rest of the eye and also for diffusion within the whole model. CSFE takes into account blood vessel properties, such as hydraulic and diffusive components. User interface tool CAD for pre- and post- processing is constructed which enables generation of geometries for patient specific purposes. Computational model provides results in a form convenient for investigation of effects of the drugs on different diseases, such as diabetic macular edema, uveitis, etc. This computational platform has potentials to become a powerful tool for optimization of therapies and simulation of different drugs.
{"title":"COMPUTATIONAL MODELING OF INTRAOCULAR DRUG TRANSPORT","authors":"M. Milošević, N. Di Trani, V. Simić, A. Grattoni, M. Kojic","doi":"10.46793/iccbi21.068m","DOIUrl":"https://doi.org/10.46793/iccbi21.068m","url":null,"abstract":"In this work we present computational model for intraocular drug transport using coupled convective-diffusive equations. Model can simulate drug transport using either injection or by state of the art implant devices. We are using Navier-Stokes equation for fluid flow in vitreous humor, and composite smeared finite element (CSFE) for convection in rest of the eye and also for diffusion within the whole model. CSFE takes into account blood vessel properties, such as hydraulic and diffusive components. User interface tool CAD for pre- and post- processing is constructed which enables generation of geometries for patient specific purposes. Computational model provides results in a form convenient for investigation of effects of the drugs on different diseases, such as diabetic macular edema, uveitis, etc. This computational platform has potentials to become a powerful tool for optimization of therapies and simulation of different drugs.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85736948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The meta-analysis provides a unique scientific conclusion with precise statistical analysis of pooled data extracted from previously reported relevant studies. That gives a better insight into the current issue with more statistical certainty than any single study observation in biomedical research. Occasionally, meta-analyses don’t provide a precise time for each step of the search strategy. The complete meta-analysis procedure is usually time-consuming, with 6-18 months reported, but it depends on the numbers of collected articles manually reviewed by two or more researchers to prevent potential bias. The purpose of this paper was to present a part of meta-analysis research with a focus on a timeline manner for extraction procedure and suggestions for preparing the database of collected articles. PRISMA guidelines were followed, and Pub Med, Scopus, and ISI Web of Science for the search were used. EndNote reference manager v.7 and Microsoft Excel 2007 were used for base preparation. Results showed that the final reference number was 4918, and 99.88% of them were excluded. A month was necessary for the search of the electronic databases. For reading titles and abstracts and extracting the papers was needed the fourth month. A month was needed for an additional search of bibliographies of the eligible papers. Even with the dedication of the team of reviewers, it is hard to predict the exact time for conducting the meta-analysis, indeed. Our results could be applicable in planning the potential systematic reviews, with or without meta-analysis, and overcoming the obstacles in the single database preparation.
荟萃分析通过对先前报道的相关研究中提取的汇总数据进行精确的统计分析，提供了独特的科学结论。这比生物医学研究中的任何单一研究观察都更有统计确定性，能更好地洞察当前的问题。有时候，元分析并不能为搜索策略的每一步提供精确的时间。完整的荟萃分析过程通常是耗时的，需要6-18个月的报告，但它取决于收集的文章的数量，由两个或更多的研究人员手工审查，以防止潜在的偏倚。本文的目的是介绍部分荟萃分析研究，重点是提取程序的时间轴方式和准备收集文章数据库的建议。遵循PRISMA指南，使用Pub Med、Scopus和ISI Web of Science进行检索。使用EndNote参考管理器v.7和Microsoft Excel 2007进行基础准备。结果最终文献号为4918篇，99.88%的文献被排除。搜索电子数据库需要一个月的时间。第四个月需要阅读标题和摘要并提取论文。又花了一个月的时间来查找符合条件的论文的参考书目。即使有审稿人团队的奉献，也很难预测进行荟萃分析的确切时间。我们的结果可以应用于计划潜在的系统评价，无论是否进行荟萃分析，并克服单一数据库准备中的障碍。
{"title":"SEARCH PROCEDURE AND DATA EXTRACTION FOR META-ANALYSIS IN BIOMEDICAL RESEARCH","authors":"J. Obradovic, V. Jurišić","doi":"10.46793/iccbi21.190o","DOIUrl":"https://doi.org/10.46793/iccbi21.190o","url":null,"abstract":"The meta-analysis provides a unique scientific conclusion with precise statistical analysis of pooled data extracted from previously reported relevant studies. That gives a better insight into the current issue with more statistical certainty than any single study observation in biomedical research. Occasionally, meta-analyses don’t provide a precise time for each step of the search strategy. The complete meta-analysis procedure is usually time-consuming, with 6-18 months reported, but it depends on the numbers of collected articles manually reviewed by two or more researchers to prevent potential bias. The purpose of this paper was to present a part of meta-analysis research with a focus on a timeline manner for extraction procedure and suggestions for preparing the database of collected articles. PRISMA guidelines were followed, and Pub Med, Scopus, and ISI Web of Science for the search were used. EndNote reference manager v.7 and Microsoft Excel 2007 were used for base preparation. Results showed that the final reference number was 4918, and 99.88% of them were excluded. A month was necessary for the search of the electronic databases. For reading titles and abstracts and extracting the papers was needed the fourth month. A month was needed for an additional search of bibliographies of the eligible papers. Even with the dedication of the team of reviewers, it is hard to predict the exact time for conducting the meta-analysis, indeed. Our results could be applicable in planning the potential systematic reviews, with or without meta-analysis, and overcoming the obstacles in the single database preparation.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"88 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74038075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jelena S. Katanić Stanković, N. Srećković, V. Mihailović
In this study, silver nanoparticles (AgNPs) have been synthesized using the aqueous extract of the aerial parts of B. purpurocaerulea, collected in Serbia. B. purpurocaerulea silver nanoparticles (Bp– AgNPs) synthesis was confirmed using UV-Vis spectroscopy and Fourier Transform Infrared Spectroscopy (FTIR). The biological potential of synthesized Bp-AgNPs was evaluated in vitro using ABTS assay for determining free radical scavenging potential and microdilution method for analysis of antimicrobial properties. Bp-AgNPs showed high antioxidant activity similar to Bp-extract, comparable to BHT. The synthesized nanoparticles exerted remarkable antibacterial effects, with minimal inhibitory concentration (MIC) values below 20 µg/mL. In the case of some bacterial strains, the results of Bp– AgNPs were comparable or similar to standard antibiotic erythromycin. The antifungal activity of Bp– AgNPs was moderate for most of the used strains. Nevertheless, several fungi were resistant to the NPs action, while two tested Penicillium species were extremely sensitive on Bp-AgNPs with MIC lower than 40 µg/mL. The antimicrobial properties of Bp-AgNPs can be useful for the development of new NPs-containing products.
{"title":"PHYTO-MEDIATED SYNTHESIS OF SILVER NANOPARTICLES USING AQUEOUS EXTRACT OF „BUGLOSSOIDES PURPUROCAERULEA“ (BORAGINACEAE) AND THEIR BIOACTIVITY","authors":"Jelena S. Katanić Stanković, N. Srećković, V. Mihailović","doi":"10.46793/iccbi21.359ks","DOIUrl":"https://doi.org/10.46793/iccbi21.359ks","url":null,"abstract":"In this study, silver nanoparticles (AgNPs) have been synthesized using the aqueous extract of the aerial parts of B. purpurocaerulea, collected in Serbia. B. purpurocaerulea silver nanoparticles (Bp– AgNPs) synthesis was confirmed using UV-Vis spectroscopy and Fourier Transform Infrared Spectroscopy (FTIR). The biological potential of synthesized Bp-AgNPs was evaluated in vitro using ABTS assay for determining free radical scavenging potential and microdilution method for analysis of antimicrobial properties. Bp-AgNPs showed high antioxidant activity similar to Bp-extract, comparable to BHT. The synthesized nanoparticles exerted remarkable antibacterial effects, with minimal inhibitory concentration (MIC) values below 20 µg/mL. In the case of some bacterial strains, the results of Bp– AgNPs were comparable or similar to standard antibiotic erythromycin. The antifungal activity of Bp– AgNPs was moderate for most of the used strains. Nevertheless, several fungi were resistant to the NPs action, while two tested Penicillium species were extremely sensitive on Bp-AgNPs with MIC lower than 40 µg/mL. The antimicrobial properties of Bp-AgNPs can be useful for the development of new NPs-containing products.","PeriodicalId":9171,"journal":{"name":"Book of Proceedings: 1st International Conference on Chemo and BioInformatics,","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80242889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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