Search results for: molecular modeling of Cdk5/p25

Authors: Dimitrios Triantakonstantis, Demetris Stathakis

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Urban areas have been expanded throughout the globe. Monitoring and modeling urban growth have become a necessity for a sustainable urban planning and decision making. Urban prediction models are important tools for analyzing the causes and consequences of urban land use dynamics. The objective of this research paper is to analyze and model the urban change, which has been occurred from 1990 to 2000 using CORINE land cover maps. The model was developed using drivers of urban changes (such as road distance, slope, etc.) under an Artificial Neural Network modeling approach. Validation was achieved using a prediction map for 2006 which was compared with a real map of Urban Atlas of 2006. The accuracy produced a Kappa index of agreement of 0,639 and a value of Cramer's V of 0,648. These encouraging results indicate the importance of the developed urban growth prediction model which using a set of available common biophysical drivers could serve as a management tool for the assessment of urban change.

Keywords: artificial neural networks, CORINE, urban atlas, urban growth prediction

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Authors: Robert Setekera, Ramses van der Toorn

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We present an extensive analysis of the temperature dependence of the local avalanche model used in most of the modern compact models for bipolar transistors. This local avalanche model uses the Chynoweth's empirical law for ionization coefficient to define the generation of the avalanche current in terms of the local electric field. We carry out the model analysis using DC-measurements taken on both Si and advanced SiGe bipolar transistors. For the advanced industrial SiGe-HBTs, we consider both high-speed and high-power devices (both NPN and PNP transistors). The limitations of the local avalanche model in modeling the temperature dependence of the avalanche current mostly in the weak avalanche region are demonstrated. In addition, the model avalanche parameters are analyzed to see if they are in agreement with semiconductor device physics.

Keywords: avalanche multiplication, avalanche current, bipolar transistors, compact modeling, electric field, impact ionization, local avalanche

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Authors: Ganiyat Soliu, Glen Bright, Chiemela Onunka

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Performance optimization plays a key role in controlling the waiting time during manufacturing in an advanced manufacturing environment to improve productivity. Queuing mathematical modeling theory was used to examine the performance of the multi-stage production line. Robotics as a disruptive technology was implemented into a virtual manufacturing scenario during the packaging process to study the effect of waiting time on productivity. The queuing mathematical model was used to determine the optimum service rate required by robots during the packaging stage of manufacturing to yield an optimum production cost. Different rates of production were assumed in a virtual manufacturing environment, cost of packaging was estimated with optimum production cost. An equation was generated using queuing mathematical modeling theory and the theorem adopted for analysis of the scenario is the Newton Raphson theorem. Queuing theory presented here provides an adequate analysis of the number of robots required to regulate waiting time in order to increase the number of output. Arrival rate of the product was fast which shows that queuing mathematical model was effective in minimizing service cost and the waiting time during manufacturing. At a reduced waiting time, there was an improvement in the number of products obtained per hour. The overall productivity was improved based on the assumptions used in the queuing modeling theory implemented in the virtual manufacturing scenario.

Keywords: performance optimization, productivity, queuing theory, robotics

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Authors: B. K. Kanungo, Monika Thakur, Minati Baral

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8-hydroxyquinoline, (8HQ), experiences a renaissance due to its utility as a building block in metallosupramolecular chemistry and its versatile use of its derivatives in various fields of analytical chemistry, materials science, and pharmaceutics. It forms stable complexes with a variety of metal ions. Assembly of more than one such unit to form a polydentate chelator enhances its coordinating ability and the related properties due to the chelate effect resulting in high stability constant. Keeping in view the above, a nonadentate chelator N-[3,5-bis(8-hydroxyquinoline-2-amido)cyclohexyl]-8-hydroxyquinoline-2-carboxamide, (TACH2OX), containing a central cis,cis-1,3,5-triaminocyclohexane appended to three 8-hydroxyquinoline at 2-position through amide linkage is developed, and its solution thermodynamics, photophysical and Density Functional Theory (DFT) studies were undertaken. The synthesis of TACH2OX was carried out by condensation of cis,cis-1,3,5-triaminocyclohexane, (TACH) with 8‐hydroxyquinoline‐2‐carboxylic acid. The brown colored solid has been fully characterized through melting point, infrared, nuclear magnetic resonance, electrospray ionization mass and electronic spectroscopy. In solution, TACH2OX forms protonated complexes below pH 3.4, which consecutively deprotonates to generate trinegative ion with the rise of pH. Nine protonation constants for the ligand were obtained that ranges between 2.26 to 7.28. The interaction of the chelator with two trivalent metal ion Fe3+ and Al3+ were studied in aqueous solution at 298 K. The metal-ligand formation constants (ML) obtained by potentiometric and spectrophotometric method agree with each other. The protonated and hydrolyzed species were also detected in the system. The in-silico studies of the ligand, as well as the complexes including their protonated and deprotonated species assessed by density functional theory technique, gave an accurate correlation with each observed properties such as the protonation constants, stability constants, infra-red, nmr, electronic absorption and emission spectral bands. The nature of electronic and emission spectral bands in terms of number and type were ascertained from time-dependent density functional theory study and the natural transition orbitals (NTO). The global reactivity indices parameters were used for comparison of the reactivity of the ligand and the complex molecules. The natural bonding orbital (NBO) analysis could successfully describe the structure and bonding of the metal-ligand complexes specifying the percentage of contribution in atomic orbitals in the creation of molecular orbitals. The obtained high value of metal-ligand formation constants indicates that the newly synthesized chelator is a very powerful synthetic chelator. The minimum energy molecular modeling structure of the ligand suggests that the ligand, TACH2OX, in a tripodal fashion firmly coordinates to the metal ion as hexa-coordinated chelate displaying distorted octahedral geometry by binding through three sets of N, O- donor atoms, present in each pendant arm of the central tris-cyclohexaneamine tripod.

Keywords: complexes, DFT, formation constant, TACH2OX

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Authors: Makhlouf Mourad, Medkour Mihoub, Bouchher Omar, Messabih Sidi Mohamed, Benrachedi Khaled

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This work is the modeling and simulation of fluid flow (liquid) through porous media. This type of flow occurs in many situations of interest in applied sciences and engineering, fluid (oil) consists of several individual substances in pure, single-phase flow is incompressible and isothermal. The porous medium is isotropic, homogeneous optionally, with the rectangular format and the flow is two-dimensional. Modeling of hydrodynamic phenomena incorporates Darcy's law and the equation of mass conservation. Correlations are used to model the density and viscosity of the fluid. A finite volume code is used in the discretization of differential equations. The nonlinearity is treated by Newton's method with relaxation coefficient. The results of the simulation of the pressure and the mobility of liquid flowing through porous media are presented, analyzed, and illustrated.

Keywords: Darcy equation, middle porous, continuity equation, Peng Robinson equation, mobility

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Authors: Furry A. Wilis, Dewi Larasati, Suhendri

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Around 96% of architecture firms in Indonesia are classified as small-medium enterprises (SME). This number shows that the SME firms have an important role in architecture, engineering, and construction (AEC) industry in Indonesia. Some of them are still using conventional system (2D based) in arranging construction project documents. This system is fragmented and not fully well-coordinated, so causes many changes in the whole project cycle. Building information modeling (BIM), as a new developed system in Indonesian construction industry, has been assumed can decrease changes in the project. But BIM has not fully implemented in Indonesian AEC industry, especially in SME architecture firms. This article identifies the challenges of implementing BIM in SME architecture firms in Indonesia. Quantitative-explorative research with questionnaire was chosen to achieve the goal of this article. The scarcity of skilled BIM user, low demand from client, high investment cost, and the unwillingness of the firm to switch into BIM were found as the result of this paper.

Keywords: architecture consultants, BIM, SME, Indonesia

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Authors: Margarita S. Tikhonova, Alireza Baniasad, Anton G. Kalmykov, Georgy A. Kalmykov, Ralf Littke

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There is a high complexity in the pore structure of organic-rich rocks caused by the combination of inter-particle porosity from inorganic mineral matter and ultrafine intra-particle porosity from both organic matter and clay minerals. Fluids are retained in that pore space, but there are major uncertainties in how and where the fluids are stored and to what extent they are accessible or trapped in 'closed' pores. A large degree of tortuosity may lead to fractionation of organic matter so that the lighter and flexible compounds would diffuse to the reservoir whereas more complicated compounds may be locked in place. Additionally, parts of hydrocarbons could be bound to solid organic matter –kerogen– and mineral matrix during expulsion and migration. Larger compounds can occupy thin channels so that clogging or oil and gas entrapment will occur. Sequential extraction of applying different solvents is a powerful tool to provide more information about the characteristics of trapped organic matter distribution. The Upper Jurassic – Lower Cretaceous Bazhenov shale is one of the most petroliferous source rock extended in West Siberia, Russia. Concerning the variable mineral composition, pore space distribution and thermal maturation, there are high uncertainties in distribution and composition of organic matter in this formation. In order to address this issue geological and geochemical properties of 30 samples including mineral composition (XRD and XRF), structure and texture (thin-section microscopy), organic matter contents, type and thermal maturity (Rock-Eval) as well as molecular composition (GC-FID and GC-MS) of different extracted materials during sequential extraction were considered. Sequential extraction was performed by a Soxhlet apparatus using different solvents, i.e., n-hexane, chloroform and ethanol-benzene (1:1 v:v) first on core plugs and later on pulverized materials. The results indicate that the studied samples are mainly composed of type II kerogen with TOC contents varied from 5 to 25%. The thermal maturity ranged from immature to late oil window. Whereas clay contents decreased with increasing maturity, the amount of silica increased in the studied samples. According to molecular geochemistry, stored hydrocarbons in open and closed pore space reveal different geochemical fingerprints. The results improve our understanding of hydrocarbon expulsion and migration in the organic-rich Bazhenov shale and therefore better estimation of hydrocarbon potential for this formation.

Keywords: Bazhenov formation, bitumen, molecular geochemistry, sequential extraction

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Authors: Sungho Kim, Dae Shik Kim, Jong Min Lee

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Fluid catalytic cracking (FCC) process is one of the most important process in modern refinery industry. This paper focuses on the fluid catalytic cracking (FCC) process. As the FCC process is difficult to model well, due to its non linearities and various interactions between its process variables, rigorous process modeling of whole FCC plant is demanded for control and plant-wide optimization of the plant. In this study, a process design for the FCC plant includes riser reactor, main fractionator, and gas processing unit was developed. A reactor model was described based on four-lumped kinetic scheme. Main fractionator, gas processing unit and other process units are designed to simulate real plant data, using a process flow sheet simulator, Aspen PLUS. The custom reactor model was integrated with the process flow sheet simulator to develop an integrated process model.

Keywords: fluid catalytic cracking, simulation, plant data, process design

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Authors: Slim Chokri

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Load forecasting is one of the central functions in power systems operations. Electricity cannot be stored, which means that for electric utility, the estimate of the future demand is necessary in managing the production and purchasing in an economically reasonable way. A majority of the recently reported approaches are based on neural network. The attraction of the methods lies in the assumption that neural networks are able to learn properties of the load. However, the development of the methods is not finished, and the lack of comparative results on different model variations is a problem. This paper presents a new approach in order to predict the Tunisia daily peak load. The proposed method employs a computational intelligence scheme based on the Fuzzy neural network (FNN) and support vector regression (SVR). Experimental results obtained indicate that our proposed FNN-SVR technique gives significantly good prediction accuracy compared to some classical techniques.

Keywords: neural network, load forecasting, fuzzy inference, machine learning, fuzzy modeling and rule extraction, support vector regression

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Authors: Cyrillus Prabandana

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Supply chain optimisation requires multiple factors as consideration or constraints. These factors are including but not limited to demand forecasting, raw material fulfilment, production capacity, inventory level, facilities locations, transportation means, and manpower availability. By knowing all manageable factors involved and assuming the uncertainty with pre-defined percentage factors, an integrated supply chain model could be developed to manage various business scenarios. This paper analyse the utilisation of geographical point of view to develop an integrated supply chain network model to optimise the distribution of finished product appropriately according to forecasted demand and available supply. The supply chain optimisation model shows that small change in one supply chain constraint is possible to largely impact other constraints, and the new information from the model should be able to support the decision making process. The model was focused on three areas, i.e. raw material fulfilment, production capacity and finished products transportation. To validate the model suitability, it was implemented in a project aimed to optimise the concrete supply chain in a mining location. The high level of operations complexity and involvement of multiple stakeholders in the concrete supply chain is believed to be sufficient to give the illustration of the larger scope. The implementation of this geographical supply chain network modeling resulted an optimised concrete supply chain from raw material fulfilment until finished products distribution to each customer, which indicated by lower percentage of missed concrete order fulfilment to customer.

Keywords: decision making, geographical supply chain modeling, supply chain optimisation, supply chain

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Authors: S. M. Dankaka, N. Abdullahi

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Context: This research was conducted to isolate and identify phenol-tolerant bacteria from petroleum-contaminated sites in the northwestern part of Nigeria. Research Aim: The aim of this study was to identify bacteria with the ability to tolerate different phenol concentrations. Methodology: Samples were obtained from different petroleum-contaminated sites, and bacteria were cultured, followed by morphological, microscopic, and molecular identification. Isolates were grown on phenol-tolerant nutrient agar. The tolerant ability of the isolates was observed at 500 mg/L, 1000 mg/L, and 1500 mg/L concentrations of phenol. Findings: Two bacteria species (NWPK and NWPKD) were obtained. The total viable counts of phenol-utilizing bacteria from NWPK and NWPKD were 2.71x10⁷ and 4.0x10⁶ cfu/g, respectively. The NWPK showed its capacity to tolerate phenol at 2.3x10⁷, 2.5x10⁷, and 1.0x10⁷ cfu/g of 500, 1000, and 1500 mg/L of phenol concentration, respectively, while NWPKD tolerance ability was 1.5x10⁷, 3.8x10⁷ and 1.0x10⁷ cfu/g of 500, 1000 and 1500 mg/L of phenol respectively. The isolates were identified as Citrobacter and Acinetobacter species, respectively, based on 16S rRNA gene sequence analysis. Conclusion: The study found that these isolates showed the ability to withstand and survive high phenol concentrations in the environment.

Keywords: phenol tolerance, bacteria, petroleum contaminated sites, 16S rRNA

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Authors: Fouad. Inel, Lakhdar. Khochemane

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This article presents a comparative response specification performance between two controllers of three and four cable based robots for various applications. The main objective of this work is: The first is to use the direct and inverse geometric model to study and simulate the end effector position of the robot with three and four cables. A graphical user interface has been implemented in order to visualizing the position of the robot. Secondly, we present the determination of static and dynamic tensions and lengths of cables required to flow different trajectories. At the end, we study the response of our systems in closed loop with a Proportional-Integrated Derivative (PID) and Proportional-Integrated (PD) controllers then this last are compared the results of the same examples using MATLAB/Simulink; we found that the PID method gives the better performance, such as rapidly speed response, settling time, compared to PD controller.

Keywords: parallel cable-based robots, geometric modeling, dynamic modeling, graphical user interface, open loop, PID/PD controllers

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Authors: B. Wang, W. H. Or, S.C. Lee, Y.C. Leung, B. Organ

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This study presents an investigation of diesel vehicle particulate-phase emissions with neat ultralow sulphur diesel (B0, ULSD) and 5% waste cooking oil-based biodiesel blend (B5) in Hong Kong. A Euro VI light duty diesel vehicle was tested under transient (New European Driving Cycle (NEDC)), steady-state and idling on a chassis dynamometer. Chemical analyses including organic carbon (OC), elemental carbon (EC), as well as 30 polycyclic aromatic hydrocarbons (PAHs) and 10 oxygenated PAHs (oxy-PAHs) were conducted. The OC fuel-based emission factors (EFs) for B0 ranged from 2.86 ± 0.33 to 7.19 ± 1.51 mg/kg, and those for B5 ranged from 4.31 ± 0.64 to 15.36 ± 3.77 mg/kg, respectively. The EFs of EC were low for both fuel blends (0.25 mg/kg or below). With B5, the EFs of total PAHs were decreased as compared to B0. Specifically, B5 reduced total PAH emissions by 50.2%, 30.7%, and 15.2% over NEDC, steady-state and idling, respectively. It was found that when B5 was used, PAHs and oxy-PAHs with lower molecular weight (2 to 3 rings) were reduced whereas PAHs/oxy-PAHs with medium or high molecular weight (4 to 7 rings) were increased. Our study suggests the necessity of taking atmospheric and health factors into account for biodiesel application as an alternative motor fuel.

Keywords: biodiesel, OC/EC, PAHs, vehicular emission

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Authors: Recep Kesli, Huseyin Bilgin, Yasar Unlu, Gokhan Gungor

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Aim: The aim of this study was to compare diagnostic values of two different molecular-based tests (GenoType® HelicoDR ve Seeplex® H. pylori-ClaR- ACE Detection) in detection presence of the H. pylori from gastric biopsy specimens. In addition to this also was aimed to determine resistance ratios of H. pylori strains against to clarytromycine and quinolone isolated from gastric biopsy material cultures by using both the genotypic (GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection) and phenotypic (gradient strip, E-test) methods. Material and methods: A total of 266 patients who admitted to Konya Education and Research Hospital Department of Gastroenterology with dyspeptic complaints, between January 2011-June 2013, were included in the study. Microbiological and histopathological examinations of biopsy specimens taken from antrum and corpus regions were performed. The presence of H. pylori in all the biopsy samples was investigated by five differnt dignostic methods together: culture (C) (Portagerm pylori-PORT PYL, Pylori agar-PYL, GENbox microaer, bioMerieux, France), histology (H) (Giemsa, Hematoxylin and Eosin staining), rapid urease test (RUT) (CLOtest, Cimberly-Clark, USA), and two different molecular tests; GenoType® HelicoDR, Hain, Germany, based on DNA strip assay, and Seeplex ® H. pylori -ClaR- ACE Detection, Seegene, South Korea, based on multiplex PCR. Antimicrobial resistance of H. pylori isolates against clarithromycin and levofloxacin was determined by GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, and gradient strip (E-test, bioMerieux, France) methods. Culture positivity alone or positivities of both histology and RUT together was accepted as the gold standard for H. pylori positivity. Sensitivity and specificity rates of two molecular methods used in the study were calculated by taking the two gold standards previously mentioned. Results: A total of 266 patients between 16-83 years old who 144 (54.1 %) were female, 122 (45.9 %) were male were included in the study. 144 patients were found as culture positive, and 157 were H and RUT were positive together. 179 patients were found as positive with GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection together. Sensitivity and specificity rates of studied five different methods were found as follows: C were 80.9 % and 84.4 %, H + RUT were 88.2 % and 75.4 %, GenoType® HelicoDR were 100 % and 71.3 %, and Seeplex ® H. pylori -ClaR- ACE Detection were, 100 % and 71.3 %. A strong correlation was found between C and H+RUT, C and GenoType® HelicoDR, and C and Seeplex ® H. pylori -ClaR- ACE Detection (r:0.644 and p:0.000, r:0.757 and p:0.000, r:0.757 and p:0.000, respectively). Of all the isolated 144 H. pylori strains 24 (16.6 %) were detected as resistant to claritromycine, and 18 (12.5 %) were levofloxacin. Genotypic claritromycine resistance was detected only in 15 cases with GenoType® HelicoDR, and 6 cases with Seeplex ® H. pylori -ClaR- ACE Detection. Conclusion: In our study, it was concluded that; GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection was found as the most sensitive diagnostic methods when comparing all the investigated other ones (C, H, and RUT).

Keywords: Helicobacter pylori, GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, antimicrobial resistance

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Authors: Nutnicha Wongpadungkiat, Suwit Siriwatanayotin, Aluck Thipayarat, Punchira Vongsawasdi, Chotika Viriyarattanasak

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Chicken products are major export product of Thailand. With a dramatically increasing consumption of chicken product in the world, there are abundant wastes from chicken meat processing industry. Recently, much research in the development of value-added products from chicken meat industry has focused on the production of protein hydrolysate, utilized as food ingredients for human diet and animal feed. The present study aimed to determine the effect of thermal pre-treatment on functional properties of chicken protein hydrolysate. Chicken breasts were heated at 40, 60, 80 and 100ºC prior to hydrolysis by Alcalase at 60ºC, pH 8 for 4 hr. The hydrolysate was freeze-dried, and subsequently used for assessment of its functional properties molecular weight by gel electrophoresis (SDS-PAGE). The obtained results show that increasing the pre-treatment temperature increased oil holding capacity and emulsion stability while decreasing antioxidant activity and water holding capacity. The SDS-PAGE analysis showed the evidence of protein aggregation in the hydrolysate treated at the higher pre-treatment temperature. These results suggest the connection between molecular weight of the hydrolysate and its functional properties.

Keywords: chicken protein hydrolysate, enzymatic hydrolysis, thermal pretreatment, functional properties

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Authors: Nadia Naseem, Farwa Batool, Nasir Mehmood, AbdulHannan Nagi

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Background: The incidence and mortality of breast cancer vary significantly in geographically distinct populations. In Pakistan, breast cancer has shown an increase in incidence in young females and is characterized by more aggressive behavior. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. This study investigated the TP53 mutations in molecular subtypes of both nodes negative and positive breast cancer in young Pakistani patients. Material and Methods: p53, Estrogen Receptor (ER), Progesterone Receptor (PR), Her-2 neu and Ki 67 expressions were analyzed immunohistochemically in a series of 75 node negative (A) and 75 node positive (B) young (aged: 19-40 years) breast cancer patients diagnosed between 2014 to 2017 at two leading hospitals of Punjab, Pakistan. Tumor tissue specimens and peripheral blood samples were examined for TP53 mutations by direct sequencing of the gene (exons 4-9). The relation of TP53 mutations to these markers and clinicopathological data was investigated. Results: Mean age of the patients was 32.4 + 9.1 SD. Invasive breast carcinoma was the most frequent histological variant (A=92%, B=94.6%). Grade 3 carcinoma was the commonest grade (A=72%, B=81.3%). Triple negative cases (ER-, PR-, Her-2) formed most of the molecular subtypes (A=44%, B=50.6%). A total of 17.2% (A: 6.6%, B: 10.6%) patients showed TP53 mutations. Mutations were significantly more frequent in triple negative cases (A: 74.8%, B: 62.2%) compared to HER2-positive patients (P < 0.0001). In the multivariate analysis of the whole patient group, the independent prognosticator were triple negative cases (P=0.021), TP53 overexpression by IHC (P=0.001) and advanced-stage disease (P=0.007). No statistically significant correlation between TP53 mutations and clinicopathological parameters was found (P < 0.05). Conclusions: It is concluded that TP53 mutations are infrequently present in breast carcinoma of young Pakistani population and there was no significant correlation between p53 mutation and early onset disease. Immunohistochemically detected TP53 expression in our resource-constrained to set up can be beneficial in predicting mutations at the younger age in our population.

Keywords: immunohistochemistry (IHC), invasive breast carcinoma (IBC), Pakistan, TP53

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Authors: Fety Nurlia Muzayanah, Arif Imam Suroso, Mukhamad Najib

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The market share of organic food in Indonesia just reaches 0.5-2 percents from the entire of agricultural products. The aim of this research is to analyze the relation of gender, work, age and final education toward the buying interest of organic food, to identify the factors influencing the resistance of the purchase of organic food, and to identify the market education process. The analysis result of Structural Equation Modeling (SEM) shows the factors causing the resistance of the purchase of organic food are the negative attitude toward organic food, the lack of affordable in range for organic food product and the lack of awareness toward organic food, while the subjective norms have no significant effect toward the buying interest. The market education process which can be done is the education about the use of the health of organic food, the organic certification and the economic value.

Keywords: market education, organic food, consumer behavior, structural equation modeling

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Authors: William Anderson, Kyle Kobold, Oleg Yakimenko

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Green microgrids using mostly renewable energy (RE) for generation, are complex systems with inherent nonlinear dynamics. Among a variety of different optimization tools there are only a few ones that adequately consider this complexity. This paper evaluates applicability of two somewhat similar optimization tools tailored for standalone RE microgrids and also assesses a machine learning tool for performance prediction that can enhance the reliability of any chosen optimization tool. It shows that one of these microgrid optimization tools has certain advantages over another and presents a detailed routine of preparing input data to simulate RE microgrid behavior. The paper also shows how neural-network-based predictive modeling can be used to validate and forecast solar power generation based on weather time series data, which improves the overall quality of standalone RE microgrid analysis.

Keywords: microgrid, renewable energy, complex systems, optimization, predictive modeling, neural networks

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Authors: Mina Kalantarzadeh, Claire Lockie-Williams, Caroline Howard

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DNA barcoding is increasingly used for identification of medicinal plants worldwide. In the last decade, a large number of DNA barcodes have been generated, and their application in species identification explored. The success of DNA barcoding process relies on the accuracy of the results from polymerase chain reaction (PCR) amplification step which could be negatively affected due to a presence of inhibitors or degraded DNA in herbal samples. An established DNA reference material can be used to support molecular characterisation protocols and prove system suitability, for fast and accurate identification of plant species. The present study describes the use of a novel reference material, the trnH-psbA British Pharmacopoeia Nucleic Acid Reference Material (trnH-psbA BPNARM), which was produced to aid in the identification of Ocimum tenuiflorum L., a widely used herb. During DNA barcoding of O. tenuiflorum, PCR amplifications of isolated DNA produced inconsistent results, suggesting an issue with either the method or DNA quality of the tested samples. The trnH-psbA BPNARM was produced and tested to check for the issues caused during PCR amplification. It was added to the plant material as control DNA before extraction and was co-extracted and amplified by PCR. PCR analyses revealed that the amplification was not as successful as expected which suggested that the amplification is affected by presence of inhibitors co-extracted from plant materials. Various potential issues were assessed during DNA extraction and optimisations were made accordingly. A DNA barcoding protocol for O. tenuiflorum was published in the British Pharmacopoeia 2016, which included the reference sequence. The trnH-psbA BPNARM accelerated degradation test which investigates the stability of the reference material over time demonstrated that it has been stable when stored at 56 °C for a year. Using this protocol and trnH-psbA reference material provides a fast and accurate method for identification of O. tenuiflorum. The optimisations of the DNA extraction using the trnH-psbA BPNARM provided a signposting method which can assist in overcoming common problems encountered when using molecular methods with medicinal plants.

Keywords: degradation, DNA extraction, nucleic acid reference material, trnH-psbA

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Authors: Asaad Y. Shamseldin

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Analytical probabilistic approach is an innovative approach for urban stormwater modeling. It can provide information about the long-term performance of a stormwater management facility without being computationally very demanding. This paper explores the application of the analytical probabilistic approach in New Zealand. The paper presents the results of a case study aimed at development of an objective way of identifying what constitutes a rainfall storm event and the estimation of the corresponding statistical properties of storms using two selected automatic rainfall stations located in the Auckland region in New Zealand. The storm identification and the estimation of the storm statistical properties are regarded as the first step in the development of the analytical probabilistic models. The paper provides a recommendation about the definition of the storm inter-event time to be used in conjunction with the analytical probabilistic approach.

Keywords: hydrology, rainfall storm, storm inter-event time, New Zealand, stormwater management

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Authors: Rudan Xue, Annika Moscati, Rehel Zeleke Kebede, Peter Johansson

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Successful buildings’ simulation and analysis inevitably require information exchange between multiple building information modeling (BIM) software. The BIM infor-mation exchange based on IFC is widely used. However, Industry Foundation Classifi-cation (IFC) files are not always reliable and information can get lost when using dif-ferent software for modeling and simulations. In this research, interviews with lighting simulation experts and a case study provided by a company producing lighting devices have been the research methods used to identify the necessary steps and data for suc-cessful information exchange between lighting simulation tools and authoring design tools. Model creation, information exchange, and model simulation have been identi-fied as key aspects for the success of information exchange. The paper concludes with recommendations for improved information exchange and more reliable simulations that take all the needed parameters into consideration.

Keywords: BIM, data exchange, interoperability issues, lighting simulations

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Authors: Ezra Yehuwalashet, Alireza Malehmir

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Blötberget mining area in central Sweden, part of the Bergslagen mineral district, is well known for its various type of mineralization particularly iron-oxide deposits since the 1600. To shed lights on the knowledge of the host rock structures, depth extent and tonnage of the mineral deposits and support deep mineral exploration potential in the study area, new ground gravity and existing aeromagnetic data (from the Geological Survey of Sweden) were used for interpretations and modelling. A major boundary separating a gravity low from a gravity high in the southern part of the study area is noticeable and likely representing a fault boundary separating two different lithological units. Gravity data and modeling offers a possible new target area in the southeast of the known mineralization while suggesting an excess high-density region down to 800 m depth.

Keywords: gravity, magnetics, ore deposit, geophysics

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Authors: Donatello Cardone

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Bilinear hysteresis models are usually used to describe the cyclic behavior of high damping rubber bearings. However, they neglect a number of phenomena (such as the interaction between axial load and shear force, buckling and post-buckling behavior, cavitation, scragging effects, etc.) that can significantly influence the dynamic behavior of such isolation devices. In this work, an advanced hysteresis model is examined and properly calibrated using consolidated procedures. Results of preliminary numerical analyses, performed in OpenSees, are shown and compared with the results of experimental tests on high damping rubber bearings and simulation analyses using alternative nonlinear models. The findings of this study can provide an useful tool for the accurate evaluation of the seismic response of structures with rubber-based isolation systems.

Keywords: seismic isolation, high damping rubber bearings, numerical modeling, axial-shear force interaction

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Authors: S. A. Naeini, A. Khalili

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Nowadays, tunnels with different applications are developed, and most of them are related to subway tunnels. The excavation of shallow tunnels that pass under municipal utilities is very important, and the surface settlement control is an important factor in the design. The study sought to analyze the settlement and also to find an appropriate model in order to predict the behavior of the tunnel in Tehran subway line-3. The displacement in these sections is also determined by using numerical analyses and numerical modeling. In addition, the Adaptive Neuro-Fuzzy Inference System (ANFIS) method is utilized by Hybrid training algorithm. The database pertinent to the optimum network was obtained from 46 subway tunnels in Iran and Turkey which have been constructed by the new Austrian tunneling method (NATM) with similar parameters based on type of their soil. The surface settlement was measured, and the acquired results were compared to the predicted values. The results disclosed that computing intelligence is a good substitute for numerical modeling.

Keywords: settlement, Subway Line, FLAC3D, ANFIS Method

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Authors: Lucian Capitanu, Virgil Florescu

Abstract:

Often for the laboratory studies, modeling of specific tribological processes raises special problems. One such problem is the modeling of some temperatures and extremely high contact pressures, allowing modeling of temperatures and pressures at which the injection or extrusion processing of thermoplastic materials takes place. Tribological problems occur mainly in thermoplastics materials reinforced with glass fibers. They produce an advanced wear to the barrels and screws of processing machines, in short time. Obtaining temperatures around 210 °C and higher, as well as pressures around 100 MPa is very difficult in the laboratory. This paper reports a simple and convenient solution to get these conditions, using friction sliding couples with linear contact, cylindrical liner plastic filled with glass fibers on plate steel samples, polished and super-finished. C120 steel, which is a steel for moulds and Rp3 steel, high speed steel for tools, were used. Obtaining the pressure was achieved by continuous request of the liner in rotational movement up to its elasticity limits, when the dry friction coefficient reaches or exceeds the hardness value of 0.5 HB. By dissipation of the power lost by friction on flat steel sample, are reached contact temperatures at the metal surface that reach and exceed 230 °C, being placed in the range temperature values of the injection. Contact pressures (in load and materials conditions used) ranging from 16.3-36.4 MPa were obtained depending on the plastic material used and the glass fibers content.

Keywords: plastics with glass fibers, dry friction, linear contact, contact temperature, contact pressure, experimental simulation

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Authors: Vrushali Guhe, Shailza Singh

Abstract:

Cutaneous leishmaniasis is neglected tropical disease present worldwide caused by the protozoan parasite Leishmania major, the therapeutic armamentarium for leishmaniasis are showing several limitations as drugs are showing toxic effects with increasing resistance by a parasite. Thus identification of novel therapeutic targets is of paramount importance. Previous studies have shown that autophagy, a cellular process, can either facilitate infection or aid in the elimination of the parasite, depending on the specific parasite species and host background in leishmaniasis. In the present study, our objective was to target the essential autophagy protein ATG8, which plays a crucial role in the survival, infection dynamics, and differentiation of the Leishmania parasite. ATG8 in Leishmania major and its homologue, LC3, in Homo sapiens, act as autophagic markers. Present study manifested the crucial role of ATG8 protein as a potential target for combating Leishmania major infection. Through bioinformatics analysis, we identified non-conserved motifs within the ATG8 protein of Leishmania major, which are not present in LC3 of Homo sapiens. Against these two non-conserved motifs, we generated a peptide library of 60 peptides on the basis of physicochemical properties. These peptides underwent a filtering process based on various parameters, including feasibility of synthesis and purification, compatibility with Selective Reaction Monitoring (SRM)/Multiple reaction monitoring (MRM), hydrophobicity, hydropathy index, average molecular weight (Mw average), monoisotopic molecular weight (Mw monoisotopic), theoretical isoelectric point (pI), and half-life. Further filtering criterion shortlisted three peptides by using molecular docking and molecular dynamics simulations. The direct interaction between ATG8 and the shortlisted peptides was confirmed through Surface Plasmon Resonance (SPR) experiments. Notably, these peptides exhibited the remarkable ability to penetrate the parasite membrane and exert profound effects on Leishmania major. The treatment with these peptides significantly impacted parasite survival, leading to alterations in the cell cycle and morphology. Furthermore, the peptides were found to modulate autophagosome formation, particularly under starved conditions, suggesting their involvement in disrupting the regulation of autophagy within Leishmania major. In vitro, studies demonstrated that the selected peptides effectively reduced the parasite load within infected host cells. Encouragingly, these findings were corroborated by in vivo experiments, which showed a reduction in parasite burden upon peptide administration. Additionally, the peptides were observed to affect the levels of LC3II within host cells. In conclusion, our findings highlight the efficacy of these novel peptides in targeting Leishmania major’s ATG8 and disrupting parasite survival. These results provide valuable insights into the development of innovative therapeutic strategies against leishmaniasis via targeting autophagy protein ATG8 of Leishmania major.

Keywords: ATG8, leishmaniasis, surface plasmon resonance, MD simulation, molecular docking, peptide designing, therapeutics

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Authors: Daniel Pinheiro Da Silva Junior, Aline Paes, Daniel De Oliveira, Christiano Lacerda Ghuerren, Marcio Duran

Abstract:

The Courts of Accounts are institutions responsible for overseeing and point out irregularities of Public Administration expenses. They have a high demand for processes to be analyzed, whose decisions must be grounded on severity laws. Despite the existing large amount of processes, there are several cases reporting similar subjects. Thus, previous decisions on already analyzed processes can be a precedent for current processes that refer to similar topics. Identifying similar topics is an open, yet essential task for identifying similarities between several processes. Since the actual amount of topics is considerably large, it is tedious and error-prone to identify topics using a pure manual approach. This paper presents a tool based on Machine Learning and Natural Language Processing to assists in building a labeled dataset. The tool relies on Topic Modelling with Latent Dirichlet Allocation to find the topics underlying a document followed by Jensen Shannon distance metric to generate a probability of similarity between documents pairs. Furthermore, in a case study with a corpus of decisions of the Rio de Janeiro State Court of Accounts, it was noted that data pre-processing plays an essential role in modeling relevant topics. Also, the combination of topic modeling and a calculated distance metric over document represented among generated topics has been proved useful in helping to construct a labeled base of similar and non-similar document pairs.

Keywords: courts of accounts, data labelling, document similarity, topic modeling

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Authors: Bilal Ahmad

Abstract:

Alzheimer’s disease (AD) is one of the most common neurodegenerative illnesses. However, how Gut-microbiota plays a role in the pathogenesis of AD is not well elucidated. The purpose of this literature review is to summarize and understand the current findings that may elucidate the gut microbiota's role in the development of AD. Methods: A literature review of all the relevant papers known to the author was conducted. Relevant articles, abstracts and research papers were collected from well-accepted web sources like PubMed, PMC, and Google Scholar. Results: Recent studies have shown that Gut-microbiota has an important role in the progression of AD via Gut-Microbiota-Brain Axis. The onset of AD supports the ‘Hygiene Hypothesis’, which shows that AD might begin in the Gut, causing dysbiosis, which interferes with the intestinal barrier by releasing pro-inflammatory cytokines and making its way up to the brain via the blood-brain barrier (BBB). Molecular mechanisms lipopolysaccharides and serotonin kynurenine (tryptophan) pathways have a direct association with inflammation, the immune system, neurodegeneration, and AD. Conclusion: The studies helped to analyze the molecular basis of AD, other neurological conditions like depression, autism, and Parkinson's disease and how they are linked to Gut-microbiota. Further, studies to explore the therapeutic effects of probiotics in AD and cognitive enhancement should be warranted to provide significant clinical and practical value.

Keywords: gut-microbiota, Alzheimer’s disease, second brain aging, lipopolysaccharides, short-chain fatty acids

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Authors: Seyed Mehrdad Gholami

Abstract:

Nowadays, using rail transport system (Metro) is increased in most cities of The world, so the need for safe and economical way of building tunnels and subway stations is felt more and more. One of the most commonly used methods for constructing underground structures in urban areas is NATM (New Austrian tunneling method). In this method, there are some key parameters such as excavation steps and cross-sectional area that have a significant effect on the surface settlement. Settlement is a very important control factor related to safe excavation. In this paper, Finite Element Method is used by Abaqus. R6 station of Tehran Metro Line 6 is built by NATM and the construction of that is studied and analyzed. Considering the outcomes obtained from numerical modeling and comparison with the results of the instrumentation and monitoring of field, finally, the excavation step of 1 meter and longitudinal distance of 14 meters between side drifts is suggested to achieve safe tunneling with allowable settlement.

Keywords: excavation step, NATM, numerical modeling, settlement.

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Authors: Christopher Mkirema Maghanga, Maurice Mghendi Mwamburi

Abstract:

Parametric modeling provides a means to deeper understand the properties of materials. Drude, Brendel, Lorentz and OJL incorporated in SCOUT® software are some of the models used to study dielectric films. In our work, we utilized Brendel and Drude models to extract the optical constants from spectroscopic data of fabricated undoped and niobium doped titanium oxide thin films. The individual contributions by the two models were studied to establish how they influence the dielectric function. The effect of dopants on their influences was also analyzed. For the undoped films, results indicate minimal contribution from the Drude term due to the dielectric nature of the films. However as doping levels increase, the rise in the concentration of free electrons favors the use of Drude model. Brendel model was confirmed to work well with dielectric films - the undoped titanium Oxide films in our case.

Keywords: modeling, Brendel model, optical constants, titanium oxide, Drude Model

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