Search results for: genome scale metabolic model

Authors: Arslan Murtaza

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Model Driven Architecture (MDA) is technique presented by OMG (Object Management Group) for software development in which different models are proposed and converted them into code. The main plan is to identify task by using PIM (Platform Independent Model) and transform it into PSM (Platform Specific Model) and then converted into code. In this review paper describes some challenges and issues that are faced in MDA, type and transformation of models (e.g. CIM, PIM and PSM), and evaluation of MDA-based methodologies.

Keywords: OMG, model driven rrchitecture (MDA), computation independent model (CIM), platform independent model (PIM), platform specific model(PSM), MDA-based methodologies

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Authors: Sujing Wang, Song Wang, Jian Zhang, Qiang Xu

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Flaring emissions during abnormal operating conditions such as plant start-ups, shut-downs, and upsets in chemical process industries (CPI) are usually significant. Flare minimization can help to save raw material and energy for CPI plants, and to improve local environmental sustainability. In this paper, a systematic methodology based on plant-wide dynamic simulation is presented for CPI plant flare minimizations under abnormal operating conditions. Since off-specification emission sources are inevitable during abnormal operating conditions, to significantly reduce flaring emission in a CPI plant, they must be either recycled to the upstream process for online reuse, or stored somewhere temporarily for future reprocessing, when the CPI plant manufacturing returns to stable operation. Thus, the off-spec products could be reused instead of being flared. This can be achieved through the identification of viable design and operational strategies during normal and abnormal operations through plant-wide dynamic scheduling, simulation, and optimization. The proposed study includes three stages of simulation works: (i) developing and validating a steady-state model of a CPI plant; (ii) transiting the obtained steady-state plant model to the dynamic modeling environment; and refining and validating the plant dynamic model; and (iii) developing flare minimization strategies for abnormal operating conditions of a CPI plant via a validated plant-wide dynamic model. This cost-effective methodology has two main merits: (i) employing large-scale dynamic modeling and simulations for industrial flare minimization, which involves various unit models for modeling hundreds of CPI plant facilities; (ii) dealing with critical abnormal operating conditions of CPI plants such as plant start-up and shut-down. Two virtual case studies on flare minimizations for start-up operation (over 50% of emission savings) and shut-down operation (over 70% of emission savings) of an ethylene plant have been employed to demonstrate the efficacy of the proposed study.

Keywords: flare minimization, large-scale modeling and simulation, plant shut-down, plant start-up

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Authors: Rituparna Nath, Shawn J. Marshall

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Glaciers are one of the main sensitive climatic indicators, as they respond strongly to small climatic shifts. We develop a flow line model of glacier dynamics to simulate the past and future extent of glaciers in the Canadian Rocky Mountains, with the aim of coupling this model within larger scale regional climate models of glacier response to climate change. This paper will focus on glacier-climate modeling and reconstructions of glacier volume from the Little Ice Age (LIA) to present for Athabasca Glacier, Alberta, Canada. Glacier thickness, volume and mass change will be constructed using flow line modelling and examination of different climate scenarios that are able to give good reconstructions of LIA ice extent. With the availability of SPOT 5 imagery, Digital elevation models and GIS Arc Hydro tool, ice catchment properties-glacier width and LIA moraines have been extracted using automated procedures. Simulation of glacier mass change will inform estimates of meltwater run off over the historical period and model calibration from the LIA reconstruction will aid in future projections of the effects of climate change on glacier recession. Furthermore, the model developed will be effective for further future studies with ensembles of glaciers.

Keywords: flow line modeling, Athabasca Glacier, glacier mass balance, Remote Sensing, Arc hydro tool, little ice age

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Authors: Abdul-Hakeem Olatunji Abiola, A. E. Adeniran, A. O. Ajimo, A. B. Lamilisa

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Introduction: Conventional wastewater treatment technology has been found to fail in developing countries because they are expensive to construct, operate and maintain. Constructed wetlands are nowadays considered as a low-cost alternative for effective wastewater treatment, especially where suitable land can be available. This study aims to evaluate the performance of the constructed wetland vegetated with water hyacinth (Eichhornia crassipes) plant for the treatment of wastewater. Methodology: The sub-surface flow wetland used for this study was an experimental scale constructed wetland consisting of four beds A, B, C, and D. Beds A, B, and D were vegetated while bed C which was used as a control was non-vegetated. This present study presents the results from bed B vegetated with water hyacinth (Eichhornia crassipes) and control bed C which was non-vegetated. The influent of the experimental scale wetland has been pre-treated with sedimentation, screening and anaerobic chamber before feeding into the experimental scale wetland. Results: pH and conductivity level were more reduced, colour of effluent was more improved, nitrate, iron, phosphate, and chromium were more removed, and dissolved oxygen was more improved in the water hyacinth bed than the control bed. While manganese, nickel, cyanuric acid, and copper were more removed from the control bed than the water hyacinth bed. Conclusion: The performance of the experimental scale constructed wetland bed planted with water hyacinth (Eichhornia crassipes) is better than that of the control bed. It is therefore recommended that plain bed without any plant should not be encouraged.

Keywords: constructed experimental scale wetland, domestic sewage, treatment, water hyacinth

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Authors: Chih-Hua Chang

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This study uses a three-dimensional (3D) fully nonlinear model to simulate the wave generation problem caused by the movement of the seabed. The numerical model is first simplified into two dimensions and then compared with the existing two-dimensional (2D) experimental data and the 2D numerical results of other shallow-water wave models. Results show that this model is different from the earlier shallow-water wave models, with the phase being closer to the experimental results of wave propagation. The results of this study are also compared with those of the 3D experimental results of other researchers. Satisfactory results can be obtained in both the waveform and the flow field. This study assesses the application of the model to simulate the wave caused by the circular (radius r0) terrain rising or falling (moving distance bm). The influence of wave-making parameters r0 and bm are discussed. This study determines that small-range (e.g., r0 = 2, normalized by the static water depth), rising, or sinking terrain will produce significant wave groups in the far field. For large-scale moving terrain (e.g., r0 = 10), uplift and deformation will potentially generate the leading solitary-like waves in the far field.

Keywords: seismic wave, wave generation, far-field waves, seabed deformation

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Authors: Prashant Motwani, Arghadeep Laskar

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The transfer of prestress force from prestressing strands to the surrounding concrete is dependent on the bond between the two materials. It is essential to understand the actual bond stress distribution along the transfer length to determine the transfer zone in pre-tensioned concrete. A 3-D nonlinear finite element model has been developed to simulate the transfer of prestress force from steel to concrete in pre-tensioned bridge girders through thermal strain technique using commercially available package ABAQUS. Full-scale bridge girder has been analyzed with thermal strain approach where the damage plasticity constitutive model has been used to model concrete. Parameters such as concrete strain, effective prestress, upward camber and longitudinal stress have been compared with analytical results. The discrepancy between numerical and analytical values was within 20%. The paper also presents a convergence study on mesh density and aspect ratio of the elements to perform the finite element study.

Keywords: aspect ratio, bridge girder, centre of gravity of strand, mesh density, finite element model, pretensioned bridge girder

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Authors: Dian Mayasari, Yosi Bayu Murti, Sylvia Utami Tunjung Pratiwi, Sudarsono

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Melastoma malabathricum L. is an Indo-Pacific herb that has been traditionally used to treat several ailments such as wounds, dysentery, diarrhea, toothache, and diabetes. This plant is common across tropical Indo-Pacific archipelagos and is tolerant of a range of soils, from low-lying areas subject to saltwater inundation to the salt-free conditions of mountain slopes. How the soil and environmental variation influences secondary metabolite production in the herb, and an understanding of the plant’s utility as traditional medicine, remain largely unknown and unexplored. The objective of this study is to evaluate the variability of the metabolic profiles of M. malabathricum L. across its geographic distribution. By employing high-performance liquid chromatography-diode array detector (HPLC-DAD), a highly established, simple, sensitive, and reliable method was employed for establishing the chemical fingerprints of 72 samples of M. malabathricum L. leaves from various geographical locations in Indonesia. Specimens collected from six terrestrial and archipelago regions of Indonesia were analyzed by HPLC to generate chromatogram peak profiles that could be compared across each region. Data corresponding to the common peak areas of HPLC chromatographic fingerprint were analyzed by hierarchical component analysis (HCA) and principal component analysis (PCA) to extract information on the most significant variables contributing to characterization and classification of analyzed samples data. Principal component values were identified as PC1 and PC2 with 41.14% and 19.32%, respectively. Based on variety and origin, the high-performance liquid chromatography method validated the chemical fingerprint results used to screen the in vitro antioxidant activity of M. malabathricum L. The result shows that the developed method has potential values for the quality of similar M. malabathrium L. samples. These findings provide a pathway for the development and utilization of references for the identification of M. malabathricum L. Our results indicate the importance of considering geographic distribution during field-collection efforts as they demonstrate regional metabolic variation in secondary metabolites of M. malabathricum L., as illustrated by HPLC chromatogram peaks and their antioxidant activities. The results also confirm the utility of this simple approach to a rapid evaluation of metabolic variation between plants and their potential ethnobotanical properties, potentially due to the environments from whence they were collected. This information will facilitate the optimization of growth conditions to suit particular medicinal qualities.

Keywords: fingerprint, high performance liquid chromatography, Melastoma malabathricum l., metabolic profiles, principal component analysis

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Authors: Stephane Laussac, Jacques Piazzola, Gilles Tedeschi

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Estimation of the impact of atmospheric aerosols on the climate evolution is an important scientific challenge. One of a major source of particles is constituted by the oceans through the generation of sea-spray aerosols. In coastal areas, marine aerosols can affect air quality through their ability to interact chemically and physically with other aerosol species and gases. The integration of accurate sea-spray emission terms in modeling studies is then required. However, it was found that sea-spray concentrations are not represented with the necessary accuracy in some situations, more particularly at short fetch. In this study, the WRF-Chem model was implemented on a North-Western Mediterranean coastal region. WRF-Chem is the Weather Research and Forecasting (WRF) model online-coupled with chemistry for investigation of regional-scale air quality which simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. One of the objectives was to test the ability of the WRF-Chem model to represent the fine details of the coastal geography to provide accurate predictions of sea spray evolution for different fetches and the anthropogenic aerosols. To assess the performance of the model, a comparison between the model predictions using a local emission inventory and the physicochemical analysis of aerosol concentrations measured for different wind direction on the island of Porquerolles located 10 km south of the French Riviera is proposed.

Keywords: sea-spray aerosols, coastal areas, sea-spray concentrations, short fetch, WRF-Chem model

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Authors: Cuong V Nguyen, Ralph Horne, John Fien, France Cheong

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Social vulnerability to climate change is increasingly being acknowledged, and proposals to measure and manage it are emerging. Building upon this work, this paper proposes an approach to social vulnerability assessment using a new mechanism to aggregate and account for causal relationships among components of a Social Vulnerability Index (SVI). To operationalize this index, the authors propose a means to develop an appropriate primary dataset, through application of a specifically-designed household survey questionnaire. The data collection and analysis, including calibration and calculation of the SVI is demonstrated through application in case study city in central coastal Vietnam. The calculation of SVI at the fine-grained local neighbourhood scale provides high resolution in vulnerability assessment, and also obviates the need for secondary data, which may be unavailable or problematic, particularly at the local scale in developing countries. The SVI household survey is underpinned by the results of a Delphi survey, an in-depth interview and focus group discussions with local environmental professionals and community members. The research reveals inherent limitations of existing SVIs but also indicates the potential for their use in assessing social vulnerability and making decisions associated with responding to climate change at the local scale.

Keywords: climate change, local scale, social vulnerability, social vulnerability index

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Authors: Mohamed Rabhi, Kouider Halim Benrahou

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The rheological properties of the carbonyl-methylcellulose (CMC), of different concentrations (25000, 50000, 60000, 80000 and 100000 ppm) and different temperatures were studied. We found that the rheological behavior of all CMC solutions presents a pseudo-plastic behavior, it follows the model of Ostwald-de Waele. The objective of this work is the modeling of flow by the CMC Cross model. The Cross model gives us the variation of the viscosity according to the shear rate. This model allowed us to adjust more clearly the rheological characteristics of CMC solutions. A comparison between the Cross model and the model of Ostwald was made. Cross the model fitting parameters were determined by a numerical simulation to make an approach between the experimental curve and those given by the two models. Our study has shown that the model of Cross, describes well the flow of "CMC" for low concentrations.

Keywords: CMC, rheological modeling, Ostwald model, cross model, viscosity

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Authors: Mostafa Sefidgar, Sohrab Zendehboudi, Hossein Bazmara, Madjid Soltani

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Based on findings from clinical applications, most drug treatments fail to eliminate malignant tumors completely even though drug delivery through systemic administration may inhibit their growth. Therefore, better understanding of tumor formation is crucial in developing more effective therapeutics. For this purpose, nowadays, solid tumor modeling and simulation results are used to predict how therapeutic drugs are transported to tumor cells by blood flow through capillaries and tissues. A solid tumor is investigated as a porous media for fluid flow simulation. Most of the studies use Darcy model for porous media. In Darcy model, the fluid friction is neglected and a few simplified assumptions are implemented. In this study, the effect of these assumptions is studied by considering Brinkman model. A multi scale mathematical method which calculates fluid flow to a solid tumor is used in this study to investigate how neglecting fluid friction affects the solid tumor simulation. In this work, the mathematical model in our previous studies is developed by considering two model of momentum equation for porous media: Darcy and Brinkman. The mathematical method involves processes such as fluid flow through solid tumor as porous media, extravasation of blood flow from vessels, blood flow through vessels and solute diffusion, convective transport in extracellular matrix. The sprouting angiogenesis model is used for generating capillary network and then fluid flow governing equations are implemented to calculate blood flow through the tumor-induced capillary network. Finally, the two models of porous media are used for modeling fluid flow in normal and tumor tissues in three different shapes of tumors. Simulations of interstitial fluid transport in a solid tumor demonstrate that the simplifications used in Darcy model affect the interstitial velocity and Brinkman model predicts a lower value for interstitial velocity than the values that Darcy model does.

Keywords: solid tumor, porous media, Darcy model, Brinkman model, drug delivery

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Authors: Vimuckthi Charika Wickramaratne, Prasansha Kumari

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Sport tourism refers to travel which involves either observing or participating in a sporting event apart from their usual environment. Sport tourism in a fast growing sector of the Sri Lankan travelling industry since Cricket are more popular sport game in the country. This study intends to analyze the impact of these popular sport events for creating and developing small scale business in the country. Primary data gathered from 100 small entrepreneurs around Keththarama Cricket Ground in Sri Lanka. Collected data analyzed using descriptive research methods. The study revealed that local and international visitors for cricket games had impacted on small scale business activities such as retail, handicraft, transport, vehicle parking, small restaurant, hotels, foods and beverage industry. In addition, it was identified that these type of small business are sessional income generating activities for the short period.

Keywords: sport tourism, small scale business, cricket, entrepreneurs

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Authors: Alex Fedoseyev

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This study explores Generalized Hydrodynamic Equations (GHE) for the simulation of turbulent flows. The GHE was derived from the Generalized Boltzmann Equation (GBE) by Alexeev (1994). GBE was obtained by first principles from the chain of Bogolubov kinetic equations and considered particles of finite dimensions, Alexeev (1994). The GHE has new terms, temporal and spatial fluctuations compared to the Navier-Stokes equations (NSE). These new terms have a timescale multiplier τ, and the GHE becomes the NSE when τ is zero. The nondimensional τ is a product of the Reynolds number and the squared length scale ratio, τ=Re*(l/L)², where l is the apparent Kolmogorov length scale, and L is a hydrodynamic length scale. The turbulence phenomenon is not well understood and is not described by NSE. An additional one or two equations are required for the turbulence model, which may have to be tuned for specific problems. We show that, in the case of the GHE, no additional turbulence model is needed, and the turbulent velocity profile is obtained from the GHE. The 2D turbulent channel and circular pipe flows were investigated using a numerical solution of the GHE for several cases. The solutions are compared with the experimental data in the circular pipes and 2D channels by Nicuradse (1932, Prandtl Lab), Hussain and Reynolds (1975), Wei and Willmarth (1989), Van Doorne (2007), theory by Wosnik, Castillo and George (2000), and the relevant experiments on Superpipe setup at Princeton, data by Zagarola (1996) and Zagarola and Smits (1998), the Reynolds number is from Re=7200 to Re=960000. The numerical solution data compared well with the experimental data, as well as with the approximate analytical solution for turbulent flow in channel Fedoseyev (2023). The obtained results confirm that the Alexeev generalized hydrodynamic theory (GHE) is in good agreement with the experiments for turbulent flows. The proposed approach is limited to 2D and 3D axisymmetric channel geometries. Further work will extend this approach by including channels with square and rectangular cross-sections.

Keywords: comparison with experimental data. generalized hydrodynamic equations, numerical solution, turbulent boundary layer, turbulent flow in channel

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Authors: Viet-Hung Truong, Seung-Eock Kim

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Rain–wind induced vibration of inclined cable is a special aerodynamic phenomenon because it is easily influenced by many factors, especially the distribution of rivulet and wind velocity. This paper proposes a new 3D model of inclined cable, based on single degree-of-freedom model. Aerodynamic forces are firstly established and verified with the existing results from a 2D model. The 3D model of inclined cable is developed. The 3D model is then applied to assess the effects of wind velocity distribution and the continuity of rivulets on the cable. Finally, an inclined cable model with small sag is investigated.

Keywords: 3D model, rain - wind induced vibration, rivulet, analytical model

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Authors: Sarah Triller, Ferdi Schüth

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The challenges encountered in upscaling the mechanochemical synthesis of high surface area α-alumina are investigated in this study. After lab-scale experiments in shaker mills and planetary ball mills, the optimization of reaction parameters of the conversion in the smallest vessel of a scalable mill, named Simoloyer, was developed. Furthermore, the future perspectives by scaling up the conversion in several steps are described. Since abrasion from the steel equipment can be problematic, the process was transferred to a ceramically lined mill, which solved the contamination problem. The recovered alpha-alumina shows a high specific surface area in all investigated scales.

Keywords: mechanochemistry, scale-up, ball milling, ceramic lining

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Authors: Mirnawati, G. Ciptaan, Ferawati

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This study aims to improve the quality of the cassava peel-leaf mixture (CPLM) through fermentation with Rhizopus oligosporusas poultry ration. This research is an experimental study using a completely randomized design (CRD) with four treatments and five replications. The treatments were cassava peel-leaf mixture (CPLM) fermented with Rhizopus oligosporus. The treatments were a combination of cassava peel and leaves with the ratio of; A (9:1), B (8:2), C (7:3), and D (6:4). The observed variables were protease enzyme activity, crude protein, crude fiber, nitrogen retention, digestibility of crude fiber, and metabolic energy. The results of the diversity analysis showed that there was a very significant (p < 0.01) effect on protease activity, crude protein, crude fiber, nitrogen retention, digestibility of crude fiber, and energy metabolism of fermented CPLM. Based on the results of the study, it can be concluded that CPLM (6:4) fermented with Rhizopus oligosporus gave the best results seen from protease activity 7,25 U/ml, 21.23% crude protein, 19.80% crude fiber, 59.65% nitrogen retention, 62.99% crude fiber digestibility and metabolic energy 2671 Kcal/kg.

Keywords: quality, Casava peel-leaf mixture, fermentation, Rhizopus oligosporus

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Authors: Adnan A. Kadi, Nasser S. Al-Shakliah, Haitham Al-Rabiah

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Zorifertinib is a novel, potent, oral, a small molecule used to treat non-small cell lung cancer (NSCLC). zorifertinib is an Epidermal Growth Factor Receptor (EGFR) inhibitor and has good blood–brain barrier permeability for (NSCLC) patients with EGFR mutations. zorifertinibis currently at phase II/III clinical trials. The current research reports the characterization and identification of in vitro, in vivo and reactive intermediates of zorifertinib. Prediction of susceptible sites of metabolism and reactivity pathways (cyanide and GSH) of zorifertinib were performed by the Xenosite web predictor tool. In-vitro metabolites of zorifertinib were performed by incubation with rat liver microsomes (RLMs) and isolated perfused rat liver hepatocytes. Extraction of zorifertinib and it's in vitro metabolites from the incubation mixtures were done by protein precipitation. In vivo metabolism was done by giving a single oral dose of zorifertinib(10 mg/Kg) to Sprague Dawely rats in metabolic cages by using oral gavage. Urine was gathered and filtered at specific time intervals (0, 6, 12, 18, 24, 48, 72,96and 120 hr) from zorifertinib dosing. A similar volume of ACN was added to each collected urine sample. Both layers (organic and aqueous) were injected into liquid chromatography ion trap mass spectrometry(LC-IT-MS) to detect vivozorifertinib metabolites. N-methyl piperizine ring and quinazoline group of zorifertinib undergoe metabolism forming iminium and electro deficient conjugated system respectively, which are very reactive toward nucleophilic macromolecules. Incubation of zorifertinib with RLMs in the presence of 1.0 mM KCN and 1.0 Mm glutathione were made to check reactive metabolites as it is often responsible for toxicities associated with this drug. For in vitro metabolites there were nine in vitro phase I metabolites, four in vitro phase II metabolites, eleven reactive metabolites(three cyano adducts, five GSH conjugates metabolites, and three methoxy metabolites of zorifertinib were detected by LC-IT-MS. For in vivo metabolites, there were eight in vivo phase I, tenin vivo phase II metabolitesofzorifertinib were detected by LC-IT-MS. In vitro and in vivo phase I metabolic pathways wereN- demthylation, O-demethylation, hydroxylation, reduction, defluorination, and dechlorination. In vivo phase II metabolic reaction was direct conjugation of zorifertinib with glucuronic acid and sulphate.

Keywords: in vivo metabolites, in vitro metabolites, cyano adducts, GSH conjugate

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Authors: Mansoureh Karimollahi, Mehriar Adrmohammadi, Mohsen Mohammadi

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Introduction: Patient satisfaction with nursing care is considered as an important indicator of the quality and effectiveness of the health care system, and improving the quality of care is not possible without paying attention to the opinions and expectations of patients. Considering that the scales for assessing satisfaction with nursing care in our country are not comprehensive and measure very few areas, therefore, in this study, psychometrically, the Persian version of the Newcastle Nursing Care Satisfaction Scale was used in patients hospitalized in the wards. Internal medicine and general surgery were discussed. Methods: This cross-sectional study was conducted on 200 patients admitted to the surgery and internal departments of hospitals affiliated to Ardabil University of Medical Sciences. The Newcastle nursing care satisfaction scale was used for the first time in Iran in comparison with the good nursing care scale from the patients' point of view to evaluate the criterion validity. The Newcastle nursing care satisfaction scale was used after translation, validity, and reliability. Results: The level of satisfaction of patients and the experience of patients with nursing care was at a favorable level, respectively, with an average of 111.8 ± 14.2 and 69.07 ± 14.8. Total CVI was estimated at 0.96 for the experience section, 0.95 for the satisfaction section, and 0.96 for the whole scale. The index (CVR) was also 0.95 for the experience section, 0.95 for the satisfaction section, and 0.95 for the whole scale. Criterion validity was also estimated using 0.725 correlation. The validity of the construct was also confirmed using the goodness of fit index (X2=1932/05, p=0.013, KMO=0.913). Convergent validity was estimated at 0.99 in the experience subscale and 0.98 in the satisfaction subscale. . The overall reliability in the experience subscale and satisfaction subscale was 94%, 92%, and 98%, respectively, which indicated the acceptable reliability of the questionnaire. Conclusion: The Persian version of the Newcastle nursing care satisfaction scale as a comprehensive tool that can be easily completed by patients and is easy to interpret, has good validity and reliability and can be used in patient care centers, in departments Surgery, and internal medicine are recommended.

Keywords: psychometrics, Newcastle nursing care satisfaction scale, nursing care satisfaction, general surgery department

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Authors: Sandra Smieszek, Jonathan Haines

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Introduction: Numerous research efforts have focused on searching for ‘longevity genes’. However, attempting to decipher the genetic component of the longevous phenotype have resulted in limited success and the mechanisms governing longevity remain to be explained. We conducted a genome-wide homozygosity analysis (GWHA) of the founder population of the Amish community in central Ohio. While genome-wide association studies using unrelated individuals have revealed many interesting longevity associated variants, these variants are typically of small effect and cannot explain the observed patterns of heritability for this complex trait. The Amish provide a large cohort of extended kinships allowing for in depth analysis via family-based approach excellent population due to its. Heritability of longevity increases with age with significant genetic contribution being seen in individuals living beyond 60 years of age. In our present analysis we show that the heritability of longevity is estimated to be increasing with age particularly on the paternal side. Methods: The present analysis integrated both phenotypic and genotypic data and led to the discovery of a series of variants, distinct for stratified populations across ages and distinct for paternal and maternal cohorts. Specifically 5437 subjects were analyzed and a subset of 893 successfully genotyped individuals was used to assess CHIP heritability. We have conducted the homozygosity analysis to examine if homozygosity is associated with increased risk of living beyond 90. We analyzed AMISH cohort genotyped for 614,957 SNPs. Results: We delineated 10 significant regions of homozygosity (ROH) specific for the age group of interest (>90). Of particular interest was ROH on chromosome 13, P < 0.0001. The lead SNPs rs7318486 and rs9645914 point to COL4A2 and our lead SNP. COL25A1 encodes one of the six subunits of type IV collagen, the C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. COL4A2 mutations have been reported with a broader spectrum of cerebrovascular, renal, ophthalmological, cardiac, and muscular abnormalities. The second region of interest points to IRS2. Furthermore we built a classifier using the obtained SNPs from the significant ROH region with 0.945 AUC giving ability to discriminate between those living beyond to 90 years of age and beyond. Conclusion: In conclusion our results suggest that a history of longevity does indeed contribute to increasing the odds of individual longevity. Preliminary results are consistent with conjecture that heritability of longevity is substantial when we start looking at oldest fifth and smaller percentiles of survival specifically in males. We will validate all the candidate variants in independent cohorts of centenarians, to test whether they are robustly associated with human longevity. The identified regions of interest via ROH analysis could be of profound importance for the understanding of genetic underpinnings of longevity.

Keywords: regions of homozygosity, longevity, SNP, Amish

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Authors: Ferry Kurniawan

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In this paper, we nowcast quarterly output growth in Indonesia by exploiting higher frequency data (monthly indicators) using a mixed-frequency factor model and exploiting both quarterly and monthly data. Nowcasting quarterly GDP in Indonesia is particularly relevant for the central bank of Indonesia which set the policy rate in the monthly Board of Governors Meeting; whereby one of the important step is the assessment of the current state of the economy. Thus, having an accurate and up-to-date quarterly GDP nowcast every time new monthly information becomes available would clearly be of interest for central bank of Indonesia, for example, as the initial assessment of the current state of the economy -including nowcast- will be used as input for longer term forecast. We consider a small scale mixed-frequency factor model to produce nowcasts. In particular, we specify variables as year-on-year growth rates thus the relation between quarterly and monthly data is expressed in year-on-year growth rates. To assess the performance of the model, we compare the nowcasts with two other approaches: autoregressive model –which is often difficult when forecasting output growth- and Mixed Data Sampling (MIDAS) regression. In particular, both mixed frequency factor model and MIDAS nowcasts are produced by exploiting the same set of monthly indicators. Hence, we compare the nowcasts performance of the two approaches directly. To preview the results, we find that by exploiting monthly indicators using mixed-frequency factor model and MIDAS regression we improve the nowcast accuracy over a benchmark simple autoregressive model that uses only quarterly frequency data. However, it is not clear whether the MIDAS or mixed-frequency factor model is better. Neither set of nowcasts encompasses the other; suggesting that both nowcasts are valuable in nowcasting GDP but neither is sufficient. By combining the two individual nowcasts, we find that the nowcast combination not only increases the accuracy - relative to individual nowcasts- but also lowers the risk of the worst performance of the individual nowcasts.

Keywords: nowcasting, mixed-frequency data, factor model, nowcasts combination

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Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

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Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular/nanoscale models is demonstrated.

Keywords: cement composite, mechanical properties, molecular dynamics, plasticizer additives

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Authors: Shittu Ahmed Tajudeen

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This study examines student-teachers’ attitude and intention towards cell-phone use for learning. The study involves one hundred and ninety (190) trainee teachers in one of the Institutes of Education in Nigeria. The data of the study was collected through a questionnaire on a rating of seven point likert-type Scale. The data collected was used to test the hypothesized model of the study using Structural Equation Modeling approach. The finding of the study revealed that Perceived Usefulness (PU), Perceived Ease of Use (PEU), Subjective Norm (SN) and Attitude significantly influence students’ intention towards adoption of cell-phone for learning. The study showed that perceived ease of use stands to be the strongest predictor of cell-phone use. The model of the study exhibits a good-fit with the data and provides an explanation on student- teachers’ attitude and intention towards cell-phone for learning.

Keywords: cell-phone, adoption, structural equation modeling, technology acceptance model

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Authors: Nurulhikma Md Isa, Intan Elya Suka, Nur Farhana Roslan, Chew Bee Lynn

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The evolutionarily conserved N-end rule pathway marks proteins for degradation by the Ubiquitin Proteosome System (UPS) based on the nature of their N-terminal residue. Proteins with a destabilizing N-terminal residue undergo a series of condition-dependent N-terminal modifications, resulting in their ubiquitination and degradation. Intensive research has been carried out in Arabidopsis previously. The group VII Ethylene Response Factor (ERFs) transcription factors are the first N-end rule pathway substrates found in Arabidopsis and their role in regulating oxygen sensing. ERFs also function as central hubs for the perception of gaseous signals in plants and control different plant developmental including germination, stomatal aperture, hypocotyl elongation and stress responses. However, nothing is known about the role of this pathway during fruit development and ripening aspect. The plant model system Arabidopsis cannot represent fleshy fruit model system therefore tomato is the best model plant to study. PROTEOLYSIS6 (PRT6) is an E3 ubiquitin ligase of the N-end rule pathway. Two homologs of PRT6 sequences have been identified in tomato genome database using the PRT6 protein sequence from model plant Arabidopsis thaliana. Homology search against Ensemble Plant database (tomato) showed Solyc09g010830.2 is the best hit with highest score of 1143, e-value of 0.0 and 61.3% identity compare to the second hit Solyc10g084760.1. Further homology search was done using NCBI Blast database to validate the data. The result showed best gene hit was XP_010325853.1 of uncharacterized protein LOC101255129 (Solanum lycopersicum) with highest score of 1601, e-value 0.0 and 48% identity. Both Solyc09g010830.2 and uncharacterized protein LOC101255129 were genes located at chromosome 9. Further validation was carried out using BLASTP program between these two sequences (Solyc09g010830.2 and uncharacterized protein LOC101255129) to investigate whether they were the same proteins represent PRT6 in tomato. Results showed that both proteins have 100 % identity, indicates that they were the same gene represents PRT6 in tomato. In addition, we used two different RNAi constructs that were driven under 35S and Polygalacturonase (PG) promoters to study the function of PRT6 during tomato developmental stages and ripening processes.

Keywords: ERFs, PRT6, tomato, ubiquitin

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Authors: Go Bong Choi, Shin Je Lee, Sung Jin Yoo, Gibaek Lee, Jong Min Lee

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In South Korea, it is difficult to obtain data for statistical pipe assessment. In this paper, to address these issues, we find that various statistical model presented before is how data mixed with noise and are whether apply in South Korea. Three major type of model is studied and if data is presented in the paper, we add noise to data, which affects how model response changes. Moreover, we generate data from model in paper and analyse effect of noise. From this we can find robustness and applicability in Korea of each model.

Keywords: proportional hazard model, survival model, water main deterioration, ecological sciences

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Authors: Ruxandra Barbulescu, Daniel Ioan, Gabriela Ciuprina

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The saltatory conduction is the way the action potential is transmitted along a myelinated axon. The potential diffuses along the myelinated compartments and it is regenerated in the Ranvier nodes due to the ion channels allowing the flow across the membrane. For an efficient simulation of populations of neurons, it is important to use reduced order models both for myelinated compartments and for Ranvier nodes and to have control over their accuracy and inner parameters. The paper presents a reduced order model of this neural system which allows an efficient simulation method for the saltatory conduction in myelinated axons. This model is obtained by concatenating reduced order linear models of 1D myelinated compartments and nonlinear 0D models of Ranvier nodes. The models for the myelinated compartments are selected from a series of spatially distributed models developed and hierarchized according to their modeling errors. The extracted model described by a nonlinear PDE of hyperbolic type is able to reproduce the saltatory conduction with acceptable accuracy and takes into account the finite propagation speed of potential. Finally, this model is again reduced in order to make it suitable for the inclusion in large-scale neural circuits.

Keywords: action potential, myelinated segments, nonlinear models, Ranvier nodes, reduced order models, saltatory conduction

Procedia PDF Downloads 140

Authors: S. Fahiminiya, J. Nadaf, F. Rauch, L. Jerome-Majewska, J. Majewski

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Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation.

Keywords: whole exome sequencing data, non-coding variants, copy number variations, rare diseases

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Authors: H. Zou, B. Wang

Abstract:

Thermal distortion of the machine tool plays a critical role in its machining accuracy. This study investigates the thermal performance of a high-precision machine frame with future-oriented mineral casting components. A thermo-mechanical finite element model (FEM) was established to evaluate the thermal behavior of the frame under environmental thermal fluctuations. The validity of the presented FEM model was confirmed experimentally by a series of laser interferometer tests. Good agreement between numerical and experimental results demonstrates that the proposed model can accurately predict the thermal deformation of the frame with thermo-mechanical coupling effect. The results also show that keeping the workshop in thermally stable conditions is crucial for improving the machine accuracy of the system with large scale components. The goal of this paper is to investigate the feasibility of innovative mineral casting material applied in high-precision drilling machine and to provide a strategy for machine tool industry seeking a perfect substitute for classic frame materials such as cast iron and granite.

Keywords: thermo-mechanical model, finite element method, laser interferometer, mineral casting frame

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Authors: Radhiyatul Hikmah Binti Abu, Zukhairi Bin Md Rahim, Siti Ujila Binti Masuri, Nur Ismarrubie Binti Zahari, Mohd Zobir Hussein

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This paper describes the synthesis of Calcium Diethylenetriamine-penta (Ca-DTPMP) Scale Inhibitor (SI) and the effect of temperature on its adsorption onto the mineral surfaces. Nanosized particles of Ca-DTPMP SI were synthesized and TEM result shows that the sizes of the synthesized particles are ranged from 10 nm to 30 nm. This synthesized nano SI was then used in static adsorption/precipitation test with various temperatures (37°C, 60°C and 100°C) to determine the effect of temperature on its adsorption ability. The performance of the SI was measured by their diffusion capability, which can be inferred by weighing the metal-SI that successfully adsorbed onto the kaolinite (mineral) surface. The kaolinite samples were analyzed using Scanning Electron Microscope (SEM) and the results show the reduction of pores on kaolinite surface as temperature increases. This indicates higher adsorption of the SI particles onto the mineral surface. Furthermore, EDX analysis shows the presence of Phosphorus (P) and Magnesium (Mg2+) on kaolinite particle surface, hence reaffirming the fact that adsorption took place on the kaolinite surface.

Keywords: adsorption, diffusivity, scale, scale inhibitor

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Authors: Nina Bijedic, Drazena Gaspar, Mirsad Hadzikadic

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Corruption is an influential and widespread problem. One part of it is so-called petty corruption, related to large-scale bribe giving by ordinary citizens trying to influence the works of public administration or public services. As it is with all means of corruption, petty corruption is related to the level of democracy (or administration efficiency) in a society. The developed model captures some of the factors related to corruptive behavior, as well as people’s attitude towards petty corruption. It has four basic elements: user’s perception of corruption in the society of interest, the influence of social interactions, the influence of penalizing mechanism, and influence of campaigns against petty corruption. The model is agent-based, developed in NetLogo, with a lot of random settings that provide a wider scope of responses. Interactions of different settings for variables of elements provide insight into the influence of each element on attitude towards petty corruption, as well as petty corruptive behavior.

Keywords: agent-based model, attitude, influence, petty corruption, society

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Authors: Safwat Mohamed, Rasha Metawi, Hadeel Khalil, Hussein Kamal

Abstract:

This paper discusses and reveals the manufacturing techniques of the leather scale armour of Tutankhamun. This armour was in critical condition and went under many conservation procedures as it suffered from some serious deterioration aspects including fragmentation. In addition, its original shape was lost, the leather scales were found scattered in the box and separated from the linen basis, and hence its outlines were blurred and incomprehensible. In view of this, the leather scale armour of Tutankhamun was desperate for urgent conservation and reconstruction interventions. Documentation measures were done before conservation. Several re-treatable conservation procedures were applied seeking for stabilizing the armour and reaching sustainable condition. The conservation treatments included many investigations and analyses that helped in revealing materials and techniques of making the armour. The leather scale armour of Tutankhamun consisted of leather scales attached to a linen support. This linen support consisted of several layers. Howard Carter assumed that the linen support consisted of 6 layers. The undertaken conservation treatments helped in revealing the actual number of layers of the linen support as well as in reaching the most sustainable condition. This paper views the importance of the conservation procedures, which were recently carried out on Tutankhamun’s leather scale armour, in identifying and revealing all materials and techniques used in its manufacturing. The collected data about manufacturing techniques were used in making a replica of the leather scale armour with the same methods and materials.

Keywords: leather scales armours, conservation, manufacturing techniques, Tutankhamun, producing a replica

Procedia PDF Downloads 73