Search results for: genomic prediction

Authors: Chen Wang, Jared Evans, Yan Asmann

Abstract:

With the quick evolvement of next-generation sequencing techniques, whole-exome or exome-panel data have become a cost-effective way for detection of small exonic mutations, but there has been a growing desire to accurately detect copy number variations (CNVs) as well. In order to address this research and clinical needs, we developed a sequencing coverage pattern-based method not only for copy number detections, data integrity checks, CNV calling, and visualization reports. The developed methodologies include complete automation to increase usability, genome content-coverage bias correction, CNV segmentation, data quality reports, and publication quality images. Automatic identification and removal of poor quality outlier samples were made automatically. Multiple experimental batches were routinely detected and further reduced for a clean subset of samples before analysis. Algorithm improvements were also made to improve somatic CNV detection as well as germline CNV detection in trio family. Additionally, a set of utilities was included to facilitate users for producing CNV plots in focused genes of interest. We demonstrate the somatic CNV enhancements by accurately detecting CNVs in whole exome-wide data from the cancer genome atlas cancer samples and a lymphoma case study with paired tumor and normal samples. We also showed our efficient reuses of existing exome sequencing data, for improved germline CNV calling in a family of the trio from the phase-III study of 1000 Genome to detect CNVs with various modes of inheritance. The performance of the developed method is evaluated by comparing CNV calling results with results from other orthogonal copy number platforms. Through our case studies, reuses of exome sequencing data for calling CNVs have several noticeable functionalities, including a better quality control for exome sequencing data, improved joint analysis with single nucleotide variant calls, and novel genomic discovery of under-utilized existing whole exome and custom exome panel data.

Keywords: bioinformatics, computational genetics, copy number variations, data reuse, exome sequencing, next generation sequencing

Procedia PDF Downloads 244

Authors: İsmail İnce

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The aim of this study is to determine index and mechanical properties of pyroclastic rock in a practical way by means of electrical resistivity method. For this purpose, electrical resistivity, uniaxial compressive strength, point load strength, P-wave velocity, density and porosity values of 10 different pyroclastic rocks were measured in the laboratory. A simple regression analysis was made among the index-mechanical properties of the samples compatible with electrical resistivity values. A strong exponentially relation was found between index-mechanical properties and electrical resistivity values. The electrical resistivity method can be used to assess the engineering properties of the rock from which it is difficult to obtain regular shaped samples as a non-destructive method.

Keywords: electrical resistivity, index-mechanical properties, pyroclastic rocks, regression analysis

Procedia PDF Downloads 453

Authors: Naseem Uddin

Abstract:

Impinging jets are used in variety of engineering and industrial applications. This paper is based on numerical simulations of heat transfer by turbulent impinging jet with velocity field excitations using different Reynolds Averaged Navier-Stokes Equations models. Also Detached Eddy Simulations are conducted to investigate the differences in the prediction capabilities of these two simulation approaches. In this paper the excited jet is simulated in non-commercial CFD code OpenFOAM with the goal to understand the influence of dynamics of impinging jet on heat transfer. The jet’s frequencies are altered keeping in view the preferred mode of the jet. The Reynolds number based on mean velocity and diameter is 23,000 and jet’s outlet-to-target wall distance is 2. It is found that heat transfer at the target wall can be influenced by judicious selection of amplitude and frequencies.

Keywords: excitation, impinging jet, natural frequency, turbulence models

Procedia PDF Downloads 257

Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

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Objective: To elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of female genital tuberculosis (FGTB) cases. Background: Female genital TB represents about 15-20% of total extra-pulmonary TB (EPTB). Female subjects with vitamin D deficiency have been shown to be at higher risk of pulmonary TB as well as FGTB. In same context few functional polymorphism in vitamin D receptor (VDR) gene has been considered as an important genetic risk factor that modulate the development of FGTB. Therefore we aimed, to elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of FGTB. Study design: Case-Control study. Sample size: Cases (60) and Controls (60). Study site: Department of Obstetrics & Gynecology & Department of Microbiology, K.G.M.U. Lucknow, (UP). Inclusion criteria: Cases: Women with age group 20-35 years, premenstrual endometrial aspiration collected and included in the study, those were positive with acid-fast bacilli (AFB)/ TB-PCR/ LJ culture/ liquid culture. Controls: Women with age group 20-35 years having no history of ATT and all test negative for TB recruited as control. Exclusion criteria: -Women with endometriosis, polycystic ovaries (PCOD), positive on Chlamydia & gonorrhea, already on anti-tubercular therapy (ATT) excluded. Materials and Methods: Blood samples were collected in EDTA tubes from cases and controls stored at -20ºC. Genomic DNA extraction was carried out by salting-out method. Genotyping of VDR gene (ApaI&TaqI) polymorphism was performed by using single amplification refractory mutation system (ARMS) PCR technique. PCR products were analyzed by electrophoresis on 2% agarose gel. Statistical analysis was done by SPSS16.3 software & computing odds ratio (OR) with 95% CI. Results: Increased risk of female genital tuberculosis was observed in AA genotype (OR =1.1419-6.212 95% CI, P*<0.036) and A allele (OR =1.255-3.518, 95% CI, P* < 0.006) in FGTB as compared to controls. Moreover A allele was found more frequent in FGTB patients. No significant difference was observed in TaqI gene polymorphism of VDR gene. Conclusion: The ApaI polymorphism is significantly associated with etiology of FGTB and plays an important role as a genetic risk factor in FGTB women.

Keywords: ARMS, ATT, EPTB, FGTB, VDR

Procedia PDF Downloads 266

Authors: Y. Galerkin, A. Rekstin, K. Soldatova

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Universal modeling method well proven for industrial compressors was applied for design of the high flow rate supersonic stage. Results were checked by ANSYS CFX and NUMECA Fine Turbo calculations. The impeller appeared to be very effective at transonic flow velocities. Stator elements efficiency is acceptable at design Mach numbers too. Their loss coefficient versus inlet flow angle performances correlates well with Universal modeling prediction. The impeller demonstrated ability of satisfactory operation at design flow rate. Supersonic flow behavior in the impeller inducer at the shroud blade to blade surface Φdes deserves additional study.

Keywords: centrifugal compressor stage, supersonic impeller, inlet flow angle, loss coefficient, return channel, shock wave, vane diffuser

Procedia PDF Downloads 451

Authors: Tayeb Aissaoui, Inas M. AlNashef

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In recent years, green solvents named deep eutectic solvents (DESs) have been found to possess significant properties and to be applicable in several technologies. Choline chloride (ChCl) mixed with urea at a ratio of 1:2 and 80 °C was the first discovered DES. In this article, chemical structure and combination mechanism of ChCl: urea based DES were investigated. Moreover, the implementation of this DES in water removal from natural gas was reported. Dehydration of natural gas by ChCl:urea shows significant absorption efficiency compared to triethylene glycol. All above operations were retrieved from COSMOthermX software. This article confirms the potential application of DESs in gas industry.

Keywords: COSMO-RS, deep eutectic solvents, dehydration, natural gas, structure, organic salt

Procedia PDF Downloads 275

Authors: Maryam Amiri, Leyli Mohammad-Khanli

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Cloud computing is becoming increasingly popular and more business applications are moving to cloud. In this regard, services that provide similar functional properties are increasing. So, the ability to select a service with the best non-functional properties, corresponding to the user preference, is necessary for the user. This paper presents an Evaluation Framework of Service Trustworthiness (EFST) that evaluates the trustworthiness of equivalent services without need to additional invocations of them. EFST extracts user preference automatically. Then, it assesses trustworthiness of services in two dimensions of qualitative and quantitative metrics based on the experiences of past usage of services. Finally, EFST determines the overall trustworthiness of services using Fuzzy Inference System (FIS). The results of experiments and simulations show that EFST is able to predict the missing values of Quality of Service (QoS) better than other competing approaches. Also, it propels users to select the most appropriate services.

Keywords: user preference, cloud service, trustworthiness, QoS metrics, prediction

Procedia PDF Downloads 271

Authors: Tarek Litim, Ouahiba Taamallah

Abstract:

The present paper is an investigation of the effect of burnishing on the surface integrity of a component made of 15NiCr6 steel. This work shows a statistical study based on regression, and Taguchi's design has allowed the development of mathematical models to predict the output responses as a function of the technological parameters studied. The response surface methodology (RSM) showed a simultaneous influence of the burnishing parameters and observe the optimal processing parameters. ANOVA analysis of the results resulted in the validation of the prediction model with a determination coefficient R=90.60% and 92.41% for roughness and hardness, respectively. Furthermore, a multi-objective optimization allowed to identify a regime characterized by P=10kgf, i=3passes, and f=0.074mm/rev, which favours minimum roughness and maximum hardness. The result was validated by the desirability of D= (0.99 and 0.95) for roughness and hardness, respectively.

Keywords: 15NiCr6 steel, burnishing, surface integrity, Taguchi, RSM, ANOVA

Procedia PDF Downloads 179

Authors: Tariq Mansoor, Lubos Hes, Vladimir Bajzik

Abstract:

Socks comfort has great significance in our daily life. This significance even increased when we have undergone a work of low or high activity. It causes the sweating of our body with different rates. In this study, plain socks with differential fibre composition were wetted to saturated level. Then after successive intervals of conditioning, these socks are characterized by thermal resistance in dry and wet states. Theoretical thermal resistance is predicted by using combined filling coefficients and thermal conductivity of wet polymers instead of dry polymer (fibre) in different models. By this modification, different mathematical models could predict thermal resistance at different moisture levels. Furthermore, predicted thermal resistance by different models has reasonable correlation range between (0.84 -0.98) with experimental results in both dry (lab conditions moisture) and wet states. "This work is supported by Technical University of Liberec under SGC-2019. Project number is 21314".

Keywords: thermal resistance, mathematical model, plain socks, moisture loss rate

Procedia PDF Downloads 178

Authors: Richard Ren

Abstract:

Air pollution is a serious danger to international well-being and economies - it will kill an estimated 7 million people every year, costing world economies $2.6 trillion by 2060 due to sick days, healthcare costs, and reduced productivity. In the United States alone, 60,000 premature deaths are caused by poor air quality. For this reason, there is a crucial need to develop effective methods to forecast air quality, which can mitigate air pollution’s detrimental public health effects and associated costs by helping people plan ahead and avoid exposure. The goal of this study is to propose an artificial intelligence framework for predicting future air quality based on timing variables (i.e. season, weekday/weekend), future weather forecasts, as well as past pollutant and air quality measurements. The proposed framework utilizes multiple machine learning algorithms (logistic regression, random forest, neural network) with different specifications and averages the results of the three top-performing models to eliminate inaccuracies, weaknesses, and biases from any one individual model. Over time, the proposed framework uses new data to self-adjust model parameters and increase prediction accuracy. To demonstrate its applicability, a prototype of this framework was created to forecast air quality in Los Angeles, California using datasets from the RP4 weather data repository and EPA pollutant measurement data. The results showed good agreement between the framework’s predictions and real-life observations, with an overall 92% model accuracy. The combined model is able to predict more accurately than any of the individual models, and it is able to reliably forecast season-based variations in air quality levels. Top air quality predictor variables were identified through the measurement of mean decrease in accuracy. This study proposed and demonstrated the efficacy of a comprehensive air quality prediction framework leveraging multiple machine learning algorithms to overcome individual algorithm shortcomings. Future enhancements should focus on expanding and testing a greater variety of modeling techniques within the proposed framework, testing the framework in different locations, and developing a platform to automatically publish future predictions in the form of a web or mobile application. Accurate predictions from this artificial intelligence framework can in turn be used to save and improve lives by allowing individuals to protect their health and allowing governments to implement effective pollution control measures.Air pollution is a serious danger to international wellbeing and economies - it will kill an estimated 7 million people every year, costing world economies $2.6 trillion by 2060 due to sick days, healthcare costs, and reduced productivity. In the United States alone, 60,000 premature deaths are caused by poor air quality. For this reason, there is a crucial need to develop effective methods to forecast air quality, which can mitigate air pollution’s detrimental public health effects and associated costs by helping people plan ahead and avoid exposure. The goal of this study is to propose an artificial intelligence framework for predicting future air quality based on timing variables (i.e. season, weekday/weekend), future weather forecasts, as well as past pollutant and air quality measurements. The proposed framework utilizes multiple machine learning algorithms (logistic regression, random forest, neural network) with different specifications and averages the results of the three top-performing models to eliminate inaccuracies, weaknesses, and biases from any one individual model. Over time, the proposed framework uses new data to self-adjust model parameters and increase prediction accuracy. To demonstrate its applicability, a prototype of this framework was created to forecast air quality in Los Angeles, California using datasets from the RP4 weather data repository and EPA pollutant measurement data. The results showed good agreement between the framework’s predictions and real-life observations, with an overall 92% model accuracy. The combined model is able to predict more accurately than any of the individual models, and it is able to reliably forecast season-based variations in air quality levels. Top air quality predictor variables were identified through the measurement of mean decrease in accuracy. This study proposed and demonstrated the efficacy of a comprehensive air quality prediction framework leveraging multiple machine learning algorithms to overcome individual algorithm shortcomings. Future enhancements should focus on expanding and testing a greater variety of modeling techniques within the proposed framework, testing the framework in different locations, and developing a platform to automatically publish future predictions in the form of a web or mobile application. Accurate predictions from this artificial intelligence framework can in turn be used to save and improve lives by allowing individuals to protect their health and allowing governments to implement effective pollution control measures.Air pollution is a serious danger to international wellbeing and economies - it will kill an estimated 7 million people every year, costing world economies $2.6 trillion by 2060 due to sick days, healthcare costs, and reduced productivity. In the United States alone, 60,000 premature deaths are caused by poor air quality. For this reason, there is a crucial need to develop effective methods to forecast air quality, which can mitigate air pollution’s detrimental public health effects and associated costs by helping people plan ahead and avoid exposure. The goal of this study is to propose an artificial intelligence framework for predicting future air quality based on timing variables (i.e. season, weekday/weekend), future weather forecasts, as well as past pollutant and air quality measurements. The proposed framework utilizes multiple machine learning algorithms (logistic regression, random forest, neural network) with different specifications and averages the results of the three top-performing models to eliminate inaccuracies, weaknesses, and biases from any one individual model. Over time, the proposed framework uses new data to self-adjust model parameters and increase prediction accuracy. To demonstrate its applicability, a prototype of this framework was created to forecast air quality in Los Angeles, California using datasets from the RP4 weather data repository and EPA pollutant measurement data. The results showed good agreement between the framework’s predictions and real-life observations, with an overall 92% model accuracy. The combined model is able to predict more accurately than any of the individual models, and it is able to reliably forecast season-based variations in air quality levels. Top air quality predictor variables were identified through the measurement of mean decrease in accuracy. This study proposed and demonstrated the efficacy of a comprehensive air quality prediction framework leveraging multiple machine learning algorithms to overcome individual algorithm shortcomings. Future enhancements should focus on expanding and testing a greater variety of modeling techniques within the proposed framework, testing the framework in different locations, and developing a platform to automatically publish future predictions in the form of a web or mobile application. Accurate predictions from this artificial intelligence framework can in turn be used to save and improve lives by allowing individuals to protect their health and allowing governments to implement effective pollution control measures.

Keywords: air quality prediction, air pollution, artificial intelligence, machine learning algorithms

Procedia PDF Downloads 103

Authors: Damiaa Saad Khudor

Abstract:

The paper describes an investigation for the thermal design of a fluidized bed cooler and prediction of heat transfer rate among the media categories. It is devoted to the thermal design of such equipment and their application in the industrial fields. It outlines the strategy for the fluidization heat transfer mode and its implementation in industry. The thermal design for fluidized bed cooler is used to furnish a complete design for a fluidized bed cooler of Sodium Bicarbonate. The total thermal load distribution between the air-solid and water-solid along the cooler is calculated according to the thermal equilibrium. The step by step technique was used to accomplish the thermal design of the fluidized bed cooler. It predicts the load, air, solid and water temperature along the trough. The thermal design for fluidized bed cooler revealed to the installation of a heat exchanger consists of (65) horizontal tubes with (33.4) mm diameter and (4) m length inside the bed trough.

Keywords: fluidization, powder technology, thermal design, heat exchangers

Procedia PDF Downloads 495

Authors: Zhi-Jun Lu, Qi Lu, Meng Wu, Qian Xiang, Jun Gu

Abstract:

The analysis of perforated steel members is a 3D problem in nature, therefore the traditional analytical expressions for the ultimate load of thin-walled steel sections cannot be used for the perforated steel member design. In this study, finite element method (FEM) and artificial neural network (ANN) were used to simulate the process of stub column tests based on specific codes. Results show that compared with those of the FEM model, the ultimate load predictions obtained from ANN technique were much closer to those obtained from the physical experiments. The ANN model for the solving the hard problem of complex steel perforated sections is very promising.

Keywords: artificial neural network (ANN), finite element method (FEM), perforated sections, thin-walled Steel, ultimate load

Procedia PDF Downloads 333

Authors: Warda Khan, Remo Lachmann, Adarsh S. Garakahally

Abstract:

The increasing complexity of software and its applicability in a wide range of industries, e.g., automotive, call for enhanced quality assurance techniques. Test automation is one option to tackle the prevailing challenges by supporting test engineers with fast, parallel, and repetitive test executions. A high degree of test automation allows for a shift from mundane (manual) testing tasks to a more analytical assessment of the software under test. However, a high initial investment of test resources is required to establish test automation, which is, in most cases, a limitation to the time constraints provided for quality assurance of complex software systems. Hence, a computer-aided creation of automated test cases is crucial to increase the benefit of test automation. This paper proposes the application of machine learning for the generation of automated test cases. It is based on supervised learning to analyze test specifications and existing test implementations. The analysis facilitates the identification of patterns between test steps and their implementation with test automation components. For the test case generation, this approach exploits historical data of test automation projects. The identified patterns are the foundation to predict the implementation of unknown test case specifications. Based on this support, a test engineer solely has to review and parameterize the test automation components instead of writing them manually, resulting in a significant time reduction for establishing test automation. Compared to other generation approaches, this ML-based solution can handle different writing styles, authors, application domains, and even languages. Furthermore, test automation tools require expert knowledge by means of programming skills, whereas this approach only requires historical data to generate test cases. The proposed solution is evaluated using various multi-label evaluation criteria (EC) and two small-sized real-world systems. The most prominent EC is ‘Subset Accuracy’. The promising results show an accuracy of at least 86% for test cases, where a 1:1 relationship (Multi-Class) between test step specification and test automation component exists. For complex multi-label problems, i.e., one test step can be implemented by several components, the prediction accuracy is still at 60%. It is better than the current state-of-the-art results. It is expected the prediction quality to increase for larger systems with respective historical data. Consequently, this technique facilitates the time reduction for establishing test automation and is thereby independent of the application domain and project. As a work in progress, the next steps are to investigate incremental and active learning as additions to increase the usability of this approach, e.g., in case labelled historical data is scarce.

Keywords: machine learning, multi-class, multi-label, supervised learning, test automation

Procedia PDF Downloads 114

Authors: A. Hocine, A. Ghouaoula, S. M. Medjdoub, M. Cherifi

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The present paper proposed a meso–macro model describing the mechanical behaviour composite laminates of staking sequence [+θ/-θ]s under tensil loading. The behaviour of a layer is ex-pressed through elasticity coupled to damage. The elastic strain is due to the elasticity of the layer and can be modeled by using the classical laminate theory, and the laminate is considered as an orthotropic material. This means that no coupling effect between strain and curvature is considered. In the present work, the damage is associated to cracking of the matrix and parallel to the fibers and it being taken into account by the changes in the stiffness of the layers. The anisotropic damage is completely described by a single scalar variable and its evolution law is specified from the principle of maximum dissipation. The stress/strain relationship is investigated in plane stress loading.

Keywords: damage, behavior modeling, meso-macro model, composite laminate, membrane loading

Procedia PDF Downloads 460

Authors: Kais A. Kadhim

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This paper is a semantic analysis of the English modals in Obama’s speech. The main objective of this study is to analyze selected modal auxiliaries identified in selected speeches of Obama’s campaign based on Coates’ (1983) semantic clusters. A total of fifteen speeches of Obama’s campaign were selected as the primary data and the modal auxiliaries selected for analysis include will, would, can, could, should, must, ought, shall, may and might. All the modal auxiliaries taken from the speeches of Barack Obama were analyzed based on the framework of Coates’ semantic clusters. Such analytical framework was carried out to examine how modal auxiliaries are used in the context of persuading people in Obama’s campaign speeches. The findings reveal that modals of intention, prediction, futurity and modals of possibility, ability, permission are mostly used in Obama’s campaign speeches.

Keywords: modals, meaning, persuasion, speech

Procedia PDF Downloads 385

Authors: G. F. Okunade, M. O. Lawal, R. E. Uwadiae, D. Portnoy

Abstract:

The diversity, physico-chemical, biochemical and genomics assessment of Macrofauna species of Ologe and Badagry Lagoons were carried out between August 2016 and July 2018. The concentrations of Fe, Zn, Mn, Cd, Cr, and Pb in water were determined by Atomic Absorption Spectrophotometer (AAS). Particle size distribution was determined with wet-sieving and sedimentation using hydrometer method. Genomics analyses were carried using 25 P. fusca (quadriseriata) and 25 P.fusca from each lagoon due to abundance in both lagoons all through the two years of collection. DNA was isolated from each sample using the Mag-Bind Blood and Tissue DNA HD 96 kit; a method designed to isolate high quality. The biochemical characteristics were analysed in the dominanat species (P.aurita and T. fuscatus) using ELISA kits. Physico-chemical parameters such as pH, total dissolved solids, dissolved oxygen, conductivity and TDS were analysed using APHA standard protocols. The Physico-chemical parameters of the water quality recorded with mean values of 32.46 ± 0.66mg/L and 41.93 ± 0.65 for COD, 27.28 ± 0.97 and 34.82 ± 0.1 mg/L for BOD, 0.04 ± 4.71 mg/L for DO, 6.65 and 6.58 for pH in Ologe and Badagry lagoons with significant variations (p ≤ 0.05) across seasons. The mean and standard deviation of salinity for Ologe and Badagry Lagoons ranged from 0.43 ± 0.30 to 0.27 ± 0.09. A total of 4210 species belonging to a phylum, two classes, four families and a total of 2008 species in Ologe lagoon while a phylum, two classes, 5 families and a total of 2202 species in Badagry lagoon. The percentage composition of the classes at Ologe lagoon had 99% gastropod and 1% bivalve, while Gastropod contributed 98.91% and bivalve 1.09% in Badagry lagoon. Particle size was distributed in 0.002mm to 2.00mm, particle size distribution in Ologe lagoon recorded 0.83% gravels, 97.83% sand, and 1.33% silt particles while Badagry lagoon recorded 7.43% sand, 24.71% silt, and 67.86% clay particles hence, the excessive dredging activities going on in the lagoon. Maximum percentage of sand (100%) was seen in station 6 in Ologe lagoon while the minimum (96%) was found in station 1. P. aurita (Ologe Lagoon) and T. fuscastus (Badagry Lagoon) were the most abundant benthic species in which both contributed 61.05% and 64.35%, respectively. The enzymatic activities of P. aurita observed with mean values of 21.03 mg/dl for AST, 10.33 mg/dl for ALP, 82.16 mg/dl for ALT and 73.06 mg/dl for CHO in Ologe Lagoon While T. fuscatus observed mean values of Badagry Lagoon) recorded mean values 29.76 mg/dl, ALP with 11.69mg/L, ALT with 140.58 mg/dl and CHO with 45.98 mg/dl. There were significant variations (P < 0.05) in AST and CHO levels of activities in the muscles of the species.

Keywords: benthos, biochemical responses, genomics, metals, particle size

Procedia PDF Downloads 114

Authors: Mabrouka Morri, Amel Soualmia, Philippe Belleudy

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Vegetation affects the mean and turbulent flow structure. It may increase flood risks and sediment transport. Therefore, it is important to develop analytical approaches for the bed shear stress on vegetated bed, to predict resistance caused by vegetation. In the recent years, experimental and numerical models have both been developed to model the effects of submerged vegetation on open-channel flow. In this paper, different analytic models are compared and tested using the criteria of deviation, to explore their capacity for predicting the mean velocity and select the suitable one that will be applied in real case of rivers. The comparison between the measured data in vegetated flume and simulated mean velocities indicated, a good performance, in the case of rigid vegetation, whereas, Huthoff model shows the best agreement with a high coefficient of determination (R2=80%) and the smallest error in the prediction of the average velocities.

Keywords: analytic models, comparison, mean velocity, vegetation

Procedia PDF Downloads 260

Authors: Gianna Zou

Abstract:

Propensity score matching (PSM), introduced by Paul R. Rosenbaum and Donald Rubin in 1983, is a popular statistical matching technique which tries to estimate the treatment effects by taking into account covariates that could impact the efficacy of study medication in clinical trials. PSM can be used to reduce the bias due to confounding variables. However, PSM assumes that the response values are normally distributed. In some cases, this assumption may not be held. In this paper, a machine learning method - Bayesian Additive Regression Tree (BART), is used as a more robust method of matching. BART can work well when models are misspecified since it can be used to model heterogeneous treatment effects. Moreover, it has the capability to handle non-linear main effects and multiway interactions. In this research, a BART Matching Method (BMM) is proposed to provide a more reliable matching method over PSM. By comparing the analysis results from PSM and BMM, BMM can perform well and has better prediction capability when the response values are not normally distributed.

Keywords: BART, Bayesian, matching, regression

Procedia PDF Downloads 133

Authors: Miaomiao Zhang, Sabrina Beckmann, Haluk Ertan, Rocky Chau, Mike Manefield

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Phenazines are a large class of nitrogen-containing aromatic heterocyclic compounds, which are almost exclusively produced by bacteria from diverse genera including Pseudomonas and Streptomyces. Phenazine-1-carboxylic acid (PCA) as one of 'core' phenazines are converted from chorismic acid before modified to other phenazine derivatives in different cells. Phenazines have attracted enormous interests because of their multiple roles on biocontrol, bacterial interaction, biofilm formation and fitness of their producers. However, in spite of ecological importance, degradation as a part of phenazines’ fate only have extremely limited attention now. Here, to isolate PCA-degrading bacteria, 200 mg L-1 PCA was supplied as sole carbon, nitrogen and energy source in minimal mineral medium. Quantitative PCR and Reverse-transcript PCR were employed to study abundance and activity of functional gene MFORT 16269 in PCA degradation, respectively. Intermediates and products of PCA degradation were identified with LC-MS/MS. After enrichment and isolation, a PCA-degrading strain was selected from soil and was designated as Rhodanobacter sp. PCA2 based on full 16S rRNA sequencing. As determined by HPLC, strain PCA2 consumed 200 mg L-1 (836 µM) PCA at a rate of 17.4 µM h-1, accompanying with significant cells yield from 1.92 × 105 to 3.11 × 106 cells per mL. Strain PCA2 was capable of degrading other phenazines as well, including phenazine (4.27 µM h-1), pyocyanin (2.72 µM h-1), neutral red (1.30 µM h-1) and 1-hydroxyphenazine (0.55 µM h-1). Moreover, during the incubation, transcript copies of MFORT 16269 gene increased significantly from 2.13 × 106 to 8.82 × 107 copies mL-1, which was 2.77 times faster than that of the corresponding gene copy number (2.20 × 106 to 3.32 × 107 copies mL-1), indicating that MFORT 16269 gene was activated and played roles on PCA degradation. As analyzed by LC-MS/MS, decarboxylation from the ring structure was determined as the first step of PCA degradation, followed by cleavage of nitrogen-containing ring by dioxygenase which catalyzed phenazine to nitrosobenzene. Subsequently, phenylhydroxylamine was detected after incubation for two days and was then transferred to aniline and catechol. Additionally, genomic and proteomic analyses were also carried out for strain PCA2. Overall, the findings presented here showed that a newly isolated strain Rhodanobacter sp. PCA2 was capable of degrading phenazines through decarboxylation and cleavage of nitrogen-containing ring, during which MFORT 16269 gene was activated and played important roles.

Keywords: decarboxylation, MFORT16269 gene, phenazine-1-carboxylic acid degradation, Rhodanobacter sp. PCA2

Procedia PDF Downloads 208

Authors: I. Goual, M. S. Goual, M. K. Gueddouda, Taïbi Saïd, Abou-Bekr Nabil, A. Ferhat

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This paper presents the study of hydro mechanical behavior of this optimal mixture. A first experimental phase was carried out in order to find the optimal mixture. This showed that the material composed of 80% tuff and 20% calcareous sand provides the maximum mechanical strength. The second experimental phase concerns the study of the drying- wetting behavior of the optimal mixture was carried out on slurry samples and compacted samples at the MPO. Experimental results let to deduce the parameters necessary for the prediction of the hydro-mechanical behavior of pavement formulated from tuff and calcareous sand mixtures, related to moisture. This optimal mixture satisfies the regulation rules and hence constitutes a good local eco-material, abundantly available, for the conception of pavements.

Keywords: tuff, sandy calcareous, road engineering, hydro mechanical behaviour, suction

Procedia PDF Downloads 491

Authors: Pei-Chann Chang, Jhen-Fu Liao, Chin-Hung Teng, Meng-Hui Chen

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This research combines artificial immune system with user and item based collaborative filtering to create an efficient and accurate recommendation system. By applying the characteristic of antibodies and antigens in the artificial immune system and using Pearson correlation coefficient as the affinity threshold to cluster the data, our collaborative filtering can effectively find useful users and items for rating prediction. This research uses MovieLens dataset as our testing target to evaluate the effectiveness of the algorithm developed in this study. The experimental results show that the algorithm can effectively and accurately predict the movie ratings. Compared to some state of the art collaborative filtering systems, our system outperforms them in terms of the mean absolute error on the MovieLens dataset.

Keywords: artificial immune system, collaborative filtering, recommendation system, similarity

Procedia PDF Downloads 517

Authors: Majid Forghani, Michael Khachay

Abstract:

In genetics, the impact of neighboring amino acids on a target site is referred as the nearest-neighbor effect or simply neighbor effect. In this paper, a new method called wavelet particle decomposition representing the one-dimensional neighbor effect using wavelet packet decomposition is proposed. The main idea lies in known dependence of wavelet packet sub-bands on location and order of neighboring samples. The method decomposes the value of a signal sample into small values called particles that represent a part of the neighbor effect information. The results have shown that the information obtained from the particle decomposition can be used to create better model variables or features. As an example, the approach has been applied to improve the correlation of test and reference sequence distance with titer in the hemagglutination inhibition assay.

Keywords: antigenic variants, neighbor effect, wavelet packet, wavelet particle decomposition

Procedia PDF Downloads 136

Authors: Kevin Kellner, Nga Lao, Orla Coleman, Paula Meleady, Niall Barron

Abstract:

Chinese Hamster Ovary (CHO) cells are the prominent cell line used in biopharmaceutical production. To improve yields and find beneficial bioprocess phenotypes genetic engineering plays an essential role in recent research. The miR-23 cluster, specifically miR-24 and miR-27, was first identified as differentially expressed during hypothermic conditions suggesting a role in proliferation and productivity in CHO cells. In this study, we used sponge decoy technology to stably deplete the miRNA expression of the cluster. Furthermore, we implemented the CRISPR/Cas9 system to knockdown miRNA expression. Sponge constructs were designed for an imperfect binding of the miRNA target, protecting from RISC mediated cleavage. GuideRNAs for the CRISPR/Cas9 system were designed to target the seed region of the miRNA. The expression of mature miRNA and precursor were confirmed using RT-qPCR. For both approaches stable expressing mixed populations were generated and characterised in batch cultures. It was shown, that CRISPR/Cas9 can be implemented in CHO cells with achieving high knockdown efficacy of every single member of the cluster. Targeting of one miRNA member showed that its genomic paralog is successfully targeted as well. The stable depletion of miR-24 using CRISPR/Cas9 showed increased growth and specific productivity in a CHO-K1 mAb expressing cell line. This phenotype was further characterized using quantitative label-free LC-MS/MS showing 186 proteins differently expressed with 19 involved in proliferation and 26 involved in protein folding/translation. Targeting miR-27 in the same cell line showed increased viability in late stages of the culture compared to the control. To evaluate the phenotype in an industry relevant cell line; the miR-23 cluster, miR-24 and miR-27 were stably depleted in a Fc fusion CHO-S cell line which showed increased batch titers up to 1.5-fold. In this work, we highlighted that the stable depletion of the miR-23 cluster and its members can improve the bioprocess phenotype concerning growth and productivity in two different cell lines. Furthermore, we showed that using CRISPR/Cas9 is comparable to the traditional sponge decoy technology.

Keywords: Chinese Hamster ovary cells, CRISPR/Cas9, microRNAs, sponge decoy technology

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Authors: Maria F. Seran

Abstract:

In second language interaction, an EFL student always carries his knowledge of targeted language and sometimes gets influenced by his first language cultures which makes him transfer his utterances from the first language to the second language. The influence of L1 cultures somehow can lead to face-threatening act when it comes to responding on speech act, for instance, compliment. A speaker praises a compliment to show gratitude, and in return, he expects for compliment respond uttered by the hearer. While Western people use more acceptance continuum on compliment response, Indonesians utter more denial continuum which can somehow put the speakers into a face-threating situation and offense. This study investigated compliment response employed by EFL students and English native speakers. The study was distinct as none compliment response studies had been conducted to compare the compliment response between English native speakers and two different Indonesian EFL proficiency groups in which this research sought to meet this need. This study was significant for EFL teachers because it gave insight on cross-cultural understanding and brought pedagogical implication on explicit pragmatic instruction. Two research questions were set, 1. How do Indonesian EFL students and English native speakers respond compliments? 2. Is there any correlation between Indonesia EFL students’ proficiency and their compliment response use in English? The study involved three groups of participants; 5 English native speakers, 10 high-proficiency and 10 low-proficiency Indonesian EFL university students. The research instruments used in this study were as follows, an online TOEFL prediction test, focusing on grammar skill which was modified from Barron TOEFL exercise test, and a discourse completion task (DCT), consisting of 10 compliment respond items. Based on the research invitation, 20 second-year university students majoring in English education at Widya Mandira Catholic University, Kupang, East Nusa Tenggara, Indonesia who willingly participated in the research took the TOEFL prediction test online from the link provided. Students who achieved score 75-100 in test were categorized as high-proficiency students, while, students who attained score below 74 were considered as low-proficiency students. Then, the DCT survey was administered to these EFL groups and the native speaker group. Participants’ responses were coded and analyzed using categories of compliment response framework proposed by Tran. The study found out that 5 native speakers applied more compliment upgrades and appreciation token in compliment response, whereas, Indonesian EFL students combined some compliment response strategies in their utterance, such as, appreciation token, return and compliment downgrade. There is no correlation between students’ proficiency level and their CR responds as most EFL students in both groups produced less varied compliment responses and only 4 Indonesian high-proficiency students uttered more varied and were similar to the native speakers. The combination strategies used by EFL students can be explained as the influence of pragmatic transfer from L1 to L2; therefore, EFL teachers should explicitly teach more compliment response strategies to raise students’ awareness on English culture and elaborate their speaking to be more competence as close to native speakers as possible.

Keywords: compliment response, English native speakers, Indonesian EFL students, speech acts

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Authors: Ihsane Modhaffar

Abstract:

Fiber orientation is essential for the physical properties of composite materials. The theoretical parameters of a given reinforcement are usually known and widely used to predict the behavior of the material. In this work, we propose an image processing approach to estimate true principal directions and fiber orientation during injection molding processes of short fiber reinforced thermoplastics. Generally, a group of fibers are described in terms of probability distribution function or orientation tensor. Numerical techniques for the prediction of fiber orientation are also considered for concentrated situations. The flow was considered to be incompressible, and behave as Newtonian fluid containing suspensions of short-fibers. The governing equations, of this problem are: the continuity, the momentum and the energy. The obtained results were compared to available experimental findings. A good agreement between the numerical results and the experimental data was achieved.

Keywords: injection, composites, short-fiber reinforced thermoplastics, fiber orientation, incompressible fluid, numerical simulation

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Authors: Liu Zhiyuan, Sun Zongdi

Abstract:

In this paper, the BP neural network model is established to predict the carbon trading price and carbon trading volume in Shanghai City. First of all, we find the data of carbon trading price and carbon trading volume in Shanghai City from September 30, 2015 to December 23, 2016. The carbon trading price and trading volume data were processed to get the average value of each 5, 10, 20, 30, and 60 carbon trading price and trading volume. Then, these data are used as input of BP neural network model. Finally, after the training of BP neural network, the prediction values of Shanghai carbon trading price and trading volume are obtained, and the model is tested.

Keywords: Carbon trading price, carbon trading volume, BP neural network model, Shanghai City

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Authors: Diego Tancara, Raul Coto, Ariel Norambuena, Hoseein T. Dinani, Felipe Fanchini

Abstract:

Quantum machine learning is a growing research field that aims to perform machine learning tasks assisted by a quantum computer. Kernel-based quantum machine learning models are paradigmatic examples where the kernel involves quantum states, and the Gram matrix is calculated from the overlapping between these states. With the kernel at hand, a regular machine learning model is used for the learning process. In this paper we investigate the quantum support vector machine and quantum kernel ridge models to predict the degree of non-Markovianity of a quantum system. We perform digital quantum simulation of amplitude damping and phase damping channels to create our quantum dataset. We elaborate on different kernel functions to map the data and kernel circuits to compute the overlapping between quantum states. We observe a good performance of the models.

Keywords: quantum, machine learning, kernel, non-markovianity

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Authors: Chen Xi, Lao Xuerui, Li Junjie, Jiang Yike, Wang Hanwei, Zeng Zihao

Abstract:

To further promote the development of smart cities, the microscopic "nerve endings" of the City Intelligent Model (CIM) are extended to be more sensitive. In this paper, we develop a pedestrian trajectory twin terminal based on the CIM and CNN technology. It also uses 5G networks, architectural and geoinformatics technologies, convolutional neural networks, combined with deep learning networks for human behaviour recognition models, to provide empirical data such as 'pedestrian flow data and human behavioural characteristics data', and ultimately form spatial performance evaluation criteria and spatial performance warning systems, to make the empirical data accurate and intelligent for prediction and decision making.

Keywords: urban planning, urban governance, CIM, artificial intelligence, convolutional neural network

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Authors: Osama Elsarrar, Marjorie Darrah, Richard Devin

Abstract:

This paper discusses the idea of capturing an expert’s knowledge in the form of human understandable rules and then inserting these rules into a dynamic cell structure (DCS) neural network. The DCS is a form of self-organizing map that can be used for many purposes, including classification and prediction. This particular neural network is considered to be a topology preserving network that starts with no pre-structure, but assumes a structure once trained. The DCS has been used in mission and safety-critical applications, including adaptive flight control and health-monitoring in aerial vehicles. The approach is to insert expert knowledge into the DCS before training. Rules are translated into a pre-structure and then training data are presented. This idea has been demonstrated using the well-known Iris data set and it has been shown that inserting the pre-structure results in better accuracy with the same training.

Keywords: neural network, self-organizing map, rule extraction, rule insertion

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Authors: Maxim A. Kadatskiy, Konstantin V. Khishchenko

Abstract:

Iron alloys are widespread components in various types of structural materials which are exposed to intensive thermal and mechanical loads. Various quantum-statistical cell models with the approximation of self-consistent field can be used for the prediction of the behavior of these materials under extreme conditions. The application of these models is even more valid, the higher the temperature and the density of matter. Results of Hugoniot calculation for iron alloys in the framework of three quantum-statistical (the Thomas–Fermi, the Thomas–Fermi with quantum and exchange corrections and the Hartree–Fock–Slater) models are presented. Results of quantum-statistical calculations are compared with results from other reliable models and available experimental data. It is revealed a good agreement between results of calculation and experimental data for terra pascal pressures. Advantages and disadvantages of this approach are shown.

Keywords: alloy, Hugoniot, iron, terapascal pressure

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