Search results for: genome scale metabolic model

Authors: M. Acin-Albiac, P. Filannino, R. Coda, Carlo G. Rizzello, M. Gobbetti, R. Di Cagno

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Demand for smart management of large amounts of agro-food by-products has become an area of major environmental and economic importance worldwide. Brewers' spent grain (BSG), the most abundant by-product generated in the beer-brewing process, represents an example of valuable raw material and source of health-promoting compounds. To the date, the valorization of BSG as a food ingredient has been limited due to poor technological and sensory properties. Tailored bioprocessing through lactic acid bacteria (LAB) fermentation is a versatile and sustainable means for the exploitation of food industry by-products. Indigestible carbohydrates (e.g., hemicelluloses and celluloses), high phenolic content, and mostly lignin make of BSG a hostile environment for microbial survival. Hence, the selection of tailored starters is required for successful fermentation. Our study investigated the metabolic strategies of Leuconostoc pseudomesenteroides and Lactobacillus plantarum strains to exploit BSG as a food ingredient. Two distinctive BSG samples from different breweries (Italian IT- and Finish FL-BSG) were microbially and chemically characterized. Growth kinetics, organic acid profiles, and the evolution of phenolic profiles during the fermentation in two BSG model media were determined. The results were further complemented with gene expression targeting genes involved in the degradation cellulose, hemicelluloses building blocks, and the metabolism of anti-nutritional factors. Overall, the results were LAB genus dependent showing distinctive metabolic capabilities. Leuc. pseudomesenteroides DSM 20193 may degrade BSG xylans while sucrose metabolism could be furtherly exploited for extracellular polymeric substances (EPS) production to enhance BSG pro-technological properties. Although L. plantarum strains may follow the same metabolic strategies during BSG fermentation, the mode of action to pursue such strategies was strain-dependent. L. plantarum PU1 showed a great preference for β-galactans compared to strain WCFS1, while the preference for arabinose occurred at different metabolic phases. Phenolic compounds profiling highlighted a novel metabolic route for lignin metabolism. These findings will allow an improvement of understanding of how lactic acid bacteria transform BSG into economically valuable food ingredients.

Keywords: brewery by-product valorization, metabolism of plant phenolics, metabolism of lactic acid bacteria, gene expression

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Authors: Abdullah Pandang, Mantasiah Rivai, Nur Fadhilah Umar, Azam Arifyadi

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This study aims to measure the validity of the politeness behaviour scale and obtain a model that fits the scale. The researcher developed the Politeness Behavior on Communicating (PBC) scale. The research method uses descriptive quantitative by developing the PBC scale. The population in this study were students in three provinces, namely South Sulawesi, West Sulawesi, and Central Sulawesi, recorded in the 2022/2023 academic year. The sampling technique used stratified random sampling by determining the number of samples using the Slovin formula. The sample of this research is 1200 students. This research instrument uses the PBC scale, which consists of 5 (five) indicators: self-regulation of compensation behaviour, self-efficacy of compensation behaviour, fulfilment of social expectations, positive feedback, and no strings attached. The PBC scale consists of 34 statement items. The data analysis technique is divided into two types: the validity test on the correlated item values and the item reliability test referring to Cronbach's and McDonald's alpha standards using the JASP application. Furthermore, the data were analyzed using confirmatory factor analysis (CFA) and exploratory factor analysis (EFA). The results showed that the adaptation of the Politeness Behavior on Communicating (PBC) scale was on the Fit Index with a chi-square value (711,800/375), RMSEA (0.53), GFI (0.990), CFI (0.987), GFI (0.985).

Keywords: polite behavior in communicating, positive communication, exploration factor analysis, confirmatory factor analysis

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Authors: Aude Pérard Lecomte, Georges Fokoua, Amine Mehel, Anne Tanière

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Air quality in urban areas is deteriorated by pollution, mainly due to the constant increase of the traffic of different types of ground vehicles. In particular, particulate matter pollution with important concentrations in urban areas can cause serious health issues. Characterizing and understanding particle dynamics is therefore essential to establish recommendations to improve air quality in urban areas. To analyze the effects of turbulence on particulate pollutants dispersion, the first step is to focus on the single-phase flow structure and turbulence characteristics in the wake of a heavy truck model. To achieve this, Computational Fluid Dynamics (CFD) simulations were conducted with the aim of modeling the wake airflow of a full- and reduced-scale heavy truck. The Reynolds Average Navier-Stokes (RANS) approach with the Reynolds Stress Model (RSM)as the turbulence model closure was used. The simulations highlight the apparition of a large vortex coming from the under trailer. This vortex belongs to the recirculation region, located in the near-wake of the heavy truck. These vortical structures are expected to have a strong influence on particle dynamics that are emitted by the truck.

Keywords: CDF, heavy truck, recirculation region, reduced scale

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Authors: Mary Kay Bacallao

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New research on the human genome has revealed secrets to the variation in skin pigmentation found in all human populations. Application of this research to multicultural education has a profound effect on students from all backgrounds. This paper identifies the four locations in the human genome that code for variation in skin pigmentation worldwide. The research makes this new knowledge accessible to students of all ages as they participate in an art project that brings these scientific multicultural concepts to life. Students participate in the application of breakthrough scientific principles through hands-on art activities where they simulate the work of the DNA coding to create their own skin tone using the colors expressed to varying degrees in every people group. As students create their own artwork handprint from the pallet of colors, they realize that each color on the pallet is essential to creating every tone of skin. This research project serves to bring people together and appreciate the variety and diversity in skin tones. As students explore the variations, they create pigmentation with the use of the eumelanins, which are the black-brown sources of pigmentation, and the pheomelanins, which are the yellow-reddish-brown sources of pigmentation. The research project dispels myths about skin tones that have divided people in the past. As a group project, this research leads to greater appreciation and understanding of the diverse family groups.

Keywords: diversity, multicultural, skin pigmentation, eumelanins, pheomelanins, handprint, artwork, science, genome, human

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Authors: Saheed Olakunle Sanusi, Israel Ajibade Adedeji

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The study analysed the effect of microfinance on the profit level of small and medium scale enterprises in Lagos. The data for the study were obtained by simple random sampling, and total of one hundred and fifty (150) small and medium scale enterprises (SMEs) were sampled for the study. Seventy-five (75) each are microfinance users and non-users. Data were analysed using descriptive statistics, logit model, t-test and ordinary least square (OLS) regression. The mean profit of the enterprises using microfinance is ₦16.8m, while for the non-users of microfinance is ₦5.9m. The mean profit of microfinance users is statistically different from the non-users. The result of the logit model specified for the determinant of access to microfinance showed that three of specified variables- educational status of the enterprise head, credit utilisation and volume of business investment are significant at P < 0.01. Enterprises with many years of experience, highly educated enterprise heads and high volume of business investment have more potential access to microfinance. The OLS regression model indicated that three parameters namely number of school years, the volume of business investment and (dummy) participation in microfinance were found to be significant at P < 0.05. These variables are therefore significant determinants of impacts of microfinance on profit level in the study area. The study, therefore, concludes and recommends that to improve the status of small and medium scale enterprises for an increase in profit, the full benefit of access to microfinance can be enhanced through investment in social infrastructure and human capital development. Also, concerted efforts should be made to encouraged non-users of microfinance among SMEs to use it in order to boost their profit.

Keywords: credit utilisation, logit model, microfinance, small and medium enterprises

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Authors: Can Huang, Xiaoliang Wang, Qingquan Liu

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Soil‒water coupling is an important process in landslide-generated impulse waves (LGIW) problems, accompanied by large deformation of soil, strong interface coupling and three-dimensional effect. A meshless particle method, smooth particle hydrodynamics (SPH) has great advantages in dealing with complex interface and multiphase coupling problems. This study presents an improved soil‒water coupled model to simulate LGIW problems based on an open source code DualSPHysics (v4.0). Aiming to solve the low efficiency problem in modeling real large-scale LGIW problems, graphics processing unit (GPU) acceleration technology is implemented into this code. An experimental example, subaerial landslide-generated water waves, is simulated to demonstrate the accuracy of this model. Then, the Huangtian LGIW, a real large-scale LGIW problem is modeled to reproduce the entire disaster chain, including landslide dynamics, fluid‒solid interaction, and surge wave generation. The convergence analysis shows that a particle distance of 5.0 m can provide a converged landslide deposit and surge wave for this example. Numerical simulation results are in good agreement with the limited field survey data. The application example of the Huangtian LGIW provides a typical reference for large-scale LGIW assessments, which can provide reliable information on landslide dynamics, interface coupling behavior, and surge wave characteristics.

Keywords: soil‒water coupling, landslide-generated impulse wave, large-scale, SPH

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Authors: Z. Abdessemed, N. Messaâdia, M. Houhamdi

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The PAH (Polycyclic Aromatic Hydrocarbons) represent a persistent source of pollution for oil field soils. Their degradation, essentially dominated by the aerobic bacterial and fungal flora, exhibits certain aspects for remediation of these soils microbial oxygenases have, as their substrates, a large range of PAH. The variety and the performance of these enzymes allow the initiation of the biodegradation of any PAH through many different metabolic pathways. These pathways are very important for the recycling of the PAH in the biosphere, where substances supposed indigestible by living organisms are rapidly transformed into simples compounds, directly assimilated by the intermediate metabolism of other microorganisms.

Keywords: polycyclic aromatic hydrocarbons, microbial oxygenases, biodegradation, metabolic pathways

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Authors: Nuha Alamro

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Besides achieving of weight loss, Bariatric surgery (BS) shown metabolic improvement including reduction of cardiovascular disease, insulin resistance and diabetes. This study aimed to measure BS effects on Framingham Risk Score (FRS) and metabolic syndrome (MetS) among patients who underwent BS. Additionally, to determine the effect of BS on TSH among euthyroid obese patients. A Retrospective follow-up study was conducted in King Abdullah Medical City. A total of 160 participants who underwent BS and completed one year of follow ups. Medical history, biochemical, anthropometric, and hormonal parameters were evaluated at baseline and 3-12 months after BS. International Diabetes Federation (IDF) criteria were used to diagnose MetS pre and postoperative. The mean age of participants was 41.9 ± 10.6 with Body Mass Index (BMI) of 48.8 ± 7.3. After 3 months, Systolic, Diastolic blood pressure (SBP, DBP), glycated haemoglobin (HBA1C), Low-density lipoprotein (LDL), cholesterol, triglycerides and Thyroid stimulating hormone (TSH) were significantly decrease (P < 0.001). Significant decrease was seen in Mets, BMI, FRS, SBP, DBP, HBA1C, LDL, triglycerides, cholesterol, liver enzyme, with significant increase in high-density lipoprotein (HDL) level 12 months post-op (P < 0.001). After 1 year, the prevalence of MetS, DM, HTN, FRS were significantly decrease from 72.5%, 43.1%, 78.1%, 11.4 to 16.3%, 9.4%, 22.5% and 5.4, respectively. Besides achieving substantial weight loss, MetS resolution was linked to improvement in cardiovascular risk profile.

Keywords: bariatric surgery, cardiovascular disease, metabolic syndrome, thyroid stimulating hormone

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Authors: Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Piet Jones, Nancy Engle, David Kainer, Wellington Muchero, Daniel Jacobson, Timothy J. Tschaplinski

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Uridine diphosphate-glycosyltransferases (UGTs) are enzymes that catalyze sugar transfer to a variety of plant metabolites. UGT substrates, which include plant secondary metabolites involved in lignification, demonstrate new activities and incorporation when glycosylated. Knowledge of UGT function, substrate specificity, and enzyme products is important for plant engineering efforts, especially related to increasing plant biomass through lignification. UGTs in Populus trichocarpa, a biofuel feedstock, and model woody plant, were selected from a pool of gene candidates using rapid prioritization strategies. A functional genomics workflow, consisting of a metabolite genome-wide association study (mGWAS), expression of synthetic codon-optimized genes, and high-throughput biochemical assays with mass spectrometry-based analysis, was developed for determining the substrates and products of previously-uncharacterized enzymes. A total of 40 UGTs from P. trichocarpa were profiled, and the biochemical assay results were compared to predicted mGWAS connections. Assay results confirmed seven of 11 leaf mGWAS associations and demonstrated varying levels of substrate specificity among candidate UGTs. P. trichocarpa UGT substrate processing confirms the role of these newly-characterized enzymes in lignan, flavonoid, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress responses.

Keywords: Populus, metabolite-gene associations, GWAS, bio feedstocks, glycosyltransferase

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Authors: Anas H. Aljemely, Jianping Xuan

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Rolling bearing fault diagnosis plays a pivotal issue in the rotating machinery of modern manufacturing. In this research, a raw vibration signal and improved deep learning method for bearing fault diagnosis are proposed. The multi-dimensional scales of raw vibration signals are selected for evaluation condition monitoring system, and the deep learning process has shown its effectiveness in fault diagnosis. In the proposed method, employing an Exponential linear unit (ELU) layer in a convolutional neural network (CNN) that conducts the identical function on positive data, an exponential nonlinearity on negative inputs, and a particular convolutional operation to extract valuable features. The identification results show the improved method has achieved the highest accuracy with a 100-dimensional scale and increase the training and testing speed.

Keywords: bearing fault prognostics, developed CNN model, multiple-scale evaluation, deep learning features

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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Authors: Yi-Hsiang Pan, Chen-Hui Huang, Ching-Hsiang Chen, Wei-Ting Hsu

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The purposes of the study were to explore the students' learning effect of physical education curriculum between merging Teaching Personal and Social Responsibility (TPSR) with sport education model and TPSR with traditional teaching model, which these learning effects included sport self-efficacy, sport enthusiastic, group cohesion, responsibility and game performance. The participants include 3 high school physical education teachers and 6 physical education classes, 133 participants with experience group 75 students and control group 58 students, and each teacher taught an experimental group and a control group for 16 weeks. The research methods used questionnaire investigation, interview, focus group meeting. The research instruments included personal and social responsibility questionnaire, sport enthusiastic scale, group cohesion scale, sport self-efficacy scale and game performance assessment instrument. Multivariate Analysis of covariance and Repeated measure ANOVA were used to test difference of students' learning effects between merging TPSR with sport education model and TPSR with traditional teaching model. The findings of research were: 1) The sport education model with TPSR could improve students' learning effects, including sport self-efficacy, game performance, sport enthusiastic, group cohesion and responsibility. 2) The traditional teaching model with TPSR could improve students' learning effect, including sport self-efficacy, responsibility and game performance. 3) the sport education model with TPSR could improve more learning effects than traditional teaching model with TPSR, including sport self-efficacy, sport enthusiastic,responsibility and game performance. 4) Based on qualitative data about learning experience of teachers and students, sport education model with TPSR significant improve learning motivation, group interaction and game sense. The conclusions indicated sport education model with TPSR could improve more learning effects in physical education curriculum. On other hand, the curricular projects of hybrid TPSR-Sport Education model and TPSR-Traditional Teaching model are both good curricular projects of moral character education, which may be applied in school physical education.

Keywords: character education, sport season, game performance, sport competence

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Authors: Enrique Castañeda, Tomas Hernadez, Mario Ulloa

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Recent studies related to submarine pipelines under high pressure, temperature and buried, forces us to make bibliographical and documentary research to make us of references applicable to our problem. This paper presents an experimental methodology to the implementation of results obtained in a scale model, bibliography soil mechanics and finite element simulation. The model consists of a tank of 0.60 x 0.90 x 0.60 basis equipped high side windows, tires and digital hardware devices for measuring different variables to be applied to the model, where the mechanical properties of the soil are determined, simulation of drag a pipeline buried in a non-cohesive seafloor of the Gulf of Mexico, estimate the failure surface and application of each of the variables for the determination of mechanical elements.

Keywords: static friction coefficient, maximum passive force resistant soil, normal, tangential stress

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Authors: Omar Qaftan

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Earthquakes can cause tremendous loss of human life and can result in severe damage to a several of civil engineering structures especially the tall buildings. The response of a multistory structure subjected to earthquake loading is a complex task, and it requires to be studied by physical and numerical modelling. For many circumstances, the scale models on shaking table may be a more economical option than the similar full-scale tests. A shaking table apparatus is a powerful tool that offers a possibility of understanding the actual behaviour of structural systems under earthquake loading. It is required to use a set of scaling relations to predict the behaviour of the full-scale structure. Selecting the scale factors is the most important steps in the simulation of the prototype into the scaled model. In this paper, the principles of scaling modelling procedure are explained in details, and the simulation of scaled multi-storey concrete structure for dynamic studies is investigated. A procedure for a complete dynamic simulation analysis is investigated experimentally and numerically with a scale factor of 1/50. The frequency domain accounting and lateral displacement for both numerical and experimental scaled models are determined. The procedure allows accounting for the actual dynamic behave of actual size porotype structure and scaled model. The procedure is adapted to determine the effects of the tall multi-storey structure on a raft foundation. Four generated accelerograms were used as inputs for the time history motions which are in complying with EC8. The output results of experimental works expressed regarding displacements and accelerations are compared with those obtained from a conventional fixed-base numerical model. Four-time history was applied in both experimental and numerical models, and they concluded that the experimental has an acceptable output accuracy in compare with the numerical model output. Therefore this modelling methodology is valid and qualified for different shaking table experiments tests.

Keywords: structure, raft, soil, interaction

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Authors: Mustafa M. Donma, Orkide Donma

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A well-defined insulin resistance (IR) is one of the requirements for the good understanding and evaluation of metabolic syndrome (MetS). However, underlying causes for the development of IR are not clear. Endothelial dysfunction also participates in the pathogenesis of this disease. IR indices are being determined in various obesity groups and also in diagnosing MetS. Components of MetS have been well established and used in adult studies. However, there are some ambiguities particularly in the field of pediatrics. The aims of this study were to compare the performance of fasting blood glucose (FBG), one of MetS components, with some other IR indices and check whether FBG may be replaced by some other parameter or ratio for a better evaluation of pediatric MetS. Five-hundred and forty-nine children were involved in the study. Five groups were constituted. Groups 109, 40, 100, 166, 110, 24 children were included in normal-body mass index (N-BMI), overweight (OW), obese (OB), morbid obese (MO), MetS with two components (MetS2) and MetS with three components (MetS3) groups, respectively. Age and sex-adjusted BMI percentiles tabulated by World Health Organization were used for the classification of obesity groups. MetS components were determined. Aside from one of the MetS components-FBG, eight measures of IR [homeostatic model assessment of IR (HOMA-IR), homeostatic model assessment of beta cell function (HOMA-%β), alanine transaminase-to-aspartate transaminase ratio (ALT/AST), alanine transaminase (ALT), insulin (INS), insulin-to-FBG ratio (INS/FBG), the product of fasting triglyceride and glucose (TyG) index, McAuley index] were evaluated. Statistical analyses were performed. A p value less than 0.05 was accepted as the statistically significance degree. Mean values for BMI of the groups were 15.7 kg/m², 21.0 kg/m², 24.7 kg/m², 27.1 kg/m², 28.7 kg/m², 30.4 kg/m² for N-BMI, OW, OB, MO, MetS2, MetS3, respectively. Differences between the groups were significant (p < 0.001). The only exception was MetS2-MetS3 couple, in spite of an increase detected in MetS3 group. Waist-to-hip circumference ratios significantly differed only for N-BMI vs, OB, MO, MetS2; OW vs MO; OB vs MO, MetS2 couples. ALT and ALT/AST did not differ significantly among MO-MetS2-MetS3. HOMA-%β differed only between MO and MetS2. INS/FBG, McAuley index and TyG were not significant between MetS2 and MetS3. HOMA-IR and FBG were not significant between MO and MetS2. INS was the only parameter, which showed statistically significant differences between MO-MetS2, MO-MetS3, and MetS2-MetS3. In conclusion, these findings have suggested that FBG presently considered as one of the five MetS components, may be replaced by INS during the evaluation of pediatric morbid obesity and MetS.

Keywords: children, insulin resistance indices, metabolic syndrome, obesity

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Authors: D. Touil, L. Ouadah

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An industrial model of cement grinding circuit is proposed on the basis of sampling surveys undertaken in the Meftah cement plant in Algiers, Algeria. The ball mill is described by a series of equal fully mixed stages that incorporates the effect of air sweeping. The kinetic parameters of this material in the energy normalized form obtained using the data of batch dry ball milling are taken into account in developing the present scale-up procedure. The dynamic separator is represented by the air classifier selectivity equation corrected by empirical factors. The model is incorporated in computer program that predict full size distributions and mass flow rates for all streams in a circuit under a particular set of operating conditions.

Keywords: grinding circuit, clinker, cement, modeling, population balance, energy

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Authors: F. Arslan, S.D. Guven, A. Özcan, H. Vatansev, Ö. Taşgin

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Weight, hypertension and dyslipidemia control and increased physical activity are required for the treatment of metabolic syndrome (METS). The purpose of this study was to investigate the effect of core exercise, reflexology and intake chrome picolinate on METS. This study comprised a twelve-week randomized controlled trial. A total of 25 university workers with metabolic risk factors participated in this study voluntarily. They were randomly divided into three groups: Those undertaking a core exercise program (n=7), reflexology intervention group (n=8) and intake chrome group (n=10). The subjects took part in a core exercise program for one hour per day, three days a week and a reflexology interfered for thirty minutes per day, one days a week and chrome group took chrome picolinate every day in week for twelve weeks. The components of metabolic syndrome were analyzed before and after the completion of all the intervention. There were significant differences at pre-prandial blood glucose in the core exercise group and at systolic blood pressure in chrome group after the twelve week interventions (p < 0.005). While High Density Lipoprotein (HDL) excluding the components of METS decreased after the interventions on the all groups; levels of HDL and the other components of METS decreased in reflexology group. There was a clear response to the twelve-week interventions in terms of METS control. Besides, the reflexology intervention should not be applied to individuals with low HDL levels and core exercise and intake chrome picolinate suggested to improve the components of METS.

Keywords: blood pressure, body mass index, exercise, METS, pre-prandial blood glucose

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Authors: Jae Woong Sull, Sun Ha Jee

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High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Nataly De La Pava, Christian S. A. Silva-Torres, Arodí P. Favaris, José Maurício S. Bento

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The lady beetles Tenuisvalve notata and Cryptolaemus montrouzieri are important predators of mealybugs (Hemiptera: Pseudococcidae). Similar to the prey, these lady beetles produce wax filaments that cover their body during the larval stage. It has been hypothesized that lady beetle body wax chemical profiles are similar to their prey as i) a mechanism of camouflage and ii) conveying protection to the lady beetle larvae against aphid-tending predatory ants. In this study, we tested those hypotheses for the predators T. notata and C. montrouzieri and two mealybug prey species, Ferissia dasyrilii, and Planococcus citri. Next, we evaluated the influence of feeding on cuticular chemistry during predator development and identified possible metabolic costs associated with wax production. Cuticular wax samples were analyzed by GC-MS and GC-FID. Also, the metabolic cost linked to wax production was evaluated in the 4th instar larvae of the two predators when subjected to body wax removal from 0 to 4 times. Results showed that predator body wax profiles are not similar to the chemical profile of prey body wax. There was a metabolic cost associated with wax removal; predators (male and female) showed a significant reduction in adult body weight when the wax was removed. This suggests the reallocation of energy to wax replacement instead of growth. In addition, it was detected effects of wax removal on fecundity and egg viability. The results do not support the hypothesis that predators mimic the cuticular wax composition of prey as a means of camouflage.

Keywords: biological control, body wax, coccinellids, cuticular hydrocarbons, metabolism cost, reproduction

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Authors: Jingjue Bao, Ye Li, Yujie Qi

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The explosive growth of ride-hailing has reshaped residents' travel behavior and plays a crucial role in urban mobility within the built environment. Contributing to the research of the spatial variation of ride-hailing demand and its relationship to the built environment and socioeconomic factors, this study utilizes multi-source data from Haikou, China, to construct a Multi-scale Geographically Weighted Regression model (MGWR), considering spatial scale heterogeneity. The regression results showed that MGWR model was demonstrated superior interpretability and reliability with an improvement of 3.4% on R2 and from 4853 to 4787 on AIC, compared with Geographically Weighted Regression model (GWR). Furthermore, to precisely identify the surrounding environment of sampling point, DeepLabv3+ model is employed to segment street-level images. Features extracted from these images are incorporated as variables in the regression model, further enhancing its rationality and accuracy by 7.78% improvement on R2 compared with the MGWR model only considered region-level variables. By integrating multi-scale geospatial data and utilizing advanced computer vision techniques, this study provides a comprehensive understanding of the spatial dynamics between ride-hailing demand and the urban built environment. The insights gained from this research are expected to contribute significantly to urban transportation planning and policy making, as well as ride-hailing platforms, facilitating the development of more efficient and effective mobility solutions in modern cities.

Keywords: travel behavior, ride-hailing, spatial relationship, built environment, street-level image

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Authors: C. Pallis

Abstract:

Induced-Gravity inflation is a model of chaotic inflation where the inflaton is identified with a Higgs-like modulus whose the vacuum expectation value controls the gravitational strength. Thanks to a strong enough coupling between the inflaton and the Ricci scalar curvature, inflation is attained even for subplanckian values of the inflaton with the corresponding effective theory being valid up to the Planck scale. In its simplest realization, induced-gravity inflation is based on a quatric potential and a quadratic non-minimal coupling and the inflationary observables turn out to be in agreement with the Planck data. Its supersymmetrization can be formulated within no-scale Supergravity employing two gauge singlet chiral superfields and applying a continuous $R$ and a discrete Zn symmetry to the proposed superpotential and Kahler potential. Modifying slightly the non-minimal coupling to Gravity, the model can account for the recent results of BICEP2. These modifications can be also accommodated beyond the no-scale SUGRA considering the fourth order term of the Kahler potential which mixes the inflaton with the accompanying non-inflaton field and small deviations from the prefactor $-3$ encountered in the adopted Kahler potential.

Keywords: cosmology, supersymmetric models, supergravity, modified gravity

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Authors: J. M. Lee, W. R. Noh, C. Y. Kim, M. G. Lee

Abstract:

Delamination of oxide scale has been often discovered at the interface between Fe carbon steel and oxide scale. Among several mechanisms of this delamination behavior, the normal tensile stress to the substrate-scale interface has been described as one of the main factors. The stress distribution at the interface is also known to be affected by thermal expansion mismatch between substrate and oxide scale, creep behavior during cooling and the geometry of the interface. In this study, stress states near the interface in a Fe carbon steel with oxide scale have been investigated using FE simulations. The thermal and mechanical properties of oxide scales are indicated in literature and Fe carbon steel is measured using tensile testing machine. In particular, the normal and shear stress components developed at the interface during bending are investigated. Preliminary numerical sensitivity analyses are provided to explain the effects of the interface geometry and oxide thickness on the delamination behavior.

Keywords: oxide scale, delamination, Fe analysis, roughness, thickness, stress state

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Authors: Kingsley Nnaemeka Ogbu, Constantine Mbajiorgu

Abstract:

Vegetation has a marked effect on runoff and has become an important component in hydrologic model. The watershed Resources Management (WRM) model, a process-based, continuous, distributed parameter simulation model developed for hydrologic and soil erosion studies at the watershed scale lack a crop growth component. As such, this model assumes a constant parameter values for vegetation and hydraulic parameters throughout the duration of hydrologic simulation. Our approach is to develop a crop growth algorithm based on the original plant growth model used in the Environmental Policy Integrated Climate Model (EPIC) model. This paper describes the development of a single crop growth model which has the capability of simulating all crops using unique parameter values for each crop. Simulated crop growth processes will reflect the vegetative seasonality of the natural watershed system. An existing model was employed for evaluating vegetative resistance by hydraulic and vegetative parameters incorporated into the WRM model. The improved WRM model will have the ability to evaluate the seasonal variation of the vegetative roughness coefficient with depth of flow and further enhance the hydrologic model’s capability for accurate hydrologic studies

Keywords: crop yield, roughness coefficient, PAR, WRM model

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Authors: N. Othman, J. Ujang, M. N. Ismail, R. Noordin, B. H. Lim

Abstract:

Amoebiasis is caused by the Entamoeba histolytica and still endemic in many parts of the tropical region, worldwide. Currently, there is no available vaccine against amoebiasis. Hence, there is an urgent need to develop a vaccine. The excretory secretory antigen (ESA) of E. histolytica is a suitable biomarker for the vaccine candidate since it can modulate the host immune response. Hence, the objective of this study is to identify the proteome of the ESA towards finding suitable biomarker for the vaccine candidate. The non-gel based and gel-based proteomics analyses were performed to identify proteins. Two kinds of mass spectrometry with different ionization systems were utilized i.e. LC-MS/MS (ESI) and MALDI-TOF/TOF. Then, the functional proteins classification analysis was performed using PANTHER software. Combination of the LC -MS/MS for the non-gel based and MALDI-TOF/TOF for the gel-based approaches identified a total of 273 proteins from the ESA. Both systems identified 29 similar proteins whereby 239 and 5 more proteins were identified by LC-MS/MS and MALDI-TOF/TOF, respectively. Functional classification analysis showed the majority of proteins involved in the metabolic process (24%), primary metabolic process (19%) and protein metabolic process (10%). Thus, this study has revealed the proteome the E. histolytica ESA and the identified proteins merit further investigations as a vaccine candidate.

Keywords: E. histolytica, ESA, proteomics, biomarker

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Authors: Chuan Yang, Jing Bie, Panagiotis Psimoulis, Zhong Wang

Abstract:

Modelling and understanding vehicle volume distribution over the urban network are essential for urban design and transport planning. The space syntax approach was widely applied as the main conceptual and methodological framework for contemporary vehicle volume models with the help of the statistical method of multiple regression analysis (MRA). However, the MRA model with space syntax variables shows a limitation in vehicle volume predicting in accounting for the crossed effect of the urban configurational characters and socio-economic factors. The aim of this paper is to construct models by interacting with the combined impact of the street network structure and socio-economic factors. In this paper, we present a multilevel linear (ML) and an agent-based (AB) vehicle volume model at an urban scale interacting with space syntax theoretical framework. The ML model allowed random effects of urban configurational characteristics in different urban contexts. And the AB model was developed with the incorporation of transformed space syntax components of the MRA models into the agents’ spatial behaviour. Three models were implemented in the same urban environment. The ML model exhibit superiority over the original MRA model in identifying the relative impacts of the configurational characters and macro-scale socio-economic factors that shape vehicle movement distribution over the city. Compared with the ML model, the suggested AB model represented the ability to estimate vehicle volume in the urban network considering the combined effects of configurational characters and land-use patterns at the street segment level.

Keywords: space syntax, vehicle volume modeling, multilevel model, agent-based model

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Authors: Avinoam Rabinovich

Abstract:

CO₂ geological storage is a proven technology for reducing anthropogenic carbon emissions, which is paramount for achieving the ambitious net zero emissions goal. Core flooding experiments are an important step in any CO₂ storage project, allowing us to gain information on the flow of CO₂ and brine in the porous rock extracted from the reservoir. This information is important for understanding basic mechanisms related to CO₂ geological storage as well as for reservoir modeling, which is an integral part of a field project. In this work, a different method for constructing accurate models of CO₂-brine core flooding will be presented. Results for synthetic cases and real experiments will be shown and compared with numerical models to exhibit their predictive capabilities. Furthermore, the various mechanisms which impact the CO₂ distribution and trapping in the rock samples will be discussed, and examples from models and experiments will be provided. The new method entails solving an inverse problem to obtain a three-dimensional permeability distribution which, along with the relative permeability and capillary pressure functions, constitutes a model of the flow experiments. The model is more accurate when data from a number of experiments are combined to solve the inverse problem. This model can then be used to test various other injection flow rates and fluid fractions which have not been tested in experiments. The models can also be used to bridge the gap between small-scale capillary heterogeneity effects (sub-core and core scale) and large-scale (reservoir scale) effects, known as the upscaling problem.

Keywords: CO₂ geological storage, residual trapping, capillary heterogeneity, core flooding, CO₂-brine flow

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Salim Belouettar, Kodjo Attipou

Abstract:

The thermal wrinkling behavior of thin membranes is investigated. The Fourier double scale series are used to deduce the macroscopic membrane wrinkling equations. The obtained equations account for the global and local wrinkling modes. Numerical examples are conducted to assess the validity of the approach developed. Compared to the finite element full model, the present model needs only few degrees of freedom to recover accurately the bifurcation curves and wrinkling paths. Different parameters such as membrane’s aspect ratio, wave number, pre-stressed membranes are discussed from a numerical point of view and the properties of the wrinkles (critical load, wavelength, size and location) are presented.

Keywords: wrinkling, thermal stresses, Fourier series, thin membranes

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Authors: J. Sharon Mano Pappu, Sathyanarayana N. Gummadi

Abstract:

Growth of Debaryomyces nepalensis on mixed substrates in batch culture follows diauxic pattern of completely utilizing glucose during the first exponential growth phase, followed by an intermediate lag phase and a second exponential growth phase consuming xylose. The present study deals with the development of cybernetic mathematical model for prediction of xylitol production and yield. Production of xylitol from xylose in batch fermentation is investigated in the presence of glucose as the co-substrate. Different ratios of glucose and xylose concentrations are assessed to study the impact of multi substrate on production of xylitol in batch reactors. The parameters in the model equations were estimated from experimental observations using integral method. The model equations were solved simultaneously by numerical technique using MATLAB. The developed cybernetic model of xylose fermentation in the presence of a co-substrate can provide answers about how the ratio of glucose to xylose influences the yield and rate of production of xylitol. This model is expected to accurately predict the growth of microorganism on mixed substrate, duration of intermediate lag phase, consumption of substrate, production of xylitol. The model developed based on cybernetic modelling framework can be helpful to simulate the dynamic competition between the metabolic pathways.

Keywords: co-substrate, cybernetic model, diauxic growth, xylose, xylitol

Procedia PDF Downloads 303