Search results for: genome scale model

Authors: Jali Octariady, Ida Herliningsih, Ade K. Mulyana, Annisa Fitria, Diaz C. K. Yuwana

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Awareness of the importance large-scale maps for development of a country is growing in all walks of life, especially for governments in Indonesia. Various parties, especially local governments throughout Indonesia demanded for immediate availability the large-scale maps of 1:5000 for regional development. But in fact, the large-scale maps of 1:5000 is only available less than 5% of the entire territory of Indonesia. Unavailability precise GCP at the entire territory of Indonesia is one of causes of slow availability the large scale maps of 1:5000. This research was conducted to find an alternative solution to this problem. This study was conducted to assess the accuracy of ArcGIS base maps coordinate when it shall be used as GCP for creating a map scale of 1:5000. The study was conducted by comparing the GCP coordinate from Field survey using GPS Geodetic than the coordinate from ArcGIS basemaps in various locations in Indonesia. Some areas are used as a study area are Lombok Island, Kupang City, Surabaya City and Kediri District. The differences value of the coordinates serve as the basis for assessing the accuracy of ArcGIS basemaps coordinates. The results of the study at various study area show the variation of the amount of the coordinates value given. Differences coordinate value in the range of millimeters (mm) to meters (m) in the entire study area. This is shown the inconsistency quality of ArcGIS base maps coordinates. This inconsistency shows that the coordinate value from ArcGIS Basemaps is careless. The Careless coordinate from ArcGIS Basemaps indicates that its cannot be used as GCP for large-scale mapping on the entire territory of Indonesia.

Keywords: accuracy, ArcGIS base maps, GCP, large scale maps

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Authors: Daria Grechishnikova, Maria Poptsova

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Transposable elements play an important role in the evolution of various species from bacteria to human. Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs) are two major classes of retrotransposons that occupy a considerable part of any genome and their copy numbers can range form several hundreds to a million. Both LINEs and SINEs multiply through a copy-and-paste mechanism. LINEs encode proteins, which make them capable of self-propagation while SINEs are parasitic and require the machinery of LINEs to multiply. The mechanisms how LINE and SINE RNA is recognized by the LINE-encoded reverse transcriptase (RT) remain unclear. For some SINE-LINE pairs, it was shown that they share a common 3’-end with a stem-loop structure. Majority of the SINE-LINE pairs do not have a common 3’-end. Recently we have shown that in the human genome Alu-L1 pairs have structurally similar stem-loop structure at the 3’-end. Here we extended our analysis to a wide range of species and analyzed LINEs from 161 different species from Repbase and 217 SINE sequences from SINEBase. It appeared that all of the analyzed sequences contained stem-loop structures at the 3’-end. Here we conclude that it is very likely that a common evolutionary mechanism of transposon RNA recognition requires the presence of stem-loop structures at their 3’-end.

Keywords: LINE, SINE, mechanisms of retrotransposition, retrotransposons, stem-loop, stem-loop structures, transposons

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Authors: Gideon J. Bonthuys, Marco van Dijk, Jay N. Bhagwan

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Small scale hydropower used to play a very important role in the provision of energy to urban and rural areas of South Africa. The national electricity grid, however, expanded and offered cheap, coal generated electricity and a large number of hydropower systems were decommissioned. Unfortunately, large numbers of households and communities will not be connected to the national electricity grid for the foreseeable future due to high cost of transmission and distribution systems to remote communities due to the relatively low electricity demand within rural communities and the allocation of current expenditure on upgrading and constructing of new coal fired power stations. This necessitates the development of feasible alternative power generation technologies. A feasibility and implementation model was developed to assist in designing and financially evaluating small-scale hydropower (SSHP) plants. Several sites were identified using the model. The SSHP plants were designed for the selected sites and the designs for the different selected sites were priced using pricing models (civil, mechanical and electrical aspects). Following feasibility studies done on the designed and priced SSHP plants, a feasibility analysis was done and a design chart developed for future similar potential SSHP plant projects. The methodology followed in conducting the feasibility analysis for other potential sites consisted of developing cost and income/saving formulae, developing net present value (NPV) formulae, Capital Cost Comparison Ratio (CCCR) and levelised cost formulae for SSHP projects for the different types of plant installations. It included setting up a model for the development of a design chart for a SSHP, calculating the NPV, CCCR and levelised cost for the different scenarios within the model by varying different parameters within the developed formulae, setting up the design chart for the different scenarios within the model and analyzing and interpreting results. From the interpretation of the develop design charts for feasible SSHP in can be seen that turbine and distribution line cost are the major influences on the cost and feasibility of SSHP. High head, short transmission line and islanded mini-grid SSHP installations are the most feasible and that the levelised cost of SSHP is high for low power generation sites. The main conclusion from the study is that the levelised cost of SSHP projects indicate that the cost of SSHP for low energy generation is high compared to the levelised cost of grid connected electricity supply; however, the remoteness of SSHP for rural electrification and the cost of infrastructure to connect remote rural communities to the local or national electricity grid provides a low CCCR and renders SSHP for rural electrification feasible on this basis.

Keywords: cost, feasibility, rural electrification, small-scale hydropower

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Authors: Ahmed. A. Hossam Eldin, Karim H. Youssef, Kareem M. AboRas

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Recent current rapid industrial development and energy shortage are essential problems, which face most of the developing countries. Moreover, increased prices of fossil fuel and advanced energy conversion technology lead to the need for renewable energy resources. A study, modelling and simulation of an outdoor micro scale stand alone wind turbine was carried out. For model validation an experimental study was applied. In this research the aim was to clarify effects of real outdoor operating conditions and the instantaneous fluctuations of both wind direction and wind speed on the actual produced power. The results were compared with manufacturer’s data. The experiments were carried out in Borg Al-Arab, Alexandria. This location is on the north Western Coast of Alexandria. The results showed a real max output power for outdoor micro scale wind turbine, which is different from manufacturer’s value. This is due to the fact that the direction of wind speed is not the same as that of the manufacturer’s data. The measured wind speed and direction by the portable metrological weather station anemometer varied with time. The blade tail response could not change the blade direction at the same instant of the wind direction variation. Therefore, designers and users of micro scale wind turbine stand alone system cannot rely on the maker’s name plate data to reach the required power.

Keywords: micro-turbine, wind turbine, inverters, renewable energy, hybrid system

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Authors: Marc Toutain, Pascale Leconte, Antoine Gauthier

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Introduction: Eating Disorders (ED), such as anorexia, bulimia, and binge eating, are psychiatric illnesses that mostly affect young people. The main symptoms concern eating (restriction, excessive food intake) and weight control behaviors (laxatives, vomiting). Psychological comorbidities (depression, executive function disorders, etc.) and problematic behaviors toward physical activity (PA) are commonly associated with ED. Acquaintances on ED risk factors are still lacking, and more community sample studies are needed to improve prevention and early detection. To our knowledge, studies are needed to specifically investigate the link between ED risk level, PA, and psychological risk factors in a community sample of adolescents. The aim of this study is to assess the relation between ED risk level, exercise (type, frequency, and motivations for engaging in exercise), and psychological factors based on the Jacobi risk factors model. We suppose that a high risk of ED will be associated with the practice of high caloric cost PA, motivations oriented to weight and shape control, and psychological disturbances. Method: An online survey destined for students has been sent to several middle schools and colleges in northwest France. This survey combined several questionnaires, the Eating Attitude Test-26 assessing ED risk; the Exercise Motivation Inventory–2 assessing motivations toward PA; the Hospital Anxiety and Depression Scale assessing anxiety and depression, the Contour Drawing Rating Scale; and the Body Esteem Scale assessing body dissatisfaction, Rosenberg Self-esteem Scale assessing self-esteem, the Exercise Dependence Scale-Revised assessing PA dependence, the Multidimensional Assessment of Interoceptive Awareness assessing interoceptive awareness and the Frost Multidimensional Perfectionism Scale assessing perfectionism. Machine learning analysis will be performed in order to constitute groups with a tree-based model clustering method, extract risk profile(s) with a bootstrap method comparison, and predict ED risk with a prediction method based on a decision tree-based model. Expected results: 1044 complete records have already been collected, and the survey will be closed at the end of May 2022. Records will be analyzed with a clustering method and a bootstrap method in order to reveal risk profile(s). Furthermore, a predictive tree decision method will be done to extract an accurate predictive model of ED risk. This analysis will confirm typical main risk factors and will give more data on presumed strong risk factors such as exercise motivations and interoceptive deficit. Furthermore, it will enlighten particular risk profiles with a strong level of proof and greatly contribute to improving the early detection of ED and contribute to a better understanding of ED risk factors.

Keywords: eating disorders, risk factors, physical activity, machine learning

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Authors: Maryam Beiranvand

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Multi-drug resistance in various microorganisms has increased globally in many healthcare facilities. Less effective antimicrobial activity of drug therapies for infection control becomes trouble. Since 1980, no new type of antimicrobial drug has been identified, even though combinations of antibiotic drugs have been discovered almost every decade. Between 1981 and 2006, over 70% of novel pharmaceuticals and chemical agents came from natural sources. Microorganisms have yielded almost 22,000 natural compounds. The identification of antimicrobial components from endophytes bacteria could help overcome the threat posed by multi-drug resistant strains. The project aims to analyze and identify antimicrobial peptides isolated from entophytic bacteria and their activity against multidrug-resistant Gram-negative bacteria in South Korea. Endophytic Paenibacillus polymyxa. 4G3 isolated from the plant, Gynura procumbery exhibited considerable antimicrobial activity against Methicillin-resistant Staphylococcus aureus, and Escherichia coli. The Rapid Annotations using Subsystems Technology showed that the total size of the draft genome was 5,739,603bp, containing 5178 genes with 45.8% G+C content. Genome annotation using antiSMASH version 6.0.0 was performed, which predicted the most common types of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). In this study, diethyl aminoethyl cellulose (DEAEC) resin was used as the first step in purifying for unknown peptides, and then the target protein was identified using hydrophilic and hydrophobic solutions, optimal pH, and step-by-step tests for antimicrobial activity. This crude was subjected to C18 chromatography and elution with 0, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 100% methanol, respectively. Only the fraction eluted with 20% -60% methanol demonstrated good antimicrobial activity against MDR E. coli. The concentration of the active fragment was measured by the Brad-ford test, and Protein A280 - Thermo Fisher Scientific at the end by examining the SDS PAGE Resolving Gel, 10% Acrylamide and purity were confirmed. Our study showed that, based on the combined results of the analysis and purification. P polymyxa. 4G3 has a high potential exists for producing novel functions of polymyxin E and bacitracin against bacterial pathogens.

Keywords: endophytic bacteria, antimicrobial activity, antimicrobial peptide, whole genome sequencing analysis, multi -drug resistance gram negative bacteria

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Authors: Norsyamimi Hassim, Masturah Markom

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Supercritical fluid extraction (SFE) has been known as a sustainable and safe extraction technique for plant extraction due to the minimal usage of organic solvent. In this study, a scale-up process for the selected herbal plant (Phyllanthus niruri) was investigated by using supercritical carbon dioxide (SC-CO2) with food-grade (ethanol-water) cosolvent. The quantification of excess ethanol content in the final dry extracts was conducted to determine the safety of enriched extracts. The extraction yields obtained by scale-up SFE unit were not much different compared to the predicted extraction yields with an error of 2.92%. For component contents, the scale-up extracts showed comparable quality with laboratory-scale experiments. The final dry extract showed that the excess ethanol content was 1.56% g/g extract. The fish embryo toxicity test (FETT) on the zebrafish embryos showed no toxicity effects by the extract, where the LD50 value was found to be 505.71 µg/mL. Thus, it has been proven that SFE with food-grade cosolvent is a safe extraction technique for the production of bioactive compounds from P. niruri.

Keywords: scale-up, supercritical fluid extraction, enriched extract, toxicity, ethanol content

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Authors: Ehsan Motamedian

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Finding all optimal flux distributions of a metabolic model is an important challenge in systems biology. In this paper, a new algorithm is introduced to identify all alternate optimal solutions of a large scale metabolic network. The algorithm reduces the model to decrease computations for finding optimal solutions. The algorithm was implemented on the Escherichia coli metabolic model to find all optimal solutions for lactate and acetate production. There were more optimal flux distributions when acetate production was optimized. The model was reduced from 1076 to 80 variable fluxes for lactate while it was reduced to 91 variable fluxes for acetate. These 11 more variable fluxes resulted in about three times more optimal flux distributions. Variable fluxes were from 12 various metabolic pathways and most of them belonged to nucleotide salvage and extra cellular transport pathways.

Keywords: flux variability, metabolic network, mixed-integer linear programming, multiple optimal solutions

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Authors: Ritu Raj, Hrishikesh Dubey

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This paper presents the results of the experimental investigations carried out on two intricate plan shaped buildings to evaluate aerodynamic performance of the building. The purpose is to study the associated environment arising due to wind forces in isolated and interference conditions on a model of scale 1:300 with a prototype having 180m height. Experimental tests were carried out at the boundary layer wind tunnel considering isolated conditions with 0° to 180° isolated wind directions and four interference conditions of twin building (separately for both the models). The research has been undertaken in Terrain Category-II, which is the most widely available terrain in India. A comparative assessment of the two models is performed out in an attempt to comprehend the various consequences of diverse conditions that may emerge in real-life situations, as well as the discrepancies amongst them. Experimental results of wind pressure coefficients of Model-1 and Model-2 shows good agreement with various wind incidence conditions with minute difference in the magnitudes of mean Cp. On the basis of wind tunnel studies, it is distinguished that the performance of Model-2 is better than Model-1in both isolated as well as interference conditions for all wind incidences and orientations respectively.

Keywords: interference factor, tall buildings, wind direction, mean pressure-coefficients

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Authors: Vasujeet Singh, Pruthiviraj Nemalipuri, Vivek Vitankar, Harish Chandra Das

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For the correct prediction of thermal and hydraulic performance (bed voidage, suspension density, pressure drop, heat transfer, and combustion kinetics), one should incorporate the correct parameters in the computational fluid dynamics simulation of a fluidized bed gasifier. Scarcity of fossil fuels, and to fulfill the energy demand of the increasing population, researchers need to shift their attention to the alternative to fossil fuels. The current research work focuses on hydrodynamics behavior and gasification of sawdust inside a 2D industrial scale FBG using the Eulerian-Eulerian multifluid model. The present numerical model is validated with experimental data. Further, this model extended for the prediction of gasification characteristics of sawdust by incorporating eight heterogeneous moisture release, volatile cracking, tar cracking, tar oxidation, char combustion, CO₂ gasification, steam gasification, methanation reaction, and five homogeneous oxidation of CO, CH₄, H₂, forward and backward water gas shift (WGS) reactions. In the result section, composition of gasification products is analyzed, along with the hydrodynamics of sawdust and sand phase, heat transfer between the gas, sand and sawdust, reaction rates of different homogeneous and heterogeneous reactions is being analyzed along the height of the domain.

Keywords: devolatilization, Eulerian-Eulerian, fluidized bed gasifier, mathematical modelling, sawdust gasification

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Authors: Mina Hojat Ansari, Kamran Bagheri Lankarani, Mohammad Reza Fattahi, Ali Reza Safarpour

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Irritable bowel syndrome (IBS) is a common bowel disorder which is usually diagnosed through the abdominal pain, fecal irregularities and bloating. Alteration in the intestinal microbial composition is implicating to inflammatory and functional bowel disorders which is recently also noted as an IBS feature. Owing to the potential importance of microbiota implication in both efficiencies of the treatment and prevention of the diseases, we examined the association between the intestinal microbiota and different bowel patterns in a cohort of subjects with IBS and healthy controls. Fresh fecal samples were collected from a total of 50 subjects, 30 of whom met the Rome IV criteria for IBS and 20 Healthy control. Total DNA was extracted and library preparation was conducted following the standard protocol for small whole genome sequencing. The pooled libraries sequenced on an Illumina Nextseq platform with a 2 × 150 paired-end read length and obtained sequences were analyzed using several bioinformatics programs. The majority of sequences obtained in the current study assigned to bacteria. However, our finding highlighted the significant microbial taxa variation among the studied groups. The result, therefore, suggests a significant association of the microbiota with symptoms and bowel characteristics in patients with IBS. These alterations in fecal microbiota could be exploited as a biomarker for IBS or its subtypes and suggest the modification of the microbiota might be integrated into prevention and treatment strategies for IBS.

Keywords: irritable bowel syndrome, intestinal microbiota, small whole genome sequencing, fecal samples, Illumina

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Authors: Mauricio Gracia, Luis Leal, Bharat Verma

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Computational fluid dynamics (CFD) has become nowadays an important tool in the process of hydrodynamic design of modern ships. CFD is used to model any phenomena related to fluid flow in a control volume like a ship or any offshore structure in the sea. In the present study, the current force drag coefficients for a Colombian Navy Frigate in deep and shallow water are estimated through the application of CFD. The study shows the process of simulating the ship current drag coefficients using the CFD simulations method, which is conducted using STAR-CCM+ software package. The Almirante Padilla class Frigate ship scale model is investigated. The results show the ship current drag coefficient calculated considering a current speed of 1 knot with a 90° drift angle for the full-scale ship. Predicted results were compared against the current drag coefficients published in the Lloyds register OCIMF report. It is shown that the simulation results agree fairly well with the published results and that STAR-CCM+ code can predict current drag coefficients.

Keywords: CFD, current draft coefficient, STAR-CCM+, OCIMF, Bollard pull

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Authors: Nur Iffika Ruslan, Ahmad Rosly Abbas, Munirah Stapah@Salleh, Nurfaziera Rahim

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Increased concerns and awareness of environmental hazards by fossil fuels burning for energy have become the major factor driving the transition toward green energy. It is expected that an additional of 2,000 MW of renewable energy is to be recorded from the renewable sources by 2025 following the implementation of Large Scale Solar projects in Peninsular Malaysia, including Large Scale Floating Solar projects. Floating Solar has better advantages over its landed counterparts such as the requirement for land acquisition is relatively insignificant. As part of the site selection process established by TNB Research Sdn. Bhd., a set of mandatory and rejection criteria has been developed in order to identify only sites that are feasible for the future development of Large Scale Floating Solar power plant. There are a total of 85 lakes and reservoirs identified within Peninsular Malaysia. Only lakes and reservoirs with a minimum surface area of 120 acres will be considered as potential sites for the development of Large Scale Floating Solar power plant. The result indicates a total of 10 potential Large Scale Floating Solar sites identified which are located in Selangor, Johor, Perak, Pulau Pinang, Perlis and Pahang. This paper will elaborate on the various mandatory and rejection criteria, as well as on the various site selection process required to identify potential (suitable) Large Scale Floating Solar sites in Peninsular Malaysia.

Keywords: Large Scale Floating Solar, Peninsular Malaysia, Potential Sites, Renewable Energy

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Authors: Carlos Gonzales, Zaida Quiroz, Marcos Prates

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Several spatial variables collected at the same location that share a common spatial distribution can be modeled simultaneously through a multivariate geostatistical model that takes into account the correlation between these variables and the spatial autocorrelation. The main goal of this model is to perform spatial prediction of these variables in the region of study. Here we focus on a geostatistical multivariate formulation that relies on sharing common spatial random effect terms. In particular, the first response variable can be modeled by a mean that incorporates a shared random spatial effect, while the other response variables depend on this shared spatial term, in addition to specific random spatial effects. Each spatial random effect is defined through a Gaussian process with a valid covariance function, but in order to improve the computational efficiency when the data are large, each Gaussian process is approximated to a Gaussian random Markov field (GRMF), specifically to the block nearest neighbor Gaussian process (Block-NNGP). This approach involves dividing the spatial domain into several dependent blocks under certain constraints, where the cross blocks allow capturing the spatial dependence on a large scale, while each individual block captures the spatial dependence on a smaller scale. The multivariate geostatistical model belongs to the class of Latent Gaussian Models; thus, to achieve fast Bayesian inference, it is used the integrated nested Laplace approximation (INLA) method. The good performance of the proposed model is shown through simulations and applications for massive data.

Keywords: Block-NNGP, geostatistics, gaussian process, GRMF, INLA, multivariate models.

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Authors: Mehrnoosh Pirhayati

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In this study, the researcher tried to propose a model of Translation Criticism (TC) regarding the phenomenon of Translation Quality Assessment (TQA). With changing the general view on re/writing as an illegal act, the researcher defined a scale for the act of translation and determined the redline of translation with other products. This research attempts to show TC as a related phenomenon to TQA. This study shows that TQA with using the rules and factors of TC as depicted in both product-oriented analysis and process-oriented analysis, determines the orientation or the level of the quality of translation. This study also depicts that TC, regarding TQA’s perspective, reveals the aim of the translation of original text and the root of ideological manipulation and re/writing. On the other hand, this study stresses the existence of a direct relationship between the linguistic materials and semiotic codes of a text or book. This study can be fruitful for translators, scholars, translation criticizers, and translation quality assessors, and also it is applicable in the area of pedagogy.

Keywords: a model of translation criticism, a model of translation quality assessment, critical discourse analysis (CDA), re/writing, translation criticism (TC), translation quality assessment (TQA)

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Authors: Wondmnew Derebe Yohannis

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Farming irrigation plays a crucial role in rural development strategies, impacting both annual household income and livelihood. This research aims to evaluate the factors influencing irrigation participation and assess the impact of small-scale irrigation on rural households' annual income. The study collected data from 287 farmers in the Dahana district of northern Ethiopia. The research investigates the driving forces behind farmers' decisions to adopt small-scale irrigation and its effect on annual income gain. The findings reveal that several factors positively influence the probability of adoption, including access to credit, cultivated land size, livestock holding, extension contact, and the education level of the household head. Conversely, the distance to local markets and water schemes negatively affects the likelihood of adoption. To understand the differences in annual income between farm households that adopted irrigation and those that did not, a simultaneous equations model with endogenous switching regression is estimated. This accounts for the heterogeneity in the adoption decision and unobservable characteristics of farmers and their farms. The analysis compares the expected income gain under actual and counterfactual scenarios, considering whether the farm household adopted irrigation or not. The study reveals that the group of farm households that adopted irrigation has distinct characteristics compared to those that did not adopt it. Furthermore, the research demonstrates that the adoption of irrigation practices leads to an increase in annual income. Interestingly, the impact of small-scale irrigation on annual income is greater for the farm households that actually adopted irrigation compared to those in the counterfactual scenario where they did not adopt. Based on the findings, the researcher concludes that small-scale irrigation is a practical solution for meeting household financial needs in the study area. It is recommended that investments in small-scale irrigation continue to further improve the livelihoods of rural farming communities by enhancing annual income gains.

Keywords: small-scale irrigation, income, rural farm households, endogenous switching regression, user, non-user

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Authors: Amira Abdelrasoul, Huu Doan, Ali Lohi

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An efficient and well-planned ultrafiltration process is becoming a necessity for monetary returns in the industrial settings. The aim of the present study was to develop a mathematical model for an accurate prediction of ultrafiltration membrane fouling of latex effluent applied to homogeneous and heterogeneous membranes with uniform and non-uniform pore sizes, respectively. The models were also developed for an accurate prediction of power consumption that can handle the large-scale purposes. The model incorporated the fouling attachments as well as chemical and physical factors in membrane fouling for accurate prediction and scale-up application. Both Polycarbonate and Polysulfone flat membranes, with pore sizes of 0.05 µm and a molecular weight cut-off of 60,000, respectively, were used under a constant feed flow rate and a cross-flow mode in ultrafiltration of the simulated paint effluent. Furthermore, hydrophilic ultrafilic and hydrophobic PVDF membranes with MWCO of 100,000 were used to test the reliability of the models. Monodisperse particles of 50 nm and 100 nm in diameter, and a latex effluent with a wide range of particle size distributions were utilized to validate the models. The aggregation and the sphericity of the particles indicated a significant effect on membrane fouling.

Keywords: membrane fouling, mathematical modeling, power consumption, attachments, ultrafiltration

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Authors: Ewelina Wisnik, Zsolt Regdon, Kinga Chmielewska, Laszlo Virag, Agnieszka Robaszkiewicz

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Apart from protecting genome, PARP1 has been documented to regulate many intracellular processes inter alia gene transcription by physically interacting with chromatin bound proteins and by their ADP-ribosylation. Our recent findings indicate that expression of PARP1 decreases during the differentiation of human CD34+ hematopoietic stem cells to monocytes as a consequence of differentiation-associated cell growth arrest and formation of E2F4-RBL2-HDAC1-SWI/SNF repressive complex at the promoter of this gene. Since the RBL2 complexes repress genes in a E2F-dependent manner and are widespread in the genome in G0 arrested cells, we asked (a) if RBL2 directly contributes to defining monocyte phenotype and function by targeting gene promoters and (b) if RBL2 controls gene transcription indirectly by repressing PARP1. For identification of genes controlled by RBL2 and/or PARP1,we used primer libraries for surface receptors and TLR signaling mediators, genes were silenced by siRNA or shRNA, analysis of gene promoter occupation by selected proteins was carried out by ChIP-qPCR, while statistical analysis in GraphPad Prism 5 and STATISTICA, ChIP-Seq data were analysed in Galaxy 2.5.0.0. On the list of 28 genes regulated by RBL2, we identified only four solely repressed by RBL2-E2F4-HDAC1-BRM complex. Surprisingly, 24 out of 28 emerged genes controlled by RBL2 were co-regulated by PARP1 in six different manners. In one mode of RBL2/PARP1 co-operation, represented by MAP2K6 and MAPK3, PARP1 was found to associate with gene promoters upon RBL2 silencing, which was previously shown to restore PARP1 expression in monocytes. PARP1 effect on gene transcription was observed only in the presence of active EP300, which acetylated gene promoters and activated transcription. Further analysis revealed that PARP1 binding to MA2K6 and MAPK3 promoters enabled recruitment of EP300 in monocytes, while in proliferating cancer cell lines, which actively transcribe PARP1, this protein maintained EP300 at the promoters of MA2K6 and MAPK3. Genome-wide analysis revealed a similar distribution of PARP1 and EP300 around transcription start sites and the co-occupancy of some gene promoters by PARP1 and EP300 in cancer cells. Here, we described a new RBL2/PARP1/EP300 axis which controls gene transcription regardless of the cell type. In this model cell, cycle-dependent transcription of PARP1 regulates expression of some genes repressed by RBL2 upon cell cycle limitation. Thus, RBL2 may indirectly regulate transcription of some genes by controlling the expression of EP300-recruiting PARP1. Acknowledgement: This work was financed by Polish National Science Centre grants nr DEC-2013/11/D/NZ2/00033 and DEC-2015/19/N/NZ2/01735. L.V. is funded by the National Research, Development and Innovation Office grants GINOP-2.3.2-15-2016-00020 TUMORDNS, GINOP-2.3.2-15-2016-00048-STAYALIVE and OTKA K112336. AR is supported by Polish Ministry of Science and Higher Education 776/STYP/11/2016.

Keywords: retinoblastoma transcriptional co-repressor like 2 (RBL2), poly(ADP-ribose) polymerase 1 (PARP1), E1A binding protein p300 (EP300), monocytes

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Authors: Olga Blagova, Yuliya Osipova, Evgeniya Kogan, Alexander Nedostup

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Purpose: to quantify the value of various clinical, laboratory and instrumental signs in the diagnosis of myocarditis in comparison with morphological studies of the myocardium. Methods: in 100 patients (65 men, 44.7±12.5 years) with «idiopathic» arrhythmias (n = 20) and dilated cardiomyopathy (DCM, n = 80) were performed 71 endomyocardial biopsy (EMB), 13 intraoperative biopsy, 5 study of explanted hearts, 11 autopsy with virus investigation (real-time PCR) of the blood and myocardium. Anti-heart antibodies (AHA) were also measured as well as cardiac CT (n = 45), MRI (n = 25), coronary angiography (n = 47). The comparison group included of 50 patients (25 men, 53.7±11.7 years) with non-inflammatory heart diseases who underwent open heart surgery. Results. Active/borderline myocarditis was diagnosed in 76.0% of the study group and in 21.6% of patients of the comparison group (p < 0.001). The myocardial viral genome was observed more frequently in patients of comparison group than in study group (group (65.0% and 40.2%; p < 0.01. Evaluated the diagnostic value of noninvasive markers of myocarditis. The panel of anti-heart antibodies had the greatest importance to identify myocarditis: sensitivity was 81.5%, positive and negative predictive value was 75.0 and 60.5%. It is defined diagnostic value of non-invasive markers of myocarditis and diagnostic algorithm providing an individual assessment of the likelihood of myocarditis is developed. Conclusion. The greatest significance in the diagnosis of latent myocarditis in patients with 'idiopathic' arrhythmias and DCM have AHA. The use of complex of noninvasive criteria allows estimate the probability of myocarditis and determine the indications for EMB.

Keywords: myocarditis, "idiopathic" arrhythmias, dilated cardiomyopathy, endomyocardial biopsy, viral genome, anti-heart antibodies

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Authors: Pouya Karimi, Ramin Gasemi Shayan, Parsa Sheykhzade

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Ease shotgun DNA sequencing is changing the microbial sciences. Sequencing instruments are compelling to the point that example planning is currently the key constraining element. Here, we present a microfluidic test readiness stage that incorporates the key strides in cells to grouping library test groundwork for up to 96 examples and decreases DNA input prerequisites 100-overlay while keeping up or improving information quality. The universally useful microarchitecture we show bolsters work processes with subjective quantities of response and tidy up or catch steps. By decreasing the example amount necessities, we empowered low-input (∼10,000 cells) entire genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil miniaturized scale settlements with prevalent outcomes. We additionally utilized the upgraded throughput to succession ∼400 clinical Pseudomonas aeruginosa libraries and exhibit magnificent single-nucleotide polymorphism discovery execution that clarified phenotypically watched anti-toxin opposition. Completely coordinated lab-on-chip test arrangement beats specialized boundaries to empower more extensive organization of genomics across numerous fundamental research and translational applications.

Keywords: clinical microbiology, DNA, microbiology, microbial genomics

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Authors: Trapti Sharma, Devesh Kumar Srivastava

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This paper is basically a analysis study of above MapReduce implementation and also to verify and validate the MapReduce solution model for Parallel K-Mediod algorithm on Hadoop Cluster. MapReduce is a programming model which authorize the managing of huge amounts of data in parallel, on a large number of devices. It is specially well suited to constant or moderate changing set of data since the implementation point of a position is usually high. MapReduce has slowly become the framework of choice for “big data”. The MapReduce model authorizes for systematic and instant organizing of large scale data with a cluster of evaluate nodes. One of the primary affect in Hadoop is how to minimize the completion length (i.e. makespan) of a set of MapReduce duty. In this paper, we have verified and validated various MapReduce applications like wordcount, grep, terasort and parallel K-Mediod clustering algorithm. We have found that as the amount of nodes increases the completion time decreases.

Keywords: hadoop, mapreduce, k-mediod, validation, verification

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Authors: Mahdi Saadat, Abbas Taheri

Abstract:

Understanding the cracking response of crystalline rocks at mineralogical scale is of great importance during the design procedure of mining structures. A grain-based distinct element model (GBM) is employed to numerically study the cracking response of Barre granite at micro- and macro-scales. The GBM framework is augmented with a proposed distinct element-based cohesive model to reproduce the micro-cracking response of the inter- and intra-grain contacts. The cohesive GBM framework is implemented in PFC2D distinct element codes. The microstructural properties of Barre granite are imported in PFC2D to generate synthetic specimens. The microproperties of the model is calibrated against the laboratory uniaxial compressive and Brazilian split tensile tests. The calibrated model is then used to simulate the fracturing behaviour of pre-cracked Barre granite with different flaw configurations. The numerical results of the proposed model demonstrate a good agreement with the experimental counterparts. The GBM framework proposed thus appears promising for further investigation of the influence of grain microstructure and mineralogical properties on the cracking behaviour of crystalline rocks.

Keywords: discrete element modelling, cohesive grain-based model, crystalline rock, fracturing behavior

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Authors: Zuhair Kadhim Jahanger, S. Joseph Antony

Abstract:

The available studies in the literature which dealt with the scale effects of strip footings on different sand packing systematically still remain scarce. In this research, the variation of ultimate bearing capacity and deformation pattern of soil beneath strip footings of different widths under plane-strain condition on the surface of loose, medium-dense and dense sand have been systematically studied using experimental and noninvasive methods for measuring microscopic deformations. The presented analyses are based on model scale compression test analysed using Particle Image Velocimetry (PIV) technique. Upper bound analysis of the current study shows that the maximum vertical displacement of the sand under the ultimate load increases for an increase in the width of footing, but at a decreasing rate with relative density of sand, whereas the relative vertical displacement in the sand decreases for an increase in the width of the footing. A well agreement is observed between experimental results for different footing widths and relative densities. The experimental analyses have shown that there exists pronounced scale effect for strip surface footing. The bearing capacity factors Nγ rapidly decrease up to footing widths B=0.25 m, 0.35 m, and 0.65 m for loose, medium-dense and dense sand respectively, after that there is no significant decrease in Nγ. The deformation modes of the soil as well as the ultimate bearing capacity values have been affected by the footing widths. The obtained results could be used to improve settlement calculation of the foundation interacting with granular soil.

Keywords: DPIV, granular mechanics, scale effect, upper bound analysis

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Authors: Mehdi Montakhabrazlighi, Ercan Balikci

Abstract:

The neural network (NN) method is applied to alloy development of single crystal Ni-base Superalloys with low density and improved mechanical strength. A set of 1200 dataset which includes chemical composition of the alloys, applied stress and temperature as inputs and density and time to rupture as outputs is used for training and testing the network. Thermodynamic phase diagram modeling of the screened alloys is performed with Thermocalc software to model the equilibrium phases and also microsegregation in solidification processing. The model is first trained by 80% of the data and the 20% rest is used to test it. Comparing the predicted values and the experimental ones showed that a well-trained network is capable of accurately predicting the density and time to rupture strength of the Ni-base superalloys. Modeling results is used to determine the effect of alloying elements, stress, temperature and gamma-prime phase volume fraction on rupture strength of the Ni-base superalloys. This approach is in line with the materials genome initiative and integrated computed materials engineering approaches promoted recently with the aim of reducing the cost and time for development of new alloys for critical aerospace components. This work has been funded by TUBITAK under grant number 112M783.

Keywords: neural network, rupture strength, superalloy, thermocalc

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Authors: Thierno Diop, Michel Fortin, Jean Deteix

Abstract:

Since the precise formulation of the elastic part is irrelevant for the description of the algorithm, we shall consider a generic case. In practice, however, we will have to deal with a non linear material (for instance a Mooney-Rivlin model). We are interested in solving a finite element approximation of the problem, leading to large-scale non linear discrete problems and, after linearization, to large linear systems and ultimately to calculations needing iterative methods. This also implies that penalty method, and therefore augmented Lagrangian method, are to be banned because of their negative effect on the condition number of the underlying discrete systems and thus on the convergence of iterative methods. This is in rupture to the mainstream of methods for contact in which augmented Lagrangian is the principal tool. We shall first present the problem and its discretization; this will lead us to describe a general solution algorithm relying on a preconditioner for saddle-point problems which we shall describe in some detail as it is not entirely standard. We will propose an iterative approach for solving three-dimensional frictional contact problems between elastic bodies, including contact with a rigid body, contact between two or more bodies and also self-contact.

Keywords: frictional contact, three-dimensional, large-scale, iterative method

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Authors: Alibakhsh Kasaeian, Mohammad Sameti, Zahra Noori, Mona Rastgoo Bahambari

Abstract:

Nowadays, the parabolic trough solar collector technology has become the most promising large-scale technology among various solar thermal generations. In this paper, a detailed numerical heat transfer model for a parabolic trough collector with nanofluid is presented based on the finite difference approach for which a MATLAB code was developed. The model was used to simulate the performance of a parabolic trough solar collector’s linear receiver, called a heat collector element (HCE). In this model, the heat collector element of the receiver was discretized into several segments in axial directions and energy balances were used for each control volume. All the heat transfer correlations, the thermodynamic equations and the optical properties were considered in details and the set of algebraic equations were solved simultaneously using iterative numerical solutions. The modeling assumptions and limitations are also discussed, along with recommendations for model improvement.

Keywords: heat transfer, nanofluid, numerical analysis, trough

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Authors: Mdluli Fezile, Schmidt Stefan, Thamaga-Chitja Joyce

Abstract:

In view of the frequently reported foodborne disease outbreaks caused by contaminated fresh produce, consumers have a preference for foods that meet requisite hygiene standards to reduce the risk of foodborne illnesses. Producing good quality fresh produce then becomes critical in improving market access and food security, especially for small-scale farmers. Questions of hygiene and subsequent microbiological quality in the rural small-scale farming sector of South Africa are even more crucial, given the policy drive to develop small-scale farming as a measure for reinforcement of household food security and reduction of poverty. Farming practices and methods, throughout the fresh produce value chain, influence the quality of the final product, which in turn determines its success in the market. This study’s aim was to therefore determine the extent to which training on organic farming methods, including modules such as Importance of Production Hygiene, influenced the hygienic farming practices employed by eTholeni small-scale organic farmers in uMbumbulu, KwaZulu-Natal- South Africa. Questionnaires were administered to 73 uncertified organic farmers and analysis showed that a total of 33 farmers were trained and supplied the local Agri-Hub while 40 had not received training. The questionnaire probed respondents’ attitudes, knowledge of hygiene and composting practices. Data analysis included descriptive statistics such as the Chi-square test and a logistic regression model. Descriptive analysis indicated that a majority of the farmers (60%) were female, most of which (73%) were above the age of 40. The logistic regression indicated that factors such as farmer training and prior experience in the farming sector had a significant influence on hygiene practices both at 5% significance levels. These results emphasize the importance of training, education and farming experience in implementing good hygiene practices in small-scale farming. It is therefore recommended that South African policies should advocate for small-scale farmer training, not only for subsistence purposes, but also with an aim of supplying produce markets with high fresh produce.

Keywords: small-scale farmers, leafy salad vegetables, organic produce, food safety, hygienic practices, food security

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

Abstract:

Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

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Authors: Jose A. Aznar-Moreno, Xi Jiang, Stefan Burén, Luis M. Rubio

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Integration of prokaryotic nitrogen fixation (nif) genes into the plastid genome for expression of functional nitrogenase components could render plants capable of assimilating atmospheric N2 making their crops less dependent of nitrogen fertilizers. The nitrogenase Fe protein component (NifH) has been used as proxy for expression and targeting of Nif proteins within plant and yeast cells. Here we use tobacco plants with the Azotobacter vinelandii nifH and nifM genes integrated into the plastid genome. NifH and its maturase NifM were constitutively produced in leaves, but not roots, during light and dark periods. Nif protein expression in transplastomic plants was stable throughout development. Chloroplast NifH was soluble, but it only showed in vitro activity when isolated from leaves collected at the end of the dark period. Exposing the plant extracts to elevated temperatures precipitated NifM and apo-NifH protein devoid of [Fe4S4] clusters, dramatically increasing the specific activity of remaining NifH protein. Our data indicate that the chloroplast endogenous [Fe-S] cluster biosynthesis was insufficient for complete NifH maturation, albeit a negative effect on NifH maturation due to excess NifM in the chloroplast cannot be excluded. NifH and NifM constitutive expression in transplastomic plants did not affect any of the following traits: seed size, germination time, germination ratio, seedling growth, emergence of the cotyledon and first leaves, chlorophyll content and plant height throughout development.

Keywords: NifH, chloroplast, nitrogen fixation, crop improvement, transplastomic plants, fertilizer, biotechnology

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Authors: Dora Vajda, Somayyeh Mohammadi, Sandor Rozsa

Abstract:

Predicting the relationship satisfaction based on the personality characteristics of both partners has a long history. The association between relationship quality and personality traits has been previously demonstrated. Personality traits are most commonly assessed using the Five-Factor Model. The present study has focused on Cloninger's psychobiological model of personality that accounts for dimensions of both temperament and character. The goal of this study was to examine the actor and partner effect of couple's personality on relationship outcomes. In total, 184 heterosexual couples completed the Temperament and Character Inventory (TCI) and the Dyadic Adjustment Scale. The analysis was based on Actor-Partner Interdependence Model (APIM) using multilevel modeling (MLwiN). Results showed that character dimensions Self-Directedness and Cooperativeness had a statistically meaningful actor and partner effect on both partner's relationship quality. However, male's personality temperament dimension Reward Dependence had an only actor effect on his relationship quality. The findings contribute to the literature by highlighting the role of character dimensions of personality in romantic relationships.

Keywords: APIM (actor-partner interdependence model), MLwiN, personality, relationship quality

Procedia PDF Downloads 391