Search results for: genomic prediction

Authors: Majid Rezayi, Sh. Shahaboddin, HNM E. Mahmud, A. Yadollah, A. Saeid, A. Yatimah

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In this study, the adaptive neuro-fuzzy inference system (ANFIS) was applied to obtain the membrane composition model affecting the potential response of our reported polymeric PVC sensor for determining the titanium (III) ions. The performance statistics of the artificial neural network (ANN) and linear regression models for potential slope prediction of membrane composition of titanium (III) ion selective electrode were compared with ANFIS technique. The results show that the ANFIS model can be used as a practical tool for obtaining the Nerntian slope of the proposed sensor in this study.

Keywords: adaptive neuro fuzzy inference, PVC sensor, titanium (III) ions, Nerntian slope

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Lely A. Luengas, Pedro R. Vizcaya, Giovanni Sánchez

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In this paper, a methodology is presented to obtain the Static Alignment Model for any transtibial amputee person. The proposed methodology starts from experimental data collected on the Hospital Militar Central, Bogotá, Colombia. The effects of transtibial prosthesis malalignment on amputees were measured in terms of joint angles, center of pressure (COP) and weight distribution. Some statistical tools are used to obtain the model parameters. Mathematical predictive models of prosthetic alignment were created. The proposed models are validated in amputees and finding promising results for the prosthesis Static Alignment. Static alignment process is unique to each subject; nevertheless the proposed methodology can be used in each transtibial amputee.

Keywords: information theory, prediction model, prosthetic alignment, transtibial prosthesis

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Authors: Lihua Zhu, Jianfeng Du, Yu Wang, Zhiqiang Wu

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Collision avoidance problems of a swarm of unmanned air vehicles (UAVs) flying in an obstacle-laden environment are investigated in this paper. Given that the UAV swarm needs to adapt to the obstacle distribution in dynamic operation, a priority configuration is designed to guide the UAVs to pass through the obstacles in turn. Based on the collision cone approach and the prediction of the collision time, a collision evaluation model is established to judge the urgency of the imminent collision of each UAV, and the evaluation result is used to assign the priority of each UAV to further instruct them going through the obstacles in descending order. At last, the simulation results provide the promising validation in terms of the efficiency and scalability of the proposed approach.

Keywords: UAV swarm, collision avoidance, complex environment, online priority design

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Authors: Hari Mohan Kushwaha, Santosh Kumar Sahu

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In the present study, analysis of heat transfer is carried out in the slip flow region for the fluid flowing between two parallel plates by employing the asymmetric heat fluxes at surface of the plates. The flow is assumed to be hydrodynamically and thermally fully developed for the analysis. The second order velocity slip and viscous dissipation effects are considered for the analysis. Closed form expressions are obtained for the Nusselt number as a function of Knudsen number and modified Brinkman number. The limiting condition of the present prediction for Kn = 0, Kn2 = 0, and Brq1 = 0 is considered and found to agree well with other analytical results.

Keywords: Knudsen number, modified Brinkman number, slip flow, velocity slip

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Authors: Christopher Deekia Nwimae, Nigel Simms, Liyun Lao

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Erosion in pipe bends caused by particles is a major obstacle in the oil and gas fields and might cause the breakdown of production equipment. This work studied the effects imposed by flow velocity and impact of solid particles diameter in an elbow; erosion rate was verified with experimental data using the computational fluid dynamics (CFD) approach. Two-way coupled Euler-Lagrange and discrete phase model was employed to calculate the air/solid particle flow in an elbow. One erosion model and three-particle rebound models were used to predict the erosion rate on the 90° elbows. The generic erosion model was used in the CFD-based erosion model, and after comparing it with experimental data, results showed agreement with the CFD-based predictions as observed.

Keywords: erosion, prediction, elbow, computational fluid dynamics

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Authors: Firas M. Tuaimah

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This paper presents an Artificial Neural Network based approach for short-term load forecasting and exactly for two days ahead. Two seasons have been discussed for Iraqi power system, namely summer and winter; the hourly load demand is the most important input variables for ANN based load forecasting. The recorded daily load profile with a lead time of 1-48 hours for July and December of the year 2012 was obtained from the operation and control center that belongs to the Ministry of Iraqi electricity. The results of the comparison show that the neural network gives a good prediction for the load forecasting and for two days ahead.

Keywords: short-term load forecasting, artificial neural networks, back propagation learning, hourly load demand

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Authors: Andy H. Clark

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This research looks into the relationship between language comprehension and production with a specific focus on the role of salience in shaping these processes. Salience, our most immediate perception of what is most probable out of all possible situations and outcomes strongly affects our perception and action in language production and comprehension. This study investigates the impact of geographic and emotional attachments to the target language on the differences in the learners’ comprehension and production abilities. Using quantitative research methods (Qualtrics, SPSS), this study examines preferential choices of two groups of Japanese English language learners: those residing in the United States and those in Japan. By comparing and contrasting these two groups, we hope to gain a better understanding of how salience of linguistics cues influences language processing.

Keywords: intercultural pragmatics, salience, production, comprehension, pragmatics, action, perception, cognition

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Authors: Begum Koru, Isik Aybay, Demet Celik Ulusoy

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The discipline of law is quite complex and has its own terminology. Apart from written legal rules, there is also living law, which refers to legal practice. Basic legal rules aim at the happiness of individuals in social life and have different characteristics in different branches such as public or private law. On the other hand, law is a national phenomenon. The law of one nation and the legal system applied on the territory of another nation may be completely different. People who are experts in a particular field of law in one country may have insufficient expertise in the law of another country. Today, in addition to the local nature of law, international and even supranational law rules are applied in order to protect basic human values and ensure the protection of human rights around the world. Systems that offer algorithmic solutions to legal problems using artificial intelligence (AI) tools will perhaps serve to produce very meaningful results in terms of human rights. However, algorithms to be used should not be developed by only computer experts, but also need the contribution of people who are familiar with law, values, judicial decisions, and even the social and political culture of the society to which it will provide solutions. Otherwise, even if the algorithm works perfectly, it may not be compatible with the values of the society in which it is applied. The latest developments involving the use of AI techniques in legal systems indicate that artificial law will emerge as a new field in the discipline of law. More AI systems are already being applied in the field of law, with examples such as predicting judicial decisions, text summarization, decision support systems, and classification of documents. Algorithms for legal systems employing AI tools, especially in the field of prediction of judicial decisions and decision support systems, have the capacity to create automatic decisions instead of judges. When the judge is removed from this equation, artificial intelligence-made law created by an intelligent algorithm on its own emerges, whether the domain is national or international law. In this work, the aim is to make a general analysis of this new topic. Such an analysis needs both a literature survey and a perspective from computer experts' and lawyers' point of view. In some societies, the use of prediction or decision support systems may be useful to integrate international human rights safeguards. In this case, artificial law can serve to produce more comprehensive and human rights-protective results than written or living law. In non-democratic countries, it may even be thought that direct decisions and artificial intelligence-made law would be more protective instead of a decision "support" system. Since the values of law are directed towards "human happiness or well-being", it requires that the AI algorithms should always be capable of serving this purpose and based on the rule of law, the principle of justice and equality, and the protection of human rights.

Keywords: AI and law, artificial law, protection of human rights, AI tools for legal systems

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Authors: B. Gepts, E. Meex, E. Nuyts, E. Knaepen, G. Verbeeck

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The importance of resource efficiency and environmental impact assessment has raised the interest in knowing the amount of materials used in buildings. If no BIM model or energy performance certificate is available, material quantities can be obtained through an estimation or time-consuming calculation. For the interior wall area, no validated estimation method exists. However, in the case of environmental impact assessment or evaluating the existing building stock as future material banks, knowledge of the material quantities used in interior walls is indispensable. This paper presents a validated method for the estimation of the interior wall area for dwellings based on easy-to-collect building characteristics. A database of 4963 residential buildings spread all over Belgium is used. The data are collected through onsite measurements of the buildings during the construction phase (between mid-2010 and mid-2017). The interior wall area refers to the area of all interior walls in the building, including the inner leaf of exterior (party) walls, minus the area of windows and doors, unless mentioned otherwise. The two predictive modelling techniques used are 1) a (stepwise) linear regression and 2) a decision tree. The best estimation method is selected based on the best R² k-fold (5) fit. The research shows that the building volume is by far the most important variable to estimate the interior wall area. A stepwise regression based on building volume per building, building typology, and type of house provides the best fit, with R² k-fold (5) = 0.88. Although the best R² k-fold value is obtained when the other parameters ‘building typology’ and ‘type of house’ are included, the contribution of these variables can be seen as statistically significant but practically irrelevant. Thus, if these parameters are not available, a simplified estimation method based on only the volume of the building can also be applied (R² k-fold = 0.87). The robustness and precision of the method (output) are validated three times. Firstly, the prediction of the interior wall area is checked by means of alternative calculations of the building volume and of the interior wall area; thus, other definitions are applied to the same data. Secondly, the output is tested on an extension of the database, so it has the same definitions but on other data. Thirdly, the output is checked on an unrelated database with other definitions and other data. The validation of the estimation methods demonstrates that the methods remain accurate when underlying data are changed. The method can support environmental as well as economic dimensions of impact assessment, as it can be used in early design. As it allows the prediction of the amount of interior wall materials to be produced in the future or that might become available after demolition, the presented estimation method can be part of material flow analyses on input and on output.

Keywords: buildings as material banks, building stock, estimation method, interior wall area

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Authors: Angga S. Fajar, A. Aminullah, J. Kiyono, R. A. Safitri

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This paper discusses about the application of ANN for optimizing of bridge structure design. ANN has been applied in various field of science concerning prediction and optimization. The structural optimization has several benefit including accelerate structural design process, saving the structural material, and minimize self-weight and mass of structure. In this paper, there are three types of bridge structure that being optimized including PSC I-girder superstructure, composite steel-concrete girder superstructure, and RC bridge pier. The different optimization strategy on each bridge structure implement back propagation method of ANN is conducted in this research. The optimal weight and easier design process of bridge structure with satisfied error are achieved.

Keywords: bridge structures, ANN, optimization, back propagation

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Authors: Tusar Kanti Dash, Ganapati Panda

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The evaluation of speech quality and intelligence is critical to the overall effectiveness of the Speech Enhancement Algorithms. Several intrusive and non-intrusive measures are employed to calculate these parameters. Non-Intrusive Evaluation is most challenging as, very often, the reference clean speech data is not available. In this paper, a novel non-intrusive speech evaluation measure is proposed using audio features derived from the Stockwell transform. These features are used with the Light Gradient Boosting Machine for the effective prediction of speech quality and intelligibility. The proposed model is analyzed using noisy and reverberant speech from four databases, and the results are compared with the standard Intrusive Evaluation Measures. It is observed from the comparative analysis that the proposed model is performing better than the standard Non-Intrusive models.

Keywords: non-Intrusive speech evaluation, S-transform, light GBM, speech quality, and intelligibility

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Authors: M. A. Ghebouli, A. Bouhemadou, H. Choutri, L. Louaila

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Some physical properties of the cubic perovskites CsXF3 (X = Sr, Ca, and Hg) have been investigated using pseudopotential plane–wave (PP-PW) method based on the density functional theory (DFT). The calculated lattice constants within GGA (PBE) and LDA (CA-PZ) agree reasonably with the available experiment data. The elastic constants and their pressure derivatives are predicted using the static finite strain technique. We derived the bulk and shear moduli, Young’s modulus, Poisson’s ratio and Lamé’s constants for ideal polycrystalline aggregates. The analysis of B/G ratio indicates that CsXF3 (X = Ca, Sr, and Hg) are ductile materials. The thermal effect on the volume, bulk modulus, heat capacities CV, CP, and Debye temperature was predicted.

Keywords: perovskite, PP-PW method, elastic constants, electronic band structure

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Authors: A. M. Byrne, E. Bonfiglio, C. Rigby, N. Edelstyn

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Introduction: Neuromarketing employs numerous methodologies when investigating products and advertisement effectiveness. Electroencephalography (EEG), a non-invasive measure of electrical activity from the brain, is commonly used in neuromarketing. EEG data can be considered using time-frequency (TF) analysis, where changes in the frequency of brainwaves are calculated to infer participant’s mental states, or event-related potential (ERP) analysis, where changes in amplitude are observed in direct response to a stimulus. This presentation discusses the findings of a systematic review of EEG measures in neuromarketing. A systematic review summarises evidence on a research question, using explicit measures to identify, select, and critically appraise relevant research papers. Thissystematic review identifies which EEG measures are the most robust predictor of customer preference and purchase intention. Methods: Search terms identified174 papers that used EEG in combination with marketing-related stimuli. Publications were excluded if they were written in a language other than English or were not published as journal articles (e.g., book chapters). The review investigated which TF effect (e.g., theta-band power) and ERP component (e.g., N400) most consistently reflected preference and purchase intention. Machine-learning prediction was also investigated, along with the use of EEG combined with physiological measures such as eye-tracking. Results: Frontal alpha asymmetry was the most reliable TF signal, where an increase in activity over the left side of the frontal lobe indexed a positive response to marketing stimuli, while an increase in activity over the right side indexed a negative response. The late positive potential, a positive amplitude increase around 600 ms after stimulus presentation, was the most reliable ERP component, reflecting the conscious emotional evaluation of marketing stimuli. However, each measure showed mixed results when related to preference and purchase behaviour. Predictive accuracy was greatly improved through machine-learning algorithms such as deep neural networks, especially when combined with eye-tracking or facial expression analyses. Discussion: This systematic review provides a novel catalogue of the most effective use of each EEG measure commonly used in neuromarketing. Exciting findings to emerge are the identification of the frontal alpha asymmetry and late positive potential as markers of preferential responses to marketing stimuli. Predictive accuracy using machine-learning algorithms achieved predictive accuracies as high as 97%, and future research should therefore focus on machine-learning prediction when using EEG measures in neuromarketing.

Keywords: EEG, ERP, neuromarketing, machine-learning, systematic review, time-frequency

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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A huge revolution has emerged in genome engineering by the discovery of CRISPR (clustered regularly interspaced palindromic repeats) and CRISPR-associated system genes (Cas) in bacteria. The function of type II Streptococcus pyogenes (Sp) CRISPR/Cas9 system has been confirmed in various species. Other S. thermophilus (St) CRISPR-Cas systems, CRISPR1-Cas and CRISPR3-Cas, have been also reported for preventing phage infection. The CRISPR1-Cas system interferes by cleaving foreign dsDNA entering the cell in a length-specific and orientation-dependant manner. The S. thermophilus CRISPR3-Cas system also acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed in the CRISPR1-Cas system. It is worth mentioning, for the effective DNA cleavage activity, RNA-guided Cas9 orthologs require their own specific PAM (protospacer adjacent motif) sequences. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of target site for the three orthogonals of Cas9 protein, a well-organized procedure will be required for high-throughput and accurate mining of possible target sites in a large genomic dataset. Consequently, we created a reliable procedure to explore potential gRNA sequences for type I (Streptococcus thermophiles), II (Streptococcus pyogenes), and III (Streptococcus thermophiles) CRISPR/Cas systems. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows: i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. The output of such procedure highlights the power of comparative genome mining for different CRISPR/Cas systems. This could yield a repertoire of Cas9 variants with expanded capabilities of gRNA design, and will pave the way for further advance genome and epigenome engineering.

Keywords: CRISPR/Cas systems, gRNA mining, Streptococcus pyogenes, Streptococcus thermophiles

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Authors: Jialin Wu, Zhiwei Lian, Jieyu Tang, Jingyun Shen

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Tornado is a serious and unpredictable natural disaster, which has an important impact on people's production and life. The probability of being hit by tornadoes in China was analyzed considering the principles of tornado formation. Then some suggestions on layout and shapes for newly-built buildings were provided combined with the characteristics of tornado wind fields. Fuzzy clustering and inverse closeness methods were used to evaluate the probability levels of tornado risks in various provinces based on classification and ranking. GIS was adopted to display the results. Finally, wind field single-vortex tornado was studied to discuss the optimized design of rural low-rise houses in Yancheng, Jiangsu as an example. This paper may provide enough data to support building and urban design in some specific regions.

Keywords: tornado probability, computational fluid dynamics, fuzzy mathematics, optimal design

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Authors: Mohammad Asadpour, Maryam Sadeghi, Mahmoud Jafari

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The transformation of carbon dioxide into fuels and commodity chemicals is considered one of the most attractive methods to meet energy demands and reduce atmospheric CO₂ levels. Cobalt complexes have previously shown high faradaic efficiency in the reduction of CO₂ to CO. In this study, a nanostructure, referred to as a porphyrin-like buckyball, is simulated and analyzed for its electrical properties. The investigation aims to understand the unique characteristics of this material and its potential applications in electronic devices. Through computational simulations and analysis, the electrocatalytic reduction of CO₂ to CO by Cobalt-porphyrin-like buckyball is explored. The findings of this study offer valuable insights into the electrocatalytic properties of this predicted structure, paving the way for further research and development in the field of nanotechnology.

Keywords: porphyrin-like buckyball, DFT, nanomaterials, CO₂ to CO

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Authors: Pacharaporn Lekyan

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The purpose of this study is to explore the conflict management affecting the workplace and analyze the ability of the prediction of leadership of the headman and the methods to handle the conflict in an organization. The quantitative research and developed the questionnaire in order to collect information from the respondents from 200 samples from leader or manager who worked in frozen food factories in Thailand. The result analysis shows about the problem of the relationship between conflict management factors, leadership, and the confliction in organization. The emotion of the leader in the organization is not the only factor that can affect conflict management but also the emotion of surrounding people which this factor can happen all the time and shows that four out of five factors of interpersonal conflict management have affected on emotion intelligence and also shows that the behaviors of leadership have an influence on conflict management.

Keywords: conflict management, emotional intelligence, leadership, factories' employee

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Authors: Yeliz Ekinci, Melis Koyuncu

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Successful planning of solid waste management systems requires successful prediction of the amount of solid waste generated in an area. Waste management planning can protect the environment and human health, hence it is tremendously important for countries. The lack of information in waste generation can cause many environmental and health problems. Turkey is a country that plans to join European Union, hence, solid waste management is one of the most significant criteria that should be handled in order to be a part of this community. Solid waste management system requires a good forecast of solid waste generation. Thus, this study aims to forecast solid waste generation in Turkey. Artificial Neural Network and Linear Regression models will be used for this aim. Many models will be run and the best one will be selected based on some predetermined performance measures.

Keywords: forecast, solid waste generation, solid waste management, Turkey

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Authors: Ruixia Liu

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Qinghai-Tibet Plateau has an important influence on the precipitation of its lower reaches. Data from remote sensing has itself advantage and numerical prediction model which assimilates RS data will be better than other. We got the assimilation data of MHS and terrestrial and sounding from GSI, and introduced the result into WRF, then got the result of RH and precipitation forecast. We found that assimilating MHS and terrestrial and sounding made the forecast on precipitation, area and the center of the precipitation more accurate by comparing the result of 1h,6h,12h, and 24h. Analyzing the difference of the initial field, we knew that the data assimilating about Qinghai-Tibet Plateau influence its lower reaches forecast by affecting on initial temperature and RH.

Keywords: Qinghai-Tibet Plateau, precipitation, data assimilation, GSI

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Authors: Hussam Elias, Ninovic Perez, Holger Hirsch

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The completion of the EMC regulations worldwide is growing steadily as the usage of electronics in our daily lives is increasing more than ever. In this paper, we introduce a novel method to perform the final phase of Electromagnetic compatibility (EMC) measurement and to reduce the required test time according to the norm EN 55032 by using a developed tool and the conventional neural network(CNN). The neural network was trained using real EMC measurements, which were performed in the Semi Anechoic Chamber (SAC) by CETECOM GmbH in Essen, Germany. To implement our proposed method, we wrote software to perform the radiated electromagnetic interference (EMI) measurements and use the CNN to predict and determine the position of the turntable that meets the maximum radiation value.

Keywords: conventional neural network, electromagnetic compatibility measurement, mean absolute error, position error

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Authors: Janneth Gonzalez, Andrés Pinzon Velasco, Maria Angarita

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Astrocytes play an important role in various processes in the brain, including pathological conditions such as neurodegenerative diseases. Recent studies have shown that the increase in saturated fatty acids such as palmitic acid (PA) triggers pro-inflammatorypathways in the brain. The use of synthetic neurosteroids such as tibolone has demonstrated neuro-protective mechanisms. However, broad studies with a systemic point of view on the neurodegenerative role of PA and the neuro-protective mechanisms of tibolone are lacking. In this study, we performed the integration of multi-omic data (transcriptome and proteome) into a human astrocyte genomic scale metabolic model to study the astrocytic response during palmitate treatment. We evaluated metabolic fluxes in three scenarios (healthy, induced inflammation by PA, and tibolone treatment under PA inflammation). We also applied a control theory approach to identify those reactions that exert more control in the astrocytic system. Our results suggest that PA generates a modulation of central and secondary metabolism, showing a switch in energy source use through inhibition of folate cycle and fatty acid β‐oxidation and upregulation of ketone bodies formation. We found 25 metabolic switches under PA‐mediated cellular regulation, 9 of which were critical only in the inflammatory scenario but not in the protective tibolone one. Within these reactions, inhibitory, total, and directional coupling profiles were key findings, playing a fundamental role in the (de)regulation of metabolic pathways that may increase neurotoxicity and represent potential treatment targets. Finally, the overall framework of our approach facilitates the understanding of complex metabolic regulation, and it can be used for in silico exploration of the mechanisms of astrocytic cell regulation, directing a more complex future experimental work in neurodegenerative diseases.

Keywords: astrocytes, data integration, palmitic acid, computational model, multi-omics

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Farid Khosravikia, Patricia Clayton

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The main objective of this study is to evaluate the advantages and disadvantages of various machine learning techniques in forecasting ground-motion intensity measures given source characteristics, source-to-site distance, and local site condition. Intensity measures such as peak ground acceleration and velocity (PGA and PGV, respectively) as well as 5% damped elastic pseudospectral accelerations at different periods (PSA), are indicators of the strength of shaking at the ground surface. Estimating these variables for future earthquake events is a key step in seismic hazard assessment and potentially subsequent risk assessment of different types of structures. Typically, linear regression-based models, with pre-defined equations and coefficients, are used in ground motion prediction. However, due to the restrictions of the linear regression methods, such models may not capture more complex nonlinear behaviors that exist in the data. Thus, this study comparatively investigates potential benefits from employing other machine learning techniques as a statistical method in ground motion prediction such as Artificial Neural Network, Random Forest, and Support Vector Machine. The algorithms are adjusted to quantify event-to-event and site-to-site variability of the ground motions by implementing them as random effects in the proposed models to reduce the aleatory uncertainty. All the algorithms are trained using a selected database of 4,528 ground-motions, including 376 seismic events with magnitude 3 to 5.8, recorded over the hypocentral distance range of 4 to 500 km in Oklahoma, Kansas, and Texas since 2005. The main reason of the considered database stems from the recent increase in the seismicity rate of these states attributed to petroleum production and wastewater disposal activities, which necessities further investigation in the ground motion models developed for these states. Accuracy of the models in predicting intensity measures, generalization capability of the models for future data, as well as usability of the models are discussed in the evaluation process. The results indicate the algorithms satisfy some physically sound characteristics such as magnitude scaling distance dependency without requiring pre-defined equations or coefficients. Moreover, it is shown that, when sufficient data is available, all the alternative algorithms tend to provide more accurate estimates compared to the conventional linear regression-based method, and particularly, Random Forest outperforms the other algorithms. However, the conventional method is a better tool when limited data is available.

Keywords: artificial neural network, ground-motion models, machine learning, random forest, support vector machine

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Authors: Prachi Desai, Ankita Gandhi, Mitali Acharya

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Rainfall forecast is mainly used for predictions of rainfall in a specified area and determining their future rainfall conditions. Rainfall is always a global issue as it affects all major aspects of one's life. Agricultural, fisheries, forestry, tourism industry and other industries are widely affected by these conditions. The studies have resulted in insufficient availability of water resources and an increase in water demand in the near future. We already have a new forecast system that uses the deep Convolutional Neural Network (CNN) to forecast monthly rainfall and climate changes. We have also compared CNN against Artificial Neural Networks (ANN). Machine Learning techniques that are used in rainfall predictions include ARIMA Model, ANN, LR, SVM etc. The dataset on which we are experimenting is gathered online over the year 1901 to 20118. Test results have suggested more realistic improvements than conventional rainfall forecasts.

Keywords: ANN, CNN, supervised learning, machine learning, deep learning

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Authors: Martin Kendra, Jaroslav Mašek, Juraj Čamaj, Matej Babin

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The railway transport is considered as a one of the most environmentally friendly mode of transport. With future prediction of increasing of freight transport there are lines facing problems with demanded capacity. Increase of the track capacity could be achieved by infrastructure constructive adjustments. The contribution shows how the travel time can be minimized and the track capacity increased by changing some of the basic infrastructure and operation parameters, for example, the minimal curve radius of the track, the number of tracks, or the usable track length at stations. Calculation of the necessary parameter changes is based on the fundamental physical laws applied to the train movement, and calculation of the occupation time is dependent on the changes of controlling the traffic between the stations.

Keywords: curve radius, maximum curve speed, track mass capacity, reconstruction

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Authors: Zulaika Mohd Khasiran

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The capability of ionic liquids in various applications makes them attracted by many researchers. They have potential to be developed as “green” solvents for gas separation, especially H2S gas. In this work, it is attempted to predict the solubility of hydrogen sulfide (H2S) in ILs by COSMO-RS method. Since H2S is a toxic pollutant, it is difficult to work on it in the laboratory, therefore an appropriate model will be necessary in prior work. The COSMO-RS method is implemented to predict the Henry’s law constants and activity coefficient of H2S in 140 ILs with various combinations of cations and anions. It is found by the screening that more H2S can be absorbed in ILs with [Cl] and [Ac] anion. The solubility of H2S in ILs with different alkyl chain at the cations not much affected and with different type of cations are slightly influence H2S capture capacities. Even though the cations do not affect much in solubility of H2S, we still need to consider the effectiveness of cation in different way. The prediction results only show their physical absorption ability, but the absorption of H2S need to be consider chemically to get high capacity of absorption of H2S.

Keywords: H2S, hydrogen sulfide, ionic liquids, COSMO-RS

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Authors: Iman Farasat, Howard M. Salis

Abstract:

The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

Procedia PDF Downloads 406

Authors: S. Belhour, A. K. Ferouani, C. Azizi

Abstract:

In recent years, a considerable effort (experience, numerical simulation, and theoretical prediction models) has characterised by high efficiency and low cost. Then an improved physics analytical model for simulating is proposed. The performance of GaAs MESFETs has been developed for use in device design for high frequency. This model is based on mathematical analysis, and a new approach for the standard model is proposed, this approach allowed to conceive applicable model for MESFET’s operating in the turn-one or pinch-off region and valid for the short-channel and the long channel MESFET’s in which the two dimensional potential distribution contributed by the depletion layer under the gate is obtained by conventional approximation. More ever, comparisons between the analytical models with different values of mobility are proposed, and a good agreement is obtained.

Keywords: analytical, gallium arsenide, MESFET, mobility, models

Procedia PDF Downloads 74

Authors: B. Y. Danjuma, A. Archibong-Eso, Aliyu M. Aliyu, H. Yeung

Abstract:

In this experimental investigation, a new data for slugging frequency for high viscosity oil-gas flow are reported. Scale experiments were carried out using a mixture of air and mineral oil as the liquid phase in a 17 m long horizontal pipe with 0.0762 ID. The data set was acquired using two high-speed Gamma Densitometers at a data acquisition frequency of 250 Hz over a time interval of 30 seconds. For the range of flow conditions investigated, increase in liquid oil viscosity was observed to strongly influence the slug frequency. A comparison of the present data with prediction models available in the literature revealed huge discrepancies. A new correlation incorporating the effect of viscosity on slug frequency has been proposed for the horizontal flow, which represents the main contribution of this work.

Keywords: gamma densitometer, flow pattern, pressure gradient, slug frequency

Procedia PDF Downloads 412