Search results for: genetic breeding models

Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

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Authors: Mafarja Majdi, Salwani Abdullah, Najmeh S. Jaddi

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One of the global combinatorial optimization problems in machine learning is feature selection. It concerned with removing the irrelevant, noisy, and redundant data, along with keeping the original meaning of the original data. Attribute reduction in rough set theory is an important feature selection method. Since attribute reduction is an NP-hard problem, it is necessary to investigate fast and effective approximate algorithms. In this paper, we proposed two feature selection mechanisms based on memetic algorithms (MAs) which combine the genetic algorithm with a fuzzy record to record travel algorithm and a fuzzy controlled great deluge algorithm to identify a good balance between local search and genetic search. In order to verify the proposed approaches, numerical experiments are carried out on thirteen datasets. The results show that the MAs approaches are efficient in solving attribute reduction problems when compared with other meta-heuristic approaches.

Keywords: rough set theory, attribute reduction, fuzzy logic, memetic algorithms, record to record algorithm, great deluge algorithm

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Authors: Keneilwe Maremi, Marlien Herselman, Adele Botha

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The main purpose and focus of this paper are to determine the Interoperability Maturity Models to consider when using School Management Systems (SMS). The importance of this is to inform and help schools with knowing which Interoperability Maturity Model is best suited for their SMS. To address the purpose, this paper will apply a scoping review to ensure that all aspects are provided. The scoping review will include papers written from 2012-2019 and a comparison of the different types of Interoperability Maturity Models will be discussed in detail, which includes the background information, the levels of interoperability, and area for consideration in each Maturity Model. The literature was obtained from the following databases: IEEE Xplore and Scopus, the following search engines were used: Harzings, and Google Scholar. The topic of the paper was used as a search term for the literature and the term ‘Interoperability Maturity Models’ was used as a keyword. The data were analyzed in terms of the definition of Interoperability, Interoperability Maturity Models, and levels of interoperability. The results provide a table that shows the focus area of concern for each Maturity Model (based on the scoping review where only 24 papers were found to be best suited for the paper out of 740 publications initially identified in the field). This resulted in the most discussed Interoperability Maturity Model for consideration (Information Systems Interoperability Maturity Model (ISIMM) and Organizational Interoperability Maturity Model for C2 (OIM)).

Keywords: interoperability, interoperability maturity model, school management system, scoping review

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Authors: Anushka Naidoo, Veron Ramsuran, Maxwell Chirehwa, Paolo Denti, Kogieleum Naidoo, Helen McIlleron, Nonhlanhla Yende-Zuma, Ravesh Singh, Sinaye Ngcapu, Nesri Padayatachi

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Background: Despite efforts to introduce new drugs and shorter drug regimens for drug-susceptible tuberculosis (TB), the standard first-line treatment has not changed in over 50 years. Rifampicin, isoniazid, and pyrazinamide are critical components of the current standard treatment regimens. Some studies suggest that microbiologic failure and acquired drug resistance are primarily driven by low drug concentrations that result from pharmacokinetic (PK) variability independent of adherence to treatment. Wide between-patient pharmacokinetic variability for rifampin, isoniazid, and pyrazinamide has been reported in prior studies. There may be several reasons for this variability. However, genetic variability in genes coding for drug metabolizing and transporter enzymes have been shown to be a contributing factor for variable tuberculosis drug exposures. Objective: We describe the pharmacokinetics of first-line TB drugs rifampicin, isoniazid, and pyrazinamide and assess the effect of genetic variability in relevant selected drug metabolizing and transporter enzymes on pharmacokinetic parameters of isoniazid and rifampicin. Methods: We conducted the randomized-controlled Improving retreatment success TB trial in Durban, South Africa. The drug regimen included rifampicin, isoniazid, and pyrazinamide. Drug concentrations were measured in plasma, and concentration-time data were analysed using nonlinear-mixed-effects models to quantify the effects of relevant covariates and single nucleotide polymorphisms (SNP’s) of drug metabolizing and transporter genes on rifampicin, isoniazid and pyrazinamide exposure. A total of 25 SNP’s: four NAT2 (used to determine acetylator status), four SLCO1B1, three Pregnane X receptor (NR1), six ABCB1 and eight UGT1A, were selected for analysis in this study. Genotypes were determined for each of the SNP’s using a TaqMan® Genotyping OpenArray™. Results: Among fifty-eight patients studied; 41 (70.7%) were male, 97% black African, 42 (72.4%) HIV co-infected and 40 (95%) on efavirenz-based ART. Median weight, fat-free mass (FFM), and age at baseline were 56.9 kg (interquartile range, IQR: 51.1-65.2), 46.8 kg (IQR: 42.5-50.3) and 37 years (IQR: 31-42), respectively. The pharmacokinetics of rifampicin and pyrazinamide was best described using one-compartment models with first-order absorption and elimination, while for isoniazid two-compartment disposition was used. The median (interquartile range: IQR) AUC (h·mg/L) and Cmax (mg/L) for rifampicin, isoniazid, and pyrazinamide were; 25.62 (23.01-28.53) and 4.85 (4.36-5.40), 10.62 (9.20-12.25) and 2.79 (2.61-2.97), 345.74 (312.03-383.10) and 28.06 (25.01-31.52), respectively. Eighteen percent of patients were classified as rapid acetylators, and 34% and 43% as slow and intermediate acetylators, respectively. Rapid and intermediate acetylator status based on NAT 2 genotype resulted in 2.3 and 1.6 times higher isoniazid clearance than slow acetylators. We found no effects of the SLCO1B1 genotypes on rifampicin pharmacokinetics. Conclusion: Plasma concentrations of rifampicin, isoniazid, and pyrazinamide were low overall in our patients. Isoniazid clearance was high overall and as expected higher in rapid and intermediate acetylators resulting in lower drug exposures. In contrast to reports from previous South African or Ugandan studies, we did not find any effects of the SLCO1B1 or other genotypes tested on rifampicin PK. However, our findings are in keeping with more recent studies from Malawi and India emphasizing the need for geographically diverse and adequately powered studies. The clinical relevance of the low tuberculosis drug concentrations warrants further investigation.

Keywords: rifampicin, isoniazid pharmacokinetics, genetics, NAT2, SLCO1B1, tuberculosis

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Authors: Seraj Makkawi, Abdulaziz A. Alqarni, Himyan Alghaythee, Suzan Y. Alharbi, Anmar Fatani, Reem Adas, Ahmad R. Abuzinadah

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Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is a neurodegenerative disease that involves both the upper and lower motor neurons. Familial ALS, including superoxide dismutase 1 (SOD1) mutation, accounts for 5-10% of all cases of ALS. Typically, the symptoms of ALS are purely motor, though coexistent sensory symptoms have been reported in rare cases. In this report, we describe the case of a 47- year-old man who presented with progressive bilateral lower limb weakness and numbness for the last four years. A nerve conduction study (NCS) showed evidence of coexistent axonal sensorimotor polyneuropathy in addition to the typical findings of ALS in needle electromyography. Genetic testing confirmed the diagnosis of familial ALS secondary to the SOD1 genetic mutation. This report highlights that the presence of sensory symptoms should not exclude the possibility of ALS in an appropriate clinical setting.

Keywords: Saudi Arabia, polyneuropathy, SOD1 gene mutation, familial amyotrophic lateral sclerosis, amyotrophic lateral sclerosis

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Authors: Ivan Župan

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Critical infrastructure is essential for the functioning of a country and is designated for special protection by governments worldwide. Due to the increase in smart technology usage in every facet of the industry, including critical infrastructure, the exposure to malicious cyber-physical attacks has grown in the last few years. Proper security measures must be undertaken in order to defend against cyber-physical threats that can disrupt the normal functioning of critical infrastructure and, consequently the functioning of the country. This paper provides a review of the scientific literature of models, methods and technologies used to protect from cyber-physical threats in industries. The focus of the literature was observed from three aspects. The first aspect, resilience, concerns itself with the robustness of the system’s defense against threats, as well as preparation and education about potential future threats. The second aspect concerns security risk management for systems with cyber-physical aspects, and the third aspect investigates available testbed environments for testing developed models on scaled models of vulnerable infrastructure.

Keywords: critical infrastructure, cyber-physical security, smart industry, security methodology, security technology

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Authors: Anderson S. Fonseca, Italo F. S. Da Silva, Robert D. A. Santos, Mayara G. Da Silva, Pedro H. C. Vieira, Antonio M. S. Sobrinho, Victor H. B. Lemos, Petterson S. Diniz, Anselmo C. Paiva, Eliana M. G. Monteiro

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In Brazil, the National Electric Energy Agency (ANEEL) establishes that electrical energy companies are responsible for measuring and billing their customers. Among these regulations, it’s defined that a company must bill your customers within 27-33 days. If a relocation or a change of period is required, the consumer must be notified in writing, in advance of a billing period. To make it easier to organize a workday’s measurements, these companies create a reading plan. These plans consist of grouping customers into reading groups, which are visited by an employee responsible for measuring consumption and billing. The creation process of a plan efficiently and optimally is a capacitated clustering problem with constraints related to homogeneity and compactness, that is, the employee’s working load and the geographical position of the consuming unit. This process is a work done manually by several experts who have experience in the geographic formation of the region, which takes a large number of days to complete the final planning, and because it’s human activity, there is no guarantee of finding the best optimization for planning. In this paper, the GBKMeans method presents a technique based on K-Means and genetic algorithms for creating a capacitated cluster that respects the constraints established in an efficient and balanced manner, that minimizes the cost of relocating consumer units and the time required for final planning creation. The results obtained by the presented method are compared with the current planning of a real city, showing an improvement of 54.71% in the standard deviation of working load and 11.97% in the compactness of the groups.

Keywords: capacitated clustering, k-means, genetic algorithm, districting problems

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Authors: Koteswara Rao Pagolu, Raghava Rao Tamanam

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The present study was aimed to find out the prevalence of DD's in Visakhapatnam, one of the north coastal districts of Andhra Pradesh, India during a span of five years. A cross-sectional investigation was held at District early intervention center (DEIC), Visakhapatnam from 2016 to 2020. To identify the pattern and trend of different DD's including seasonal variations, a retrospective analysis of the health center's inpatient database for the past 5 years was done. Male and female children aged 2 months-18 years are included in the study with the prior permission of the concerned medical officer. The screening tool developed by the Ministry of health and family welfare, India, was used for the study. Among 26,423 cases, children with birth defects are 962, 2229 with deficiencies, 7516 with diseases, and 15716 with disabilities were admitted during the study period. From birth defects, congenital deafness occurred in large numbers with 22.66%, and neural tube defect observed in a small number of cases with 0.83% during the period. From the side of deficiencies, severe acute malnutrition has mostly occurred (66.80 %) and a small number of children were affected with goiter (1.70%). Among the diseases, dental carriers (67.97%) are mostly found and these cases were at peak during the years 2016 and 2019. From disabilities, children with vision impairment (20.55%) have mostly approached the center. Over the past 5 years, the admission rate of down's syndrome and congenital deafness cases showed a rising trend up to 2019 and then declined. Hearing impairment, motor delay, and learning disorder showed a steep rise and gradual decline trend, whereas severe anemia, vitamin-D deficiency, otitis media, reactive airway disease, and attention deficit hyperactivity disorder showed a declining trend. However, congenital heart diseases, dental caries, and vision impairment admission rates showed a zigzag pattern over the past 5 years. This center had inadequate diagnostic facilities related to genetic disease management. For advanced confirmation, the cases are referred to a district government hospital or private diagnostic laboratories in the city for genetic tests. Information regarding the overall burden and pattern of admissions in the health center is obtained by the review of DEIC records. Through this study, it is observed that the incidence of birth defects, as well as genetic disease burden, is high in the Visakhapatnam district. Hence there is a need for strengthening of management services for these diseases in this region.

Keywords: child health screening, developmental delays, district early intervention center, genetic disease management, infrastructural facility, Visakhapatnam district

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Authors: Ali Hesari, Arezoo Esmaeeli

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Regarding to dramatic changes of fertility and higher order births during recent decades in Iran, access to knowledge about affecting factors on different birth orders has crucial importance. In this study, According to hierarchical structure of many of social sciences data and the effect of variables of different levels of social phenomena that determine different birth orders in 365 days ending to 1390 census have been explored by multilevel approach. In this paper, 2% individual row data for 1390 census is analyzed by HLM software. Three different hierarchical linear regression models are estimated for data analysis of the first and second, third, fourth and more birth order. Research results displays different outcomes for three models. Individual level variables entered in equation are; region of residence (rural/urban), age, educational level and labor participation status and province level variable is GDP per capita. Results show that individual level variables have different effects in these three models and in second level we have different random and fixed effects in these models.

Keywords: fertility, birth order, hierarchical approach, fixe effects, random effects

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Authors: Ehsan Eshtehardian, Saeed Khodaverdi

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This paper surveys the studies on construction change and reveals some of the potential future works. A full-scale investigation of change literature, including change definitions, types, causes and effects, and change management systems, is accomplished to explore some of the coming change trends. It is tried to pick up the critical works in each section to deduct a true timeline of construction changes. The findings show that leaping from best practice guides in late 1990s and generic process models in the early 2000s to very advanced modeling environments in the mid-2000s and the early 2010s have made gaps along with opportunities for change researchers in order to develop some more easy and applicable models. Another finding is that there is a compelling similarity between the change and risk prediction models. Therefore, integrating these two concepts, specifically from proactive management point of view, may lead to a synergy and help project teams avoid rework. Also, the findings show that exploitation of cause-effect relationship models, in order to facilitate the dispute resolutions, seems to be an interesting field for future works.

Keywords: construction change, change management systems, dispute resolutions, change literature

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Authors: Suren Chilingaryan

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We study two models describing a single two-level system coupled to two boson field modes in either a parallel or orthogonal setup. Both models may be feasible for experimental realization through Raman adiabatic driving in cavity QED. We study their ground state configurations; that is, we find the quantum precursors of the corresponding semi-classical phase transitions. We found that the ground state configurations of both models present the same critical coupling as the quantum Rabi model. Around this critical coupling, the ground state goes from the so-called normal configuration with no excitation, the qubit in the ground state and the fields in the quantum vacuum state, to a ground state with excitations, the qubit in a superposition of ground and excited state, while the fields are not in the vacuum anymore, for the first model. The second model shows a more complex ground state configuration landscape where we find the normal configuration mentioned above, two single-mode configurations, where just one of the fields and the qubit are excited, and a dual-mode configuration, where both fields and the qubit are excited.

Keywords: quantum optics, quantum phase transition, cavity QED, circuit QED

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Authors: Salah Alrabeei, Mohammad Yousuf

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The goal of option pricing theory is to help the investors to manage their money, enhance returns and control their financial future by theoretically valuing their options. However, most of the option pricing models have no analytical solution. Furthermore, not all the numerical methods are efficient to solve these models because they have nonsmoothing payoffs or discontinuous derivatives at the exercise price. In this paper, we solve the American option under jump diffusion models by using efficient time-dependent numerical methods. several techniques are integrated to reduced the overcome the computational complexity. Fast Fourier Transform (FFT) algorithm is used as a matrix-vector multiplication solver, which reduces the complexity from O(M2) into O(M logM). Partial fraction decomposition technique is applied to rational approximation schemes to overcome the complexity of inverting polynomial of matrices. The proposed method is easy to implement on serial or parallel versions. Numerical results are presented to prove the accuracy and efficiency of the proposed method.

Keywords: integral differential equations, jump–diffusion model, American options, rational approximation

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Authors: Yasaman Mohammadi

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Emotion regulation is a complex process that allows individuals to manage and modulate their emotional responses in order to adaptively respond to environmental demands. As individuals age, emotion regulation abilities may decline, leading to an increased vulnerability to mood disorders and other negative health outcomes. Advances in neuroimaging techniques have greatly enhanced our understanding of the neural substrates underlying emotion regulation and age-related changes in these neural systems. Additionally, genetic research has identified several candidate genes that may influence age-related changes in emotion regulation. In this paper, we review recent findings from neuroimaging and genetic research on age-related changes in the neural substrates of emotion regulation, highlighting the mechanisms and consequences of these changes. We also discuss potential interventions, including cognitive and behavioral approaches, that may be effective in mitigating age-related declines in emotion regulation. We propose that a better understanding of the mechanisms underlying age-related changes in emotion regulation may lead to the development of more targeted interventions aimed at promoting healthy emotional functioning in older adults. Overall, this paper highlights the importance of studying age-related changes in emotion regulation and provides a roadmap for future research in this field.

Keywords: emotion regulation, aging, neural substrates, neuroimaging, emotional functioning, healthy aging

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Authors: Hany Mohamed Abdu, Mohamed Hassan Gadallah, El-Giushi Mokhtar, Yehia Mahmoud Ismail

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Laser beam cutting is one nontraditional machining process. This paper optimizes the parameters of Laser beam cutting machining parameters of Stainless steel (316L) by considering the effect of input parameters viz. power, oxygen pressure, frequency and cutting speed. Statistical design of experiments are carried in three different levels and process responses such as 'Average kerf taper (Ta)' and 'Surface Roughness (Ra)' are measured accordingly. A quadratic mathematical model (RSM) for each of the responses is developed as a function of the process parameters. Responses predicted by the models (as per Taguchi’s L27 OA) are employed to search for an optimal parametric combination to achieve desired yield of the process. RSM models are developed for mean responses, S/N ratio, and standard deviation of responses. Optimization models are formulated as single objective problem subject to process constraints. Models are formulated based on Analysis of Variance (ANOVA) using MATLAB environment. Optimum solutions are compared with Taguchi Methodology results.

Keywords: optimization, laser cutting, robust design, kerf width, Taguchi method, RSM and DOE

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Authors: D. S. C. Soares, D. G. Costa, J. T. S., A. K. S. Abud, T. P. Nunes, A. M. Oliveira Júnior

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Mathematical models of drying are used for the purpose of understanding the drying process in order to determine important parameters for design and operation of the dryer. The jackfruit is a fruit with high consumption in the Northeast and perishability. It is necessary to apply techniques to improve their conservation for longer in order to diffuse it by regions with low consumption. This study aimed to analyse several mathematical models (Page, Lewis, and Midilli) to indicate one that best fits the conditions of convective drying process using performance indicators associated with each model: accuracy (Af) and noise factors (Bf), mean square error (RMSE) and standard error of prediction (% SEP). Jackfruit drying was carried out in convective type tray dryer at a temperature of 50°C for 9 hours. It is observed that the model Midili was more accurate with Af: 1.39, Bf: 1.33, RMSE: 0.01%, and SEP: 5.34. However, the use of the Model Midilli is not appropriate for purposes of control process due to need four tuning parameters. With the performance indicators used in this paper, the Page model showed similar results with only two parameters. It is concluded that the best correlation between the experimental and estimated data is given by the Page’s model.

Keywords: drying, models, jackfruit, biotechnology

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Authors: T. Y. Liu, C. H. Lin, Y. M. Ferng

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Wind energy is one of the clean renewable energy. However, the low frequency (20-200HZ) noise generated from the wind turbine blades, which bothers the residents, becomes the major problem to be developed. It is useful for predicting the aerodynamic noise by flow field and pressure distribution analysis on the wind turbine blades. Therefore, the main objective of this study is to use different turbulence models to analyse the flow field and pressure distributions of the wing blades. Three-dimensional Computation Fluid Dynamics (CFD) simulation of the flow field was used to calculate the flow phenomena for the National Renewable Energy Laboratory (NREL) Phase VI horizontal axis wind turbine rotor. Two different flow cases with different wind speeds were investigated: 7m/s with 72rpm and 15m/s with 72rpm. Four kinds of RANS-based turbulence models, Standard k-ε, Realizable k-ε, SST k-ω, and v2f, were used to predict and analyse the results in the present work. The results show that the predictions on pressure distributions with SST k-ω and v2f turbulence models have good agreements with experimental data.

Keywords: horizontal axis wind turbine, turbulence model, noise, fluid dynamics

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Authors: Abdellatif Chebboub

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Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change’s representative concentration pathway with end-of-century radiative forcing of 8.5 W/m2. The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

Keywords: climate change, agriculture, weather change, danger of climate change

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Authors: Ferhat Demir

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Even if strategic management is highly critical for all types of organizations, only a few maturity models have been proposed in business literature for the area of strategic management activities. This paper updates previous studies and presents a new conceptual model for assessing the maturity of strategic management in any organization. Strategic management maturity model (S-3M) is basically composed of 6 maturity levels with 7 dimensions. The biggest contribution of S-3M is to put innovation into agenda of strategic management. The main objective of this study is to propose a model to align innovation with business strategies. This paper suggests that innovation (breakthrough new products/services and business models) is the only way of creating sustainable growth and strategy studies cannot ignore this aspect. Maturity models should embrace innovation to respond dynamic business environment and rapidly changing customer behaviours.

Keywords: strategic management, innovation, business model, maturity model

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Authors: Leah Lee

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This paper examines the correlation between deep learning models and emotions with noises to see whether or not noises mask emotions. The deep learning models used are plain convolutional neural networks (CNN), auto-encoder, long short-term memory (LSTM), and Visual Geometry Group-16 (VGG-16). Emotion datasets used are Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS), Crowd-sourced Emotional Multimodal Actors Dataset (CREMA-D), Toronto Emotional Speech Set (TESS), and Surrey Audio-Visual Expressed Emotion (SAVEE). To make it four times bigger, audio set files, stretch, and pitch augmentations are utilized. From the augmented datasets, five different features are extracted for inputs of the models. There are eight different emotions to be classified. Noise variations are white noise, dog barking, and cough sounds. The variation in the signal-to-noise ratio (SNR) is 0, 20, and 40. In summation, per a deep learning model, nine different sets with noise and SNR variations and just augmented audio files without any noises will be used in the experiment. To compare the results of the deep learning models, the accuracy and receiver operating characteristic (ROC) are checked.

Keywords: auto-encoder, convolutional neural networks, long short-term memory, speech emotion recognition, visual geometry group-16

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Authors: Artem Kim, Clara Savary, Christele Dubourg, Wilfrid Carre, Houda Hamdi-Roze, Valerie Dupé, Sylvie Odent, Marie De Tayrac, Veronique David

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Holoprosencephaly (HPE) is a rare congenital brain malformation resulting from the incomplete separation of the two cerebral hemispheres. It is characterized by a wide phenotypic spectrum and a high degree of locus heterogeneity. Genetic defects in 16 genes have already been implicated in HPE, but account for only 30% of cases, suggesting that a large part of genetic factors remains to be discovered. HPE has been recently redefined as a complex multigenic disorder, requiring the joint effect of multiple mutational events in genes belonging to one or several developmental pathways. The onset of HPE may result from accumulation of the effects of multiple rare variants in functionally-related genes, each conferring a moderate increase in the risk of HPE onset. In order to decipher the genetic basis of HPE, unconventional patterns of inheritance involving multiple genetic factors need to be considered. The primary objective of this study was to uncover possible disease causing combinations of multiple rare variants underlying HPE by performing trio-based Whole Exome Sequencing (WES) of familial cases where no molecular diagnosis could be established. 39 families were selected with no fully-penetrant causal mutation in known HPE gene, no chromosomic aberrations/copy number variants and without any implication of environmental factors. As the main challenge was to identify disease-related variants among a large number of nonpathogenic polymorphisms detected by WES classical scheme, a novel variant prioritization approach was established. It combined WES filtering with complementary gene-level approaches: transcriptome-driven (RNA-Seq data) and clinically-driven (public clinical data) strategies. Briefly, a filtering approach was performed to select variants compatible with disease segregation, population frequency and pathogenicity prediction to identify an exhaustive list of rare deleterious variants. The exome search space was then reduced by restricting the analysis to candidate genes identified by either transcriptome-driven strategy (genes sharing highly similar expression patterns with known HPE genes during cerebral development) or clinically-driven strategy (genes associated to phenotypes of interest overlapping with HPE). Deeper analyses of candidate variants were then performed on a family-by-family basis. These included the exploration of clinical information, expression studies, variant characteristics, recurrence of mutated genes and available biological knowledge. A novel bioinformatics pipeline was designed. Applied to the 39 families, this final integrated workflow identified an average of 11 candidate variants per family. Most of candidate variants were inherited from asymptomatic parents suggesting a multigenic inheritance pattern requiring the association of multiple mutational events. The manual analysis highlighted 5 new strong HPE candidate genes showing recurrences in distinct families. Functional validations of these genes are foreseen.

Keywords: complex genetic disorder, holoprosencephaly, multiple rare variants, whole exome sequencing

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Authors: Dev Ras Pandey, Bharat Mishra, S. K. Tripathi

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Cloud computing is ready to transform the structure of businesses and learning through supplying the real-time applications and provide an immediate help for small to medium sized businesses. The ability to run a hypervisor inside a virtual machine is important feature of virtualization and it is called nested virtualization. In today’s growing field of information technology, many of the virtualization models are available, that provide a convenient approach to implement, but decision for a single model selection is difficult. This paper explains the applications of operating system based virtualization in cloud computing with an appropriate/suitable model with their different specifications and user’s requirements. In the present paper, most popular models are selected, and the selection was based on container and hypervisor based virtualization. Selected models were compared with a wide range of user’s requirements as number of CPUs, memory size, nested virtualization supports, live migration and commercial supports, etc. and we identified a most suitable model of virtualization.

Keywords: virtualization, OS based virtualization, container based virtualization, hypervisor based virtualization

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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

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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

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Authors: Mst. Tuhin Akter, Sharun Akter Khushbu, S. M. Shaqib

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A real-time system architecture is highly effective for monitoring and detecting various damaged products or fruits that may deteriorate over time or become infected with diseases. Deep learning models have proven to be effective in building such architectures. However, building a deep learning model from scratch is a time-consuming and costly process. A more efficient solution is to utilize deep neural network (DNN) based transfer learning models in the real-time monitoring architecture. This study focuses on using a novel strawberry dataset to develop effective transfer learning models for the proposed real-time monitoring system architecture, specifically for evaluating and detecting strawberry freshness. Several state-of-the-art transfer learning models were employed, and the best performing model was found to be Xception, demonstrating higher performance across evaluation metrics such as accuracy, recall, precision, and F1-score.

Keywords: strawberry freshness evaluation, deep neural network, transfer learning, image augmentation

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Authors: Thiago Ribeiro De Alencar, Jacyro Gramulia Junior, Patricia Teixeira Leite Asano

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The area of the electricity sector that deals with energy needs by the hydropower and thermoelectric in a coordinated way is called Planning Operating Hydrothermal Power Systems. The aim of this area is to find a political operative to provide electrical power to the system in a specified period with minimization of operating cost. This article proposes a computational tool for solving the planning problem. In addition, this article will be introducing a methodology to find new transfer points between reservoirs increasing energy production in hydroelectric power plants cascade systems. The computational tool proposed in this article applies: i) genetic algorithms to optimize the water transfer and operation of hydroelectric plants systems; and ii) Ant Colony algorithm to find the trajectory with the least energy pumping for the construction of pipes transfer between reservoirs considering the topography of the region. The computational tool has a database consisting of 35 hydropower plants and 41 reservoirs, which are part of the southeastern Brazilian system, which has been implemented in an individualized way.

Keywords: ant colony system, genetic algorithms, hydroelectric, hydrothermal systems, optimization, water transfer between rivers

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

Abstract:

Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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Authors: Auwal Ibrahim Magashi, Lawan Dan Larai Fagwalawa, Muhammad Bello Ibrahim

Abstract:

A research was conducted to study genetic variability of some quantitative traits in varieties of cowpea (Vigna unguiculata L. [Walp]) under water stressed from Zaria, Nigeria. Seeds of seven varieties of cowpea (Sampea 1, Sampea 2, IAR1074, Sampea 7, Sampea 8, Sampea 10 and Sampea 12) collected from Institute for Agricultural Research (IAR), Samaru, Zaria were screened for water stressed tolerance. The seeds were then sown in poly bags containing sandy-loam arranged in Completely Randomized Design with three replications for quantitative traits evaluation. The nutritional composition of the seeds obtained from the water stress tolerant varieties of cowpea were analyzed. The result obtained revealed highly significant difference (P ≤ 0.01) in the effects of water stress on the number of wilted and dead plants at 40 days after sowing (DAS) and significant (P ≤ 0.05) 34 DAS. However, sampea 10 has the highest mean performance in terms of number of wilted plants at 34 DAS while sampea 2 and IAR 1074 has the lowest mean performance. However, sampea 7 was found to have the highest mean performance for the number of wilted plants at 40 DAS and sampea 2 is lowest. The result for quantitative traits study indicated highly significant difference (P ≤ 0.01) in the plant height, number of days to 50% flowering, number of days to maturity, number of pods per plant, pod length, number of seeds per plant and 100 seed weight; and significant (P ≤ 0.05) at seedling height and number of branches per plant. Similarly, IAR1074 was found to have high performance in terms of most of the quantitative traits under study. However, sampea 8 has the highest mean performance at nutritional level. It was therefore concluded that, all the seven cowpea genotypes were water stress tolerant and produced considerable yield that contained significant nutrients. It was recommended that IAR1074 should be grown for yield while sampea 8 should be grown for protein supplements.

Keywords: cowpea, genetic variability, quantitative traits, water stress

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Authors: Elif Aykin Dincer, Mustafa Erbas

Abstract:

The vacuum drying behavior of beef slices (10 x 4 x 0.2 cm3) was experimentally investigated at the temperature of 60, 70, and 80°C under 25 mbar ultimate vacuum pressure and the mathematical models (Lewis, Page, Midilli, Two-term, Wangh and Singh and Modified Henderson and Pabis) were used to fit the vacuum drying of beef slices. The increase in drying air temperature resulted in a decrease in drying time. It took approximately 206, 180 and 157 min to dry beef slices from an initial moisture content to a final moisture content of 0.05 kg water/kg dry matter at 60, 70 and 80 °C of vacuum drying, respectively. It is also observed that the drying rate increased with increasing drying temperature. The coefficients (R2), the reduced chi-square (x²) and root mean square error (RMSE) values were obtained by application of six models to the experimental drying data. The best model with the highest R2 and, the lowest x² and RMSE values was selected to describe the drying characteristics of beef slices. The Page model has shown a better fit to the experimental drying data as compared to other models. In addition, the effective moisture diffusivities of beef slices in the vacuum drying at 60 - 80 °C varied in the range of 1.05 – 1.09 x 10-10 m2/s. Consequently, this results can be used to simulate vacuum drying process of beef slices and improve efficiency of the drying process.

Keywords: beef slice, drying models, effective diffusivity, vacuum

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Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua

Abstract:

Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.

Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune

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