Search results for: Bouallegue Ridha

Authors: Samia Dardouri, Ridha Bouallegue

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Scheduling is the process of dynamically allocating physical resources to User Equipment (UE) based on scheduling algorithms implemented at the LTE base station. Various algorithms have been proposed by network researchers as the implementation of scheduling algorithm which represents an open issue in Long Term Evolution (LTE) standard. This paper makes an attempt to study and compare the performance of PF, MLWDF and EXP/PF scheduling algorithms. The evaluation is considered for a single cell with interference scenario for different flows such as Best effort, Video and VoIP in a pedestrian and vehicular environment using the LTE-Sim network simulator. The comparative study is conducted in terms of system throughput, fairness index, delay, packet loss ratio (PLR) and total cell spectral efficiency.

Keywords: LTE, multimedia flows, scheduling algorithms, mobile computing

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Authors: Laabidi Mounira, Zayani Rafk, Bouallegue Ridha

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Filter Bank Multicarrier with Offset Quadrature Amplitude Modulation (FBMC/OQAM) is presently known as a sustainable alternative to conventional Orthogonal Frequency Division Multiplexing (OFDM) for signal transmission over multi-path fading channels. Like all multicarrier systems, FBMC/OQAM suffers from high Peak to Average Power Ratio (PAPR). Due to the symbol overlap inherent in the FBMC/OQAM system, the direct application of conventional OFDM PAPR reduction scheme is far from being effective. This paper suggests a novel scheme termed Multi-Blocks Selective Mapping (MB-SLM) whose simulation results show that its performance in terms of PAPR reduction is almost identical to that of OFDM system.

Keywords: FBMC/OQAM, multi-blocks, OFDM, PAPR, SLM

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Authors: Raida Zouari, Iness Ahriz, Rafik Zayani, Ali Dziri, Ridha Bouallegue

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This paper proposes a room level indoor localization algorithm based on the use Multi-Layer Neural Network (MLNN) classifiers and one versus one strategy. Seven parameters of the Channel Impulse Response (CIR) were used and Gram-Shmidt Orthogonalization was performed to study the relevance of the extracted parameters. Simulation results show that when relevant CIR parameters are used as position fingerprint and when optimal MLNN architecture is selected good room level localization score can be achieved. The current study showed also that some of the CIR parameters are not correlated to the location and can decrease the localization performance of the system.

Keywords: mobile indoor localization, multi-layer neural network (MLNN), channel impulse response (CIR), Gram-Shmidt orthogonalization

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Authors: Mounira Laabidi, Rafik Zayani, Ridha Bouallegue, Daniel Roviras

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The Filter Bank multicarrier with Offset Quadrature Amplitude Modulation (FBMC-OQAM) has been introduced to overcome the poor spectral characteristics and the waste in both bandwidth and energy caused by the use of the cyclic prefix. However, the FBMC-OQAM signals suffer from the high Peak to Average Power Ratio (PAPR) problem. Due to the overlapping structure of the FBMC-OQAM signals, directly applying the PAPR reduction schemes conceived for the OFDM one turns out to be ineffective. In this paper, we address the problem of PAPR reduction for FBMC-OQAM systems by suggesting a new scheme based on an improved version of Active Constellation Extension scheme (ACE) of OFDM. The proposed scheme, named Rolling Window ACE, takes into consideration the overlapping naturally emanating from the FBMC-OQAM signals.

Keywords: ACE, FBMC, OQAM, OFDM, PAPR, rolling-window

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Authors: Marwane Ben Hcine, Ridha Bouallegue

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The aim of this work is to provide an original analytical framework for downlink effective SINR evaluation in LTE networks. The classical single carrier SINR performance evaluation is extended to multi-carrier systems operating over frequency selective channels. Extension is achieved by expressing the link outage probability in terms of the statistics of the effective SINR. For effective SINR computation, the exponential effective SINR mapping (EESM) method is used on this work. Closed-form expression for the link outage probability is achieved assuming a log skew normal approximation for single carrier case. Then we rely on the lognormal approximation to express the exponential effective SINR distribution as a function of the mean and standard deviation of the SINR of a generic subcarrier. Achieved formulas is easily computable and can be obtained for a user equipment (UE) located at any distance from its serving eNodeB. Simulations show that the proposed framework provides results with accuracy within 0.5 dB.

Keywords: LTE, OFDMA, effective SINR, log skew normal approximation

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Authors: Kaouther Selmi, Alaeddine Sridi, Mohamed Bouallegue, Kais Bouallegue

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Neurons are the fundamental units of the brain and the nervous system. The variable structure model of neurons consists of a system of differential equations with various parameters. By optimizing these parameters, we can create a unique model that describes the dynamic behavior of a single neuron. We introduce a neural network based on neurons with multiple dendrites employing an activation function with a variable structure. In this paper, we present a model for heart behavior. Finally, we showcase our successful simulation of the heart's ECG diagram using our Variable Structure Neuron Model (VSMN). This result could provide valuable insights into cardiology.

Keywords: neural networks, neuron, dendrites, heart behavior, ECG

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Authors: Jamel Miri, Bechir Nsiri, Ridha Bouallegue

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Ultra WidBand-IR physical layer technology has seen a great development during the last decade which makes it a promising candidate for short range wireless communications, as they bring considerable benefits in terms of connectivity and mobility. However, like all wireless communication they suffer from vulnerabilities in terms of security because of the open nature of the radio channel. To face these attacks, distance bounding protocols are the most popular counter measures. In this paper, we presented a protocol based on distance bounding to thread the most popular attacks: Distance Fraud, Mafia Fraud and Terrorist fraud. In our work, we study the way to adapt the best secure distance bounding protocols to mapping code of ultra-wideband (TH-UWB) radios. Indeed, to ameliorate the performances of the protocol in terms of security communication in TH-UWB, we combine the modified protocol to ultra-wideband impulse radio technology (IR-UWB). The security and the different merits of the protocols are analyzed.

Keywords: distance bounding, mapping code ultrawideband, terrorist fraud, physical layer technology

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Authors: Ameni Mejri, Moufida Hajjaj, Salem Hasnaoui, Ridha Bouallegue

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The technology advances have most lately made the millimeter wave (mmWave) communication possible. Due to the huge amount of spectrum that is available in MmWave frequency bands, this promising candidate is considered as a key technology for the deployment of 5G cellular networks. In order to enhance system capacity and achieve spectral efficiency, very large antenna arrays are employed at mmWave systems by exploiting array gain. However, it has been shown that conventional beamforming strategies are not suitable for mmWave hardware implementation. Therefore, new features are required for mmWave cellular applications. Unlike traditional multiple-input-multiple-output (MIMO) systems for which only digital precoders are essential to accomplish precoding, MIMO technology seems to be different at mmWave because of digital precoding limitations. Moreover, precoding implements a greater number of radio frequency (RF) chains supporting more signal mixers and analog-to-digital converters. As RF chain cost and power consumption is increasing, we need to resort to another alternative. Although the hybrid precoding architecture has been regarded as the best solution based on a combination between a baseband precoder and an RF precoder, we still do not get the optimal design of hybrid precoders. According to the mapping strategies from RF chains to the different antenna elements, there are two main categories of hybrid precoding architecture. Given as a hybrid precoding sub-array architecture, the partially-connected structure reduces hardware complexity by using a less number of phase shifters, whereas it sacrifices some beamforming gain. In this paper, we treat the hybrid precoder design in mmWave MIMO systems as a problem of matrix factorization. Thus, we adopt the alternating minimization principle in order to solve the design problem. Further, we present our proposed algorithm for the partially-connected structure, which is based on the iterative hard thresholding method. Through simulation results, we show that our hybrid precoding algorithm provides significant performance gains over existing algorithms. We also show that the proposed approach reduces significantly the computational complexity. Furthermore, valuable design insights are provided when we use the proposed algorithm to make simulation comparisons between the hybrid precoding partially-connected structure and the fully-connected structure.

Keywords: alternating minimization, hybrid precoding, iterative hard thresholding, low-complexity, millimeter wave communication, partially-connected structure

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Authors: Mechlouch Ridha Fethi

Abstract:

This paper presents a recent mathematical model in political sciences concerning democracy. The model is represented by a logarithmic equation linking the Relative Index of Democracy (RID) to Participation Ratio (PR). Firstly the meanings of the different parameters of the model were presented; and the variation curve of the RID according to PR with different critical areas was discussed. Secondly, the model was applied to a virtual group where we show that the model can be applied depending on the gender. Thirdly, it was observed that the model can be extended to different language models of democracy and that little use to assess the state of democracy for some International organizations like UNO.

Keywords: democracy, mathematic, modelization, quantification

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Authors: Ridha Salhi, Mondher Labidi, Fethi Choubani

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Metamaterials have attracted much attention in recent years because of their electromagnetic exquisite proprieties. We will present, in this paper, the modeling of three metamaterial structures by equivalent circuit model. We begin by modeling the SRR (Split Ring Resonator), then we model the HIS (High Impedance Surfaces), and finally, we present the model of the CPW (Coplanar Wave Guide). In order to validate models, we compare the results obtained by an equivalent circuit models with numerical simulation.

Keywords: metamaterials, SRR, HIS, CPW, IDC

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Authors: Ridha Zgolli, Ahmed Belhaj, Maroua Ennouri

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This study presents a new method to predict cavitation area that may be eroded. It is based on the post-treatment of URANS simulations in cavitant flows. The most RANS calculations with incompressible consideration are based on cavitation model using mixture fluid with density (ρm) calculated as a function of liquid density (ρliq), vapour or gas density (ρvap) and vapour or gas volume fraction α (ρm = αρvap + (1-α) ρliq). The calculations are performed on hydrofoil geometries and compared with experimental works concerning flows characteristics (size of pocket, pressure, velocity). We present here the used cavitation model and the approach followed to evaluate the value of α fixing the shape of pocket around wall before collapsing.

Keywords: flows, CFD, cavitation, erosion

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Authors: S. Ben Brahim, T. H. Vuong, J. David, R. Bouallegue, M. Pietrzak-David

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Electrical machine monitoring is important to protect motor from unexpected problems. Today, using wireless communication for electrical machines is interesting for both real time monitoring and diagnostic purposes. In this paper, we propose a system based on wireless communication IEEE 802.11 to control electrical machine. IEEE 802.11 standard is recommended for this type of applications because it provides a faster connection, better range from the base station, and better security. Therefore, our contribution is to study a new technique to control and monitor the rotating electrical machines (motors, generators) using wireless communication. The reliability of radio channel inside rotating electrical machine is also discussed. Then, the communication protocol, software and hardware design used for the proposed system are presented in detail and the experimental results of our system are illustrated.

Keywords: control, DFIM machine, electromagnetic field, EMC, IEEE 802.11, monitoring, rotating electrical machines, wireless communication

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Authors: Ridha Zgolli, Hatem Kanfoudi

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Cavitating flows inside a diesel injection nozzle hole were simulated using a mixture model. A 2D numerical model is proposed in this paper to simulate steady cavitating flows. The Reynolds-averaged Navier-Stokes equations are solved for the liquid and vapor mixture, which is considered as a single fluid with variable density which is expressed as function of the vapor volume fraction. The closure of this variable is provided by the transport equation with a source term TEM. The processes of evaporation and condensation are governed by changes in pressure within the flow. The source term is implanted in the CFD code ANSYS CFX. The influence of numerical and physical parameters is presented in details. The numerical simulations are in good agreement with the experimental data for steady flow.

Keywords: cavitation, injection nozzle, numerical simulation, k–ω

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Authors: Marwa Ben Abdessalem, Amin Zribi, Ammar Bouallègue

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In this paper, a Joint Source Channel coding scheme based on LDPC codes is investigated. We consider two concatenated LDPC codes, one allows to compress a correlated source and the second to protect it against channel degradations. The original information can be reconstructed at the receiver by a joint decoder, where the source decoder and the channel decoder run in parallel by transferring extrinsic information. We investigate the performance of the JSC LDPC code in terms of Bit-Error Rate (BER) in the case of transmission over an Additive White Gaussian Noise (AWGN) channel, and for different source and channel rate parameters. We emphasize how JSC LDPC presents a performance tradeoff depending on the channel state and on the source correlation. We show that, the JSC LDPC is an efficient solution for a relatively low Signal-to-Noise Ratio (SNR) channel, especially with highly correlated sources. Finally, a source-channel rate optimization has to be applied to guarantee the best JSC LDPC system performance for a given channel.

Keywords: AWGN channel, belief propagation, joint source channel coding, LDPC codes

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Authors: Boubaker Fezzani, Ridha Ben Cheikh, Tarek Rouissi

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In this work the original ADM1, implemented in the simulation software package MATLAB/Simulink, was modified and adapted and applied to reproduce the experimental results of the mesophilic anaerobic digestion of Esperto paper industry wastewater in a batch digester. The data set from lab-scale experiment runs were used to calibrate and validate the model. The simulations’ results indicated that the modified ADM1 was able to predict reasonably well the steady state results of gas flows, methane and carbon dioxide contents, pH and total volatile fatty acids (TVFA) observed with all influents concentrations.

Keywords: anaerobic digestion, mathematical modelling, Simulation, ADM1, batch digester, esparto paper industry effluent, mesophilic temperature

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Authors: E. Ghayoula, M. Haj Taieb, A. Bouallegue, J. Y. Chouinard, R. Ghayoula

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This paper evaluates the bit error rate (BER) performance of MIMO systems for wireless communication. MIMO uses multiple transmitting antennas, multiple receiving antennas and the space-time block codes to provide diversity. MIMO transmits signal encoded by space-time block (STBC) encoder through different transmitting antennas. These signals arrive at the receiver at slightly different times. Spatially separated multiple receiving antennas are employed to provide diversity reception to combat the effect of fading in the channel. This paper presents a detailed study of diversity coding for MIMO systems. STBC techniques are implemented and simulation results in terms of the BER performance with varying number of MIMO transmitting and receiving antennas are presented. Our results show how increasing the number of both transmit and receive antenna improves system performance and reduces the bit error rate.

Keywords: MIMO systems, diversity, BER, MRRC, SIMO, MISO, STBC, alamouti, SNR

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Authors: Ridha Fethi Mechlouch, Ahlem Ayadi, Ammar Ben Brahim

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Given the importance of the preservation of polyphenols and carotenoids during thermal processing, we attempted in this study to investigate the variation of these two parameters in faba beans during microwave treatment using different power densities (1; 2; and 3W/g), then to perform a mathematical modeling by using non-linear regression analysis to evaluate the models constants. The variation of the carotenoids and polyphenols ratio of faba beans and the models are tested to validate the experimental results. Exponential models were found to be suitable to describe the variation of caratenoid ratio (R²= 0.945, 0.927 and 0.946) for power densities (1; 2; and 3W/g) respectively, and polyphenol ratio (R²= 0.931, 0.989 and 0.982) for power densities (1; 2; and 3W/g) respectively. The effect of microwave power density Pd(W/g) on the coefficient k of models were also investigated. The coefficient is highly correlated (R² = 1) and can be expressed as a polynomial function.

Keywords: microwave treatment, power density, carotenoid, polyphenol, modeling

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Authors: Rifda Naufalin, Nurul Latifasari, Siti Nuryanti, Muna Ridha Hanifah

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Kecombrang is a Zingiberaceae plant which has antioxidant properties. The high antioxidant content in kecombrang flowers has the potential to be processed as a functional beverage raw material so that it can be used as an ingredient in making herbal teas. The purpose of this study was to determine the chemical components, physicochemistry, antioxidant activity and sensory characteristics of kecombrang tea. The research methodology was carried out by using a completely randomized design with processing factors of kecombrang tea namely blanching and non-blanching, fermentation and non-fermentation, and the optimal time for drying kecombrang tea. The best treatment combination based on the effective index method is the treatment of the blanching process followed by drying at a temperature of 50ᵒC until the 2% moisture content can produce kecombrang tea with a total phenol content of 5.95 mg Tannic Acid Equivalent (TAE) / gram db, total flavonoid 3%, pH 4.5, and antioxidant activity 82.95%, red color, distinctive aroma of tea, fresh taste, and preferred by panelists.

Keywords: kecombrang tea, blanching, fermentation, total phenol, and antioxidant activity

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Authors: Abir Touati, Syed Jawad Hussain, Farid Touati, Ammar Bouallegue

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Although there has been a growing interest in the hybrid free-space optical link and radio frequency FSO/RF communication system, the current literature is limited to results obtained in moderate or cold environment. In this paper, using a soft switching approach, we investigate the effect of weather inhomogeneities on the strength of turbulence hence the channel refractive index under Qatar harsh environment and their influence on the hybrid FSO/RF availability. In this approach, either FSO/RF or simultaneous or none of them can be active. Based on soft switching approach and a finite state Markov Chain (FSMC) process, we model the channel fading for the two links and derive a mathematical expression for the outage probability of the hybrid system. Then, we evaluate the behavior of the hybrid FSO/RF under hazy and harsh weather. Results show that the FSO/RF soft switching renders the system outage probability less than that of each link individually. A soft switching algorithm is being implemented on FPGAs using Raptor code interfaced to the two terminals of a 1Gbps/100 Mbps FSO/RF hybrid system, the first being implemented in the region. Experimental results are compared to the above simulation results.

Keywords: atmospheric turbulence, haze, hybrid FSO/RF, outage probability, refractive index

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Authors: Zahia Aliche, Fatiha Boudjema, Benyoucef Khelidj, Selma Mettai, Zohra Bouriahi, Saliha Mohammed Belkebir, Ridha Mazouz

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The purpose of this work is the study of the viscoelastic behaviour formulating gels based plant extractions. The extracts of Zingibar officinale and Cinnamomum cassia were included in the gel at different concentrations of these plants in order to be applied in anti-inflammatory drugs. The yield of ethanolic extraction of Zingibar o. is 3.98% and for Cinnamomum c., essential oil by hydrodistillation is 1.67 %. The ethanolic extract of Zingibar.o, the essential oil of Cinnamomum c. and the mixture showed an anti-DPPH radicals’ activity, presented by EC50 values of 11.32, 13.48 and 14.39 mg/ml respectively. A gel based on different concentrations of these extracts was prepared. Microbiological tests conducted against Staphylococcus aureus and Escherichia colishowed moderate inhibition of Cinnamomum c. gel and less the gel based on Cinnamomum c./ Zingibar o. (20/80). The yeast Candida albicansis resistant to gels. The viscoelastic formulation property was carried out in dynamic and creep and modeled with the Kelvin-Voigt model. The influence of some parameters on the stability of the gel (time, temperature and applied stress) has been studied.

Keywords: Cinnamomum cassia, Zingibar officinale, antioxidant activity, antimicrobien activity, gel, viscoelastic behaviour

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Authors: Fatema Salman, Ridha Hammam, Fatima Khairallah, Fatima Aradi, Nafeesa Abdulla, Mohammed Alsafar

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Purpose: This study aims at measuring the extent of nurses’ knowledge and attitudes toward the use of physical restraints in different hospital wards at Salmaniya Medical Complex (SMC). Background: The habitual use of physical restraint is a widespread practice among nurses working in the clinical settings. Restraints inflict many deleterious consequences on patients physically and psychologically which in turn increases their morbidity and mortality risk and jeopardizes care quality. Nurses’ knowledge and attitudes toward physical restraints are crucial determinants of the persistence of this practice. Literature review: the evidence of lack of knowledge among nurses regarding the use of physical restraints is overwhelming in various clinical settings, especially in two main areas which are the negative consequences and the available alternatives to physical restraints. Studies explored nurses’ attitudes toward physical restraints yielded inconsistent findings. Equally comparable, some studies found that nurses hold positive attitudes toward the use of physical restraints while some others reported just the opposite. Methods: Self-administered knowledge and attitudes scales to 106 nurses working in the SMC. Findings: nurses hold the moderate level of knowledge about restraints (M=58%) with weak negative attitudes (M = -20%) toward using it. Significant moderately-strong negative correlation (r= -0.57, r2= 0.32, p= 0.000) was uncovered between nurses knowledge and their attitudes which provided an empirical explanation of this phenomenon (use of physical restraints). Recommendations: Induction of awareness program that especially focuses on the negative consequences and encourages the use of alternatives is an evident need. This effort necessarily should be adjoined with policy and procedure adjustments.

Keywords: attitudes, knowledge, nurses, restraints

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Authors: Chargui Ridha, Agrebi Sameh

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The integration of phase change materials (PCM) for the storage of thermal energy during the period of sunshine before being released during the night is a complement of free energy to improve the system formed by a solar collector, tank storage, and a heat exchanger. This paper is dedicated to the design of a thermal storage tank based on a PCM-based heat exchanger. The work is divided into two parts: an experimental part using paraffin as PCM was carried out within the Laboratory of Thermal Processes of Borj Cedria in order to improve the performance of the system formed by the coupling of a flat solar collector and a thermal storage tank and to subsequently determine the influence of PCM on the whole system. This phase is based on the measurement instrumentation, namely, a differential scanning calorimeter (DSC) and the thermal analyzer (hot disk: HOT DISK) in order to determine the physical properties of the paraffin (PCM), which has been chosen. The second phase involves the detailed design of the PCM heat exchanger, which is incorporated into a thermal storage tank and coupled with a solar air collector installed at the Research and Technology Centre of Energy (CRTEn). A numerical part based on the TRANSYS and Fluent software, as well as the finite volume method, was carried out for the storage reservoir systems in order to determine the temperature distribution in each chosen system.

Keywords: phase change materials, storage tank, heat exchanger, flat plate collector

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Authors: Ridha Abdulla Al Hammam

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Purpose: to measure the extent of perceived structural empowerment and work commitment the intensive care unit in SMC have in their work place. Background: nurses’ access to power structures (information, recourses, opportunity, and support) directly influences their productivity, retention, and job satisfaction. Exploring nurses’ level and sources of work commitment (affective, normative, and continuance) is very essential to guide nursing leaders making decisions to improve work environment to facilitate effective nursing care. Both concepts (Structural Empowerment and Work Commitment) were never investigated in our critical care unit. Methods: a sample of 50 nurses attained from the Intensive Care Unit (Adult). Conditions for Workplace Effectiveness Questionnaire and Three-Component Model Employee Commitment Survey were used to measure the two concepts respectively. The study is quantitative, descriptive, and correlational in design. Results: the participants reported moderate structural empowerment provided by their work place (M=15 out of 20). The sample perceived high access to opportunity mainly through gaining more skills (M=4.45 out of 5) where the rest power structures were perceived with moderate accessibility. The participants’ affective commitment (M=5.6 out of 7) to work in the ICU overweighed their normative and continuance commitment (M=5.1, M=4.9 out of 7) implying a stronger emotional connection with their unit. Strong positive and significant correlations were observed between the participants’ structural empowerment scores and all work commitment sources. Conclusion: these results provided an insight on aspects of work environment that need to be fostered and improved in our intensive care unit which have a direct linkage to nurses’ work commitment and potentially to their quality of care they provide.

Keywords: structural empowerment, commitment, intensive care, nurses

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Authors: Wade Ghribi, Abdelmoty M. Ahmed, Ahmed Said Badawy, Belgacem Bouallegue

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In higher education institutions, the most pressing priority is to improve student performance and retention. Large volumes of student data are used in Educational Data Mining techniques to find new hidden information from students' learning behavior, particularly to uncover the early symptom of at-risk pupils. On the other hand, data with noise, outliers, and irrelevant information may provide incorrect conclusions. By identifying features of students' data that have the potential to improve performance prediction results, comparing and identifying the most appropriate ensemble learning technique after preprocessing the data, and optimizing the hyperparameters, this paper aims to develop a reliable students' performance prediction model for Higher Education Institutions. Data was gathered from two different systems: a student information system and an e-learning system for undergraduate students in the College of Computer Science of a Saudi Arabian State University. The cases of 4413 students were used in this article. The process includes data collection, data integration, data preprocessing (such as cleaning, normalization, and transformation), feature selection, pattern extraction, and, finally, model optimization and assessment. Random Forest, Bagging, Stacking, Majority Vote, and two types of Boosting techniques, AdaBoost and XGBoost, are ensemble learning approaches, whereas Decision Tree, Support Vector Machine, and Artificial Neural Network are supervised learning techniques. Hyperparameters for ensemble learning systems will be fine-tuned to provide enhanced performance and optimal output. The findings imply that combining features of students' behavior from e-learning and students' information systems using Majority Vote produced better outcomes than the other ensemble techniques.

Keywords: educational data mining, student performance prediction, e-learning, classification, ensemble learning, higher education

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Authors: Wafa Toumi, Alessandro Ripalti, Luigi Ricciardiello, Dalila Gargouri, Jamel Kharrat, Abderraouf Cherif, Ahmed Bouhafa, Slim Jarboui, Mohamed Zili, Ridha Khelifa

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Background & aims: Colorectal cancer (CRC) is one of the most common malignancies throughout the world. Several risk factors, both genetic and environmental, including viral infections, have been linked to colorectal carcinogenesis. A few studies report the detection of human polyomavirus JC (JCV) DNA and transformation antigen (T-Ag) in a fraction of the colorectal tumors studied and suggest an association of this virus with CRC. In order to investigate whether such an association of JCV with CRC will hold in a different epidemiological setting, we looked for the presence of JCV DNA and T-Ag expression in a group of Tunisian CRC patients. Methods: Fresh colorectal mucosa biopsies were obtained from 17 healthy volunteers and from both colorectal tumors and adjacent normal tissues of 47 CRC patients. DNA was extracted from fresh biopsies or from formalin-fixed, paraffin-embedded tissue sections using the Invitrogen Purelink Genomic DNA mini Kit. A simple PCR and a nested PCR were used to amplify a region of the T-Ag gene. The obtained PCR products revealed a 154 bp and a 98 bp bands, respectively. Specificity was confirmed by sequencing of the PCR products. T-Ag expression was determined by immunohistochemical staining using a mouse monoclonal antibody (clone PAb416) directed against SV40 T-Ag that cross reacts with JCV T-Ag. Results: JCV DNA was found in 12 (25%) and 22 (46%) of the CRC tumors by simple PCR and by nested PCR, respectively. All paired adjacent normal mucosa biopsies were negative for viral DNA. Sequencing of the DNA amplicons obtained confirmed the authenticity of T-Ag sequences. Immunohistochemical staining showed nuclear T-Ag expression in all 22 JCV DNA- positive samples and in 3 additional tumor samples which appeared DNA-negative by PCR. Conclusions: These results suggest an association of JCV with a subpopulation of Tunisian colorectal tumors.

Keywords: colorectal cancer, immunohistochemistry, Polyomavirus JC, PCR

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Authors: Inam Ridha, Christine L. Kuryla, Madhuranga Thilakasiri Madugoda Ralalage Don, Norman J. Kleiman, Yunro Chung, Jin Park, Vel Murugan, Joshua LaBaer

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To date, more than 275 million people worldwide have been diagnosed with COVID-19 and the rapid spread of the omicron variant suggests many millions more will soon become infected. Many infections are asymptomatic, while others result in mild to moderate illness. Unfortunately, some infected individuals exhibit more serious symptoms including respiratory distress, thrombosis, cardiovascular disease, multi-organ failure, cognitive difficulties, and, in roughly 2% of cases, death. Studies indicate other coronaviruses can alter the host cell's epigenetic profile and lead to alterations in the immune response. To better understand the mechanism(s) by which SARS-CoV-2 infection causes serious illness, DNA methylation profiles in peripheral blood mononuclear cells (PBMCs) from 90 hospitalized severely ill COVID-19 patients were compared to profiles from uninfected control subjects. Exploratory epigenome-wide DNA methylation analyses were performed using multiplexed methylated DNA immunoprecipitation (MeDIP) followed by pathway enrichment analysis. The findings demonstrated significant DNA methylation changes in infected individuals as compared to uninfected controls. Pathway analysis indicated that apoptosis, cell cycle control, Toll-like receptors (TLR), cytokine interactions, and T cell differentiation were among the most affected metabolic processes. In addition, changes in specific gene methylation were compared to SARS-CoV-2 induced changes in RNA expression using published RNA-seq data from 3 patients with severe COVID-19. These findings demonstrate significant correlations between differentially methylated and differentially expressed genes in a number of critical pathways.

Keywords: COVID19, epigenetics, DNA mathylation, viral infection

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