Search results for: genetic drift

Authors: Jacqueline P. Davies

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Introduction: Student nurses must develop skills in observation, communication and reflection as well as public health knowledge from their first year of training. This paper will explain a method developed for students to collect their own findings about public health in urban areas. These areas are both rich in the history of old public health that informs the content of many traditional public health walks, but are also locations where new public health concerns about chronic disease are concentrated. The learning method explained in this paper enables students to collect their own data and write original work as first year students. Examples of their findings will be given. Methodology: In small groups, health care students are instructed to walk in neighbourhoods near to the hospitals they will soon attend as apprentice nurses. On their walks, they wander slowly, engage in conversations, and enter places open to the public. As they drift, they observe with all five senses in the real three dimensional world to collect data for their reflective accounts of old and new public health. They are encouraged to stop for refreshments and taste, as well as look, hear, smell, and touch while on their walk. They reflect as a group and later develop an individual reflective account in which they write up their deep reflections about what they observed on their walk. In preparation for their walk, they are encouraged to look at studies of quality of Life and other neighbourhood statistics as well as undertaking a risk assessment for their walk. Findings: Reflecting on their walks, students apply theoretical concepts around social determinants of health and health inequalities to develop their understanding of communities in the neighbourhoods visited. They write about the treasured historical architecture made of stone, bronze and marble which have outlived those who built them; but also how the streets are used now. The students develop their observations into thematic analyses such as: what we drink as illustrated by the empty coke can tossed into a now disused drinking fountain; the shift in home-life balance illustrated by streets where families once lived over the shop which are now walked by commuters weaving around each other as they talk on their mobile phones; and security on the street, with CCTV cameras placed at regular intervals, signs warning trespasses and barbed wire; but little evidence of local people watching the street. Conclusion: In evaluations of their first year, students have reported the health walk as one of their best experiences. The innovative approach was commended by the UK governing body of nurse education and it received a quality award from the nurse education funding body. This approach to education allows students to develop skills in the real world and write original work.

Keywords: education, innovation, nursing, urban

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Authors: Harun Aydilek, Asiye Aydilek, Ali Allahverdi

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Our objective is to minimize the total tardiness in an m-machine two-stage assembly flowshop scheduling problem. The objective is an important performance measure because of the fact that the fulfillment of due dates of customers has to be taken into account while making scheduling decisions. In the literature, the problem is considered with zero setup times which may not be realistic and appropriate for some scheduling environments. Considering separate setup times from processing times increases machine utilization by decreasing the idle time and reduces total tardiness. We propose two new algorithms and adapt four existing algorithms in the literature which are different versions of simulated annealing and genetic algorithms. Moreover, a dominance relation is developed based on the mathematical formulation of the problem. The developed dominance relation is incorporated in our proposed algorithms. Computational experiments are conducted to investigate the performance of the newly proposed algorithms. We find that one of the proposed algorithms performs significantly better than the others, i.e., the error of the best algorithm is less than those of the other algorithms by minimum 50%. The newly proposed algorithm is also efficient for the case of zero setup times and performs better than the best existing algorithm in the literature.

Keywords: algorithm, assembly flowshop, scheduling, simulation, total tardiness

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Authors: Varun Singh, Mainak Bandyopadhyay, Maharana Pratap Singh

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The shortest path (SP) problem concerns with finding the shortest path from a specific origin to a specified destination in a given network while minimizing the total cost associated with the path. This problem has widespread applications. Important applications of the SP problem include vehicle routing in transportation systems particularly in the field of in-vehicle Route Guidance System (RGS) and traffic assignment problem (in transportation planning). Well known applications of evolutionary methods like Genetic Algorithms (GA), Ant Colony Optimization, Particle Swarm Optimization (PSO) have come up to solve complex optimization problems to overcome the shortcomings of existing shortest path analysis methods. It has been reported by various researchers that PSO performs better than other evolutionary optimization algorithms in terms of success rate and solution quality. Further Geographic Information Systems (GIS) have emerged as key information systems for geospatial data analysis and visualization. This research paper is focused towards the application of PSO for solving the shortest path problem between multiple points of interest (POI) based on spatial data of Allahabad City and traffic speed data collected using GPS. Geovisualization of results of analysis is carried out in GIS.

Keywords: particle swarm optimization, GIS, traffic data, outliers

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Authors: Mohsen S. Sajadieha, Danyar Molavia

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In this paper, a truck scheduling problem is investigated at a two-touch cross-docking center with due dates for outbound trucks as a hard constraint. The objective is to minimize the total cost comprising penalty and delivery cost of delayed shipments. The sequence of unloading shipments is considered and is assumed that shipments are sent to shipping dock doors immediately after unloading and a First-In-First-Out (FIFO) policy is considered for loading the shipments. A mixed integer programming model is developed for the proposed model. Two meta-heuristic algorithms including genetic algorithm (GA) and variable neighborhood search (VNS) are developed to solve the problem in medium and large sized scales. The numerical results show that increase in due dates for outbound trucks has a crucial impact on the reduction of penalty costs of delayed shipments. In addition, by increase the due dates, the improvement in the objective function arises on average in comparison with the situation that the cross-dock is multi-touch and shipments are sent to shipping dock doors only after unloading the whole inbound truck.

Keywords: cross-docking, truck scheduling, fixed due date, door assignment

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Authors: Mohammed Sghir Taleb

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Located at the northwest corner of the African continent between 21 ° and 36 ° north latitude and between the 1st and the 17th degree of west longitude, Morocco, with a total area of 715,000 km², enjoys a privileged position with a coastline of 3 446 km long opening to the Mediterranean and the Atlantic Ocean. Its privileged location with a double coastline and its diverse mountain with four major mountain ranges: the Rif, Middle Atlas, High Atlas, and Anti Atlas, with altitudes exceeding 2000 m in the Rif, 3000 m in the Middle Atlas, and 4000 m in the High Atlas. Morocco is characterized by an important forest genetic diversity represented by a rich and varied flora and many ecosystems: forest, preforest, presteppe, steppe, Sahara that spans a range of bioclimatic zones: arid, semiarid, subhumid, and humid. The vascular flora of Morocco is rich and highly diversified, with a very significant degree of endemism. Natural flora and ecosystems provide important services to populations represented by grazing, timber harvest, harvesting of medicinal and aromatic plants. This work will be focused on the Moroccan biodiversity and natural ecosystem services and on the interaction between local populations and ecosystems

Keywords: biodiversity, forest, ecosystem, services, Morocco

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Authors: Ayse Ozge Demir, Nihat Mert

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This study has been carried out in order to determine the polymorphic traits of various biochemical parameters in goat breeds which are native to Turkey. For this purpose, Angora and Hair goats breeds were chosen as live materials. Two different herds for each breed were selected from Ankara and Antalya, respectively. Blood samples were taken from a total of 120 goats aged between 2 and 4 which was made up of 60 Angora goats and 60 Hair goats. All which derived equally from 4 lots of herds. Analyses were performed for the polymorphic determination of the Haemoglobin (Hb), Transferrine (Tf), Ceruloplasmin (Cp) and Glutathione (GSH). Hb types were determined by starch gel electrophoresis and Tf types were detected by SDS-PAGE electrophoresis. Furthermore, Cp and GSH analyses were performed by spectrophotometrically. Following the analysis, Hb types were found as 3 genotypes (AA, AB, BB) controlled by 2 allel genes. Tf types were found as 6 genotypes (AA, AB, AC, BB, BC, CC) controlled by 3 allele genes. Findings for Hb was in line with the Hardy-Weinberg Equilibrium (HWE) in Angora goats while the Hair goat was not found to be in line. Moreover, Tf was found in line with the HWE for 2 separate goat breeds. The levels of Cp and GSH of two breeds were significantly different from other (P<0.0001). The findings are recorded as a source of reference for prospective polymorphism studies.

Keywords: electrophoresis, genetic resources, goats, spectrophotometer

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Authors: Andrew Anis Fakhrey Mosaad

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Introduction: Sports- and physical activity-related injuries may be more likely if there is a genetic predisposition, improper coaching and/or training, and no follow-up care from sports medicine. Goal: To evaluate the frequency of injuries among athletes receiving care at a sportsfocused physical therapy clinic. Methods: The survey of injuries in athletes' treatment records over a period of eight years of activity was done to obtain data. The data collected included: the patient's features, the sport, the type of injury, the injury's characteristics, and the body portion injured. Results: The athletes were drawn from 1090 patient/athlete records, had an average age of 25, participated in 44 different sports, and were 75% men on average. Joint injuries were the most frequent type of injury, then damage to the muscles and bones. The most prevalent type of injury was chronic (47%), while the knee, ankle, and shoulder were the most frequently damaged body parts. The most injured athletes were seen in soccer, futsal, and track and field, respectively, out of all the sports. Conclusion: The most popular sport among injured players was soccer, and the most common injury type was joint damage, with the knee being the most often damaged body area. The majority of the injuries were chronic.

Keywords: sports injuries, athletes, joint injuries, injured players

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Authors: Nadir Sidiqi

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Biodiversity conservation is humanity’s building block to sustain lives - ultimately allowing all living and nonliving creatures to interact in a balanced proportion. Humanity’s challenge in the 21st century is to maintain biodiversity without harming the natural habitat of plants, animals and beneficial microorganisms. There are many good reasons to consider why biodiversity is important to every nation around the world, especially for a nation like Afghanistan. One of the major values of biodiversity is its economic value: biodiversity provides goods and services to the Afghan nation directly through links and components such as the maintenance of traditional crops, medicine, fruits, animals, grazing, fuel, timber, harvesting, fishing, hunting and related supplies. Biodiversity is the variety of the living components, such as humans, plants, animals, and microorganisms, and nonliving components interaction, including air, water, sunlight, soil, humidity and environmental factors in an area. There are many ways of gauging the value of biodiversity. As an ecosystem, biodiversity includes such benefits as soil fertility, erosion control, crop pollination, crop rotation, and pest control. The conservation of biodiversity is crucial for these benefits, which would be impossible to replace. Biodiversity conservation also has heritage values; this wealth of genetic diversity provides backup to rural people living close together.

Keywords: Afghanistan, biodiversity, conservation, economy, environment

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Authors: Muhammad Fiaz, Muhammad Saqlain, Bernard M. Y. Cheung, S. M. Saqlan Naqvi, Ghazala Kaukab Raja

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Background: Association of C allele of rs662799 SNP of APOA5 gene with metabolic syndrome (MetS) has been reported in different populations around the world. A case control study was conducted to explore the relationship of rs662799 variants (T/C) with the MetS and the associated risk phenotypes in a population of Pakistani origin. Methods: MetS was defined according to the IDF criteria. Blood samples were collected from the Pakistan Institute of Medical Sciences, Islamabad, Pakistan for biochemical profiling and DNA extraction. Genotyping of rs662799 was performed using mass ARRAY, iPEX Gold technology. A total of 712 unrelated case and control subjects were genotyped. Data were analyzed using Plink software and SPSS 16.0. Results: The risk allele C of rs662799 showed highly significant association with MetS (OR=1.5, Ρ=0.002). Among risk phenotypes, dyslipidemia, and obesity showed strong association with SNP (OR=1.49, p=0.03; OR =1.46, p=0.01) respectively in models adjusted for age and gender. Conclusion: The rs662799C allele is a significant risk marker for MetS in the local Pakistani population studied. The effect of the SNP is more on dyslipidemia than the other components of the MetS.

Keywords: metabolic syndrome, APOA5, rs662799, dyslipidemia, obesity

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Authors: Alice Petzold, Alexandre Hassanin

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The number of giraffe species has been in focus of interest since the exploration of sub-Saharan Africa by European naturalists during the 18th and 19th centuries, as previous taxonomists, like Geoffroy Saint-Hilaire, Richard Owen or William Edward de Winton, recognized two or three species of Giraffa. For the last decades, giraffes were commonly considered as a single species subdivided into nine subspecies. In this study, we have re-examined available nuclear and mitochondrial data. Our genetic admixture analyses of seven introns support three species: G. camelopardalis (i.e., northern giraffes including reticulated giraffes), G. giraffa (southern giraffe) and G. tippelskirchi (Masai giraffe). However, the nuclear alignments show small variation and our phylogenetic analyses provide high support only for the monophyly of G. camelopardalis. Comparisons with the mitochondrial tree revealed a robust conflict for the position and monophyly of G. giraffa and G. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe, and secondly, by gene flow mediated by male dispersal between southern populations (subspecies angolensis and giraffa). We conclude that current data gives only moderate support for three giraffe species and point out that additional nuclear data need to be studied to revise giraffe taxonomy.

Keywords: autosomal markers, Giraffidae, mitochondrial introgression, taxonomy

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Authors: Vinay Kumar Vanjakula, Frank Adam

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The generation of electricity through wind power is one of the leading renewable energy generation methods. Due to abundant higher wind speeds far away from shore, the construction of offshore wind turbines began in the last decades. However, the installation of offshore foundation-based (monopiles) wind turbines in deep waters are often associated with technical and financial challenges. To overcome such challenges, the concept of floating wind turbines is expanded as the basis of the oil and gas industry. For such a floating system, stabilization in harsh conditions is a challenging task. For that, a robust heavy-weight gravity anchor is needed. Transportation of such anchor requires a heavy vessel that increases the cost. To lower the cost, the gravity anchor is designed with ballast chambers that allow the anchor to float while towing and filled with water when lowering to the planned seabed location. The presence of such a large structure may influence the flow field around it. The changes in the flow field include, formation of vortices, turbulence generation, waves or currents flow breaking and pressure differentials around the seabed sediment. These changes influence the installation process. Also, after installation and under operating conditions, the flow around the anchor may allow the local seabed sediment to be carried off and results in Scour (erosion). These are a threat to the structure's stability. In recent decades, rapid developments of research work and the knowledge of scouring on fixed structures (bridges and monopiles) in rivers and oceans have been carried out, and very limited research work on scouring around a bluff-shaped gravity anchor. The objective of this study involves the application of different numerical models to simulate the anchor towing under waves and calm water conditions. Anchor lowering involves the investigation of anchor movements at certain water depths under wave/current. The motions of anchor drift, heave, and pitch is of special focus. The further study involves anchor scour, where the anchor is installed in the seabed; the flow of underwater current around the anchor induces vortices mainly at the front and corners that develop soil erosion. The study of scouring on a submerged gravity anchor is an interesting research question since the flow not only passes around the anchor but also over the structure that forms different flow vortices. The achieved results and the numerical model will be a basis for the development of other designs and concepts for marine structures. The Computational Fluid Dynamics (CFD) numerical model will build in OpenFOAM and other similar software.

Keywords: anchor lowering, anchor towing, gravity anchor, computational fluid dynamics, scour

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Authors: Ying Qi Chan, Chunyu Li, Xu Rou Yoyo Ma, Yaya Li, Saber Khederzadeh

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In the ever-evolving landscape of genome extraction protocols, the existing methodologies grapple with issues ranging from sub-optimal yields and compromised quality to time-intensive procedures and reliance on hazardous reagents, often necessitating substantial tissue quantities. This predicament is particularly challenging for scientists in developing countries, where resources are limited. Our investigation presents a protocol for the efficient extraction of high-yield RNA from various tissues such as muscle, insect, and plant samples. Noteworthy for its advantages, our protocol stands out as the safest, swiftest (completed in just 38 minutes), most cost-effective (coming in at a mere US$0.017), and highly efficient method in comparison to existing protocols. Notably, our method avoids the use of hazardous or toxic chemicals such as chloroform and phenol and enzymatic agents like RNase and Proteinase K. Our RNA extraction protocol has demonstrated clear advantages over other methods, including commercial kits, in terms of yield. This nucleic acid extraction protocol is more environmentally and research-friendly, suitable for a range of tissues, even in tiny volumes, hence facilitating various genetic diagnosis and researches across the globe.

Keywords: RNA extraction, rapid protocol, universal method, diverse tissues

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Authors: Naso Isaiah Thanavisuth, Patompong Satapornpong

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Introduction: Covid-19 has been a global pandemic for some time now, causing severe symptoms to patients that received the virus. However, there has been no report on this gene in the Thai population. Objective: Our aim in this study is to explore and compare the frequency of HLA-C allele that is associated with severe COVID-19 symptoms in Thais and other populations. Method: 200 general Thai population were enrolled in this study. The genotyping of HLA -C alleles were determined by the polymerase chain reaction with sequence-specific oligonucleotide probes (PCR-SSOP) and Luminex®IS 100 system (Luminex Corporation, Austin, Texas, USA). Results: We found that the frequency of alleles HLA-C* 01:02 (16.00%), HLA-C* 08:01(10.50%), HLA-C* 03:04 (10.25%),HLA-C* 07:02 (10.00%), HLA-C* 03:02 (9.25%), HLA-C* 07:01 (6.75%), HLA-C* 04:01 (5.00%), HLA-C* 06:02 (4.00%), HLA-C* 04:03 (4.00%), and HLA-C* 07:04 (3.75%) were more common in the Thai population. HLA-C* 01:02 (16.00%) allele was the highest frequency in the North, Center, and North East groups in Thailand, but there was the South region that was not significantly different when compared with the other groups of the region. Additionally, HLA-C∗14:02 allele was similarly distributed in Thais (3.00%), African Americans (1.98%), Caucasians (2.08%), Hispanics (1.71%), North American Natives (1.34%) and Asians (5.01%) by p-value = 0.6506, 0.6506, 0.6506, 0.6135 and 0.7182, respectively. Conclusion: Genetic variation database is important to identify HLA can be a risk factor for severe COVID-19 in many populations. In this study, we will support the research of the HLA markers for screening severe COVID-19 in many populations.

Keywords: HLA-C * 14:02, COVID-19, allele frequency, Thailand

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Authors: Anna Ouskova Leonteva, Michel Risser, Anne Jeannin-Girardon, Pierre Parrend, Pierre Collet

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This paper proposes an efficient optimization tool for an active magnetic regenerator (AMR) model, operating in two modes: magnetic refrigeration system (MRS) and thermo-magnetic generator (TMG). The aim of this optimizer is to improve the design of the AMR by applying a multi-physics multi-scales numerical model as a core of evaluation functions to achieve industrial requirements for refrigeration and energy conservation systems. Based on the multi-objective non-dominated sorting genetic algorithm 3 (NSGA3), it maximizes four different objectives: efficiency and power density for MRS and TMG. The main contribution of this work is in the simultaneously application of a CPU-parallel NSGA3 version to the AMR model in both modes for studying impact of control and design parameters on the performance. The parametric study of the optimization results are presented. The main conclusion is that the common (for TMG and MRS modes) optimal parameters can be found by the proposed tool.

Keywords: ecological refrigeration systems, active magnetic regenerator, thermo-magnetic generator, multi-objective evolutionary optimization, industrial optimization problem, real-world application

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Authors: Nasir Khalid, S. Thirumalaichelvam

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In most buildings, according to US Department of Energy Data Book, the electrical consumption attributable to centralized heating and ventilation of air- condition (HVAC) component can be as high as 40-60% of the total electricity consumption for an entire building. To provide efficient energy management for the market today, researchers are finding new ways to develop a system that can save electrical consumption of buildings even more. In this concept paper, a system known as Intelligent Chiller Energy Efficiency (iCEE) System is being developed that is capable of saving up to 25% from the chiller’s existing electrical energy consumption. In variable frequency drives (VFDs), research has found significant savings up to 30% of electrical energy consumption. Together with the VFDs at specific Air Handling Unit (AHU) of HVAC component, this system will save even more electrical energy consumption. The iCEE System is compatible with any make, model or age of centrifugal, rotary or reciprocating chiller air-conditioning systems which are electrically driven. The iCEE system uses engineering principles of efficiency analysis, enthalpy analysis, heat transfer, mathematical prediction, modified genetic algorithm, psychometrics analysis, and optimization formulation to achieve true and tangible energy savings for consumers.

Keywords: variable frequency drives, adjustable speed drives, ac drives, chiller energy system

Procedia PDF Downloads 558

Authors: Beata J. Lehka, Samuel A. Bradley, Frederik G. Hansson, Khem B. Adhikari, Daniela Rago, Paulina Rubaszka, Ahmad K. Haidar, Ling Chen, Lea G. Hansen, Olga Gudich, Konstantina Giannakou, Yoko Nakamura, Thomas Dugé de Bernonville, Konstantinos Koudounas, Sarah E. O’Connor, Vincent Courdavault, Jay D. Keasling, Jie Zhang, Michael K. Jensen

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Monoterpenoid indole alkaloids (MIAs) represent a large class of natural plant products with marketed pharmaceutical activities against a wide range of applications, including cancer and mental disorders. Halogenated MIAs have shown improved pharmaceutical properties; however, characterisation and synthesis of new-to-nature halogenated MIAs remain a challenge in slow-growing plants with limited genetic tractability. Here, we demonstrate a platform for de novo biosynthesis of two bioactive MIAs, serpentine and alstonine, in baker’s yeast Saccharomyces cerevisiae, reaching titers of 8.85 mg/L and 4.48 mg/L, respectively, when cultivated in fed-batch micro bioreactors. Using this MIA biosynthesis platform, we undertake a systematic exploration of the derivative space surrounding these compounds and produce halogenated MIAs. The aim of the current study is to develop a fermentation process for halogenated MIAs.

Keywords: monoterpenoid indole alkaloids, Saccharomyces cerevisiae, halogenated derivatives, fermentation

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Authors: Akshay B. Pawar, Rohit Y. Parasnis

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Heart Rate Variability (HRV) is a widely used indicator of the regulation between the autonomic nervous system (ANS) and the cardiovascular system. Besides being non-invasive, it also has the potential to predict mortality in cases involving critical injuries. The gold standard method for determining HRV is based on the analysis of RR interval time series extracted from ECG signals. However, because it is much more convenient to obtain photoplethysmogramic (PPG) signals as compared to ECG signals (which require the attachment of several electrodes to the body), many researchers have used pulse cycle intervals instead of RR intervals to estimate HRV. They have also compared this method with the gold standard technique. Though most of their observations indicate a strong correlation between the two methods, recent studies show that in healthy subjects, except for a few parameters, the pulse-based method cannot be a surrogate for the standard RR interval- based method. Moreover, the former tends to overestimate short-term variability in heart rate. This calls for improvements in or alternatives to the pulse-cycle interval method. In this study, besides the systolic peak-peak interval method (PP method) that has been studied several times, four recent PPG-based techniques, namely the first derivative peak-peak interval method (P1D method), the second derivative peak-peak interval method (P2D method), the valley-valley interval method (VV method) and the tangent-intersection interval method (TI method) were compared with the gold standard technique. ECG and PPG signals were obtained from 10 young and healthy adults (consisting of both males and females) seated in the armchair position. In order to de-noise these signals and eliminate baseline drift, they were passed through certain digital filters. After filtering, the following HRV parameters were computed from PPG using each of the five methods and also from ECG using the gold standard method: time domain parameters (SDNN, pNN50 and RMSSD), frequency domain parameters (Very low-frequency power (VLF), Low-frequency power (LF), High-frequency power (HF) and Total power or “TP”). Besides, Poincaré plots were also plotted and their SD1/SD2 ratios determined. The resulting sets of parameters were compared with those yielded by the standard method using measures of statistical correlation (correlation coefficient) as well as statistical agreement (Bland-Altman plots). From the viewpoint of correlation, our results show that the best PPG-based methods for the determination of most parameters and Poincaré plots are the P2D method (shows more than 93% correlation with the standard method) and the PP method (mean correlation: 88%) whereas the TI, VV and P1D methods perform poorly (<70% correlation in most cases). However, our evaluation of statistical agreement using Bland-Altman plots shows that none of the five techniques agrees satisfactorily well with the gold standard method as far as time-domain parameters are concerned. In conclusion, excellent statistical correlation implies that certain PPG-based methods provide a good amount of information on the pattern of heart rate variation, whereas poor statistical agreement implies that PPG cannot completely replace ECG in the determination of HRV.

Keywords: photoplethysmography, heart rate variability, correlation coefficient, Bland-Altman plot

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Authors: Yooncheol Lee, Jeongmin Kim, Kwang Ryel Ryu

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This paper deals with the establishment of a short-term operational plan for an air conditioner for efficient energy management of exhibition hall. The short-term operational plan is composed of a time series of operational schedules, which we have searched using genetic algorithms. Establishing operational schedule should be considered the future trends of the variables affecting the exhibition hall environment. To reflect continuously changing factors such as external temperature and occupant, short-term operational plans should be updated in real time. But it takes too much time to evaluate a short-term operational plan using EnergyPlus, a building emulation tool. For that reason, it is difficult to update the operational plan in real time. To evaluate the short-term operational plan, we designed prediction models based on machine learning with fast evaluation speed. This model, which was created by learning the past operational data, is accurate and fast. The collection of operational data and the verification of operational plans were made using EnergyPlus. Experimental results show that the proposed method can save energy compared to the reactive control method.

Keywords: exhibition hall, energy management, predictive model, simulation-based optimization

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Authors: Sara Canas Pedrosa, Esther Moraleda SepuLveda

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Angelman Syndrome (AS) and Prader-Willi Syndrome (PWS) are considered rare genetic disorders that share the same chromosomal region: 15q11.2-q13. This is why both share some common characteristics, such as, delay in language development. However, there is still little research that specifically focuses on the linguistic profile in these populations. Therefore, the objective of this study was to know the characteristics of oral and written language that Angelman Syndrome and Prader-Willi Syndrome present from the point of view of parents. The sample consisted of 36 families (with children between 6 and 17 years old), of which 23 had children with AS and 13 had children with PWS. All of them answered the Language Assessment Scale of the standardized test CELF-4, Spanish Clinical Evaluation of Language Fundamentals-4 (Wiig, Secord & Semel, 2006). The scale is made up of 40 items that assesses the perception of parents in areas such as: difficulty of listening, speaking, reading and writing. The results indicate that the majority of parents manifest problems in almost all the sub-areas related to oral language and written language, taking into account that many do not achieve a literacy level, with similar results in comparison with both syndromes. These data support the importance of working on oral language delay and its relationship with the subsequent learning of literacy throughout its development.

Keywords: Angelman Syndrome , development, language, Prader-Willi Syndrome

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Authors: Alime Cengiz, Talip Kahyaoglu

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Roasting process has the major importance to obtain desired aromatic taste of nuts. In this study, two kinds of roasting process were applied to hulled sesame seeds - vacuum oven and hot air roasting. Efficiency of Gene Expression Programming (GEP), a new soft computing technique of evolutionary algorithm that describes the cause and effect relationships in the data modelling system, and response surface methodology (RSM) were examined in the modelling of roasting processes over a range of temperature (120-180°C) for various times (30-60 min). Color attributes (L*, a*, b*, Browning Index (BI)), textural properties (hardness and fracturability) and moisture content were evaluated and modelled by RSM and GEP. The GEP-based formulations and RSM approach were compared with experimental results and evaluated according to correlation coefficients. The results showed that both GEP and RSM were found to be able to adequately learn the relation between roasting conditions and physical and textural parameters of roasted seeds. However, GEP had better prediction performance than the RSM with the high correlation coefficients (R2 >0.92) for the all quality parameters. This result indicates that the soft computing techniques have better capability for describing the physical changes occuring in sesame seeds during roasting process.

Keywords: genetic expression programming, response surface methodology, roasting, sesame seed

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Authors: Jianli Dong, Fangling Xu, Gengming Huang

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Human endogenous retroviral elements (HERVs) comprise approximately 8% of the human genome. They are thought to be germline-integrated genetic remnants of retroviral infections. Although HERV sequences are highly defective, some, especially the K type (HERV-K), have been shown to be expressed and may have biological activities in the pathogenesis of cancer, chronic inflammation and autoimmune diseases. We found that HERV-K GAG and ENV proteins were strongly expressed in pleomorphic melanoma cells. We also detected a critical role of HERV-K ENV in mediating intercellular fusion and colony formation of melanoma cells. Interestingly, we found that levels of HERV-K GAG and ENV expression correlated with the activation of ERK and loss of p16INK4A in melanoma cells, and inhibition of MEK or CDK4, especially in combination, reduced HERV-K expression in melanoma cells. We also performed a reverse transcription-polymerase chain reaction (RT-PCR) assay using DNase I digestion to remove “contaminating” HERV-K genomic DNA and examined HERV-K RNA expression in plasma samples from HIV-1 infected individuals. We found a covariation between HERV-K RNA expression and CD4 cell counts in HIV-1 positive samples. Although a causal link between HERV-K activation and melanoma development, and between HERV-K activation, HIV-1 infection and CD4 cell count have yet to be determined, existing data support the further research efforts in HERV-K.

Keywords: CD4 cell, HERV-K, HIV-1, melanoma

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Authors: Lavinia Ruta, Ileana Farcasanu

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The yeast surface display (YSD) technique enables the expression of proteins on yeast cell surfaces, facilitating the identification and isolation of proteins with targeted binding properties, such as nanobodies. Nanobodies, derived from camelid species, are single-domain antibody fragments renowned for their high affinity and specificity towards target proteins, making them valuable in research and potentially in therapeutics. Their advantages include a compact size (~15 kDa), robust stability, and the ability to target challenging epitopes. The project endeavors to establish and validate a platform for producing Green Fluorescent Protein (GFP) and mCherry nanobodies using the yeast surface display method. mCherry, a prevalent red fluorescent protein sourced from coral species, is commonly utilized as a genetic marker in biological studies due to its vibrant red fluorescence. The GFP-nanobody, a single variable domain of heavy-chain antibodies (VHH), exhibits specific binding to GFP, offering a potent means for isolating and engineering fluorescent protein fusions across various biological research domains. Both GFP and mCherry nanobodies find specific utility in cellular imaging and protein analysis applications.

Keywords: YSD, nanobodies, GFP, Saccharomyces cerevisiae

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Authors: Loo Fung Ying, Loo Fung Chiat

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The formation of a musical identity that shapes the nation in this multiracial country reveals many complexities, conundrums, and contingencies. Creativity and identity formation at the level of an individual or a collective group further diversified musical expression, representation, and style, which has led to an absence of regularities. In addition, ‘contemporizing accretion,’ borrowing a term used by Schnelle in theology (2009), further complicates musical identity, authenticity, conception, and realization. Thus, in this paper, we attempt to define the issues surrounding the teaching and learning of the multiracial Malaysian national music identity. We also discuss unnecessary power hierarchies, interracial conflicts, and sentiments in the construct of a multiracial national music identity by referring to genetic origins, the evolution of music, and the neglected issues of representation and reception at a global level from a diachronic perspective. Lastly, by synthesizing Ladson-Billings, Gay, Kruger, and West-Burns’s culturally relevant/responsive pedagogical theories, we discuss possible analytic tools for consideration that are more multiculturally relevant and responsive for the teaching, learning, and construction of a multiracial Malaysian national music identity.

Keywords: Malaysia, music, multiracial, national music identity, culturally relevant/responsive pedagogy

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Authors: Mahmoud Nadir, Adel Ghenaiet

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The main purpose of this study is the thermodynamic modeling, the parametric analysis, and the optimization of three pressure level reheat HRSG (Heat Recovery Steam Generator) using PSO method (Particle Swarm Optimization). In this paper, a parametric analysis followed by a thermodynamic optimization is presented. The chosen objective function is the specific work of the steam cycle that may be, in the case of combined cycle (CC), a good criterion of thermodynamic performance analysis, contrary to the conventional steam turbines in which the thermal efficiency could be also an important criterion. The technologic constraints such as maximal steam cycle temperature, minimal steam fraction at steam turbine outlet, maximal steam pressure, minimal stack temperature, minimal pinch point, and maximal superheater effectiveness are also considered. The parametric analyses permitted to understand the effect of design parameters and the constraints on steam cycle specific work variation. PSO algorithm was used successfully in HRSG optimization, knowing that the achieved results are in accordance with those of the previous studies in which genetic algorithms were used. Moreover, this method is easy to implement comparing with the other methods.

Keywords: combined cycle, HRSG thermodynamic modeling, optimization, PSO, steam cycle specific work

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Authors: Khaoula Azraiel, Mohamed Mehdi Abassi, Amel Sadraoui, Walid Hammami, Azouz Msaddek, Imed Cheikh, Maria Mancebo, Elisabet Perez-Navarro, Antonio Caruz, Henda Triki, Ahlem Djebbi

Abstract:

IL28B rs12979860 genotype is confirmed as an important predictor of response to peginterferon/ribavirin therapy in patients with chronic hepatitis C (CHC). IFNL4 ss469415590 is a newly discovered polymorphism that could also affect the sustained virological response (SVR). The aim of this study was to evaluate the association of IL28B and IFNL4 genotypes with peginterferon/ribavirin treatment response in Tunisians patients with CHC and to determine which of these SNPs, was the stronger marker. A total of 120 patients were genotyped for both rs12979860 and ss469415590 polymorphisms. The association of each genetic marker with SVR was analyzed and comparison between the two SNPs was calculated by logistic regression models. For rs12979860, 69.6% of patients with CC, 41.8% with CT and 42.8% with TT achieved SVR (p = 0.003). Regarding ss469415590, 70.4% of patients with TT/TT genotype achieved SVR compared to 42.8% with TT/ΔG and 37.5% with ΔG /ΔG (p = 0.002). The presence of CC and TT/TT genotypes was independently associated with treatment response with an OR of 3.86 for each. In conclusion, both IL28B rs12979860 and IFNL4 ss469415590 variants were associated with response to pegIFN/RBV in Tunisian patients, without any additional benefit in performance for IFNL4. Our results are different from those detected in Sub-Saharan Africa countries.

Keywords: Hepatitis C virus, IFNL4, IL28B, Peginterferon/ribavirin, polymorphism

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Authors: Alexander Dao, Oscar Wambuguh

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Irritable Bowel Syndrome (IBS) is a heterogeneous functional bowel disease that is characterized by chronic visceral abdominal pain and abnormal bowel function and habits. Its multifactorial pathophysiology and mechanisms are still largely a mystery to the contemporary biomedical community, although there are many hypotheses to try to explain IBS’s presumed physiological, psychosocial, genetic, and environmental etiologies. IBS’s symptomatic presentation is varied and divided into four major subtypes: IBS-C, IBS-D, IBS-M, and IBS-U. Given its diverse presentation and unclear mechanisms, diagnosis is done through a combination of positive identification utilizing the “Rome IV Irritable Bowel Syndrome Criteria'' (Rome IV) diagnostic criteria while also excluding other potential conditions with similar symptoms. Treatment of IBS is focused on the management of symptoms using an assortment of pharmaceuticals, lifestyle changes, and dietary changes, with future potential in microbial treatment and psychotherapy as other therapy methods. Its chronic, heterogeneous nature and disruptive gastrointestinal (GI) symptoms are negatively impactful on patients’ daily lives, health systems, and society. However, with a better understanding of the gaps in knowledge and technological advances in IBS’s pathophysiology, management, and treatment options, there is optimism for the millions of people worldwide who are suffering from the debilitating effects of IBS.

Keywords: irritable bowel syndrome, lifestyle, diet, functional gastrointestinal disorder

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Authors: Guangyuan Zhao, Nan Huang, Xuesong Han, Xu Huang

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In order to solve the problem of sample dilution in the traditional particle filter algorithm and achieve accurate state estimation in a nonlinear system, a particle filter method based on an improved artificial bee colony (ABC) algorithm was proposed. The algorithm simulated the process of bee foraging and optimization and made the high likelihood region of the backward probability of particles moving to improve the rationality of particle distribution. The opposition-based learning (OBL) strategy is introduced to optimize the initial population of the artificial bee colony algorithm. The convergence factor is introduced into the neighborhood search strategy to limit the search range and improve the convergence speed. Finally, the crossover and mutation operations of the genetic algorithm are introduced into the search mechanism of the following bee, which makes the algorithm jump out of the local extreme value quickly and continue to search the global extreme value to improve its optimization ability. The simulation results show that the improved method can improve the estimation accuracy of particle filters, ensure the diversity of particles, and improve the rationality of particle distribution.

Keywords: particle filter, impoverishment, state estimation, artificial bee colony algorithm

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Authors: Yin-Yann Chen, Jia-Ying Li

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Assembly line balancing problems can be categorized into one-sided, two-sided, and multi-manned ones by using the number of operators deployed at workstations. This study explores the balancing problem of a resource-constrained assembly line with multi-manned workstations. Resources include machines or tools in assembly lines such as jigs, fixtures, and hand tools. A mathematical programming model was developed to carry out decision-making and planning in order to minimize the numbers of workstations, resources, and operators for achieving optimal production efficiency. To improve the solution-finding efficiency, a genetic algorithm (GA) and a simulated annealing algorithm (SA) were designed and developed in this study to be combined with a practical case in car making. Results of the GA/SA and mathematics programming were compared to verify their validity. Finally, analysis and comparison were conducted in terms of the target values, production efficiency, and deployment combinations provided by the algorithms in order for the results of this study to provide references for decision-making on production deployment.

Keywords: heuristic algorithms, line balancing, multi-manned workstation, resource-constrained

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Authors: G. Tamilpavai, C. Vishnuppriya

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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM

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Authors: Zi-Han Li, Zi-Jun Sun, Dong-Yuan Chang, Li Zhu, Min Chen, Ming-Hui Zhao

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Aims: A genome-wide association study (GWAS) reported that patients with the rs55703767 minor allele in collagen type IV α3 chain encoding gene COL4A3 showed protection against diabetic kidney disease (DKD) in type 1 diabetes mellitus (T1DM). However, the role of rs55703767 in type 2 DKD has not been elucidated. The aim of the current study was to investigate the association between COL4A3 variant rs55703767 and DKD risk in Chinese patients with type 2 diabetes mellitus (T2DM). Methods: This nested case-control study was performed on 1311 patients who had T2DM for at least 10 years, including 580 with DKD and 731 without DKD. We detected the genotypes of all patients by TaqMan SNP Genotyping Assay and analyzed the association between COL4A3 variant rs55703767 and DKD risk. Results: Genetic analysis revealed that there was no significant difference between T2DM patients with DKD and those without DKD regarding allele or genotype frequencies of rs55703767, and the effect of this variant was not hyperglycemia specific. Conclusion: Our findings suggested that there was no detectable association between the COL4A3 variant rs55703767 and the susceptibility to DKD in the Chinese T2DM population.

Keywords: collagen type IV α3 chain, gene polymorphism, type 2 diabetes, diabetic kidney disease

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