Search results for: genetic polymorphisms

Authors: Ali Kuzu

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There are about 800 thousand chemicals in our environment and the number is increasing more than a thousand every year. While most of these chemicals are used as components in various consumer products, some are faced as industrial waste in the environment. Unfortunately, many of these chemicals are hazardous and affect humans. According to the “International Program on Chemical Safety” of World Health Organization; Among the chronic health effects of chemicals, cancer is of major concern. Many substances have found in recent years to be carcinogenic in one or more species of laboratory animals. Especially with respect to long-term effects, the response to a chemical may vary, quantitatively or qualitatively, in different groups of individuals depending on predisposing conditions, such as nutritional status, disease status, current infection, climatic extremes, and genetic features, sex and age of the individuals. Understanding the response of such specific risk groups is an important area of toxicology research. People with age 65+ is defined as “aged (or elderly)”. The elderly population in the world is about 600 million, which corresponds to ~8 percent of the world population. While every 1 of each 4 people is aged in Japan, the elderly population is quite close to 20 percent in many developed countries. And elderly population in these countries is growing more rapidly than the total population. The negative effects of chemicals on elderly take an important place in health-care related issues in last decades. The aged population is more susceptible to the harmful effects of environmental chemicals. According to the poor health of the organ systems in elderly, the ability of their body to eliminate the harmful effects and chemical substances from their body is also poor. With the increasing life expectancy, more and more people will face problems associated with chemical residues.

Keywords: elderly, chemicals’ effects, aged care, care need

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Authors: Savjot Kaur, Mridula Mahajan, AJS Bhanwer, Santokh Singh, Kawaljit Matharoo

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Background: Disorders of lipid metabolism and genetic predisposition are CAD risk factors. ApoA1 is the apolipoprotein component of anti-atherogenic high density lipoprotein (HDL) particles. The protective action of HDL and ApoA1 is attributed to their central role in reverse cholesterol transport (RCT). Aim: This study was aimed at identifying sequence variations in ApoA1 (-75G>A) and its association with serum ApoA1 levels. Methods: A total of 300 CAD patients and 300 Normal individuals (controls) were analyzed. PCR-RFLP method was used to determine the DNA polymorphism in the ApoA1 gene, PCR products digested with restriction enzyme MspI, followed by Agarose Gel Electrophoresis. Serum apolipoprotein A1 concentration was estimated with immunoturbidimetric method. Results: Deviation from Hardy- Weinberg Equilibrium (HWE) was observed for this gene variant. The A- allele frequency was higher among Coronary Artery disease patients (53.8) compared to controls (45.5), p= 0.004, O.R= 1.38(1.11-1.75). Under recessive model analysis (AA vs. GG+GA) AA genotype of ApoA1 G>A substitution conferred ~1 fold increased risk towards CAD susceptibility (p= 0.002, OR= 1.72(1.2-2.43). With serum ApoA1 levels < 107 A allele frequency was higher among CAD cases (50) as compared to controls (43.4) [p=0.23, OR= 1.2(0.84-2)] and there was zero % occurrence of A allele frequency in individuals with ApoA1 levels > 177. Conclusion: Serum ApoA1 levels were associated with ApoA1 promoter region variation and influence CAD risk. The individuals with the APOA1 -75 A allele confer excess hazard of developing CAD as a result of its effect on low serum concentrations of ApoA1.

Keywords: apolipoprotein A1 (G>A) gene polymorphism, coronary artery disease (CAD), reverse cholesterol transport (RCT)

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Authors: Yitao Lei, Xingxiang Zhai, Burra Venkata Durga Kumar

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As the quantity and complexity of computing in large-scale software systems increase, distributed system computing becomes increasingly important. The distributed system realizes high-performance computing by collaboration between different computing resources. If there are no efficient resource scheduling resources, the abuse of distributed computing may cause resource waste and high costs. However, resource scheduling is usually an NP-hard problem, so we cannot find a general solution. However, some optimization algorithms exist like genetic algorithm, ant colony optimization, etc. The large scale of distributed systems makes this traditional optimization algorithm challenging to work with. Heuristic and machine learning algorithms are usually applied in this situation to ease the computing load. As a result, we do a review of traditional resource scheduling optimization algorithms and try to introduce a deep reinforcement learning method that utilizes the perceptual ability of neural networks and the decision-making ability of reinforcement learning. Using the machine learning method, we try to find important factors that influence the performance of distributed system computing and help the distributed system do an efficient computing resource scheduling. This paper surveys the application of deep reinforcement learning on distributed system computing resource scheduling proposes a deep reinforcement learning method that uses a recurrent neural network to optimize the resource scheduling, and proposes the challenges and improvement directions for DRL-based resource scheduling algorithms.

Keywords: resource scheduling, deep reinforcement learning, distributed system, artificial intelligence

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Authors: Bawa Yusuf Muhammad, Musa Abubakar Kana, Aminatu Abdulrahman, Kerry Goetz

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Background: Inherited eye diseases are disorders that affect globally, 1 in 1000 people. The six main world populations have created databases containing information on eye genotypes. Aim: The aim of the scoping review was to mine and present the available information to date on the genetics of inherited eye diseases within the African continent. Method: Literature Search Strategy was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). PubMed and Google Scholar searched for articles on inherited eye diseases from inception to 20th June 2022. Both Original and review articles that report on inherited, genetic or developmental/congenital eye diseases within the African Continent were included in the research. Results: A total of 1162 citations were obtained, but only 37 articles were reviewed based on the inclusion and exclusion criteria. The highest output of publications on inherited eye diseases comes from South Africa and Tunisia (about 43%), followed by Morocco and Egypt (27%), then Sub-Saharan Africa and North Africa (13.50%), while the remaining articles (16.5%) originated from Nigeria, Ghana, Mauritania Cameroon, Zimbabwe and combined article between Zimbabwe and Cameroon. Glaucoma and inherited retinal disorders represent the most studied diseases, followed by Albinism and congenital cataracts, respectively. Conclusion: Despite the growing research from Tunisia, Morocco, Egypt and South Africa, Sub-Saharan Africa remains almost a virgin region to explore the genetics of eye diseases.

Keywords: inherited eye diseases, Africa, scoping review, longitudinal eye study

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Authors: Seema Garcha, Sheetal Chopra, Navraj Sarao

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Plant hormones play a role in internal colonization by beneficial microbes and also systemic acquired resistance. They define qualitative and quantitative nature of root microbiome and also influence dynamics of root rhizospheric soil. The present study is an attempt to relate salicylic acid (signal molecule) content and qualitative nature of root endophytes at various stages in the growth of rice varieties of commercial value- Parmal 121 and Basmati 1121. Root seedlings of these varieties were raised using tissue culture techniques and then they were transplanted in the fields. Cultivation was done using conventional methods in agriculture. Field soil contained 0.39% N, 75.12 Kg/hectare of phosphorus and 163.0 Kg/hectare of potassium. Microfloral profiling of the root tissue was done using the selective microbiological medium. The salicylic acid content was estimated using HPLC-Agilent 1100 HPLC Series. Salicylic acid level of Basmati 1121 remained relatively low at the time of transplant and 90 days after transplant. It increased marginally at 60 days. A similar trend was observed with Parmal 121 as well. However, Parmal variety recorded 0.935 ug/g of salicylic acid at 60 days after transplant. Salicylic acid content decreased after 90 days as both the rice varieties remained disease free. The endophytic root microflora was established by 60 days after transplant in both the varieties after which their population became constant. Rhizobium spp dominated over Azotobacter spp. Genetic profiling of endophytes for nitrogen-fixing ability is underway.

Keywords: plant-microbe interaction, rice, root microbiome, salicylic acid

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Authors: Hesham Abd Elkhalek, Sherif M. Hafez, Yasser M. El Fahham

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Allocating limited budget to maintain bridge networks and selecting effective maintenance strategies for each bridge represent challenging tasks for maintenance managers and decision makers. In Egypt, bridges are continuously deteriorating. In many cases, maintenance works are performed due to user complaints. The objective of this paper is to develop a practical and reliable framework to manage the maintenance, repair, and rehabilitation (MR&R) activities of Bridges network considering performance and budget limits. The model solves an optimization problem that maximizes the average condition of the entire network given the limited available budget using Genetic Algorithm (GA). The framework contains bridge inventory, condition assessment, repair cost calculation, deterioration prediction, and maintenance optimization. The developed model takes into account multiple parameters including serviceability requirements, budget allocation, element importance on structural safety and serviceability, bridge impact on network, and traffic. A questionnaire is conducted to complete the research scope. The proposed model is implemented in software, which provides a friendly user interface. The framework provides a multi-year maintenance plan for the entire network for up to five years. A case study of ten bridges is presented to validate and test the proposed model with data collected from Transportation Authorities in Egypt. Different scenarios are presented. The results are reasonable, feasible and within acceptable domain.

Keywords: bridge management systems (BMS), cost optimization condition assessment, fund allocation, Markov chain

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Authors: Abdurzag Kerban, Mostfa M. Abou-Ahmed, Abdelrof M. Ghallab, Mona H. Shaker

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Preservation of semen had a major impact on sheep genetic breeding. The aim of this study was to evaluate the effect of protected fat, probiotic and zinc-enriched diets on semen freezability. Twenty two Barki rams were randomly assigned into four groups; Group I (n=5) was fed the basal diet enriched with 3.7% of dry fat/kg concentration/day, Group II (n=5) was fed a basal diet-enriched with 10gm of probiotic /head/day, Group III (n=6) was fed on the basal diet enriched with 100 ppm of 10% zinc chelated with methionine/kg dry matter/day and Group IV (n=6) was served as control. A pool of three to four ejaculates were pooled from rams within a period of ten weeks. Semen was diluted in egg yolk-Tris diluent and processed in 0.25 ml straw. Motility was evaluated after dilution, before freezing and post-thawing at 0, 1, 2 and 3 hour incubation. Viability index, acrosome integrity and leakage of intracellular enzymes (Aspartat aminotransferase and Alkline phosphatase) were also evaluated. Spermatozoa exhibited highly significant (P<0.01) percentages of motility at 0, 1, 2, and 3 hours incubation after thawing, viability index and acrosome integrity in rams fed a diet enriched with protected fat and zinc groups as compared with probiotic and control groups. Also, the mean value of extracellular leakage of AST was significantly lower in fat and zinc group as compared with probiotic and control groups. In conclusion, semen freezability was improved in animals fed a diet fortified with fat and zinc with no significant improvement in animals fed the probiotic-enriched diet.

Keywords: Barki ram semen, freezing, straw, feed additives

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Authors: Kyu Jin Kim, Byung Kwan Oh, Hyo Seon Park

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The seismic responses-based structural health monitoring system has been performed to prevent seismic damage. Structural seismic damage of building is caused by the instantaneous stress concentration which is related with dynamic characteristic of earthquake. Meanwhile, seismic response analysis to estimate the dynamic responses of building demands significantly high computational cost. To prevent the failure of structural members from the characteristic of the earthquake and the significantly high computational cost for seismic response analysis, this paper presents an artificial neural network (ANN) based prediction model for dynamic responses of building considering specific time length. Through the measured dynamic responses, input and output node of the ANN are formed by the length of specific time, and adopted for the training. In the model, evolutionary radial basis function neural network (ERBFNN), that radial basis function network (RBFN) is integrated with evolutionary optimization algorithm to find variables in RBF, is implemented. The effectiveness of the proposed model is verified through an analytical study applying responses from dynamic analysis for multi-degree of freedom system to training data in ERBFNN.

Keywords: structural health monitoring, dynamic response, artificial neural network, radial basis function network, genetic algorithm

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Authors: Mehdi Nasr Esfahani, Abdal-Rasool Gholamalian, Abdelfattah A. Dababat

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Wheat, Triticum aestivum L. is one of the most important and strategic crops in the human diet. Several diseases threaten this particular crop. Common root rot disease of wheat by a fungal agent, Bipolaris sorokiniana is one of the important diseases, causing considerable losses worldwide. Resistant sources are the only feasible and effective method of control for managing diseases. In this study, the response of 33 domestic and exotic wheat genotypes, including cultivars and promising lines were screened to B. sorokiniana at greenhouse and field conditions, based on five scoring scale indexes of 0 to 100 severity percentage. The screening was continued on resistant wheat genotypes and repeated several times to confirm the greenhouse and field results. Statistical and cluster analysis of data was performed using SAS and SPSS software, respectively. The results showed that, the response of wheat genotypes to the disease in the greenhouse and field conditions was highly significant. The highest rate of common root rot disease infection, B. sorokiniana in the greenhouse and field, was of CVS. Karkheh and Beck Cross-Roshan with 60.83% and 59.16% disease severity respectively, and the lowest one were in cv. Alvand with 18.33%, followed by cv. Baharan with 19.16% disease severity, with a highly significant difference respectively. The remaining wheat genotypes were located in between these two highest and lowest infected groups to B. sorokiniana significantly. There was a high correlation coefficient between the related statistical groups and cluster analysis.

Keywords: wheat, rot, root, crown, fungus, genotype, resistance

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Authors: S. Bahrami, A. Rezaie, Z. Boroumand, S. Ghavami

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Neospora caninum is protozoan parasite which can cause a serious disease in dogs and cattle. It has been shown that birds may be a permissive intermediate host for N. caninum since parasite DNA has been detected in tissues from birds. It is showed that embryonated chicken egg can be used as an animal model for experimental infection. The aim of present study was to compare experimental infection of Neospora in chicken and pigeons embryonated eggs. An infection with N. caninum Nc1 isolate was conducted in chicken and pigeons embryonated eggs to evaluate LD50. After calculation of LD50, 2LD50 of tachyzoites were injected to eggs. Macroscopic changes of each embryo were noticed and to investigate the parasite distribution in tissues immunohistochemistry (IHC) and molecular methods were used. In the present study, histopathological changes were considered and sections to those used for histopathological examination including heart, liver, brain and chorioallantoic (CA) membrane were subjected to IHC, too. For PCR procedure, primer pair Np21/Np6 was used for amplification of the Nc5 gene. Pigeon's embryo showed more macroscopic changes than chicken embryo. A hemorrhage of the CA was the main grass lesion. All the infected tissues had histopathological changes. Microscopic examination of tissues revealed acute neosporosis due to hemorrhage, necrosis and infiltration of mononuclear inflammatory cells. Based on IHC and molecular results, the parasite aggregation in the heart was more predominant than in the other tissues. These results reinforce that there is genetic susceptibility to N. caninum in pigeons embryonated eggs like chickens embryonated eggs and provide new insights to research an inexpensive and available animal model for N. caninum.

Keywords: immunohistochemistry, Neospora caninum, PCR, pigeon embryonated egg

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Authors: Maryam Torabi, Habibi, Abdolahi, Mohammadi, Hassanzadeh, Darban Maghami, Baghi

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Sheeppox Virus (SPPV) and goatpox virus (GTPV) are considerable diseases of sheep, and goats, caused by viruses of the Capripoxvirus (CaPV) genus. They are responsible for economic losses. Animal mortality, morbidity, cost of vaccinations, and restrictions in animal products’ trade are the reasons of economic losses. Control and eradication of CaPV depend on early detection of outbreaks so that molecular detection and genetic analysis could be effective to this aim. This study was undertaken to molecularly characterize SPPV and GTPV strains that have been circulating in Iran. 120 skin papules and nodule biopsies were collected from different regions of Iran and were examined for SPPV, GTPV viruses using TaqMan Real -Time PCR. Some of these amplified genes were sequenced, and phylogenetic trees were constructed. Out of the 120 samples analysed, 98 were positive for CaPV by Real- Time PCR (81.6%), and most of them wereSPPV. then 10 positive samples were sequenced and characterized by amplifying the ORF 103CaPV gene. sequencing and phylogenetic analysis for these positive samples revealed a high percentage of identity with SPPV isolated from different countries in Middle East. In conclusions, molecular characterization revealed nearly complete identity with all recent SPPVs strains in local countries that requires further studies to monitor the virus evolution and transmission pathways to better understand the virus pathobiology that will help for SPPV control.

Keywords: molecular epidemiology, Real-Time PCR, phylogenetic analysis, capripoxviruses

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Authors: Frikha Rim, Abdelmoula Bouayed Nouha, Rebai Tarek

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Pregnancy is a hypercoagulable state which causing a defective maternal haemostatic response and leading to thrombosis of the uteroplacental vasculature, that might cause pregnancy complications as recurrent pregnancy loss (RPL). Since heritable Thrombophilic defects are associated with increased thrombosis, their prevalence was evaluated in patients with special emphasis on combinations of the above pathologies. Especially, Factor V Leiden (FVL) G1691A, methylene tetra hydro folate reductase (MTHFR) C677T, and factor II (FII) G20210A mutations are three important causes of thrombophilia, which might be related to recurrent pregnancy loss (RPL). In this study we evaluated the presence of these three mutations [factor V Leiden (FVL), prothrombin G20210A (PTG) and methylenetetrahydrofolate reductase (MTHFR) C677T] amongst 35 Tunisian women with more than 2 miscarriages, referred to our genetic counseling. DNA was extracted from peripheral blood samples and PCR-RFLP was performed for the molecular diagnosis of each mutation. Factor V Leiden and Prothrombin mutation were detected respectively in 5.7% and 2.9% of women with particular history of early fetal loss and thrombotic events. Despites the luck of strength of this study, we insist that testing for the most inherited thrombophilia (FVL and FII mutation) should be performed in women with RPL in the context of thrombotic events. Multi-centre collaboration is necessary to clarify the real impact of thrombotic molecular defects on the pregnancy outcome, to ascertain the effect of thrombophilia on recurrent pregnancy loss and then to evaluate the appropriate therapeutic approach.

Keywords: thrombophilia, recurrent pregnancy loss, factor V Leiden, prothrombin G20210A, methylene tetra hydro folate reductase

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Authors: Ogbonnaya O. Iroanya, Samson T. Fakorede, Osamudiamen J. Edosa, Hadiat A. Azeez

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The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes.

Keywords: hypervariable region, indels, mitochondrial DNA, polymorphism, random match probability

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Authors: O. M. M. Sabry, Abeer M. El Sayed

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The essential oils from the aerial parts and flowers of Haplophyllum tuberculatum (Forsskal) Adr. Juss (Rutaceae) growing in Libya were obtained separately by hydro-distillation using a Clevenger-type apparatus. The essential oils yield were (0.4, 1.5w/w%) respectively based on the dry weight of the plant. The oils were analyzed by GC-MS. Twenty four constituents, amounting to 96.6%, were identified in the oil of the aerial parts. The predominant compounds were among the non oxygenated terpenoids (82.4%) as monoterpene hydrocarbons, represented by sabinen (26.4 %), δ-terpinen (26 %), β-phellandrene (10.4%) and 3-carene (3.86%). Zingiberine (0.4%) and β-sesquiphellandrene (0.12%) were the major sesquiterpene hydrocarbons identified. Oxygenated monoterpenes were represented by eucalyptol (5.5%) and piperitone (5.55%). Twenty six constituents, equivalent to 99.5%, were identified in the oil of the flowers. The dominance of monoterpene hydrocarbons in the flowers oil can be attributed to the high percentage of γ-terpinen (38.44%), β-phellandrene (10.0%), α- phellandrene (2.33%), 3,4-dimethyl-1,5-cyclooctadiene (6.67%), β-myrecene (6.04%), 3-carene (5.43%) and α-pinene (1.3%).While the oxygenated monoterpenes can be contributed to the trans-piperitol (4.67%) and piperitone (2.07%). Sesquiterpene hydrocarbons were not identified in the oil of the flower of H. tuberculatum. Variation in constitution between oils of Libyan H. tuberculatum and that obtained from other countries can be due to both environmental and genetic factors. The essential oils have demonstrated variable antimicrobial activities against certain micro-organisms. Also have revealed marked in vitro cytotoxicity against lung (H1299), liver (HEPG2) carcinoma cell line and variably effective as anti-inflammatory and antioxidant.

Keywords: Halpophyllum tuberculatum, rutaceae, essential oil, antimicrobial, anti-inflammatory, antitumor, antioxidant, Libya

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Authors: Joseph J. Okoh, Samuel T. Mbap, Tahir Ibrahim, Yusuf P. Mancha

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The influence of plumage colour on measurable attributes of 6176 adult indigenous chickens of mixed-sex from four states of the North Central Zone of Nigeria namely; Nasarawa, Niger, Benue, Kogi and the Federal Capital Territory (FCT) Abuja were assessed. The overall average body weight of the chickens was 1.95 ± 0.03kg. The body weights of black, white, black/white, brown, black/brown, grey and mottled chicken however were 1.87 ± 0.04, 1.94 ± 0.04, 1.95 ± 0.03, 1.93 ± 0.03, 2.01 ± 0.04, 1.96 ± 0.04 and 1.94±0.14kg respectively. Only body length did not vary by plumage colour. The others; body weight and width, shank, comb and breast length, breast height (p < 0.001), beak and wing lengths (p < 0.001) varied significantly. Generally, no colour was outrightly superior to others in all body measurements. However, body weight and breast height were both highest in black/brown chickens which also had the second highest breast length. Body width, shank, beak, comb and wing lengths were highest in grey chickens but lowest in those with white colour and combinations. Egg quality was on the other hand mostly lowest in grey chickens. In selection for genetic improvement in body measurements, black/brown and grey chickens should be favoured. However, in view of the known negative relationship between body weight and egg attributes, selection in favour of grey plumage may result in chickens of poor egg attributes. Therefore, grey chickens should be selected against egg quality.

Keywords: body weight, indigenous chicken, measurements, plumage colour

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Authors: Misganaw Abebe Baye, Ji-Woo Park, Beom-Soo Kang

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The product quality of multi-point dieless forming (MDF) is identified to be dependent on the process parameters. Moreover, a certain variation of friction and material properties may have a substantially worse influence on the final product quality. This study proposed on how to compensate the MDF product defects by minimizing the sensitivity of noise parameter variations. This can be attained by reliability-based robust optimization (RRO) technique to obtain the optimal process setting of the controllable parameters. Initially two MDF Finite Element (FE) simulations of AA3003-H14 saddle shape showed a substantial amount of dimpling, wrinkling, and shape error. FE analyses are consequently applied on ABAQUS commercial software to obtain the correlation between the control process setting and noise variation with regard to the product defects. The best prediction models are chosen from the family of metamodels to swap the computational expensive FE simulation. Genetic algorithm (GA) is applied to determine the optimal process settings of the control parameters. Monte Carlo Analysis (MCA) is executed to determine how the noise parameter variation affects the final product quality. Finally, the RRO FE simulation and the experimental result show that the amendment of the control parameters in the final forming process leads to a considerably better-quality product.

Keywords: dimpling, multi-point dieless forming, reliability-based robust optimization, shape error, variation, wrinkling

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Authors: Areej Javaid, Nishat Fatima, Mehwish Naseer

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There is a tremendous use of biofertilizers in agriculture to increase crop productivity. Pakistan spends a huge amount on the purchase of synthetic fertilizers every year. The use of natural compounds to harness crop productivity is the major area of interest nowadays due to being safe for human health and the environment as well. Legumes have the intrinsic quality to enrich the nutrient status of soil because of the presence of nitrogen fixation bacteria on nodules. This research determined the effect of biofertilizer on nodulation attributes and yield of the pea plant. Seeds of pea varieties were treated with a slurry of biofertilizer prepared in a 10% sugar solution just before seed sowing. The impact of biofertilizer on different parameters of growth, yield and nodulation was observed. Analysis of variance showed that plant height, days to flowering, number of nodes, days to first pod, root length and plant height exhibited significant genetic variation. All the yield parameters, including the number of pods per plant, number of seeds per pod, seed fresh and dry weight showed significant results under treatment. Among nodulation parameters, nodule number responded positively to biofertilizer treatment. Genotypes 2001-40 showed better performance followed by 2001-20 and LINA-PAK in all the parameters, whereas 2001-40 and 2001-20 performed well in nodulation and yield parameters. Consequently, seed treatment with biofertilizer before sowing is recommended to obtain higher crop yield.

Keywords: biological nitrogen fixation, correlation analysis, quantitative inheritance, varietal responses

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Authors: G. Shahzadi, A. Soulaimani

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This research work aims to identify the physical parameters of the constitutive soil model in the design of a rockfill dam by inverse analysis. The best parameters of the constitutive soil model, are those that minimize the objective function, defined as the difference between the measured and numerical results. The Finite Element code (Plaxis) has been utilized for numerical simulation. Polynomial and neural network-based response surfaces have been generated to analyze the relationship between soil parameters and displacements. The performance of surrogate models has been analyzed and compared by evaluating the root mean square error. A comparative study has been done based on objective functions and optimization techniques. Objective functions are categorized by considering measured data with and without uncertainty in instruments, defined by the least square method, which estimates the norm between the predicted displacements and the measured values. Hydro Quebec provided data sets for the measured values of the Romaine-2 dam. Stochastic optimization, an approach that can overcome local minima, and solve non-convex and non-differentiable problems with ease, is used to obtain an optimum value. Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Differential Evolution (DE) are compared for the minimization problem, although all these techniques take time to converge to an optimum value; however, PSO provided the better convergence and best soil parameters. Overall, parameter identification analysis could be effectively used for the rockfill dam application and has the potential to become a valuable tool for geotechnical engineers for assessing dam performance and dam safety.

Keywords: Rockfill dam, parameter identification, stochastic analysis, regression, PLAXIS

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Authors: Natida Thongsima, Patompong Satapornpong

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Introduction: Lamotrigine is widely used in the treatment of epilepsy and bipolar disorder. However, lamotrigine leads to adverse drug reactions (ADRs) consist of severe cutaneous adverse reactions (SCARs) include Stevens–Johnson syndrome (SJS), toxic epidermal necrolysis (TEN) and drug rash with eosinophilia and systemic symptoms (DRESS). Moreover, lamotrigine-induced SCARs are usually manifested between 2 and 8 weeks after treatment initiation. According to a previous study, the association between HLA-B*15:02 and lamotrigine-induced cutaneous adverse drug reactions in the Thai population (odds ratio 4.89; 95% CI 1.28–18.66; p-value = 0.014) was found. Therefore, the distribution of pharmacogenetics markers a major role in predicting the culprit drugs for SCARs in many populations. Objective: In this study, we want to investigate the prevalence of HLA-B allele, which correlates with lamotrigine-induced SCARs in the healthy Thai population. Materials and Methods: We enrolled 350 healthy Thai individuals and were approved by the ethics committee of Rangsit University. HLA-B alleles were genotyped by the Lifecodes HLA SSO typing kits (Immucor, West Avenue, Stamford, USA). Results: The results presented HLA-B allele frequency in healthy Thai population were 14.71% (HLA-B*46:01), 8.57% (HLA-B*15:02), 6.71% (HLA-B*40:01), 5.86% (HLA-B*13:01), 5.71% (HLA-B*58:01), 5.14% (HLA-B*38:02), 4.86% (HLA-B*18:01), 4.86% (HLA-B*51:01), 3.86% (HLA-B*44:03) and 2.71% (HLA-B*07:05). Especially, HLA-B*15:02 allele was the high frequency in the Thais (8.57%), Han Chinese (7.30%), Vietnamese (13.50%), Malaysian (6.06%) and Indonesian (11.60%). Nevertheless, this allele was much lower in other populations, namely, Africans, Caucasians, and Japanese. Conclusions: Although the sample size of the healthy Thai population in this research was limited, there were found the frequency of the HLA-B*15:02 allele could predispose them toward to lamotrigine-induced SCARs in Thailand.

Keywords: lamotrigine, cutaneous adverse drug reactions, HLA-B, Thai population

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Authors: Zoe Goldberger, Priscilla S. Briquez, Jeffrey A. Hubbell

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Tumor cells have mutations resulting from genetic instability that the immune system can actively recognize. Immune checkpoint immunotherapy (ICI) is commonly used in the clinic to re-activate immune reactions against mutated proteins, called neoantigens, resulting in tumor remission in cancer patients. However, only around 20% of patients show durable response to ICI. While tumor mutational burden (TMB) has been approved by the Food and Drug Administration (FDA) as a criterion for ICI therapy, the relevance of the subcellular localizations of the mutated proteins within the tumor cell has not been investigated. Here, we hypothesized that localization of mutations impacts the effect of immune responsiveness to ICI. We analyzed publicly available tumor mutation sequencing data of ICI treated patients from 3 independent datasets. We extracted the subcellular localization from the UniProtKB/Swiss-Prot database and quantified the proportion of membrane, cytoplasmic, nuclear, or secreted mutations per patient. We analyzed this information in relation to response to ICI treatment and overall survival of patients showing with 1722 ICI-treated patients that high mutational burden localized at the membrane (mTMB), correlate with ICI responsiveness, and improved overall survival in multiple cancer types. We anticipate that our results will ameliorate predictability of cancer patient response to ICI with potential implications in clinical guidelines to tailor ICI treatment. This would not only increase patient survival for those receiving ICI, but also patients’ quality of life by reducing the number of patients enduring non-effective ICI treatments.

Keywords: cancer, immunotherapy, membrane neoantigens, efficacy prediction, biomarkers

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Authors: Hossein Miri, Zhou YongQi, Chan Bormei-Suy

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The development of advanced technologies and innovative solutions has opened up exciting new possibilities for revolutionizing healthcare systems. One such emerging concept is the use of virtual and holographic health information platforms that aim to provide interactive and personalized medical information to users. This paper provides a review of notable virtual and holographic health information platforms. It begins by highlighting the need for information visualization and 3D representation in healthcare. It then proceeds to provide background knowledge on information visualization and historical developments in 3D visualization technology. Additional domain knowledge concerning holography, holographic computing, and mixed reality is then introduced, followed by highlighting some of their common applications and use cases. After setting the scene and defining the context, the need and importance of virtual and holographic visualization in medicine are discussed. Subsequently, some of the current research areas and applications of digital holography and holographic technology are explored, alongside the importance and role of virtual and holographic visualization in genetics and genomics. An analysis of the key principles and concepts underlying virtual and holographic health information systems is presented, as well as their potential implications for healthcare are pointed out. The paper concludes by examining the most notable existing mixed-reality applications and systems that help doctors visualize diagnostic and genetic data and assist in patient education and communication. This paper is intended to be a valuable resource for researchers, developers, and healthcare professionals who are interested in the use of virtual and holographic technologies to improve healthcare.

Keywords: virtual, holographic, health information platform, personalized interactive medical information

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Authors: Kusmayadi Ita Nursita, Sundoro Ali

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Cleft lip and palate are one of the most common congenital abnormalities in the face. It could happen to anyone, but mostly affect Asian population including Indonesia. Factors that influence the occurrence of cleft lip and palate vary from genetic to environmental factors. Children with cleft lip and palate will often have various problems such as airway disorders, eating disorders, speech and language developmental disorders, hearing disorders and psycho-social disorders, one of which is caused by appearance disorders. During his life, the child will experience multidisciplinary surgery and non-surgical treatment and can be accompanied by a psychological and financial burden on himself and his family. In Indonesia, there are no detailed scientific data on the prevalence and characteristic of cleft lip and palate patients. It was mainly caused by the absence of a national level organization, differences in geographical location, and the absence of national guidelines. This study aimed to describe the characteristic and prevalence of cleft lip and palate patients in Bandung Cleft Lip and Palate Center from 1 January 2016 to 31 December 2017. A total of 560 patients were included in the study. The highest percentage of cases are left unilateral cleft lip and palate with higher number of female patient and labioplasty as the most often surgical procedure to be conducted in Bandung Cleft Lip and Palate Center. In order to improve quality of life in patients with cleft lip and palate, early recognition and early treatment based on actual comprehensive data should be conducted. The data from Bandung Cleft Lip and Palate Center as one of the largest center of cleft lip and palate in West Java Indonesia hopefully could provide a big step of further comprehensive data collection in Indonesia and for the better overall management of cleft lip and palate in the future.

Keywords: cleft lip, cleft palate, characteristic, prevalence

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Authors: Debjani Ghosh, Goutam Chowdhury, Prosenjit Samanta, Asish Kumar Mukhopadhyay

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Acute diarrhoea caused by diarrheagenic Escherichia coli (DEC) is one of the major public health problem in developing countries, mainly in Asia and Africa. DEC consists of six pathogroups, but the majority of the cases were associated with the three pathogropus, enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), and enteropathogenic E. coli (EPEC). Hence, we studied the prevalence and antimicrobial resistance of these three major DEC pathogroups in hospitalized diarrheal patients in Kolkata, India, during 2012-2019 with a large sample size. 8,891 stool samples were processed, and 7.8% of them was identified as DEC infection screened by multiplex PCR, in which ETEC was most common (47.7%) followed by EAEC (38.4%) and EPEC (13.9%). Clinical patient history suggested that children <5 years of age were mostly affected with ETEC and EAEC, whereas people within >5-14 years of age were significantly associated with EPEC and ETEC infections. Antibiogram profile showed a high prevalence of multidrug resistant (MDR) isolates among DEC (56.9%), in which 9% were resistant to antibiotics of six different antimicrobial classes. Screening of the antibiotic resistance conferring genes in DEC showed the presence of blaCTX-M (30.2%) in highest number followed by blaTEM (27.5%), tetB (18%), sul2 (12.6%), strA (11.8%), aadA1 (9.8%), blaOXA-1 (9%), dfrA1 (1.6%) and blaSHV (1.2%) which indicates the existence of mobile genetic elements in those isolates. Therefore, the presence of MDR DEC strains in higher number alarms the public health authorities to take preventive measures before the upsurge of the DEC caused diarrhea cases in near future.

Keywords: diarrheagenic escherichia coli, ETEC, EAEC, EPEC

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Authors: L. M. Al-Harbi, A. M. Shokry, J. S. M. Sabir, A. Chaudhary, J. Manikandan, K. S. Saini

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Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations.

Keywords: breast cancer, molecular biology, ecology, environment

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: C. Nathanailides, S. Anastasiou, A. Dimitroglou, P. Logothetis, G. Kanlis

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In the present work we reviewed historical data of the Greek Marine aquaculture industry including adoption of new methods and technological innovation. The results indicate that the industry exhibited a rapid rise in production efficiency, employment and adoption of new technologies which reduced outbreaks of diseases, reduced production risk and the price of the farmed fish. The improvements of total quality practices and technological input on the Greek Aquaculture industry include improved survival, growth and body shape of farmed fish, which resulted from development of new aquaculture feeds and the genetic selection of the bloodstock. Also improvements in the quality of the final product were achieved via technological input in the methods and technology applied during harvesting, packaging, and transportation-preservation of farmed fish ensuring high quality of the product from the fish farm to the plate of the consumers. These parameters (health management, nutrition, genetics, harvesting and post-harvesting methods and technology) changed significantly over the last twenty years and the results of these improvements are reflected in the production efficiency of the Aquaculture industry and the quality of the final product. It is concluded that the Greek aquaculture industry exhibited a rapid growth, adoption of technologies and supply was stabilized after the global financial crisis, nevertheless, the development of the Greek aquaculture industry is currently limited by international trade sanctions, credit crunch, and increased taxation and not by limited technology or resources.

Keywords: innovation, aquaculture, total quality, management

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Authors: Alaa Sheta

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Economic Load Dispatch (ELD) is one of the vital optimization problems in power system planning. Solving the ELD problems mean finding the best mixture of power unit outputs of all members of the power system network such that the total fuel cost is minimized while sustaining operation requirements limits satisfied across the entire dispatch phases. Many optimization techniques were proposed to solve this problem. A famous one is the Quadratic Programming (QP). QP is a very simple and fast method but it still suffer many problem as gradient methods that might trapped at local minimum solutions and cannot handle complex nonlinear functions. Numbers of metaheuristic algorithms were used to solve this problem such as Genetic Algorithms (GAs) and Particle Swarm Optimization (PSO). In this paper, another meta-heuristic search algorithm named Differential Evolution (DE) is used to solve the ELD problem in power systems planning. The practicality of the proposed DE based algorithm is verified for three and six power generator system test cases. The gained results are compared to existing results based on QP, GAs and PSO. The developed results show that differential evolution is superior in obtaining a combination of power loads that fulfill the problem constraints and minimize the total fuel cost. DE found to be fast in converging to the optimal power generation loads and capable of handling the non-linearity of ELD problem. The proposed DE solution is able to minimize the cost of generated power, minimize the total power loss in the transmission and maximize the reliability of the power provided to the customers.

Keywords: economic load dispatch, power systems, optimization, differential evolution

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Authors: M. Ntswane, N. Mbuma, M. Labuschagne, A. Mofokeng, M. Rantso

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Cowpea is an essential legume for the nutrition and health of millions of people in different regions. The production and productivity of the crop are very limited in South Africa due to a lack of adapted and stable genotypes. The improvement of nutritional quality is made possible by manipulating the genes of diverse cowpea genotypes available around the world. Assessing the adaptability and stability of the cowpea mutant genotypes for yield and nutritional quality requires examining them in different environments. The objective of the study was to determine the adaptability and stability of cowpea mutant genotypes under South African conditions and to identify the superior genotypes that combine grain yield components, antioxidants, and nutritional quality. Thirty-one cowpea genotypes were obtained from the Agricultural Research Council grain crops (ARC-GC) and were planted in Glen, Mafikeng, Polokwane, Potchefstroom, Taung, and Vaalharts during the 2021/22 summer cropping season. Significant genotype by location interactions indicated the possibility of genetic improvement of these traits. The genotype plus genotype by environment indicated broad adaptability and stability of mutant genotypes. The principal component analysis identified the association of the genotypes with the traits. Phenotypic correlation analysis showed that Zn and protein content were significant and positively correlated and suggested the possibility of indirect selection of these traits. Results from this study could be used to help plant breeders in making informed decisions and developing nutritionally improved cowpea genotypes with the aim of addressing the challenges of poor nutritional quality.

Keywords: cowpea seeds, adaptability, stability, mineral elements, protein content

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: Abdullah A. Al Qurashi, Hattan A. Hassani, Bader K. Alaslap

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Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (ARVD/C) is an uncommon, inheritable cardiac disorder characterized by the progressive substitution of cardiac myocytes by fibro-fatty tissues. This pathologic substitution predisposes patients to ventricular arrhythmias and right ventricular failure. The underlying genetic defect predominantly involves genes encoding for desmosome proteins, particularly plakophilin-2 (PKP2). These aberrations lead to impaired cell adhesion, heightening the susceptibility to fibrofatty scarring under conditions of mechanical stress. Primarily, ARVD/C affects the right ventricle, but it can also compromise the left ventricle, potentially leading to biventricular heart failure. Clinical presentations can vary, spanning from asymptomatic individuals to those experiencing palpitations, syncopal episodes, and, in severe instances, sudden cardiac death. The establishment of a diagnostic criterion specifically tailored for ARVD/C significantly aids in its accurate diagnosis. Nevertheless, the task of early diagnosis is complicated by the disease's frequently asymptomatic initial stages, and the overall rarity of ARVD/C cases reported globally. In some cases, as exemplified by the adult female patient in this report, the disease may advance to terminal stages, rendering therapies like Ventricular Tachycardia (VT) ablation ineffective. This case underlines the necessity for increased awareness and understanding of ARVD/C to aid in its early detection and management. Through such efforts, we aim to decrease morbidity and mortality associated with this challenging cardiac disorder.

Keywords: arrhythmogenic right ventricular dysplasia, cardiac disease, interventional cardiology, cardiac electrophysiology

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