Search results for: genetic profile

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations of previous approaches, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with attention mechanism. In a previous work on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: transformers, generative ai, gene expression design, classification

Procedia PDF Downloads 52

Authors: R. Odoh, M. S. Dauda, E. A. Kamba, N. C. Igwemmar

Abstract:

Honey and honey trade is an important economic activity for many tropical rural and urban areas worldwide. In West Africa and other part of the world, honey and honey products holds high socio–cultural, religious, medicinal and traditional values. Therefore, to maximize benefits or to enhance profit, a variety of components are added to the raw, fresh and unprocessed honey, introducing the possibility of heavy metals contaminants. Therefore the honey sold in various places, markets and shops in some states in Northern Nigeria (Benue, Nassarawa and Taraba) including Abuja FCT, in Nigeria was analyzed to determine the level of heavy metals (Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). All the honey samples contain heavy metals. The results ranged from 0.028–0.070, 0.023–0.058, 0.042–0.092, 4.231–8.589, 8.115–14.892, 0.078–0.922, 0.044–0.092, 0.041–0.087 and 18.234–28.654 μg/L for Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn respectively. The mean concentration (μg/L) of the heavy metals Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn of the regularly marketed honey is significantly higher than the mean concentration observed in raw, fresh and unprocessed honey. However, continued consumption of honey with high heavy metal content might lead to exposure to chronic heavy metal poisoning.

Keywords: honey, health, mineral profile adulteration, contamination

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Authors: Ebrahim Behrouzian Nejad, Rezvan Alipoor Sabzevari

Abstract:

Cloud computing systems are large-scale distributed systems, so that they focus more on large scale resource sharing, cooperation of several organizations and their use in new applications. One of the main challenges in this realm is resource allocation. There are many different ways to resource allocation in cloud computing. One of the common methods to resource allocation are economic methods. Among these methods, the auction-based method has greater prominence compared with Fixed-Price method. The double combinatorial auction is one of the proper ways of resource allocation in cloud computing. This method includes two phases: winner determination and resource allocation. In this paper a new method has been presented to determine winner in double combinatorial auction-based resource allocation using Imperialist Competitive Algorithm (ICA). The experimental results show that in our new proposed the number of winner users is higher than genetic algorithm. On other hand, in proposed algorithm, the number of winner providers is higher in genetic algorithm.

Keywords: cloud computing, resource allocation, double auction, winner determination

Procedia PDF Downloads 356

Authors: Anthropometric, Physical Fitness Ability Profile of Elite, Non-Elite Boxers of Manipur

Abstract:

Background: Boxing is one of the oldest combat sports where different anthropological and fitness ability parameters determine performance. It is characterized by short duration, high intensity bursts of activity. The purpose of this research was to determine anthropometric and physical fitness profile of male elite and non-elite boxers of Manipur and to compare the two groups. Materials and Methods: Nineteen subjects were selected as elite boxers and twenty-four were non-elite boxers of Manipur. A cross-sectional study was conducted on anthropometric measurements and physical fitness ability tests on 33 subjects (elite and non-elite boxers). Statistical analysis was done using descriptive statistics, t-test and logistic regression with the help of SPSS version 15 software. Results: Results showed elite boxers have significantly reduced neck girth and calf girth as compare to non-elite boxers. Elite boxers have significantly lower sub scapular skin fold (SSF) and supra iliac skin fold (SISF) than their counterparts. Higher stature, larger BTB and lower percent fat are associated with higher performance in boxing. Sit ups (SU), standing Broad Jump (SBJ), Plat taping (PT), Sit and reach (SAR) and Harvard Step Test (HST) are predicted as most contributing factors enhancing performance level among the physical fitness components. Elite boxers are found to have more functional strength (sit ups), higher explosive strength (SBJ), more agility (PT), cardio-vascular endurance and flexibility (SAR) than non-elite boxers. Conclusion: In conclusion, lower fat, higher lean body mass, larger bi-trochantric breadth, high explosive strength, agility and flexibility are significantly associated with higher performance and chance of becoming elite boxers.

Keywords: anthropometry, elite and non-elite boxers, Manipur, physical fitness

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Authors: Dale Daniel G. Bodo

Abstract:

This study investigated the status of the Laboratory Tools and Equipment of the BSHRT Program of Eastern Visayas State University, Tacloban City Campus. Descriptive-correlation method was used which Variables include profile age, gender, acquired NC II, competencies in HRT and the status of the laboratory facilities, tools, and equipment of the BSHRT program. The study also identified significant correlation between the profile of the respondents and the implementation of the BSHRT Program in terms of laboratory tools and equipment. A self-structured survey questionnaire was used to gather relevant data among eighty-seven (87) BSHRT-OJT students. To test the correlations of variables, Pearson Product Moment Coefficient Correlation or Pearson r was used. As a result, the study revealed very interesting results and various significant correlations among the paired variables and as to the implementation of the BSHRT Program. Hence, this study was done to update the status of laboratory tools and equipment of the program.

Keywords: status, BSHRT Program, laboratory tools and equipment, descriptive-correlation

Procedia PDF Downloads 183

Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

Abstract:

Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

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Authors: Ahlam Elkilani, Bayan Elsheikh Ali, Rasha Abu Romman, Amjed Al-mousa, Belal Sababha

Abstract:

The amount of energy the world uses doubles every 20 years. Green homes play an important role in reducing the residential energy demand. This paper presents a platform that is intended to learn the behavior of home residents and build a profile about their habits and actions. The proposed resident aware home controller intervenes in the operation of home appliances in order to save energy without compromising the convenience of the residents. The presented platform can be used to simulate the actions and movements happening inside a home. The paper includes several optimization techniques that are meant to save energy in the home. In addition, several test scenarios are presented that show how the controller works. Moreover, this paper shows the computed actual savings when each of the presented techniques is implemented in a typical home. The test scenarios have validated that the techniques developed are capable of effectively saving energy at homes.

Keywords: green home, resident aware, resident profile, activity learning, machine learning

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Authors: D. Leibman, D. Wolf, A. Gal-On

Abstract:

Viral diseases of tomato crops result in heavy yield losses and may even jeopardize the production of these crops. Classical tomato breeding for disease resistance against Tomato yellow leaf curl virus (TYLCV), leads to partial resistance associated with a number of recessive genes. To author’s best knowledge Pepino mosaic virus (PepMV) genetic resistance is not yet available. The generation of viral resistance by means of genetic engineering was reported and implemented for many crops, including tomato. Transgenic resistance against viruses is based, in most cases, on Post Transcriptional Gene Silencing (PTGS), an endogenous mechanism which destroys the virus genome. In this work, we developed immunity against PepMV and TYLCV in a tomato based on a PTGS mechanism. Tomato plants were transformed with a hairpin-construct-expressed transgene-derived double-strand-RNA (tr-dsRNA). In the case of PepMV, the binary construct harbored three consecutive fragments of the replicase gene from three different PepMV strains (Italian, Spanish and American), to provide resistance against a range of virus strains. In the case of TYLCV, the binary vector included three consecutive fragments of the IR, V2 and C2 viral genes constructed in a hairpin configuration. Selected transgenic lines (T0) showed a high accumulation of transgene siRNA of 21-24 bases, and T1 transgenic lines showed complete immunity to PepMV and TYLCV. Graft inoculation displayed immunity of the transgenic scion against PepMV and TYLCV. The study presents the engineering of resistance in tomato against two serious diseases, which will help in the production of high-quality tomato. However, unfortunately, these resistant plants have not been implemented due to public ignorance and opposition against breeding by genetic engineering.

Keywords: PepMV, PTGS, TYLCV, tr-dsRNA

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Authors: Humraaz Kaja, Kofi Mensah, Frasia Oosthuizen

Abstract:

Background and Aim: Vilazodone was approved in 2011 as an antidepressant to treat the major depressive disorder. As a relatively new drug, it is not clear if all adverse effects have been identified. The aim of this study was to review the adverse effects reported to the WHO Programme for International Drug Monitoring (PIDM) in order to add to the knowledge about the safety profile and adverse effects caused by vilazodone. Method: Data on adverse effects reported for vilazodone was obtained from the database VigiAccess managed by PIDM. Data was extracted from VigiAccess using Excel® and analyzed using descriptive statistics. The data collected was compared to the patient information leaflet (PIL) of Viibryd® and the FDA documents to determine adverse drug reactions reported post-marketing. Results: A total of 9708 adverse events had been recorded on VigiAccess, of which 6054 were not recorded on the PIL and the FDA approval document. Most of the reports were received from the Americas and were for adult women aged 45-64 years (24%, n=1059). The highest number of adverse events reported were for psychiatric events (19%; n=1889), followed by gastro-intestinal effects (18%; n=1839). Specific psychiatric disorders recorded included anxiety (316), depression (208), hallucination (168) and agitation (142). The systematic review confirmed several psychiatric adverse effects associated with the use of vilazodone. The findings of this study suggested that these common psychiatric adverse effects associated with the use of vilazodone were not known during the time of FDA approval of the drug and is not currently recorded in the patient information leaflet (PIL). Conclusions: In summary, this study found several adverse drug reactions not recorded in documents emanating from clinical trials pre-marketing. This highlights the importance of continued post-marketing surveillance of a drug, as well as the need for further studies on the psychiatric adverse events associated with vilazodone in order to improve the safety profile.

Keywords: adverse drug reactions, pharmacovigilance, post-marketing surveillance, vilazodone

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Authors: Rosemarie P. Ongoco, Rowena S. Badua, Kristine Joy S. Simpao, Ria L. Dizon

Abstract:

Food Technology (FT) has become a very powerful field in dealing with the processing of food making it available, safe, tasty and convenient. Bataan Peninsula State University (BPSU) has been offering FT as a major of the Bachelor of Science in Industrial Technology, both in the Main and Orani campuses since the 1970s. With the different orientation of FT offered in state universities and colleges, whether it is skill or science-based, this study aims to assess the current FT situation in BPSU. Curriculum, faculty profile and facilities of FT in BPSU were assessed and compared to the other FT related program in three state universities in Region III; Nueva Ecija University of Science and Technology, Pampanga Agricultural College, and Central Luzon State University. Data were gathered through structured interview, ocular inspection for the facilities and questionnaires for the teacher and students’ personal interest. Results show that BPSU’s FT program is more likely similar to the one offered in NEUST. PAC is offering a similar course but is more business and management-oriented BS Home Economics while CLSU is offering a science and technology-related course, BS Home Economics while CLSU is offering a science and technology-related course, BS Food Technology. BPSU students more intercede in cooking and baking while doing sales report, dishwashing and food packaging are the activities faculty and students are least interested. Mechanized machines in cooking and baking are also suggested by the majority of the students in BPSU. In conclusion, BPSU’s program in BS IT major in Food Technology must be improved in the aspects of curriculum, faculty profile, and facilities. It is recommended for the department to consider the curriculum, faculty profile, and facilities. It is recommended for the department to consider the curriculum of NEUST in the BS IT major in Food Technology.

Keywords: food technology, curriculum, technology, assessment

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Authors: Yu-Ching Cheng, Yi-Kai Juan, Daniel Castro

Abstract:

Energy consumption of buildings has been an increasing concern for researchers and practitioners in the last decade. Sustainable building renovation can reduce energy consumption and carbon dioxide emissions; meanwhile, it also can extend existing buildings useful life and facilitate environmental sustainability while providing social and economic benefits to the society. School buildings are different from other designed spaces as they are more crowded and host the largest portion of daily activities and occupants. Strategies that focus on reducing energy use but also improve the students’ learning environment becomes a significant subject in sustainable school buildings development. A decision model is developed in this study to solve complicated and large-scale combinational, discrete and determinate problems such as school renovation projects. The task of this model is to automatically search for the most cost-effective (lower cost and higher quality) renovation strategies. In this study, the search process of optimal school building renovation solutions is by nature a large-scale zero-one programming determinate problem. A* is suitable for solving deterministic problems due to its stable and effective search process, and genetic algorithms (GA) provides opportunities to acquire global optimal solutions in a short time via its indeterminate search process based on probability. These two algorithms are combined in this study to consider trade-offs between renovation cost and improved quality, this decision model is able to evaluate current school environmental conditions and suggest an optimal scheme of sustainable school buildings renovation strategies. Through adoption of this decision model, school managers can overcome existing limitations and transform school buildings into spaces more beneficial to students and friendly to the environment.

Keywords: decision model, school buildings, sustainable renovation, genetic algorithm, A* search algorithm

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Authors: Nurlaili E. P., Astuti M., Marsono Y., Naruki S.

Abstract:

Iron is an essential nutrient with limited bioavailability. Nutritional anemia caused mainly by iron deficiency is the most recognized nutritional problem in both countries as well as affluent societies. Rice (Oryza sativa L.) has become the most important cereal crop for the improvement of human health due to the starch, protein, oil, and the majority of micronutrients, particularly in Asian countries. In this study, the iron availability and profile lipid were evaluated for the extracts from Cibeusi varieties (black rices) of ancient rice brans. Results: The quality of K, B, R, E diets groups shows the same effect on the growth of rats. This indicate that groups is as efficiently utilized by the body as E diets. Hematocrit and MCHC levels of rats fed K, B, R and E diets were not significantly (P< 0.05). MCV and MCH levels of rats K, B, R were significantly (P< 0.05) with E groups but rats K, B, R were not significantly (P< 0.05). The iron content in the serum of rats fed with K, B, R and E diets were not significantly (P< 0.05). The highest level of iron in the serum was founded in the B group. The iron content in the liver of rats fed with K, B, R and E diets were not significantly (P< 0.05). The highest level of iron in the liver was founded in the R group. HDL cholesterol levels were significantly (P< 0.05) between rats of fed B, E with K, R, but K and R were not significantly (P< 0.05). LDL cholesterol levels of rats fed K and E significantly (P< 0.05) with B and R. Conclusions: the bran of pigmented rice varieties has, with some exceptions, greater antioxidant and free-radical scavenging activities. The results also show that pigmented rice extracts acted as pro-oxidants in the lipid peroxidation assay, possibly by mechanisms described for the pro-oxidant activities of tocopherol and ascorbic. Pigmented rice bran extracts more effectively increases iron stores and reduces the prevalence of iron deficiency. And reduces cholesterol, TG and LDL cholesterol and increses HDL cholesterol.

Keywords: anemia, black rice bran extract, iron, profile lipid

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Authors: Choonoh Lee, Seyeon Park, Dongyun Kang, Jaehyeong Choi, Soojee Kim, Younggeun Kim

Abstract:

Market Kurly is the first South Korean online grocery retailer that guarantees same-day, overnight shipping. More than 1.6 million customers place an average of 4.7 million orders and add 3 to 14 products into a cart per month. The company has sold almost 30,000 kinds of various products in the past 6 months, including food items, cosmetics, kitchenware, toys for kids/pets, and even flowers. The company is operating and expanding multiple dry, cold, and frozen fulfillment centers in order to store and ship these products. Due to the scale and complexity of the fulfillment, pick-pack-ship processes are planned and operated in batches, and thus, the planning that decides the batch of the customers’ orders is a critical factor in overall productivity. This paper introduces a metaheuristic optimization method that reduces the complexity of batch processing in a fulfillment center. The method is an iterative genetic algorithm with heuristic creation and evolution strategies; it aims to group similar orders into pick-pack-ship batches to minimize the total number of distinct products. With a well-designed approach to create initial genes, the method produces streamlined plans, up to 13.5% less complex than the actual plans carried out in the company’s fulfillment centers in the previous months. Furthermore, our digital-twin simulations show that the optimized plans can reduce 3% of operation time for packing, which is the most complex and time-consuming task in the process. The optimization method implements a multithreading design on the Spring framework to support the company’s warehouse management systems in near real-time, finding a solution for 4,000 orders within 5 to 7 seconds on an AWS c5.2xlarge instance.

Keywords: fulfillment planning, genetic algorithm, online grocery retail, optimization

Procedia PDF Downloads 77

Authors: Atsuko Okazaki, Jurg Ott

Abstract:

Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

Procedia PDF Downloads 115

Authors: Carolina V. Viegas, Monique Gonçalves, Gisel Chenard Diaz, Yordanka Reyes Cruz, Donato Alexandre Gomes Aranda

Abstract:

To develop the massive cultivation of microalgae, it is necessary to isolate and characterize the species, improving genetic tools in search of specific characteristics. Therefore, the detection, identification and quantification of the compounds that compose the Scenedesmus sp. were prerequisites to verify the potential of these microalgae. The main objective of this work was to carry out the characterization of Scenedesmus sp. as to the content of ash, carbohydrates, proteins and lipids as well as the determination of the composition of their lipid classes and main fatty acids. The biomass of Scenedesmus sp, showed 15,29 ± 0,23 % of ash and CaO (36,17 %) was the main component of this fraction, The total protein and carbohydrate content of the biomass was 40,74 ± 1,01 % and 23,37 ± 0,95 %, respectively, proving to be a potential source of proteins as well as carbohydrates for the production of ethanol via fermentation, The lipid contents extracted via Bligh & Dyer and in situ saponification were 8,18 ± 0,13 % and 4,11 ± 0,11 %, respectively. In the lipid extracts obtained via Bligh & Dyer, approximately 50 % of the composition of this fraction consists of fatty compounds, while the other half is composed of an unsaponifiable fraction composed mainly of chlorophylls, phytosterols and carotenes. From the lowest yield, it was possible to obtain a selectivity of 92,14 % for fatty components (fatty acids and fatty esters) confirmed through the infrared spectroscopy technique. The presence of polyunsaturated acids (~45 %) in the lipid extracts indicated the potential of this fraction as a source of nutraceuticals. The results indicate that the biomass of Scenedesmus sp, can become a promising potential source for obtaining polyunsaturated fatty acids, carotenoids and proteins as well as the simultaneous obtainment of different compounds of high commercial value.

Keywords: microalgae, Desmodesmus, lipid classes, fatty acid profile, proteins, carbohydrates

Procedia PDF Downloads 88

Authors: Babak Forouraghi

Abstract:

A genetic circuit is a collection of interacting genes and proteins that enable individual cells to implement and perform vital biological functions such as cell division, growth, death, and signaling. In cell engineering, synthetic gene circuits are engineered networks of genes specifically designed to implement functionalities that are not evolved by nature. These engineered networks enable scientists to tackle complex problems such as engineering cells to produce therapeutics within the patient's body, altering T cells to target cancer-related antigens for treatment, improving antibody production using engineered cells, tissue engineering, and production of genetically modified plants and livestock. Construction of computational models to realize genetic circuits is an especially challenging task since it requires the discovery of the flow of genetic information in complex biological systems. Building synthetic biological models is also a time-consuming process with relatively low prediction accuracy for highly complex genetic circuits. The primary goal of this study was to investigate the utility of a pre-trained bidirectional encoder transformer that can accurately predict gene expressions in genetic circuit designs. The main reason behind using transformers is their innate ability (attention mechanism) to take account of the semantic context present in long DNA chains that are heavily dependent on the spatial representation of their constituent genes. Previous approaches to gene circuit design, such as CNN and RNN architectures, are unable to capture semantic dependencies in long contexts, as required in most real-world applications of synthetic biology. For instance, RNN models (LSTM, GRU), although able to learn long-term dependencies, greatly suffer from vanishing gradient and low-efficiency problem when they sequentially process past states and compresses contextual information into a bottleneck with long input sequences. In other words, these architectures are not equipped with the necessary attention mechanisms to follow a long chain of genes with thousands of tokens. To address the above-mentioned limitations, a transformer model was built in this work as a variation to the existing DNA Bidirectional Encoder Representations from Transformers (DNABERT) model. It is shown that the proposed transformer is capable of capturing contextual information from long input sequences with an attention mechanism. In previous works on genetic circuit design, the traditional approaches to classification and regression, such as Random Forrest, Support Vector Machine, and Artificial Neural Networks, were able to achieve reasonably high R2 accuracy levels of 0.95 to 0.97. However, the transformer model utilized in this work, with its attention-based mechanism, was able to achieve a perfect accuracy level of 100%. Further, it is demonstrated that the efficiency of the transformer-based gene expression classifier is not dependent on the presence of large amounts of training examples, which may be difficult to compile in many real-world gene circuit designs.

Keywords: machine learning, classification and regression, gene circuit design, bidirectional transformers

Procedia PDF Downloads 56

Authors: Makduma Zahan Badhan, M. Abdul Matin

Abstract:

A study has been undertaken to develop a fluvial stage-discharge rating curve for Jamuna River. Past Cross-sectional survey of Jamuna River reach within Sirajgonj and Tangail has been analyzed. The analysis includes the estimation of discharge carrying capacity, possible maximum scour depth and sediment transport capacity of the selected reaches. To predict the discharge and sediment carrying capacity, stream flow data which include cross-sectional area, top width, water surface slope and median diameter of the bed material of selected stations have been collected and some are calculated from reduced level data. A well-known resistance equation has been adopted and modified to a simple form in order to be used in the present analysis. The modified resistance equation has been used to calculate the mean velocity through the channel sections. In addition, a sediment transport equation has been applied for the prediction of transport capacity of the various sections. Results show that the existing drainage sections of Jamuna channel reach under study have adequate carrying capacity under existing bank-full conditions, but these reaches are subject to bed erosion even in low flow situations. Regarding sediment transport rate, it can be estimated that the channel flow has a relatively high range of bed material concentration. Finally, stage­ discharge curves for various sections have been developed. Based on stage-discharge rating data of various sections, water surface profile and sediment-rating curve of Jamuna River have been developed and also the flooding conditions have been analyzed from predicted water surface profile.

Keywords: discharge rating, flow profile, fluvial, sediment rating

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Authors: Minto Rattan, Tania Bose, Neeraj Chamoli

Abstract:

The present paper investigates the effect of linear thermal gradient on the steady-state creep behavior of rotating isotropic disc using threshold stress based Sherby’s creep law. The composite discs made of aluminum matrix reinforced with silicon carbide particulate has been taken for analysis. The stress and strain rate distributions have been calculated for discs rotating at linear thermal gradation using von Mises’ yield criterion. The material parameters have been estimated by regression fit of the available experimental data. The results are displayed and compared graphically in designer friendly format for the above said temperature profile with the disc operating under uniform temperature profile. It is observed that radial and tangential stresses show minor variation and the strain rates vary significantly in the presence of thermal gradation as compared to disc having uniform temperature.

Keywords: creep, isotropic, steady-state, thermal gradient

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Authors: Abubakar Maikudi

Abstract:

Contrastive analysis is the method of analyzing the structure of any two languages with a view to determining the possible differential aspects of their systems irrespective of their genetic affinity or level of development. Contrastive analysis of two languages becomes useful when it is adequately describing the sound structure and grammatical structure of two languages, with comparative statements giving emphasis to the compatible items in the two systems. This research work uses comparative analysis theory to analyze adjective and adjectival phrases in Hausa and Yorùbá languages. The Hausa language belongs to the Chadic family of the Afro-Asiatic phylum, while the Yorùbá language belongs to the Benue-Congo family of the Niger-Congo phylum. The findings of the research clearly demonstrated that there are significant similarities in the adjectival phrase constructions of the two languages, i.e., nominal (Head) and post-nominal (Post-Head) use of the adjective, predicative function of an adjective, use of the reduplicative adjective, use of the comparative and superlative adjective, etc. However, there are dissimilarities in the adjectival phrase of the two languages in gender/number agreement and pre-nominal (Post-Head) use of adjectives.

Keywords: genetic affinity, contrastive analysis, phylum, pre-head, post-head

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Authors: Zhong Ma, Zhuping Wang, Congxin Liu, Xiangzeng Liu

Abstract:

Satellite imagery classification is a challenging problem with many practical applications. In this paper, we designed a deep convolution neural network (DCNN) to classify the satellite imagery. The contributions of this paper are twofold — First, to cope with the large-scale variance in the satellite image, we introduced the inception module, which has multiple filters with different size at the same level, as the building block to build our DCNN model. Second, we proposed a genetic algorithm based method to efficiently search the best hyper-parameters of the DCNN in a large search space. The proposed method is evaluated on the benchmark database. The results of the proposed hyper-parameters search method show it will guide the search towards better regions of the parameter space. Based on the found hyper-parameters, we built our DCNN models, and evaluated its performance on satellite imagery classification, the results show the classification accuracy of proposed models outperform the state of the art method.

Keywords: satellite imagery classification, deep convolution network, genetic algorithm, hyper-parameter optimization

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Authors: Agnieszka H. Ludwig-Slomczynska, Michal T. Seweryn, Przemyslaw Kapusta, Ewelina Pitera, Katarzyna Cyganek, Urszula Mantaj, Lucja Dobrucka, Ewa Wender-Ozegowska, Maciej T. Malecki, Pawel Wolkow

Abstract:

Obesity results from an imbalance between energy intake and its expenditure. Genome-Wide Association Study (GWAS) analyses have led to discovery of only about 100 variants influencing body mass index (BMI), which explain only a small portion of genetic variability. Analysis of gene epistasis gives a chance to discover another part. Since it was shown that interaction and communication between nuclear and mitochondrial genome are indispensable for normal cell function, we have looked for epistatic interactions between the two genomes to find their correlation with BMI. Methods: The analysis was performed on 366 T1DM patients using Illumina Infinium OmniExpressExome-8 chip and followed by imputation on Michigan Imputation Server. Only genes which influence mitochondrial functioning (listed in Human MitoCarta 2.0) were included in the analysis – variants of nuclear origin (MAF > 5%) in 1140 genes and 42 mitochondrial variants (MAF > 1%). Gene expression analysis was performed on GTex data. Association analysis between genetic variants and BMI was performed with the use of Linear Mixed Models as implemented in the package 'GENESIS' in R. Analysis of association between mRNA expression and BMI was performed with the use of linear models and standard significance tests in R. Results: Among variants involved in epistasis between mitochondria and nucleus we have identified one in mitochondrial transcription factor, TFB2M (rs6701836). It interacted with mitochondrial variants localized to MT-RNR1 (p=0.0004, MAF=15%), MT-ND2 (p=0.07, MAF=5%) and MT-ND4 (p=0.01, MAF=1.1%). Analysis of the interaction between nuclear variant rs6701836 (nuc) and rs3021088 localized to MT-ND2 mitochondrial gene (mito) has shown that the combination of the two led to BMI decrease (p=0.024). Each of the variants on its own does not correlate with higher BMI [p(nuc)=0.856, p(mito)=0.116)]. Although rs6701836 is intronic, it influences gene expression in the thyroid (p=0.000037). rs3021088 is a missense variant that leads to alanine to threonine substitution in the MT-ND2 gene which belongs to complex I of the electron transport chain. The analysis of the influence of genetic variants on gene expression has confirmed the trend explained above – the interaction of the two genes leads to BMI decrease (p=0.0308). Each of the mRNAs on its own is associated with higher BMI (p(mito)=0.0244 and p(nuc)=0.0269). Conclusıons: Our results show that nuclear-mitochondrial epistasis can influence BMI in T1DM patients. The correlation between transcription factor expression and mitochondrial genetic variants will be subject to further analysis.

Keywords: body mass index, epistasis, mitochondria, type 1 diabetes

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

Abstract:

Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease

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

Abstract:

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

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

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

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

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

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

Abstract:

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

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

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Authors: Amel Hannech, Mehdi Adda, Hamid Mcheick

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In this paper, we propose a generic model of user profile integrating several elements that may positively impact the research process. We exploit the classical behavior of users and integrate a delimitation process of their research activities into several research sessions enriched with contextual and temporal information, which allows reflecting the current interests of these users in every period of time and infer data freshness. We argue that the annotation of resources gives more transparency on users' needs. It also strengthens social links among resources and users, and can so increase the scope of the user profile. Based on this idea, we integrate the social tagging practice in order to exploit the social users' behavior to enrich their profiles. These profiles are then integrated into a recommendation system in order to predict the interesting personalized items of users allowing to assist them in their researches and further enrich their profiles. In this recommendation, we provide users new research experiences.

Keywords: user profiles, topical ontology, contextual information, folksonomies, tags' clusters, data freshness, association rules, data recommendation

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

Abstract:

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

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

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Authors: Anish Shah, Steve A. Wakelin, Derrick Moot, Aurélie Laugraud, Hayley J. Ridgway

Abstract:

A mixed pasture system of ryegrass-clover is used in New Zealand, where clovers are generally inoculated with commercially available strains of rhizobia. The community of rhizobia living in the soil and the way in which they interact with the plant are affected by different biotic and abiotic factors. In general, bacterial richness and diversity in soil varies by soil pH. pH also affects cell physiology and acts as a master variable that controls the wider soil physiochemical conditions such as P availability, Al release and micronutrient availability. As such, pH can have both primary and secondary effects on soil biology and processes. The aim of this work was to investigate the effect of soil pH on the genetic diversity and metabolic profile of Rhizobium leguminosarum strains nodulating clover. Soils were collected from 12 farms across New Zealand which had a pH(water) range of between 4.9 and 7.5, with four acidic (pH 4.9 – 5.5), four ‘neutral’ (5.8 – 6.1) and four alkaline (6.5 – 7.5) soils. Bacteria were recovered from nodules of Trifolium repens (white clover) and T. subterraneum (subterranean clover) grown in the soils. The strains were cultured and screened against a range of pH-amended media to demonstrate whether they were adapted to pH levels similar to their native soils. The strains which showed high relative growth at a given pH (~20% of those isolated) were selected for metabolic and taxonomic profiling. The Omnilog (Biolog Inc., Hayward, CA) phenotype array was used to perform assays on carbon (C) utilisation for selected strains. DNA was extracted from the strains which had differing C utilisation profiles and PCR products for both forward and reverse primers were sequenced for the following genes: 16S rRNA, recA, nodC, nodD and nifH (symbiotic).

Keywords: bacterial diversity, clover, metabolic and taxonomic profiling, pH adaptation, rhizobia

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Authors: Koteswara Rao Pagolu, Raghava Rao Tamanam

Abstract:

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

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

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Authors: Soon Young Choi, Chan Hwan Kim, Chan Hong Park, Hyung Rae Kim, Myoung Hoon Lee, Hyeon-Yeong Park

Abstract:

We performed the marine magnetic, bathymetry and seismic survey at the TA22 seamount (in the Lau basin, SW Pacific) for finding the submarine hydrothermal deposits in October 2009. We acquired magnetic and bathymetry data sets by suing Overhouser Proton Magnetometer SeaSPY (Marine Magnetics Co.), Multi-beam Echo Sounder EM120 (Kongsberg Co.). We conducted the data processing to obtain detailed seabed topography, magnetic anomaly, reduction to the pole (RTP) and magnetization. Based on the magnetic properties result, we analyzed submarine geology structure of TA22 seamount with post-processed seismic profile. The detailed bathymetry of the TA22 seamount showed the left and right crest parts that have caldera features in each crest central part. The magnetic anomaly distribution of the TA22 seamount regionally displayed high magnetic anomalies in northern part and the low magnetic anomalies in southern part around the caldera features. The RTP magnetic anomaly distribution of the TA22 seamount presented commonly high magnetic anomalies in the each caldera central part. Also, it represented strong anomalies at the inside of caldera rather than outside flank of the caldera. The magnetization distribution of the TA22 seamount showed the low magnetization zone in the center of each caldera, high magnetization zone in the southern and northern east part. From analyzed the seismic profile map, The TA22 seamount area is showed for the inferred small mounds inside each caldera central part and it assumes to make possibility of sills by the magma in cases of the right caldera. Taking into account all results of this study (bathymetry, magnetic anomaly, RTP, magnetization, seismic profile) with rock samples at the left caldera area in 2009 survey, we suppose the possibility of hydrothermal deposits at mounds in each caldera central part and at outside flank of the caldera representing the low magnetization zone. We expect to have the better results by combined modeling from this study data with the other geological data (ex. detailed gravity, 3D seismic, petrologic study results and etc).

Keywords: detailed bathymetry, magnetic anomaly, seamounts, seismic profile, SW Pacific

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