Search results for: genetic variations
2638 Advances in Sesame Molecular Breeding: A Comprehensive Review
Authors: Micheale Yifter Weldemichael
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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering
Procedia PDF Downloads 242637 Management and Genetic Characterization of Local Sheep Breeds for Better Productive and Adaptive Traits
Authors: Sonia Bedhiaf-Romdhani
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The sheep (Ovis aries) was domesticated, approximately 11,000 years ago (YBP), in the Fertile Crescent from Asian Mouflon (Ovis Orientalis). The Northern African (NA) sheep is 7,000 years old, represents a remarkable diversity of sheep populations reared under traditional and low input farming systems (LIFS) over millennia. The majority of small ruminants in developing countries are encountered in low input production systems and the resilience of local communities in rural areas is often linked to the wellbeing of small ruminants. Regardless of the rich biodiversity encountered in sheep ecotypes there are four main sheep breeds in the country with 61,6 and 35.4 percents of Barbarine (fat tail breed) and Queue Fine de l’Ouest (thin tail breed), respectively. Phoenicians introduced the Barbarine sheep from the steppes of Central Asia in the Carthaginian period, 3000 years ago. The Queue Fine de l’Ouest is a thin-tailed meat breed heavily concentrated in the Western and the central semi-arid regions. The Noire de Thibar breed, involving mutton-fine wool producing animals, has been on the verge of extinction, it’s a composite black coated sheep breed found in the northern sub-humid region because of its higher nutritional requirements and non-tolerance of the prevailing harsher condition. The D'Man breed, originated from Morocco, is mainly located in the southern oases of the extreme arid ecosystem. A genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. Genetic analysis of relationship between breeds highlighted the genetic differentiation of Noire de Thibar breed from the other local breeds, reflecting the effect of past events of introgression of European gene pool. The Queue Fine de l’Ouest breed showed a genetic heterogeneity and was close to Barbarine. The D'Man breed shared a considerable gene flow with the thin-tailed Queue Fine de l'Ouest breed. Native small ruminants breeds, are capable to be efficiently productive if essential ingredients and coherent breeding schemes are implemented and followed. Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources.Keywords: sheep, farming systems, diversity, SNPs.
Procedia PDF Downloads 1412636 Predictions of Values in a Causticizing Process
Authors: R. Andreola, O. A. A. Santos, L. M. M. Jorge
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An industrial system for the production of white liquor of a paper industry, Klabin Paraná Papé is, formed by ten reactors was modeled, simulated, and analyzed. The developed model considered possible water losses by evaporation and reaction, in addition to variations in volumetric flow of lime mud across the reactors due to composition variations. The model predictions agreed well with the process measurements at the plant and the results showed that the slaking reaction is nearly complete at the third causticizing reactor, while causticizing ends by the seventh reactor. Water loss due to slaking reaction and evaporation occurs more pronouncedly in the slaking reaction than in the final causticizing reactors; nevertheless, the lime mud flow remains nearly constant across the reactors.Keywords: causticizing, lime, prediction, process
Procedia PDF Downloads 3452635 Genetic Improvement Potential for Wood Production in Melaleuca cajuputi
Authors: Hong Nguyen Thi Hai, Ryota Konda, Dat Kieu Tuan, Cao Tran Thanh, Khang Phung Van, Hau Tran Tin, Harry Wu
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Melaleuca cajuputi is a moderately fast-growing species and considered as a multi-purpose tree as it provides fuelwood, piles and frame poles in construction, leaf essential oil and honey. It occurs in Australia, Papua New Guinea, and South-East Asia. M. cajuputi plantation can be harvested on 6-7 year rotations for wood products. Its timber can also be used for pulp and paper, fiber and particle board, producing quality charcoal and potentially sawn timber. However, most reported M. cajuputi breeding programs have been focused on oil production rather than wood production. In this study, breeding program of M. cajuputi aimed to improve wood production was examined by estimating genetic parameters for growth (tree height, diameter at breast height (DBH), and volume), stem form, stiffness (modulus of elasticity (MOE)), bark thickness and bark ratio in a half-sib family progeny trial including 80 families in the Mekong Delta of Vietnam. MOE is one of the key wood properties of interest to the wood industry. Non-destructive wood stiffness was measured indirectly by acoustic velocity using FAKOPP Microsecond Timer and especially unaffected by bark mass. Narrow-sense heritability for the seven traits ranged from 0.13 to 0.27 at age 7 years. MOE and stem form had positive genetic correlations with growth while the negative correlation between bark ratio and growth was also favorable. Breeding for simultaneous improvement of multiple traits, faster growth with higher MOE and reduction of bark ratio should be possible in M. cajuputi. Index selection based on volume and MOE showed genetic gains of 31 % in volume, 6 % in MOE and 13 % in stem form. In addition, heritability and age-age genetic correlations for growth traits increased with time and optimal early selection age for growth of M. cajuputi based on DBH alone was 4 years. Selected thinning resulted in an increase of heritability due to considerable reduction of phenotypic variation but little effect on genetic variation.Keywords: acoustic velocity, age-age correlation, bark thickness, heritability, Melaleuca cajuputi, stiffness, thinning effect
Procedia PDF Downloads 1742634 Acceleration of DNA Hybridization Using Electroosmotic Flow
Authors: Yun-Hsiang Wang, Huai-Yi Chen, Kin Fong Lei
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Deoxyribonucleic acid (DNA) hybridization is a common technique used in genetic assay widely. However, the hybridization ratio and rate are usually limited by the diffusion effect. Here, microfluidic electrode platform producing electroosmosis generated by alternating current signal has been proposed to enhance the hybridization ratio and rate. The electrode was made of aurum fabricated by microfabrication technique. Thiol-modified oligo probe was immobilized on the electrode for specific capture of target, which is modified by fluorescent tag. Alternative electroosmosis can induce local microfluidic vortexes to accelerate DNA hybridization. This study provides a strategy to enhance the rate of DNA hybridization in the genetic assay.Keywords: DNA hybridization, electroosmosis, electrical enhancement, hybridization ratio
Procedia PDF Downloads 3802633 Twenty-Five Polymorphic Microsatellite Loci Used To Genotype Some Camel Types and Subtypes From Sudan, Qatar, Chad, And Somalia
Authors: Wathig Hashim Mohamed Ibrahim
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Twenty Five polymorphic microsatellite out of 50 Loci were used to genotype some camel (Camelus dromedarius) types and subtypes in Sudan (Naylawi, Shanapla, Lahawi, Kinani, Rashaydi, Bani-Aamir, Annafi, Bishari Shallagyai and Bishari Arririt) and that from Qatar (OmmaniHJ, OmmaniKH, Majaheem, Pakistani Sindi, Pakistani Punjabi and Pakistani) and for comparative; one type from Somalia (Aarhou) and another from Chad (Spotted) were investigated. The highest number of alleles were 23 in Locus CVRL 01, and lowest were 2 in YWLL 59. The observed heterozygosity (Hobs) were 0.950 and 0.049 for VOLP08 and YWLL09, respectively, while the expected heterozygosity (HExp) were 0.915 and 0.362 for Locus VOLP67 and YWLL58, respectively, and the HExp mean was 0.7378. Polymorphic Information Content (PIC) ranged between 0.907 - 0.345 in Locus VOLP67 and YWLL58, and the PIC mean was 0.7002. The genetic distance ranged between 0.545 – 0.098 for Shallagyai (Bishari subtype) – Pakistani Sindi subtype and between Annafi - Rashaydi, respectively. The genetic distance between spotted and all types ranged between 0.223 with Arririt (Bishari subtype) and 0.463 with Punjabi (Pakistani subtype) that found in Qatar, while all types with Aarhou ranged between 0.215 for Arririt and 0.469 with Punjabi (Pakistani subtype). The dondrogram shows that there is a relationship between the genetic makeup and geographical distributions and also between the genetic makeup and phenotypic characteristic. Individual assignment was calculated, 46.62% correctly assigned and 46.87% quality index. Hardy Weinberg Equivalent (HWE) was also calculated. Key words: Camel, genotype, polymorphic microsatelliteKeywords: camel, genotype, polymorphic microsatellite, types and subtypes
Procedia PDF Downloads 762632 Genetic Association of SIX6 Gene with Pathogenesis of Glaucoma
Authors: Riffat Iqbal, Sidra Ihsan, Andleeb Batool, Maryam Mukhtar
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Glaucoma is a gathering of optic neuropathies described by dynamic degeneration of retinal ganglionic cells. It is clinically and innately heterogenous illness containing a couple of particular forms each with various causes and severities. Primary open-angle glaucoma (POAG) is the most generally perceived kind of glaucoma. This study investigated the genetic association of single nucleotide polymorphisms (SNPs; rs10483727 and rs33912345) at the SIX1/SIX6 locus with primary open-angle glaucoma (POAG) in the Pakistani population. The SIX6 gene plays an important role in ocular development and has been associated with morphology of the optic nerve. A total of 100 patients clinically diagnosed with glaucoma and 100 control individuals of age over 40 were enrolled in the study. Genomic DNA was extracted by organic extraction method. The SNP genotyping was done by (i) PCR based restriction fragment length polymorphism (RFLP) and sequencing method. Significant genetic associations were observed for rs10483727 (risk allele T) and rs33912345 (risk allele C) with POAG. Hence, it was concluded that Six6 gene is genetically associated with pathogenesis of Glaucoma in Pakistan.Keywords: genotyping, Pakistani population, primary open-angle glaucoma, SIX6 gene
Procedia PDF Downloads 1802631 Phylogenetic Studies of Six Egyptian Sheep Breeds Using Cytochrome B
Authors: Othman Elmahdy Othman, Agnés Germot, Daniel Petit, Muhammad Khodary, Abderrahman Maftah
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Recently, the control (D-loop) and cytochrome b (Cyt b) regions of mtDNA have received more attention due to their role in the genetic diversity and phylogenetic studies in different livestock which give important knowledge towards the genetic resource conservation. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. By using cytochrome B sequencing, we aimed to clarify the genetic affinities and phylogeny of six Egyptian sheep breeds. Blood samples were collected from 111 animals belonging to six Egyptian sheep breeds; Barki, Rahmani, Ossimi, Saidi, Sohagi and Fallahi. The total DNA was extracted and the specific primers were used for conventional PCR amplification of the cytochrome B region of mtDNA. PCR amplified products were purified and sequenced. The alignment of sequences was done using BioEdit software and DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 39 polymorphic sites leading to the formation of 29 haplotypes. The haplotype diversity in six tested breeds ranged from 0.643 in Rahmani breed to 0.871 in Barki breed. The lowest genetic distance was observed between Rahmani and Saidi (D: 1.436 and Dxy: 0.00127) while the highest distance was observed between Ossimi and Sohagi (D: 6.050 and Dxy: 0.00534). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of 111 analyzed samples were aligned with references sequences of different haplogroups; A, B, C, D and E. The phylogeny result showed the presence of four haplogroups; HapA, HapB, HapC and HapE in the examined samples whereas the haplogroup D was not found. The result showed that 88 out of 111 tested animals cluster with haplogroup B (79.28%), whereas 12 tested animals cluster with haplogroup A (10.81%), 10 animals cluster with haplogroup C (9.01%) and one animal belongs to haplogroup E (0.90%).Keywords: phylogeny, genetic biodiversity, MtDNA, cytochrome B, Egyptian sheep
Procedia PDF Downloads 3422630 Genetically Modified Organisms
Authors: Mudrika Singhal
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The research paper is basically about how the genetically modified organisms evolved and their significance in today’s world. It also highlights about the various pros and cons of the genetically modified organisms and the progress of India in this field. A genetically modified organism is the one whose genetic material has been altered using genetic engineering techniques. They have a wide range of uses such as transgenic plants, genetically modified mammals such as mouse and also in insects and aquatic life. Their use is rooted back to the time around 12,000 B.C. when humans domesticated plants and animals. At that humans used genetically modified organisms produced by the procedure of selective breeding and not by genetic engineering techniques. Selective breeding is the procedure in which selective traits are bred in plants and animals and then are domesticated. Domestication of wild plants into a suitable cultigen is a well known example of this technique. GMOs have uses in varied fields ranging from biological and medical research, production of pharmaceutical drugs to agricultural fields. The first organisms to be genetically modified were the microbes because of their simpler genetics. At present the genetically modified protein insulin is used to treat diabetes. In the case of plants transgenic plants, genetically modified crops and cisgenic plants are the examples of genetic modification. In the case of mammals, transgenic animals such as mice, rats etc. serve various purposes such as researching human diseases, improvement in animal health etc. Now coming upon the pros and cons related to the genetically modified organisms, pros include crops with higher yield, less growth time and more predictable in comparison to traditional breeding. Cons include that they are dangerous to mammals such as rats, these products contain protein which would trigger allergic reactions. In India presently, group of GMOs include GM microorganisms, transgenic crops and animals. There are varied applications in the field of healthcare and agriculture. In the nutshell, the research paper is about the progress in the field of genetic modification, taking along the effects in today’s world.Keywords: applications, mammals, transgenic, engineering and technology
Procedia PDF Downloads 5912629 Relay Node Placement for Connectivity Restoration in Wireless Sensor Networks Using Genetic Algorithms
Authors: Hanieh Tarbiat Khosrowshahi, Mojtaba Shakeri
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Wireless Sensor Networks (WSNs) consist of a set of sensor nodes with limited capability. WSNs may suffer from multiple node failures when they are exposed to harsh environments such as military zones or disaster locations and lose connectivity by getting partitioned into disjoint segments. Relay nodes (RNs) are alternatively introduced to restore connectivity. They cost more than sensors as they benefit from mobility, more power and more transmission range, enforcing a minimum number of them to be used. This paper addresses the problem of RN placement in a multiple disjoint network by developing a genetic algorithm (GA). The problem is reintroduced as the Steiner tree problem (which is known to be an NP-hard problem) by the aim of finding the minimum number of Steiner points where RNs are to be placed for restoring connectivity. An upper bound to the number of RNs is first computed to set up the length of initial chromosomes. The GA algorithm then iteratively reduces the number of RNs and determines their location at the same time. Experimental results indicate that the proposed GA is capable of establishing network connectivity using a reasonable number of RNs compared to the best existing work.Keywords: connectivity restoration, genetic algorithms, multiple-node failure, relay nodes, wireless sensor networks
Procedia PDF Downloads 2342628 Prevalence and Genetic Determinant of Drug Resistant Tuberculosis among Patients Completing Intensive Phase of Treatment in a Tertiary Referral Center in Nigeria
Authors: Aminu Bashir Mohammad, Agwu Ezera, Abdulrazaq G. Habib, Garba Iliyasu
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Background: Drug resistance tuberculosis (DR-TB) continues to be a challenge in developing countries with poor resources. Routine screening for primary DR-TB before commencing treatment is not done in public hospitals in Nigeria, even with the large body of evidence that shows a high prevalence of primary DR-TB. Data on drug resistance and its genetic determinant among follow up TB patients is lacking in Nigeria. Hence the aim of this study was to determine the prevalence and genetic determinant of drug resistance among follow up TB patients in a tertiary hospital in Nigeria. Methods: This was a cross-sectional laboratory-based study conducted on 384 sputum samples collected from consented follow-up tuberculosis patients. Standard microbiology methods (Zeil-Nielsen staining and microscopy) and PCR (Line Probe Assay)] were used to analyze the samples collected. Person’s Chi-square was used to analyze the data generated. Results: Out of three hundred and eighty-four (384) sputum samples analyzed for mycobacterium tuberculosis (MTB) and DR-TB twenty-five 25 (6.5%) were found to be AFB positive. These samples were subjected to PCR (Line Probe Assay) out of which 18(72%) tested positive for DR-TB. Mutations conferring resistance to rifampicin (rpo B) and isoniazid (katG, and or inhA) were detected in 12/18(66.7%) and 6/18(33.3%), respectively. Transmission dynamic of DR-TB was not significantly (p>0.05) dependent on demographic characteristics. Conclusion: There is a need to strengthened the laboratory capacity for diagnosis of TB and drug resistance testing and make these services available, affordable, and accessible to the patients who need them.Keywords: drug resistance tuberculosis, genetic determinant, intensive phase, Nigeria
Procedia PDF Downloads 2802627 Optimal Sensing Technique for Estimating Stress Distribution of 2-D Steel Frame Structure Using Genetic Algorithm
Authors: Jun Su Park, Byung Kwan Oh, Jin Woo Hwang, Yousok Kim, Hyo Seon Park
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For the structural safety, the maximum stress calculated from the stress distribution of a structure is widely used. The stress distribution can be estimated by deformed shape of the structure obtained from measurement. Although the estimation of stress is strongly affected by the location and number of sensing points, most studies have conducted the stress estimation without reasonable basis on sensing plan such as the location and number of sensors. In this paper, an optimal sensing technique for estimating the stress distribution is proposed. This technique proposes the optimal location and number of sensing points for a 2-D frame structure while minimizing the error of stress distribution between analytical model and estimation by cubic smoothing splines using genetic algorithm. To verify the proposed method, the optimal sensor measurement technique is applied to simulation tests on 2-D steel frame structure. The simulation tests are performed under various loading scenarios. Through those tests, the optimal sensing plan for the structure is suggested and verified.Keywords: genetic algorithm, optimal sensing, optimizing sensor placements, steel frame structure
Procedia PDF Downloads 5272626 Hamiltonian Related Properties with and without Faults of the Dual-Cube Interconnection Network and Their Variations
Authors: Shih-Yan Chen, Shin-Shin Kao
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In this paper, a thorough review about dual-cubes, DCn, the related studies and their variations are given. DCn was introduced to be a network which retains the pleasing properties of hypercube Qn but has a much smaller diameter. In fact, it is so constructed that the number of vertices of DCn is equal to the number of vertices of Q2n +1. However, each vertex in DCn is adjacent to n + 1 neighbors and so DCn has (n + 1) × 2^2n edges in total, which is roughly half the number of edges of Q2n+1. In addition, the diameter of any DCn is 2n +2, which is of the same order of that of Q2n+1. For selfcompleteness, basic definitions, construction rules and symbols are provided. We chronicle the results, where eleven significant theorems are presented, and include some open problems at the end.Keywords: dual-cubes, dual-cube extensive networks, dual-cube-like networks, hypercubes, fault-tolerant hamiltonian property
Procedia PDF Downloads 4592625 A Single-Channel BSS-Based Method for Structural Health Monitoring of Civil Infrastructure under Environmental Variations
Authors: Yanjie Zhu, André Jesus, Irwanda Laory
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Structural Health Monitoring (SHM), involving data acquisition, data interpretation and decision-making system aim to continuously monitor the structural performance of civil infrastructures under various in-service circumstances. The main value and purpose of SHM is identifying damages through data interpretation system. Research on SHM has been expanded in the last decades and a large volume of data is recorded every day owing to the dramatic development in sensor techniques and certain progress in signal processing techniques. However, efficient and reliable data interpretation for damage detection under environmental variations is still a big challenge. Structural damages might be masked because variations in measured data can be the result of environmental variations. This research reports a novel method based on single-channel Blind Signal Separation (BSS), which extracts environmental effects from measured data directly without any prior knowledge of the structure loading and environmental conditions. Despite the successful application in audio processing and bio-medical research fields, BSS has never been used to detect damage under varying environmental conditions. This proposed method optimizes and combines Ensemble Empirical Mode Decomposition (EEMD), Principal Component Analysis (PCA) and Independent Component Analysis (ICA) together to separate structural responses due to different loading conditions respectively from a single channel input signal. The ICA is applying on dimension-reduced output of EEMD. Numerical simulation of a truss bridge, inspired from New Joban Line Arakawa Railway Bridge, is used to validate this method. All results demonstrate that the single-channel BSS-based method can recover temperature effects from mixed structural response recorded by a single sensor with a convincing accuracy. This will be the foundation of further research on direct damage detection under varying environment.Keywords: damage detection, ensemble empirical mode decomposition (EEMD), environmental variations, independent component analysis (ICA), principal component analysis (PCA), structural health monitoring (SHM)
Procedia PDF Downloads 3002624 Analysis of Expert Possibilities While Identifying Human Teeth
Authors: Saule Mussabekova
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Forensic investigation of human teeth plays an important role in detection of crime, particularly in cases of personal identification of dead bodies changed by putrefactive processes or skeletonized bodies as well as when finding bodies of unknown persons. 152 teeth have been investigated; 85 of them belonged to men and 67 belonged to women taken from alive people of different age. Teeth have been investigated after extraction. Two types of teeth have been investigated: teeth without integrity violation of dental crown and teeth with different degrees of its violation. Additionally, 517 teeth have been investigated that were collected from dead bodies, 252 of which belonged to women and 265 belonged to men, whatever the cause of death with death limitation from 1 month to 20 years. Isohemagglutinating serums and Coliclons of different series have been used for the research of tooth-group specificity by serological methods according to the AB0 system. Standard protocols of different techniques have been used for DNA purification from teeth (by reagent Chelex 100 produced by Bio-Rad using reagent kit 'DNA IQTM System' produced by Promega company (USA) and using columns 'QIAamp DNA Investigator Kit' produced by Qiagen company). Results of comparative forensic investigation of human teeth using serological and molecular genetic methods have shown that use of serological methods for forensic identification is sensible only in cases of preselection prior to the next molecular genetic investigation as well as in cases of impossibility of corresponding genetic investigation for different objective reasons. A number of advantages of methods of molecular genetics in the dental investigation have been marked, particularly in putrefactive changes, in personal identification. Key moments of modern condition of personal identification have been reflected according to dental state. Prospective directions of advance preparation of material have been emphasized for identification of teeth in forensic practice.Keywords: dental state, forensic identification, molecular genetic analysis, teeth
Procedia PDF Downloads 1362623 A Classical Method of Optimizing Manufacturing Systems Using a Number of Industrial Engineering Techniques
Authors: John M. Ikome, Martha E. Ikome, Therese Van Wyk
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Productivity optimization of a company can significantly increase the company’s output and productivity which can be in the form of corrective actions of ineffective activities, process simplification, and reduction of variations, responsiveness, and reduction of set-up-time which are all under the classification of waste within the manufacturing environment. Deriving a means to eliminate a number of these issues has a key importance for manufacturing organization. This paper focused on a number of industrial engineering techniques which include a cause and effect diagram, to identify and optimize the method or systems being used. Based on our results, it shows that there are a number of variations within the production processes that can significantly disrupt the expected output.Keywords: optimization, fishbone, diagram, productivity
Procedia PDF Downloads 3062622 Analysis of Temporal Factors Influencing Minimum Dwell Time Distributions
Authors: T. Pedersen, A. Lindfeldt
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The minimum dwell time is an important part of railway timetable planning. Due to its stochastic behaviour, the minimum dwell time should be considered to create resilient timetables. While there has been significant focus on how to determine and estimate dwell times, to our knowledge, little research has been carried out regarding temporal and running direction variations of these. In this paper, we examine how the minimum dwell time varies depending on temporal factors such as the time of day, day of the week and time of the year. We also examine how it is affected by running direction and station type. The minimum dwell time is estimated by means of track occupation data. A method is proposed to ensure that only minimum dwell times and not planned dwell times are acquired from the track occupation data. The results show that on an aggregated level, the average minimum dwell times in both running directions at a station are similar. However, when temporal factors are considered, there are significant variations. The minimum dwell time varies throughout the day with peak hours having the longest dwell times. It is also found that the minimum dwell times are influenced by weekday, and in particular, weekends are found to have lower minimum dwell times than most other days. The findings show that there is a potential to significantly improve timetable planning by taking minimum dwell time variations into account.Keywords: minimum dwell time, operations quality, timetable planning, track occupation data
Procedia PDF Downloads 1912621 Geodynamics Behaviour of Greater Cairo as Deduced from 4D Gravity and Seismic Activities
Authors: Elsayed A. Issawy, Anwar H. Radwan
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Recent crustal deformations studies in Egypt are applied on the most active areas with relation to seismic activity. Temporal gravity variations in parallel with the geodetic technique (GPS) were used to monitor recent crustal movements in Egypt since 1997. The non-tidal gravity changes were constrained by the vertical component of surface movements derived from the GPS observations. The gravity changes were used to understand the surface tectonics and geodynamic modelling of the Greater Cairo region after the occurrence of an earthquake of 1992. It was found that there is a certain relation showed by increasing of gravity values before the main seismic activity. As example, relative considerable increase of gravity values was noticed for the network between the epochs of 2000 and 2004. Otherwise, the temporal gravity variations were reported a considerable decrease in gravity values between the two campaigns of 2004 and 2007 for the same stations. This behaviour could explain by compressive deformation and strain build-up stage before the South western Cairo earthquake (July 31, 2005 with magnitude of 4.3) and the stress release stage occurred after the main event. The geodetic measurements showed that, the estimated horizontal velocities for almost of points are 5.5 mm/year in approximately NW direction.Keywords: temporal gravity variations, geodynamics, greater Cairo, recent crustal movements, earthquakes
Procedia PDF Downloads 3612620 An Efficient Machine Learning Model to Detect Metastatic Cancer in Pathology Scans Using Principal Component Analysis Algorithm, Genetic Algorithm, and Classification Algorithms
Authors: Bliss Singhal
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Machine learning (ML) is a branch of Artificial Intelligence (AI) where computers analyze data and find patterns in the data. The study focuses on the detection of metastatic cancer using ML. Metastatic cancer is the stage where cancer has spread to other parts of the body and is the cause of approximately 90% of cancer-related deaths. Normally, pathologists spend hours each day to manually classifying whether tumors are benign or malignant. This tedious task contributes to mislabeling metastasis being over 60% of the time and emphasizes the importance of being aware of human error and other inefficiencies. ML is a good candidate to improve the correct identification of metastatic cancer, saving thousands of lives and can also improve the speed and efficiency of the process, thereby taking fewer resources and time. So far, the deep learning methodology of AI has been used in research to detect cancer. This study is a novel approach to determining the potential of using preprocessing algorithms combined with classification algorithms in detecting metastatic cancer. The study used two preprocessing algorithms: principal component analysis (PCA) and the genetic algorithm, to reduce the dimensionality of the dataset and then used three classification algorithms: logistic regression, decision tree classifier, and k-nearest neighbors to detect metastatic cancer in the pathology scans. The highest accuracy of 71.14% was produced by the ML pipeline comprising of PCA, the genetic algorithm, and the k-nearest neighbor algorithm, suggesting that preprocessing and classification algorithms have great potential for detecting metastatic cancer.Keywords: breast cancer, principal component analysis, genetic algorithm, k-nearest neighbors, decision tree classifier, logistic regression
Procedia PDF Downloads 752619 Ordinary Differentiation Equations (ODE) Reconstruction of High-Dimensional Genetic Networks through Game Theory with Application to Dissecting Tree Salt Tolerance
Authors: Libo Jiang, Huan Li, Rongling Wu
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Ordinary differentiation equations (ODE) have proven to be powerful for reconstructing precise and informative gene regulatory networks (GRNs) from dynamic gene expression data. However, joint modeling and analysis of all genes, essential for the systematical characterization of genetic interactions, are challenging due to high dimensionality and a complex pattern of genetic regulation including activation, repression, and antitermination. Here, we address these challenges by unifying variable selection and game theory through ODE. Each gene within a GRN is co-expressed with its partner genes in a way like a game of multiple players, each of which tends to choose an optimal strategy to maximize its “fitness” across the whole network. Based on this unifying theory, we designed and conducted a real experiment to infer salt tolerance-related GRNs for Euphrates poplar, a hero tree that can grow in the saline desert. The pattern and magnitude of interactions between several hub genes within these GRNs were found to determine the capacity of Euphrates poplar to resist to saline stress.Keywords: gene regulatory network, ordinary differential equation, game theory, LASSO, saline resistance
Procedia PDF Downloads 6352618 An Improved GA to Address Integrated Formulation of Project Scheduling and Material Ordering with Discount Options
Authors: Babak H. Tabrizi, Seyed Farid Ghaderi
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Concurrent planning of the resource constraint project scheduling and material ordering problems have received significant attention within the last decades. Hence, the issue has been investigated here with the aim to minimize total project costs. Furthermore, the presented model considers different discount options in order to approach the real world conditions. The incorporated alternatives consist of all-unit and incremental discount strategies. On the other hand, a modified version of the genetic algorithm is applied in order to solve the model for larger sizes, in particular. Finally, the applicability and efficiency of the given model is tested by different numerical instances.Keywords: genetic algorithm, material ordering, project management, project scheduling
Procedia PDF Downloads 2972617 Integrating a Universal Forensic DNA Database: Anticipated Deterrent Effects
Authors: Karen Fang
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Investigative genetic genealogy has attracted much interest in both the field of ethics and the public eye due to its global application in criminal cases. Arguments have been made regarding privacy and informed consent, especially with law enforcement using consumer genetic testing results to convict individuals. In the case of public interest, DNA databases have the strong potential to significantly reduce crime, which in turn leads to safer communities and better futures. With the advancement of genetic technologies, the integration of a universal forensic DNA database in violent crimes, crimes against children, and missing person cases is expected to deter crime while protecting one’s privacy. Rather than collecting whole genomes from the whole population, STR profiles can be used to identify unrelated individuals without compromising personal information such as physical appearance, disease risk, and geographical origin, and additionally, reduce cost and storage space. STR DNA profiling is already used in the forensic science field and going a step further benefits several areas, including the reduction in recidivism, improved criminal court case turnaround time, and just punishment. Furthermore, adding individuals to the database as early as possible prevents young offenders and first-time offenders from participating in criminal activity. It is important to highlight that DNA databases should be inclusive and tightly governed, and the misconception on the use of DNA based on crime television series and other media sources should be addressed. Nonetheless, deterrent effects have been observed in countries like the US and Denmark with DNA databases that consist of serious violent offenders. Fewer crimes were reported, and fewer people were convicted of those crimes- a favorable outcome, not even the death penalty could provide. Currently, there is no better alternative than a universal forensic DNA database made up of STR profiles. It can open doors for investigative genetic genealogy and fostering better communities. Expanding the appropriate use of DNA databases is ethically acceptable and positively impacts the public.Keywords: bioethics, deterrent effects, DNA database, investigative genetic genealogy, privacy, public interest
Procedia PDF Downloads 1452616 Bioinformatic Approaches in Population Genetics and Phylogenetic Studies
Authors: Masoud Sheidai
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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis
Procedia PDF Downloads 1162615 Investigation of Changes of Physical Properties of the Poplar Wood in Radial and Longitudinal Axis at Chaaloos Zone
Authors: Afshin Veisi
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In this study, the physical properties of wood in poplar wood (Populous sp.) were analyzed in longitudinal and radial directions of the stem. Three Populous Alba tree were cut in chaloos zone and from each tree, 3 discs were selected at 130cm, half of tree and under of crown. The test samples from pith to bark (heartwood to sapwood) were prepared from these discs for measuring the involved properties such as, wet, dry and critical specific gravity, porosity, volume shrinkage and swelling based on the ASTM standard, and data in two radial and longitudinal directions in the trank were statistically analyzed. Such as, variations of wet, dry and critical specific gravity had in radial direction respectively: irregular increase, increase and increase, and in longitudinal direction respectively: irregular decrease, irregular increase and increase. Results of variations to moisture content and porosity show that in radial direction respectively: irregular increasing and decreasing, and in longitudinal direction from down to up respectively: irregular decreasing and stability. Volume shrinkage and swelling variations show in radial direction irregular and in longitudinal axial regular decreasing.Keywords: poplar wood, physical properties, shrinkage, swelling, critical specific gravity, wet specific gravity, dry specific gravity
Procedia PDF Downloads 2732614 Isolate-Specific Variations among Clinical Isolates of Brucella Identified by Whole-Genome Sequencing, Bioinformatics and Comparative Genomics
Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi
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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing
Procedia PDF Downloads 3712613 Part Variation Simulations: An Industrial Case Study with an Experimental Validation
Authors: Narendra Akhadkar, Silvestre Cano, Christophe Gourru
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Injection-molded parts are widely used in power system protection products. One of the biggest challenges in an injection molding process is shrinkage and warpage of the molded parts. All these geometrical variations may have an adverse effect on the quality of the product, functionality, cost, and time-to-market. The situation becomes more challenging in the case of intricate shapes and in mass production using multi-cavity tools. To control the effects of shrinkage and warpage, it is very important to correctly find out the input parameters that could affect the product performance. With the advances in the computer-aided engineering (CAE), different tools are available to simulate the injection molding process. For our case study, we used the MoldFlow insight tool. Our aim is to predict the spread of the functional dimensions and geometrical variations on the part due to variations in the input parameters such as material viscosity, packing pressure, mold temperature, melt temperature, and injection speed. The input parameters may vary during batch production or due to variations in the machine process settings. To perform the accurate product assembly variation simulation, the first step is to perform an individual part variation simulation to render realistic tolerance ranges. In this article, we present a method to simulate part variations coming from the input parameters variation during batch production. The method is based on computer simulations and experimental validation using the full factorial design of experiments (DoE). The robustness of the simulation model is verified through input parameter wise sensitivity analysis study performed using simulations and experiments; all the results show a very good correlation in the material flow direction. There exists a non-linear interaction between material and the input process variables. It is observed that the parameters such as packing pressure, material, and mold temperature play an important role in spread on functional dimensions and geometrical variations. This method will allow us in the future to develop accurate/realistic virtual prototypes based on trusted simulated process variation and, therefore, increase the product quality and potentially decrease the time to market.Keywords: correlation, molding process, tolerance, sensitivity analysis, variation simulation
Procedia PDF Downloads 1722612 EDM for Prediction of Academic Trends and Patterns
Authors: Trupti Diwan
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Predicting student failure at school has changed into a difficult challenge due to both the large number of factors that can affect the reduced performance of students and the imbalanced nature of these kinds of data sets. This paper surveys the two elements needed to make prediction on Students’ Academic Performances which are parameters and methods. This paper also proposes a framework for predicting the performance of engineering students. Genetic programming can be used to predict student failure/success. Ranking algorithm is used to rank students according to their credit points. The framework can be used as a basis for the system implementation & prediction of students’ Academic Performance in Higher Learning Institute.Keywords: classification, educational data mining, student failure, grammar-based genetic programming
Procedia PDF Downloads 4192611 Physicians’ Knowledge and Perception of Gene Profiling in Malaysia: A Pilot Study
Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo
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Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires was returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age range from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge. However, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non-significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.Keywords: gene profiling, knowledge, Malaysia, physician
Procedia PDF Downloads 3222610 Decision Support System for Solving Multi-Objective Routing Problem
Authors: Ismail El Gayar, Ossama Ismail, Yousri El Gamal
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This paper presented a technique to solve one of the transportation problems that faces us in real life which is the Bus Scheduling Problem. Most of the countries using buses in schools, companies and traveling offices as an example to transfer multiple passengers from many places to specific place and vice versa. This transferring process can cost time and money, so we build a decision support system that can solve this problem. In this paper, a genetic algorithm with the shortest path technique is used to generate a competitive solution to other well-known techniques. It also presents a comparison between our solution and other solutions for this problem.Keywords: bus scheduling problem, decision support system, genetic algorithm, shortest path
Procedia PDF Downloads 4002609 Cadaveric Study of Lung Anatomy: A Surgical Overview
Authors: Arthi Ganapathy, Rati Tandon, Saroj Kaler
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Introduction: A thorough knowledge of variations in lung anatomy is of prime significance during surgical procedures like lobectomy, pneumonectomy, and segmentectomy of lungs. The arrangement of structures in the lung hilum act as a guide in performing such procedures. The normal pattern of arrangement of hilar structures in the right lung is eparterial bronchus, pulmonary artery, hyparterial bronchus and pulmonary veins from above downwards. In the left lung, it is pulmonary artery, principal bronchus and pulmonary vein from above downwards. The arrangement of hilar structures from anterior to posterior in both the lungs is pulmonary vein, pulmonary artery, and principal bronchus. The bronchial arteries are very small and usually the posterior most structures in the hilum of lungs. Aim: The present study aims at reporting the variations in hilar anatomy (arrangement and number) of lungs. Methodology: 75 adult formalin fixed cadaveric lungs from the department of Anatomy AIIMS New Delhi were observed for variations in the lobar anatomy. Arrangement of pulmonary hilar structures was meticulously observed, and any deviation in the pattern of presentation was recorded. Results: Among the 75 adult lung specimens observed 36 specimens were of right lung and the rest of left lung. Seven right lung specimens showed only 2 lobes with an oblique fissure dividing them and one left lung showed 3 lobes. The normal pattern of arrangement of hilar structures was seen in 22 right lungs and 23 left lungs. Rest of the lung specimens (14 right and 16 left) showed a varied pattern of arrangement of hilar structures. Some of them showed alterations in the sequence of arrangement of pulmonary artery, pulmonary veins, bronchus, and others in the number of these structures. Conclusion: Alterations in the pattern of arrangement of structures in the lung hilum are quite frequent. A compromise in knowledge of such variations will result in inadvertent complications like intraoperative bleeding during surgical procedures.Keywords: fissures, hilum, lobes, pulmonary
Procedia PDF Downloads 216