Search results for: Genetic Algorithm Logistic Regression

Authors: Yelin Zhao, Xinxiu Li, Martin Smelik, Oleg Sysoev, Firoj Mahmud, Dina Mansour Aly, Mikael Benson

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Background: Early diagnosis of pancreatic cancer is clinically challenging due to vague, or no symptoms, and lack of biomarkers. Polygenic risk score (PRS) scores may provide a valuable tool to assess increased or decreased risk of PC. This study aimed to develop such PRS by filtering genetic variants identified by GWAS using transcriptional programs identified by single-cell RNA sequencing (scRNA-seq). Methods: ScRNA-seq data from 24 pancreatic ductal adenocarcinoma (PDAC) tumor samples and 11 normal pancreases were analyzed to identify differentially expressed genes (DEGs) in in tumor and microenvironment cell types compared to healthy tissues. Pathway analysis showed that the DEGs were enriched for hundreds of significant pathways. These were clustered into 40 “programs” based on gene similarity, using the Jaccard index. Published genetic variants associated with PDAC were mapped to each program to generate program PRSs (pPRSs). These pPRSs, along with five previously published PRSs (PGS000083, PGS000725, PGS000663, PGS000159, and PGS002264), were evaluated in a European-origin population from the UK Biobank, consisting of 1,310 PDAC participants and 407,473 non-pancreatic cancer participants. Stepwise Cox regression analysis was performed to determine associations between pPRSs with the development of PC, with adjustments of sex and principal components of genetic ancestry. Results: The PDAC genetic variants were mapped to 23 programs and were used to generate pPRSs for these programs. Four distinct pPRSs (P1, P6, P11, and P16) and two published PRSs (PGS000663 and PGS002264) were significantly associated with an increased risk of developing PC. Among these, P6 exhibited the greatest hazard ratio (adjusted HR[95% CI] = 1.67[1.14-2.45], p = 0.008). In contrast, P10 and P4 were associated with lower risk of developing PC (adjusted HR[95% CI] = 0.58[0.42-0.81], p = 0.001, and adjusted HR[95% CI] = 0.75[0.59-0.96], p = 0.019). By comparison, two of the five published PRS exhibited an association with PDAC onset with HR (PGS000663: adjusted HR[95% CI] = 1.24[1.14-1.35], p < 0.001 and PGS002264: adjusted HR[95% CI] = 1.14[1.07-1.22], p < 0.001). Conclusion: Compared to published PRSs, scRNA-seq-based pPRSs may be used not only to assess increased but also decreased risk of PDAC.

Keywords: cox regression, pancreatic cancer, polygenic risk score, scRNA-seq, UK biobank

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Authors: Soodabeh Shahid Sales, Azam Rastgar Moghadam, Mehrane Mehramiz, Malihe Entezari, Kazem Anvari, Mohammad Sadegh Khorrami, Saeideh Ahmadi Simab, Ali Moradi, Seyed Mahdi Hassanian, Majid Ghayour-Mobarhan, Gordon A. Ferns, Amir Avan

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Background Esophageal cancer has been reported as the eighth most common cancer universal and the seventh cause of cancer-related death in men .recent studies have revealed that cytochrome P450, family 1, subfamily B, polypeptide 1, which plays a role in metabolizing xenobiotics, is associated with different cancers. Therefore in the present study, we investigated the impact of CYP1B1-rs1056836 on esophagus squamous cell carcinoma (ESCC) patients. Method: 317 subjects, with and without ESCC were recruited. DNA was extracted and genotyped via Real-time PCR-Based Taq Man. Kaplan Meier curves were utilized to assess overall and progression-free survival. To evaluate the relationship between patients clinicopathological data, genotypic frequencies, disease prognosis, and patients survival, Pearson chi-square and t-test were used. Logistic regression was utilized to assess the association between the risk of ESCC and genotypes. Results: the genotypic frequency for GG, GC, and CC are respectively 58.6% , 29.8%, 11.5% in the healthy group and 51.8%, 36.14% and 12% in ESCC group. With respect to the recessive genetic inheritance model, an association between the GG genotype and stage of ESCC were found. Also, statistically significant results were not found for this variation and risk of ESCC. Patients with GG genotype had a decreased risk of nodal metastasis in comparison with patients with CC/CG genotype, although this link was not statistically significant. Conclusion: Our findings illustrated the correlation of CYP1B1-rs1056836 as a potential biomarker for ESCC patients, supporting further studies in larger populations in different ethnic groups. Moreover, further investigations are warranted to evaluate the association of emerging marker with dietary intake and lifestyle.

Keywords: Cytochrome P450, esophagus squamous cell carcinoma, dietary intake, lifestyle

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Authors: Mukesh Ravi Raushan

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Despite consideration of obesity as a deadly public health issue contributing 2.6 million deaths worldwide every year developing country like India is facing malnutrition and it is more common than in Sub-Saharan Africa. About one in every three malnourished children in the world lives in India. The paper assess the nutritional health among children using data from total number of 43737 infant and young children aged 0-59 months (µ = 29.54; SD = 17.21) of the selected households by National Family Health Survey, 2005-06. The wasting was measured by a Z-score of standardized weight-for-height according to the WHO child growth standards. The impact of education with place of residence was found to be significantly associated with the complementary food diversity score (CFDS) in India. The education of mother was positively associated with the CFDS but the degree of performance was lower in rural India than their counterpart from urban. The result of binary logistic regression on wasting with WHO seven types of recommended food for children in India suggest that child who consumed the milk product food (OR: 0.87, p<0.0001) were less likely to be malnourished than their counterparts who did not consume, whereas, in case of other food items as the child who consumed food product of seed (OR: 0.75, p<0.0001) were less likely to be malnourished than those who did not. The nutritional status among children were negatively associated with the protein containing complementary food given the child as those child who received pulse in last 24 hour were less likely to be wasted (OR: 0.87, p<0.00001) as compared to the reference categories. The frequency to feed the indexed child increases by 10 per cent the expected change in child health outcome in terms of wasting decreases by 2 per cent in India when place of residence, education, religion, and birth order were controlled. The index gets improved as the risk for malnutrition among children in India decreases.

Keywords: CFDS, food diversity index, India, logistic regression

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Authors: M. Kislu Noman, Syed Mohammed Shamsul Islam, Shahriar Hassan, Raihana Pervin

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With the increasing rate of wireless devices and high bandwidth operations, wireless networking and communications are becoming over crowded. To cope with such crowdy and messy situation, massive MIMO is designed to work with hundreds of low costs serving antennas at a time as well as improve the spectral efficiency at the same time. TDD has been used for gaining beamforming which is a major part of massive MIMO, to gain its best improvement to transmit and receive pilot sequences. All the benefits are only possible if the channel state information or channel estimation is gained properly. The common methods to estimate channel matrix used so far is LS, MMSE and a linear version of MMSE also proposed in many research works. We have optimized these methods using genetic algorithm to minimize the mean squared error and finding the best channel matrix from existing algorithms with less computational complexity. Our simulation result has shown that the use of GA worked beautifully on existing algorithms in a Rayleigh slow fading channel and existence of Additive White Gaussian Noise. We found that the GA optimized LS is better than existing algorithms as GA provides optimal result in some few iterations in terms of MSE with respect to SNR and computational complexity.

Keywords: channel estimation, LMMSE, LS, MIMO, MMSE

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Authors: Lubena Achmad, Herman Kristanto, Julian Dewantiningrum

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Background: The Bishop score is a standard method used to predict the success of induction. This examination tends to be subjective with high inter and intraobserver variability, so it was presumed to have a low predictive value in terms of the outcome of labor induction. Cervical length measurement using transvaginal ultrasound is considered to be more objective to assess the cervical length. Meanwhile, this examination is not a complicated procedure and less invasive than vaginal touché. Objective: To compare transvaginal ultrasound and Bishop score in predicting successful induction. Methods: This study was a prospective cohort study. One hundred and twenty women with singleton pregnancies undergoing induction of labor at 37 – 42 weeks and met inclusion and exclusion criteria were enrolled in this study. Cervical assessment by both transvaginal ultrasound and Bishop score were conducted prior induction. The success of labor induction was defined as an ability to achieve active phase ≤ 12 hours after induction. To figure out the best cut-off point of cervical length and Bishop score, receiver operating characteristic (ROC) curves were plotted. Logistic regression analysis was used to determine which factors best-predicted induction success. Results: This study showed significant differences in terms of age, premature rupture of the membrane, the Bishop score, cervical length and funneling as significant predictors of successful induction. Using ROC curves found that the best cut-off point for prediction of successful induction was 25.45 mm for cervical length and 3 for Bishop score. Logistic regression was performed and showed only premature rupture of membranes and cervical length ≤ 25.45 that significantly predicted the success of labor induction. By excluding premature rupture of the membrane as the indication of induction, cervical length less than 25.3 mm was a better predictor of successful induction. Conclusion: Compared to Bishop score, cervical length using transvaginal ultrasound was a better predictor of successful induction.

Keywords: Bishop Score, cervical length, induction, successful induction, transvaginal sonography

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Authors: Amir Abbas Fatemi, Zahra Tabrizian, Kabir Sadeghi

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To find the location and severity of damage that occurs in a structure, characteristics changes in dynamic and static can be used. The non-destructive techniques are more common, economic, and reliable to detect the global or local damages in structures. This paper presents a non-destructive method in structural damage detection and assessment using GA and static data. Thus, a set of static forces is applied to some of degrees of freedom and the static responses (displacements) are measured at another set of DOFs. An analytical model of the truss structure is developed based on the available specification and the properties derived from static data. The damages in structure produce changes to its stiffness so this method used to determine damage based on change in the structural stiffness parameter. Changes in the static response which structural damage caused choose to produce some simultaneous equations. Genetic Algorithms are powerful tools for solving large optimization problems. Optimization is considered to minimize objective function involve difference between the static load vector of damaged and healthy structure. Several scenarios defined for damage detection (single scenario and multiple scenarios). The static damage identification methods have many advantages, but some difficulties still exist. So it is important to achieve the best damage identification and if the best result is obtained it means that the method is Reliable. This strategy is applied to a plane truss. This method is used for a plane truss. Numerical results demonstrate the ability of this method in detecting damage in given structures. Also figures show damage detections in multiple damage scenarios have really efficient answer. Even existence of noise in the measurements doesn’t reduce the accuracy of damage detections method in these structures.

Keywords: damage detection, finite element method, static data, non-destructive, genetic algorithm

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Authors: Yi-Hsien Wang, Fu-Ju Yang, Hwa-Rong Shen, Rui-Lin Tseng

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The business is notably related to the market risk according to the increase of liberalization of financial markets. Hence, the company usually utilized high financial leverage of derivatives to hedge the risk. When the company choose different hedging instruments to face a variety of exchange rate risk, we employ the Multinomial Logistic-AHP to analyze the impact of various derivatives. Hence, the research summarized the literature on relevant factors affecting managers selected exchange rate hedging instruments, using Multinomial Logistic Model and and further integrate AHP. Using Experts’ Questionnaires can test multi-level selection and hedging effect of different hedging instruments in order to calculate the hedging instruments and the multi-level factors of weights to understand the gap between the empirical results and practical operation. Finally, the Multinomial Logistic-AHP Model will sort the weights to analyze. The research findings can be a basis reference for investors in decision-making.

Keywords: exchange rate risk, derivatives, hedge, multinomial logistic-AHP

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Authors: M. Karthigayan, M. Rizon, Sazali Yaacob, R. Nagarajan, M. Muthukumaran, Thinaharan Ramachandran, Sargunam Thirugnanam

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In this paper, using a set of irregular and regular ellipse fitting equations using Genetic algorithm (GA) are applied to the lip and eye features to classify the human emotions. Two South East Asian (SEA) faces are considered in this work for the emotion classification. There are six emotions and one neutral are considered as the output. Each subject shows unique characteristic of the lip and eye features for various emotions. GA is adopted to optimize irregular ellipse characteristics of the lip and eye features in each emotion. That is, the top portion of lip configuration is a part of one ellipse and the bottom of different ellipse. Two ellipse based fitness equations are proposed for the lip configuration and relevant parameters that define the emotions are listed. The GA method has achieved reasonably successful classification of emotion. In some emotions classification, optimized data values of one emotion are messed or overlapped to other emotion ranges. In order to overcome the overlapping problem between the emotion optimized values and at the same time to improve the classification, a fuzzy clustering method (FCM) of approach has been implemented to offer better classification. The GA-FCM approach offers a reasonably good classification within the ranges of clusters and it had been proven by applying to two SEA subjects and have improved the classification rate.

Keywords: ellipse fitness function, genetic algorithm, emotion recognition, fuzzy clustering

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Authors: Aftab Khan, Ashfaq Khan

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The research paper focuses on an interesting challenge faced in Blind Image Deblurring (BID). It relates to the estimation of arbitrarily shaped or non-parametric Point Spread Functions (PSFs) of motion blur caused by camera handshake. These PSFs exhibit much more complex shapes than their parametric counterparts and deblurring in this case requires intricate ways to estimate the blur and effectively remove it. This research work introduces a novel blind deblurring scheme visualized for deblurring images corrupted by arbitrarily shaped PSFs. It is based on Genetic Algorithm (GA) and utilises the Blind/Reference-less Image Spatial QUality Evaluator (BRISQUE) measure as the fitness function for arbitrarily shaped PSF estimation. The proposed BID scheme has been compared with other single image motion deblurring schemes as benchmark. Validation has been carried out on various blurred images. Results of both benchmark and real images are presented. Non-reference image quality measures were used to quantify the deblurring results. For benchmark images, the proposed BID scheme using BRISQUE converges in close vicinity of the original blurring functions.

Keywords: blind deconvolution, blind image deblurring, genetic algorithm, image restoration, image quality measures

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Authors: Katalin Gombos, Bence Gálik, Krisztina Ildikó Kalács, Krisztina Gödöny, Ákos Várnagy, József Bódis, Attila Gyenesei, Gábor L. Kovács

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Although non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) is potentially appropriate to assess chromosomal ploidy of the embryo, practical application of it in a routine IVF center has not been started in the absence of a recommendation. We developed a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology. We performed MALBAC whole genome amplification and NGS on spent blastocyst culture media of Day 3 embryos fertilized with intra-cytoplasmic sperm injection (ICSI). Spent embryonic culture media of morphologically good quality score embryos were enrolled in further analysis with the blank culture media as background control. Chromosomal abnormalities were identified by an optimized bioinformatics pipeline applying a copy number variation (CNV) detecting algorithm. We demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A. It can be carried out within 48 h which is critical for the same-cycle blastocyst transfer, but also suitable for “freeze all” and “elective frozen embryo” strategies. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods.

Keywords: next generation sequencing, in vitro fertilization, embryo assessment, non-invasive pre-implantation genetic testing

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Authors: Harini Chakkera

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Background: Inpatient hyperglycemia is an established independent risk factor among several patient cohorts with hospital readmission. This has not been studied after kidney transplantation. Nearly one-third of patients who have undergone a kidney transplant reportedly experience 30-day readmission. Methods: Data on first-time solitary kidney transplantations were retrieved between September 2015 to December 2018. Information was linked to the electronic health record to determine a diagnosis of diabetes mellitus and extract glucometeric and insulin therapy data. Univariate logistic regression analysis and the XGBoost algorithm were used to predict 30-day readmission. We report the average performance of the models on the testing set on five bootstrapped partitions of the data to ensure statistical significance. Results: The cohort included 1036 patients who received kidney transplantation, and 224 (22%) experienced 30-day readmission. The machine learning algorithm was able to predict 30-day readmission with an average AUC of 77.3% (95% CI 75.30-79.3%). We observed statistically significant differences in the presence of pretransplant diabetes, inpatient-hyperglycemia, inpatient-hypoglycemia, and minimum and maximum glucose values among those with higher 30-day readmission rates. The XGBoost model identified the index admission length of stay, presence of hyper- and hypoglycemia and recipient and donor BMI values as the most predictive risk factors of 30-day readmission. Additionally, significant variations in the therapeutic management of blood glucose by providers were observed. Conclusions: Suboptimal glucose metrics during hospitalization after kidney transplantation is associated with an increased risk for 30-day hospital readmission. Optimizing the hospital blood glucose management, a modifiable factor, after kidney transplantation may reduce the risk of 30-day readmission.

Keywords: kidney, transplant, diabetes, insulin

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Authors: Srinivasa Rao Gadde

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In this article, we considered a group acceptance sampling plans for exponentiated half logistic distribution when the life-test is truncated at a pre-specified time. It is assumed that the index parameter of the exponentiated half logistic distribution is known. The design parameters such as the number of groups and the acceptance number are obtained by satisfying the producer’s and consumer’s risks at the specified quality levels in terms of medians and 10th percentiles under the assumption that the termination time and the number of items in each group are pre-fixed. Finally, an example is given to illustration the methodology.

Keywords: group acceptance sampling plan, operating characteristic, consumer and producer’s risks, truncated life-test

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Authors: Peter James C. Icalia, Agapita J. Salces, Loida Valenzuela, Kangseok Seo, Geronima Ludan

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This study evaluated polymorphism of 11 microsatellite markers in four local genetic groups of cattle. Batanes cattle which has never been studied using microsatellites is evaluated for its genetic distance from the Ilocos cattle while Brahman and Holstein-Sahiwal are also included as there were insemination programs by the government using these two breeds. PCR products that were genotyped for each marker were analyzed using POPGENEv32. Results showed that 55% (Fst=0.5501) of the genetic variation is due to the differences between populations while the remaining 45% is due to individual variation. The Fst value also indicates that there were very great differences from population to population using the range proposed by Sewall and Wright. The constructed phylogenetic tree based on Nei’s genetic distance using the modified neighboor joining procedure of PHYLIPv3.5 showed the admixture of Brahman and Holstein-Sahiwal having them grouped in the same clade. Batanes and Ilocos cattle were grouped in a different cluster showing that they have descended from a single parental population. This would presumably address the claim that Batanes and Ilocos cattle are genetically distant from other groups and still exist despite the artificial insemination program of the government using Brahman and other imported breeds. The knowledge about the genetic structure of this population supports the development of conservation programs for the smallholder farmers.

Keywords: microsatellites, cattle, Philippines, populations, genetic structure

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Authors: A. Ishag Mohamed, A. A. Rabah

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The objective of this research is to develop a generalized correlation for the prediction of thermal conductivity of n-Alkanes and Alkenes. There is a minority of research and lack of correlation for thermal conductivity of liquids in the open literature. The available experimental data are collected covering the groups of n-Alkanes and Alkenes.The data were assumed to correlate to temperature using Filippov correlation. Nonparametric regression of Grace Algorithm was used to develop the generalized correlation model. A spread sheet program based on Microsoft Excel was used to plot and calculate the value of the coefficients. The results obtained were compared with the data that found in Perry's Chemical Engineering Hand Book. The experimental data correlated to the temperature ranged "between" 273.15 to 673.15 K, with R2 = 0.99.The developed correlation reproduced experimental data that which were not included in regression with absolute average percent deviation (AAPD) of less than 7 %. Thus the spread sheet was quite accurate which produces reliable data.

Keywords: N-Alkanes, N-Alkenes, nonparametric, regression

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Authors: O. Ekrami, P. Claes, S. Van Dongen

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Fluctuating asymmetry (FA) has been studied for many years as an indicator of developmental stability or ‘genetic quality’ based on the assumption that perfect symmetry is ideally the expected outcome for a bilateral organism. Further studies have also investigated the possible link between FA and attractiveness or levels of masculinity or femininity. These hypotheses have been mostly examined using 2D images, and the structure of interest is usually presented using a limited number of landmarks. Such methods have the downside of simplifying and reducing the dimensionality of the structure, which will in return increase the error of the analysis. In an attempt to reach more conclusive and accurate results, in this study we have used high-resolution 3D scans of human faces and have developed an algorithm to measure and localize FA, taking a spatially-dense approach. A symmetric spatially dense anthropometric mask with paired vertices is non-rigidly mapped on target faces using an Iterative Closest Point (ICP) registration algorithm. A set of 19 manually indicated landmarks were used to examine the precision of our mapping step. The protocol’s accuracy in measurement and localizing FA is assessed using simulated faces with known amounts of asymmetry added to them. The results of validation of our approach show that the algorithm is perfectly capable of locating and measuring FA in 3D simulated faces. With the use of such algorithm, the additional captured information on asymmetry can be used to improve the studies of FA as an indicator of fitness or attractiveness. This algorithm can especially be of great benefit in studies of high number of subjects due to its automated and time-efficient nature. Additionally, taking a spatially dense approach provides us with information about the locality of FA, which is impossible to obtain using conventional methods. It also enables us to analyze the asymmetry of a morphological structures in a multivariate manner; This can be achieved by using methods such as Principal Components Analysis (PCA) or Factor Analysis, which can be a step towards understanding the underlying processes of asymmetry. This method can also be used in combination with genome wide association studies to help unravel the genetic bases of FA. To conclude, we introduced an algorithm to study and analyze asymmetry in human faces, with the possibility of extending the application to other morphological structures, in an automated, accurate and multi-variate framework.

Keywords: developmental stability, fluctuating asymmetry, morphometrics, 3D image processing

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Authors: Palash Dey, Sudip Talukdar

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In this work, a cross-breed approach is presented for obtaining both the amount of the damage intensity and location of damage existing in thin-walled members. This cross-breed approach is developed based on response surface methodology (RSM) and genetic algorithm (GA). Theoretical finite element (FE) model of cracked angle section thin walled curved beam has been linked to the developed approach to carry out trial experiments to generate response surface functions (RSFs) of free, forced and heterogeneous dynamic response data. Subsequently, the error between the computed response surface functions and measured dynamic response data has been minimized using GA to find out the optimum damage parameters (amount of the damage intensity and location). A single crack of varying location and depth has been considered in this study. The presented approach has been found to reveal good accuracy in prediction of crack parameters and possess great potential in crack detection as it requires only the current response of a cracked beam.

Keywords: damage parameters, finite element, genetic algorithm, response surface methodology, thin walled curved beam

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Authors: Masahiro Ohmura, Koh Kakusho, Takeshi Okadome

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This paper presents a regression model with autocorrelated errors in which the inputs are social moods obtained by analyzing the adjectives in Twitter posts using a document topic model. The regression model predicts Dow Jones Industrial Average (DJIA) more precisely than autoregressive moving-average models.

Keywords: stock market prediction, social moods, regression model, DJIA

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Authors: Atsuko Okazaki, Jurg Ott

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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

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Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

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The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Vishnu Pratap Singh Kirar

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Artificial Neural Network (ANN) can be trained using backpropagation (BP). It is the most widely used algorithm for supervised learning with multi-layered feed-forward networks. Efficient learning by the BP algorithm is required for many practical applications. The BP algorithm calculates the weight changes of artificial neural networks, and a common approach is to use a two-term algorithm consisting of a learning rate (LR) and a momentum factor (MF). The major drawbacks of the two-term BP learning algorithm are the problems of local minima and slow convergence speeds, which limit the scope for real-time applications. Recently the addition of an extra term, called a proportional factor (PF), to the two-term BP algorithm was proposed. The third increases the speed of the BP algorithm. However, the PF term also reduces the convergence of the BP algorithm, and criteria for evaluating convergence are required to facilitate the application of the three terms BP algorithm. Although these two seem to be closely related, as described later, we summarize various improvements to overcome the drawbacks. Here we compare the different methods of convergence of the new three-term BP algorithm.

Keywords: neural network, backpropagation, local minima, fast convergence rate

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Authors: ِAbdallah A. A. Shaheen

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Gaza Strip faces economic and political issues such as conflict, siege and urbanization; all these have led to an increase in the air pollution over Gaza Strip. In this study, Particulate matter 10 (PM10) concentration over Gaza Strip has been estimated by Landsat Thematic Mapper (TM) and Landsat Enhanced Thematic Mapper Plus (ETM+) data, based on a multispectral algorithm. Simultaneously, in-situ measurements for the corresponding particulate are acquired for selected time period. Landsat and ground data for eleven years are used to develop the algorithm while four years data (2002, 2006, 2010 and 2014) have been used to validate the results of algorithm. The developed algorithm gives highest regression, R coefficient value i.e. 0.86; RMSE value as 9.71 µg/m³; P values as 0. Average validation of algorithm show that calculated PM10 strongly correlates with measured PM10, indicating high efficiency of algorithm for the mapping of PM10 concentration during the years 2000 to 2014. Overall results show increase in minimum, maximum and average yearly PM10 concentrations, also presents similar trend over urban area. The rate of urbanization has been evaluated by supervised classification of the Landsat image. Urban sprawl from year 2000 to 2014 results in a high concentration of PM10 in the study area.

Keywords: PM10, landsat, atmospheric reflectance, Gaza strip, urbanization

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Authors: Rugang Tian

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In this study, we generated whole-genome sequence (WGS) data from110 native cattle. Together with whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of different cattle populations. Our findings revealed clustering of cattle groups in line with their geographic locations. We identified noticeable genetic diversity between indigenous cattle breeds and commercial populations. Among all studied cattle groups, lower genetic diversity measures were found in commercial populations, however, high genetic diversity were detected in some local cattle, particularly in Rashoki and Mongolian breeds. Our search for potential genomic regions under selection in native cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis.

Keywords: cattle, whole-genome, population structure, adaptation

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Authors: Haoming Ma, Guo Yu, Peiru Zhou

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Background: Previous studies show that dysglycemia, mostly hyperglycemia, hypoglycemia and glycemic variability(GV), are associated with excess mortality in critically ill patients, especially those without diabetes. Glycemic variability is an increasingly important measure of glucose control in the intensive care unit (ICU) due to this association. However, there is limited data pertaining to the relationship between different clinical factors and glycemic variability and clinical outcomes categorized by their DM status. This retrospective study of 958 intensive care unit(ICU) patients was conducted to investigate the relationship between GV and outcome in critically ill patients and further to determine the significant factors that contribute to the glycemic variability. Aim: We hypothesize that the factors contributing to mortality and the glycemic variability are different from critically ill patients with or without diabetes. And the primary aim of this study was to determine which dysglycemia (hyperglycemia\hypoglycemia\glycemic variability) is independently associated with an increase in mortality among critically ill patients in different groups (DM/Non-DM). Secondary objectives were to further investigate any factors affecting the glycemic variability in two groups. Method: A total of 958 diabetic and non-diabetic patients with severe diseases in the ICU were selected for this retrospective analysis. The glycemic variability was defined as the coefficient of variation (CV) of blood glucose. The main outcome was death during hospitalization. The secondary outcome was GV. The logistic regression model was used to identify factors associated with mortality. The relationships between GV and other variables were investigated using linear regression analysis. Results: Information on age, APACHE II score, GV, gender, in-ICU treatment and nutrition was available for 958 subjects. Predictors remaining in the final logistic regression model for mortality were significantly different in DM/Non-DM groups. Glycemic variability was associated with an increase in mortality in both DM(odds ratio 1.05; 95%CI:1.03-1.08,p＜0.001) or Non-DM group(odds ratio 1.07; 95%CI:1.03-1.11,p=0.002). For critically ill patients without diabetes, factors associated with glycemic variability included APACHE II score(regression coefficient, 95%CI:0.29,0.22-0.36,p＜0.001), Mean BG(0.73,0.46-1.01,p＜0.001), total parenteral nutrition(2.87,1.57-4.17,p＜0.001), serum albumin(-0.18,-0.271 to -0.082,p＜0.001), insulin treatment(2.18,0.81-3.55,p=0.002) and duration of ventilation(0.006,0.002-1.010,p=0.003).However, for diabetes patients, APACHE II score(0.203,0.096-0.310,p＜0.001), mean BG(0.503,0.138-0.869,p=0.007) and duration of diabetes(0.167,0.033-0.301,p=0.015) remained as independent risk factors of GV. Conclusion: We found that the relation between dysglycemia and mortality is different in the diabetes and non-diabetes groups. And we confirm that GV was associated with excess mortality in DM or Non-DM patients. Furthermore, APACHE II score, Mean BG, total parenteral nutrition, serum albumin, insulin treatment and duration of ventilation were significantly associated with an increase in GV in Non-DM patients. While APACHE II score, mean BG and duration of diabetes (years) remained as independent risk factors of increased GV in DM patients. These findings provide important context for further prospective trials investigating the effect of different clinical factors in critically ill patients with or without diabetes.

Keywords: diabetes, glycemic variability, predictors, severe disease

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Authors: Kevin Worrall, Euan McGookin

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The use of optimization algorithms is common across a large number of diverse fields. This work presents the use of a hybrid optimization algorithm applied to a mobile robot tasked with carrying out a search of an unknown environment. The algorithm is then applied to the multiple robots case, which results in a reduction in the time taken to carry out the search. The hybrid algorithm is a Random Search Algorithm fused with a Tabu mechanism. The work shows that the algorithm locates the desired points in a quicker time than a brute force search. The Tabu Random algorithm is shown to work within a simulated environment using a validated mathematical model. The simulation was run using three different environments with varying numbers of targets. As an algorithm, the Tabu Random is small, clear and can be implemented with minimal resources. The power of the algorithm is the speed at which it locates points of interest and the robustness to the number of robots involved. The number of robots can vary with no changes to the algorithm resulting in a flexible algorithm.

Keywords: algorithms, control, multi-agent, search and rescue

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Authors: Rakesh Prajapati, Purvik Patel, Hardik Patel

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Productivity and quality are two important aspects that have become great concerns in today’s competitive global market. Every production/manufacturing unit mainly focuses on these areas in relation to the process, as well as the product developed. The electrical discharge machining (EDM) process, even now it is an experience process, wherein the selected parameters are still often far from the maximum, and at the same time selecting optimization parameters is costly and time consuming. Material Removal Rate (MRR) during the process has been considered as a productivity estimate with the aim to maximize it, with an intention of minimizing surface roughness taken as most important output parameter. These two opposites in nature requirements have been simultaneously satisfied by selecting an optimal process environment (optimal parameter setting). Objective function is obtained by Regression Analysis and Analysis of Variance. Then objective function is optimized using Genetic Algorithm technique. The model is shown to be effective; MRR and Surface Roughness improved using optimized machining parameters.

Keywords: MMR, TWR, OC, DOE, ANOVA, minitab

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Authors: Ma Lei-Lei, Zhou You

Abstract:

Aiming at the problems of low detection accuracy of deep learning algorithm in traffic sign detection, this paper proposes improved EfficientDet based traffic sign detection algorithm. Multi-head self-attention is introduced in the minimum resolution layer of the backbone of EfficientDet to achieve effective aggregation of local and global depth information, and this study proposes an improved feature fusion pyramid with increased vertical cross-layer connections, which improves the performance of the model while introducing a small amount of complexity, the Balanced L1 Loss is introduced to replace the original regression loss function Smooth L1 Loss, which solves the problem of balance in the loss function. Experimental results show, the algorithm proposed in this study is suitable for the task of traffic sign detection. Compared with other models, the improved EfficientDet has the best detection accuracy. Although the test speed is not completely dominant, it still meets the real-time requirement.

Keywords: convolutional neural network, transformer, feature pyramid networks, loss function

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Authors: Dale Dzemydiene, Aurelija Burinskiene, Arunas Miliauskas, Kristina Ciziuniene

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Data flow and the purpose of reporting the data are different and dependent on business needs. Different parameters are reported and transferred regularly during freight delivery. This business practices form the dataset constructed for each time point and contain all required information for freight moving decisions. As a significant amount of these data is used for various purposes, an integrating methodological approach must be developed to respond to the indicated problem. The proposed methodology contains several steps: (1) collecting context data sets and data validation; (2) multi-objective analysis for optimizing freight transfer services. For data validation, the study involves Grubbs outliers analysis, particularly for data cleaning and the identification of statistical significance of data reporting event cases. The Grubbs test is often used as it measures one external value at a time exceeding the boundaries of standard normal distribution. In the study area, the test was not widely applied by authors, except when the Grubbs test for outlier detection was used to identify outsiders in fuel consumption data. In the study, the authors applied the method with a confidence level of 99%. For the multi-objective analysis, the authors would like to select the forms of construction of the genetic algorithms, which have more possibilities to extract the best solution. For freight delivery management, the schemas of genetic algorithms' structure are used as a more effective technique. Due to that, the adaptable genetic algorithm is applied for the description of choosing process of the effective transportation corridor. In this study, the multi-objective genetic algorithm methods are used to optimize the data evaluation and select the appropriate transport corridor. The authors suggest a methodology for the multi-objective analysis, which evaluates collected context data sets and uses this evaluation to determine a delivery corridor for freight transfer service in the multi-modal transportation network. In the multi-objective analysis, authors include safety components, the number of accidents a year, and freight delivery time in the multi-modal transportation network. The proposed methodology has practical value in the management of multi-modal transportation processes.

Keywords: multi-objective, analysis, data flow, freight delivery, methodology

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Authors: Aisling De Paor

Abstract:

Scientific and technological developments are driving genetics and genetic technologies into the public sphere. Scientists are making genetic discoveries as to the make up of the human body and the cause and effect of disease, diversity and disability amongst individuals. Technological innovation in the field of genetics is also advancing, with the development of genetic testing, and other emerging genetic technologies, including gene editing (which offers the potential for genetic modification). In addition to the benefits for medicine, health care and humanity, these genetic advances raise a range of ethical, legal and societal concerns. From an ethical perspective, such advances may, for example, change the concept of humans and what it means to be human. Science may take over in conceptualising human beings, which may push the boundaries of existing human rights. New genetic technologies, particularly gene editing techniques create the potential to stigmatise disability, by highlighting disability or genetic difference as something that should be eliminated or anticipated. From a disability perspective, use (and misuse) of genetic technologies raise concerns about discrimination and violations to the dignity and integrity of the individual. With an acknowledgement of the likely future orientation of genetic science, and in consideration of the intersection of genetics and disability, this paper highlights the main concerns raised as genetic science and technology advances (particularly with gene editing developments), and the consequences for disability and human rights. Through the use of traditional doctrinal legal methodologies, it investigates the use (and potential misuse) of gene editing as creating the potential for a unique form of discrimination and stigmatization to develop, as well as a potential gateway to a form of new, subtle eugenics. This article highlights the need to maintain caution as to the use, application and the consequences of genetic technologies. With a focus on the law and policy position in Europe, it examines the need to control and regulate these new technologies, particularly gene editing. In addition to considering the need for regulation, this paper highlights non-normative approaches to address this area, including awareness raising and education, public discussion and engagement with key stakeholders in the field and the development of a multifaceted genetics advisory network.

Keywords: disability, gene-editing, genetics, law, regulation

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Authors: Mahmoud T. Alwidyan, Ahmad Alrawashdeh, Alaa O. Oteir

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Background: Emergency medical service (EMS) providers, oftentimes, use the lights and sirens (L&S) of their ambulances to warn road users, navigate through traffic, and expedite transport to save lives of ill and injured patients. Despite the contribution of road users in the effectiveness of reducing transport time of EMS ambulances using L&S, there is a lack of empirical assessments exploring the road user’s attitude and behavior in such situations. This study, therefore, aimed to assess the attitude and behavior of road users in response to EMS ambulances with warning L&S in use. Methods: This was a cross-sectional survey developed and distributed to adult road users in Northern Jordan. The questionnaire included 20 items addressing demographics, attitudes, and behavior toward emergency ambulances. We described the participants’ responses and assessed the association between demographics and attitude statements using logistic regression. Results: A total of 1302 questionnaires were complete and appropriate for analysis. The mean age was 34.2 (SD± 11.4) years, and the majority were males (72.6%). About half of road users (47.9%) in our sample would perform inappropriate action in response to EMS ambulances with L&S in use. The multivariate logistic regression model show that being female (OR, 0.63; 95% CI = 0.48-0.81), more educated (OR, 0.68; 95% CI = 0.53-0.86), or public transport driver (OR, 0.55; 95% CI = 0.34-0.90) is significantly associated with inappropriate response to EMS ambulances. Additionally, a significant proportion of road users may perform inappropriate and lawless driving practices such as crossing red traffic lights or following the passing by EMS ambulances, which would, in turn, increase the risk on ambulances and other road users. Conclusions: A large proportion of road users in Jordan may respond inappropriately to the EMS ambulances, and many engage in risky driving behaviors due perhaps to the lack of procedural knowledge. Policy-related interventions and educational programs are crucially needed to increase public awareness of the traffic law concerning EMS ambulances and to enhance appropriate driving behavior, which, in turn, improves the efficiency of ambulance services.

Keywords: EMS ambulances, lights and sirens, road users, attitude and behavior

Procedia PDF Downloads 82