Search results for: genotype variations

Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Sung Duk Kim, Kwan U. Kim, Jin Sim, Ryong Jin Jang

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The phenomenon of seasonal variations in the Earth’s rotation velocity was discovered in the 1930s when a crystal clock was developed and analyzed in a quantitative way for the first time between 1955 and 1968 when observation data of the seasonal variations was analyzed by an atomic clock. According to the previous investigation, atmospheric circulation is supposed to be a factor affecting the seasonal variations in the Earth’s rotation velocity in many cases, but the problem has not been solved yet. In order to solve the problem, it is necessary to apply dynamics to consider the Earth’s spatial motion, rotation and change of shape of the Earth (movement of materials in and out of the Earth and change of the Earth’s figure) at the same time and in interrelation to the accuracy of post-Newtonian approximation regarding the Earth body as a system of mass points because the stability of the Earth’s rotation angular velocity is in the range of 10⁻⁸~10⁻⁹. For the purpose, the equation was derived, which can consider the 3 kinds of motion above mentioned at the same time by taking the effect of the resultant of external force on the Earth’s rotation into account in a relativistic way to the accuracy of post-Newtonian approximation. Therefore, the equation has been solved to obtain the theoretical values of periodic change in the Earth’s rotation velocity and they have been compared with the astronomical observation data, so to reveal the cause for the periodic change in the Earth’s rotation velocity.

Keywords: Earth rotation, moment function, periodic change, seasonal variation, relativistic change

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Authors: Umego Chukwudi T., Ntui Valentine O., Uyoh Edak A.

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Phosphorus (P) deficiency has been identified as a major hindrance to rice production the world over. Eleven (11) rice genotypes predominantly used by local farmers in Nigeria were studied for their responses to P deficient conditions. The characterization was based on morpho-physiologic parameters. The genotypes were screened using a hydroponic system in a modified Hoagland’s solution. Morphological and physiologic parameters, including Plant height (PH), number of tillers per plant, shoot dry weight (SDW), shoot phosphate concentration (SPC), and chlorophyll content, were recorded after exposure to three levels of phosphate concentration (0µM, 400 µM, and 800 µM). The data obtained were subjected to analysis of variance (ANOVA), and the means were separated using least significance difference tests. The results obtained showed that P starvation caused a significant (p≤0.05) reduction in PH, SDW, and tillering and also triggered a significant (p≤0.05) increase in root length among the genotypes. The Pearsons correlation coefficient was used to estimate the relationships among studied parameters, and a significant negative correlation was observed between plant height and root length. FARO63 was identified as a highly tolerant genotype to P deficiency with a low (0.24) SPC and higher (4.81) phosphate utilization efficiency (PUE). This study has identified FARO63 as a true tolerant genotype to Phosphate deficiency, which will be useful in breeding for phosphate deficiency tolerance in rice and thus combating food insecurity.

Keywords: phosphate deficiency, rice genotypes, hydroponic system, food security

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Authors: Fhajema Kunso

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People who live in the same region and who seemed to speak the same language still vary in some aspects of their language. The variation may occur in terms of pronunciation, lexicon, morphology, and syntax. This qualitative study described the phonological, morphological, and lexical variations of the Maguindanaon language among the ten Maguindanao municipalities. Purposive sampling, in-depth interviews, focus group discussion, and sorting and classifying of words according to phonological and morphological as well as lexical structures in data analysis were employed. The variations occurred through phonemic changes and other phonological processes and morphological processes. Phonological processes consisted of vowel lengthening and deletion while morphological processes included affixation, borrowing, and coinage. In the phonological variation, it was observed that there were phonemic changes in one dialect to another. For example, there was a change of phoneme /r/ to /l/. The phoneme /r/ was most likely to occur in Kabuntalan like /biru/, /kurIt/, and /kɘmɅr/ whereas in the rest of the dialects these were /bilu/, /kuIɪt/, and /kɘmɅl/ respectively. Morphologically, the affixation was the main way to know the tenses. For example, the root sarig (expect) when inserted with im becomes simarig, i.e. s + im + arig = simarig (expected). Lexical variation also existed in the Maguindanaon language. Results revealed that the variation in phonology, morphology, and lexicon were observed to be associated primarily on geographic distribution.

Keywords: applied linguistics, language, lexicon, Maguindanao, morphology, Philippines, phonology, processes, qualitative, variation

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Authors: Gulam Anwer Khan, A. Gautam

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Background: The arch of aorta is a large artery that arches over the root of the left lung and connects the ascending aorta and descending aorta. It is situated in the superior mediastinum behind the manubrium sterni. It gives off three major branches i.e. brachiocephalic trunk, left common carotid artery and left subclavian artery arising from the superior surface of arch of aorta from right to left. Material and Methods: This was a descriptive study. It was carried out in 44 cadavers, obtained during dissections for undergraduates of Department of Anatomy, Chitwan Medical College, Bharatpur, Chitwan, between March 2015 to October 2016. Cadavers of both sexes were included in the present study. The arch of aorta was dissected and exposed according to the methods described by Romanes in Cunningham’s manual of practical anatomy. Results: Out of 44 dissected cadavers, 35 (79.54%) were male and 9 (20.46%) were female cadavers. The normal branching pattern of the arch of aorta was encountered in 28 (63.64%) cadavers and the remaining 16 (36.36%) cadavers showed variations in the branching pattern of arch of aorta. Two different types of variations on the branching pattern of arch of aorta were noted in the present study, in which 12 (27.27%) cadavers had common trunk of the Arch of Aorta. In 3 (5.00%) male cadavers, we found the origin of the Thyroid ima artery. This variation was noted in 1(1.66%) female cadaver. Conclusion: The present study carried out on adult human cadavers’ revealed wide variations in the branching pattern of the arch of ao rta. These variations are of clinical significance and also very useful for the anatomists, radiologists, anesthesiologists, surgeons for practice during angiography, instrumentation, supra-aortic thoracic, head and neck surgery.

Keywords: arch of aorta, brachiocephalic trunk, left common carotid artery, left subclavian artery, Thyroidea ima artery

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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

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Authors: Anita Singh, Richa Naula, Manoj Raghav

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Nutrient rich and high-yielding varieties of fenugreek can be developed by using genotypes which are naturally high in nutrients. Gene banks harbour scanty germplasm collection of Trigonella spp. and a very little background information about its genetic diversity. The extent of genetic diversity in a specific breeding population depends upon the genotype included in it. The present investigation aims at the estimation of macronutrient (phosphorus by spectrophotometer and potassium by flame photometer), micronutrients, namely, iron, zinc, manganese, and copper from seeds of fenugreek genotypes using atomic absorption spectrophotometer, protein by Rapid N Cube Analyser and Steroidal Saponins. Twenty-eight genotypes of fenugreek along with two standard checks, namely, Pant Ragini and Pusa Early Bunching were collected from different parts of India, and nutrient contents of each genotype were determined at G. B. P. U. A. & T. Laboratory, Pantnagar. Highest potassium content was observed in PFG-35 (1207 mg/100g). PFG-37 and PFG-20 were richest in phosphorus, iron and manganese content among all the genotypes. The lowest zinc content was found in PFG-26 (1.19 mg/100g), while the maximum zinc content was found in PFG- 28 (4.43 mg/100g). The highest content of copper was found in PFG-26 (1.97 mg/100g). PFG-39 has the highest protein content (29.60 %). Significant differences were observed in the steroidal saponin among the genotypes. Saponin content ranged from 0.38 g/100g to 1.31 g/100g. Steroidal Saponins content was found the maximum in PFG-36 (1.31 g/100g) followed by PFG-17 (1.28 g/100g). Therefore, the genotypes which are rich in nutrient and oil content can be used for plant biofortification, dietary supplements, and herbal products.

Keywords: genotypes, macronutrients, micronutrient, protein, seeds

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Authors: Nidhi S. Chandra, Veena Agrawal, Debprasad Chattopadhyay

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Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in developing countries. It spreads feco orally mainly due to contamination of drinking water by sewage. There is limited data on the genotypic comparison of HEV isolates from sewage water and humans. The aim of this study was to identify genotype and conduct phylogenetic analysis of HEV isolates from sewage water and humans. Materials and Methods: 14 sewage water and 60 serum samples from acute sporadic hepatitis E cases (negative for hepatitis A, B, C) were tested for HEV-RNA by nested polymerase chain reaction (RTnPCR) using primers designed with in RdRp (RNA dependent RNA polymerase) region of open reading frame-1 (ORF-1). Sequencing was done by ABI prism 310. The sequences (343 nucleotides) were compared with each other and were aligned with previously reported HEV sequences obtained from GeneBank, using Clustal W software. A Phylogenetic tree was constructed by using PHYLIP version 3.67 software. Results: HEV-RNA was detected in 49/ 60 (81.67%) serum and 5/14 (35.71%) sewage samples. The sequences obtained from 17 serums and 2 sewage specimens belonged to genotype I with 85% similarity and clustering with previously reported human HEV sequences from India. HEV isolates from human and sewage in North West India are genetically closely related to each other. Conclusion: These finding suggest that sewage acts as reservoir of HEV. Therefore it is important that measures are taken for proper waste disposal and treatment of drinking water to prevent outbreaks and epidemics due to HEV.

Keywords: hepatitis E virus, nested polymerase chain reaction, open reading frame-1, nucleotidies

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Authors: Salah Hadjout, Mohamed Zouidi

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In Algeria, several works carried out in recent years have shown the importance of fusarium head blight in durum wheat. Indeed, this disease is caused by a complex of Fusarium genus pathogens. The research carried out reports that F. culmorum is the main species infecting cereals. These informations motivated our interest in the field evaluation of the behavior of some durum wheat genotypes (parental varieties and lines) with regard to fusarium head blight, mainly caused by four F. culmorum isolates. Our research work focused on following the evolution of symptom development throughout the grain filling, after artificial inoculation of ears by Fusarium isolates in order to establish a first image on the differences in genotype behavior to fusarium haed blight. Field disease assessment criteria are: disease assessment using a grading scale, thousand grain weight measurement and AUDPC. The results obtained revealed that the varieties and lines resulting from crosses had a quite different level of sensitivity to F. culmorum species and no genotype showed complete resistance in our culture conditions. Among the material tested, some lines showed higher resistance than their parents. The results also show a slight behavioral variability also linked to the aggressiveness of the Fusarium species studied in this work. Our results open very important research perspectives on fusarium head blight, in particular the search for toxins produced by Fusarium species.

Keywords: fusarium head blight, durum wheat, Fusarium culmorum, field disease assessment criteria, Algeria

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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

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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)

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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

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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

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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

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Authors: Alieh Farshbaf, Tayyeb Bahrami

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Introduction: Cc-chemokine receptor-5 (CCR5) is known as a main co-receptor in human immunodeficiency virus type-1 (HIV-1) infection. Many studies showed 32bp deletion (Δ32) in CCR5 gene, provide natural resistance to HIV-1 infection in homozygous individuals. Inducing the resistance mechanism by CCR5 in HIV-1 infected patients eliminated many problems of highly-active-anti retroviral therapy (HAART) drugs like as low safety, side-effects and virus rebounding from latent reservoirs. New treatments solved some restrictions that are based on gene modification and cell therapy. Literature review: The stories of the “Berlin and Boston patients” showed autologous hematopoietic stem cells transplantation (HSCT) could provide effective cure of HIV-1 infected patients. Furthermore, gene modification by zinc finger nuclease (ZFN) demonstrated another successful result again. Despite the other studies for gene therapy by ∆32 genotype, there is another mutation -CCR5 ∆32/m303- that provides HIV-1 resistant. It is a heterozygote genotype for ∆32 and T→A point mutation at nucleotide 303. These results approved the key role of CCR5 gene. Conclusion: Recent studies showed immune gene therapy and cell therapy could provide effective cure for refractory disease like as HIV. Eradication of HIV-1 from immune system was not observed by HAART, because of reloading virus genome from latent reservoirs after stopping them. It is showed that CCR5 could induce natural resistant to HIV-1 infection by the new approaches based on stem cell transplantation and gene modifying.

Keywords: CCR5, HIV-1, stem cell, immune gene therapy, gene modification

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Authors: Naser B. Almari, Salem S. Alghamdi, Muhammad Afzal, Mohamed Helmy El Shal

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Wheat landraces are a rich genetic resource for boosting agronomic qualities in breeding programs while also providing diversity and unique adaptation to local environmental conditions. These genotypes have grown increasingly important in the face of recent climate change challenges. This research aimed to look at the genetic diversity of Saudi Durum wheat landraces using morpho-phenological and molecular data. The principal components analysis (PCA) analysis recorded 78.47 % variance and 1.064 eigenvalues for the first six PCs of the total, respectively. The significant characters contributed more to the diversity are the length of owns at the tip relative to the length of the ear, culm: glaucosity of the neck, flag leaf: glaucosity of the sheath, flag leaf: anthocyanin coloration of auricles, plant: frequency of plants with recurved flag leaves, ear: length, and ear: shape in profile in the PC1. The significant wheat genotypes contributed more in the PC1 (8, 14, 497, 650, 569, 590, 594, 598, 600, 601, and 604). The cluster analysis recorded an 85.42 cophenetic correlation among the 22 wheat genotypes and grouped the genotypes into two main groups. Group, I contain 8 genotypes, however, the 2nd group contains 12 wheat genotypes, while two genotypes (13 and 497) are standing alone in the dendrogram and unable to make a group with any one of the genotypes. The second group was subdivided into two subgroups. The genotypes (14, 602, and 600) were present in the second sub-group. The genotypes were grouped into two main groups. The first group contains 17 genotypes, while the second group contains 3 (8, 977, and 594) wheat genotypes. The genotype (602) was standing alone and unable to make a group with any wheat genotype. The genotypes 650 and 13 also stand alone in the first group. Using the Mantel test, the data recorded a significant (R2 = 0.0006) correlation (phenotypic and genetic) among 22 wheat durum genotypes.

Keywords: durum wheat, PCA, cluster analysis, SRAP, genetic diversity

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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

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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

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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

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Authors: Mehmet Demir Kaya, Engin Gökhan Kulan, Onur İleri, Süleyman Avcı

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Due to variation in seed size, shape and oil content of safflower cultivars, germination and emergence performance have been severely influenced by seed characteristics. This study aimed to determine genotypic variation among safflower genotypes for one thousand seed weight, oil content, germination and seed vigor using electrical conductivity (EC) and cold test. In the study, safflower lines ES37-5, ES38-4, ES43-11, ES55-14 and ES58-11 which were developed by single seed selection method, and Dinçer and Remzibey-05 were used as standard varieties. The genotypes were grown under rainfed conditions in Eskişehir, Turkey with four replications. The seeds of each genotype were subjected to standard germination and emergence test at 25°C for 10 days with four replications and 50 seeds per replicate. Electrical conductivity test was performed at 25°C for 24 h to assess the seed vigor. Also, cold test were applied to each safflower genotype at 10°C for 4 days and 25°C for 6 days. Results showed that oil content of the safflower genotypes were different. The highest oil content was determined in ES43-11 with 36.6% while the lowest was 25.9% in ES38-4. Higher germination and emergence rate were obtained from ES55-14 with 96.5% and 73.0%, respectively. There was no significant difference among the safflower genotypes for EC values. Cold test showed that ES43-11 and ES55-14 gave the maximum germination percentages. It was concluded that genotypic factors except for soil and climatic conditions play an important role for determining seed vigor because safflower genotypes grown at the same condition produced various seed vigor values.

Keywords: Carthamus tinctorius L., germination, emergence, cold test, electrical conductivity

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Authors: Christakis Chatzichristou, Elias Kranos

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Architectural awards, especially if they are given by the state, recognize excellence in the field and, at the same time, strongly contribute to the making of the architectural culture of a place. The present research looks at the houses that have been awarded through such a system in Cyprus in order to discuss the values promoted, directly or not, by such a setup which is quite similar to other prestigious award systems such as the Mies van de Rohe Prize in Europe. In fact, many of the projects signed out through the state award system end up being selected to represent the country for the European awards. The residential architecture encouraged by such systems is quite interesting in that the most public of institutions influence how the most private unit of society is architecturally accommodated. The methodology uses both qualitative as well as quantitative research tools in order to analyze: the official state call for entries to the competition; the final report of the evaluation committee; the spatial characteristics of the houses through the Space Syntax methodology; the statements of the architects regarding their intentions and the final outcome; the feelings of the owners and users of the houses regarding the design process as well as the degree of satisfaction regarding the final product. The above-mentioned analyses allow for a more thorough discussion regarding not only the values promoted explicitly by the system through the brief that describes what the evaluation committee is looking for but also the values that are actually being promoted indirectly through the results of the actual evaluation itself. The findings suggest that: the strong emphasis in brief on bioclimatic design and issues of sustainability weakens significantly, if at all present, in the actual selection process; continuous improvement seems to be fuzzily used as a concept; most of the houses tend to have a similar spatial genotype; most of the houses have similar aesthetic qualities; discrepancies between the proposed lifestyle through the design and the actual use of the spaces do not seem to be acknowledged in the evaluation as an issue; the temporal factor seems to be ignored as the projects are required to be ‘finished projects’ as though the users and their needs do not change through time. The research suggests that, rather than preserving a critical attitude regarding the role of the architect in society, the state award system tends, like any other non-reflective social organism, to simply promote its own unexamined values as well as prejudices. This is perhaps more evident in the shared aesthetic character of the awarded houses and less so in the hidden spatial genotype to which they belong. If the design of houses is indeed a great opportunity for architecture to contribute in a more deliberate manner to the evolution of society, then what the present study shows is that this opportunity seems to be largely missed. The findings may serve better less as a verdict and more as a chance for introspection and discussion.

Keywords: award systems, houses, spatial genotype, aesthetic qualities

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Authors: Carlo Stephen O. Moneva, Sharon Rose M. Tabugo

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The present study aims to assess polymorphism in the prolactin (C576A) gene and determine the influence of different prolactin (PRL) genotypes to milk yield performance in crossbred Anglo-Nubian dairy goats raised from Awang, Opol, Misamis Oriental and Talay, Dumaguete City, Negros Oriental. Genomic DNA was extracted from hair follicles and Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for the genotyping of the C576A polymorphism located in exon 5 of goats’ prolactin gene using Eco241 restriction enzyme. Genotypic and allelic frequencies of 0.56 for AA, 0.44 for AB, 0.78 for A, and 0.22 for B were recorded. Observed heterozygosity values were higher than the expected heterozygosity. All populations followed the Hardy–Weinberg principle at p>0.05, except for dairy goats from Farm A located in Opol, Misamis Oriental. A two-way factorial (2 x 4) in a Randomized Complete Block Design was used to be able to evaluate the relationship between genotypes and milk yield performance. PRL genotypes and parity were used as main factors and farm as the blocking factor. AB genotype goats produced significantly higher average daily milk yield and total milk production than AA genotype (p<0.05), an indication that the polymorphism in the caprine PRL (C576A) gene influenced milk yield performance in the population of crossbred Anglo-Nubian goats from Opol, Misamis Oriental and Dumaguete City, Negros Oriental. However, these results have to be validated in other dairy goat breeds.

Keywords: polymorphism, prolactin, milk yield, Anglo-Nubian, PCR-RFLP

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Authors: Rajeev Manhas, M. A. Bhat, A. K. Taku, Dalip Singh, Deep Shikha, Gulzar Bader

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The study was aimed to understand the distribution of various serogroups of Pasteurella multocida in bovines, small ruminants, pig, rabbit, and poultry from Jammu, Jammu and Kashmir and to characterize the isolates with respect to LPS synthesizing genes, dermonecrotic toxin gene (toxA) gene and antibiotic resistance. For isolation, the nasopharyngeal swab procedure appeared to be better than nasal swab procedure, particularly in ovine and swine. Out of 200 samples from different animals, isolation of P. multocida could be achieved from pig and sheep (5 each) and from poultry and buffalo (2 each) samples only, which accounted for 14 isolates. Upon molecular serogrouping, 3 isolates from sheep and 2 isolates from poultry were found as serogroup A, 2 isolates from buffalo were confirmed as serogroup B and 5 isolates from pig were found to belong to serogroup D. However, 2 isolates from sheep could not be typed, hence, untypable. All the 14 isolates were subjected to mPCR genotyping. A total of 10 isolates, 5 each from pig and sheep, generated an amplicon specific to genotype L6 and L6 indicates Heddleston serovars 10, 11, 12 and 15. Similarly, 2 isolates from bovines generated an amplicon of genotype L2 which indicates Heddleston serovar 2/5. However, 2 isolates from poultry generated specific amplicon with L1 signifying Heddleston serovar 1, but these isolates also produced multiple bands with primer L5. Only, one isolate of capsular type A from sheep possessed the structural gene, toxA for dermonecrotoxin. There was variability in the antimicrobial susceptibility pattern in sheep isolates, but overall the rate of tetracycline resistance was relatively high (64.28%) in our strains while all the isolates were sensitive to streptomycin. Except for the swine isolates and one toxigenic sheep isolate, the P. multocida isolates from this study were sensitive to quinolones. Although the level of resistance to commercial antibiotics was generally low, the use of tetracycline and erythromycin was not recommended.

Keywords: antibiogram, genotyping, Pasteurella multocida, serogrouping, toxA

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Authors: Nisha Thapa, Ram Prasad Mainali, Prakriti Chand

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Broadleaf mustard is a commercialized leafy vegetable of Nepal. However, its utilization is hindered in terms of production and productivity due to the high intensity of insects, pests, and diseases causing great loss. The plant protection part of the crop’s disease and damage intensity has not been studied much from research perspectives in Nepal. The research aimed to evaluate broadleaf mustard genotypes for resistance against different diseases. A total of 35 native genotypes of broadleaf mustard were screened at weekly intervals by scoring the plants for ten weeks. Five different diseases, such as Rhizoctonia root rot, Alternaria blight, black rot, turnip mosaic virus disease, and white rust, were reported from the broad leaf mustard genotypes. Out of 35 genotypes, 23 genotypes were found with very high Rhizoctonia Root Rot severity, whereas 8 genotypes showed very high Alternaria blight severity. Likewise, 3 genotypes were found with high Black rot severity, and 1 genotype was found with very high Turnip mosaic virus disease incidence. Similarly, 2 genotypes were found to have very high White rust severity. Among the disease of national importance, Rhizoctonia root rot was found to be the most severe disease with the greatest loss. Broadleaf mustard genotypes like Rato Rayo, CO 1002, and CO 11007 showed average to the high level of field resistance; therefore, these genotypes should be used, conserved, and stored in a mustard improvement program as the disease resistance quality or susceptibility of these genotypes can be helpful for seed producing farmers, companies and other stakeholders through varietal improvement and developmental works that further aids in sustainable disease management of the vegetable.

Keywords: genotype, disease resistance, Rhizoctonia root rot severity, varietal improvement

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Raden Suhartono, Alexander Jayadi Utama, Patrianef Darwis, S. Dwi Anita, Luluk Yunaini, Kemas Dahlan

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Introduction: Vascular endothelial growth factor (VEGF) gene shows association with various angiogenesis conditions including Diabetic Foot Ulcer (DFU) disease. In this study, we performed this study to examine VEGF gene polymorphism associated with DFU. Methods: Case-control study of polymorphism of VEGF gene +405 C>G and -460 T>C, of diabetes mellitus (DM) type 2 with Diabetic Foot Ulcer (DFU) in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. Results: There were 203 patients, 102 patients with DFU and 101 patients without DFU. Forty-nine point 8 percent of total samples is male and 50,2% female with mean age 56,06 years. Distribution of the wild-type genotype VEGF +405 C>G wild type CC was found in 6,9% of respondents, the number of mutant heterozygote CG was 69,5% and mutant homozygote GG was 19,7%. Cumulatively, there were 6,9% wild-type and 85,2% mutant and 3,9% of total blood samples could not be detected on PCR-RFLP. Distribution of VEGF allele +405 C>G C alleles were 43% and G alleles were 57%. Distribution of genotype from VEGF gene -460 T>C is wild type TT 42,9%, mutant heterozygote TC 37,9% and mutant homozygote CC 13,3%. Cumulatively, there were 42,9% wild-type and 51% mutant type. Distribution of VEGF -460 T>C were 62% T allele and 38% C allele. Conclusion: In this study we found the distribution of alleles from VEGF +405 C>G is C 43% and G 57% and from VEGF -460 T>C; T 62% and C 38%. We propose that G allele in VEGF +405 C>G can act as a protective allele and on the other hands T allele in VEGF -460 T>C could be acted as a risk factor for DFU in diabetic patients.

Keywords: diabetic foot ulcer, diabetes mellitus, polymorphism, VEGF

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Authors: Chethan Purushothama

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Coronary artery disease is one of the major causes of death in developing countries. The coronary arteries show wide range of variations and these variations have not been dealt with different population groups. The present study aims to focus on the pattern and variations of coronary artery in south Indian population. The study was performed to analyze the coronary artery dominance and divisions of main trunk of left coronary artery in 81 isolated adult human cadaveric hearts of South Indian population. The specimens were fixed in 10% formalin and were dissected manually. In our specimens, 74.1% of the hearts were right dominant, 11.1% were left dominant, and 14.8% were co-dominant. Bifurcation, trifurcation, and quadrifurcation of main trunk of left coronary artery were seen in 49.4%, 48.1%, and 2.5% cases respectively. The right dominant hearts had bifurcation, trifurcation and quadrifurcation of main trunk of left coronary artery in 46.7%, 50% and 3.3% hearts respectively. The left dominant hearts had bifurcation and trifurcation of main trunk of left coronary artery in 55.6% and 44.4% cases respectively. The co-dominant hearts had bifurcation and trifurcation of main trunk of left coronary artery in 58.3% and 41.7% respectively. Quadrifurcation of main trunk of left coronary artery were seen only in right dominant hearts. We believe that the data obtained from the present study are important to the interventional cardiologists and radiologists. The details obtained will also be helpful for the clinical anatomists.

Keywords: bifurcation, coronary artery, trifurcation, quadrifurcation

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Authors: Aurelien Boutin

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In optical systems such as Variable Optical Delay Lines, where a collimated beam has to go back and forth, corner cubes are used in order to keep the reflected beam parallel to the incoming beam. However, the reflected beam can be laterally shifted, which will lead to losses. In this paper, we report on a patented optical design that allows keeping the reflected beam with the exact same position and direction whatever the displacement of the corner cube leading to zero losses. After explaining how the optical design works and theoretically allows to compensate for any defects in the translation of the corner cube, we will present the results of experimental comparisons between a standard layout (i.e., only corner cubes) and our optical layout. To compare both optical layouts, we used a fiber-to-fiber coupling setup. It consists of a couple of lights from one fiber to the other, thanks to two lenses. The ensemble [fiber+lense] is fixed and called a collimator so that the light is coupled from one collimator to another. Each collimator was precisely made in order to have a precise working distance. In the experiment, we measured and compared the Insertion Losses (IL) variations between both collimators with the distance between them (i.e., natural Gaussian beam coupling losses) and between both collimators in the different optical layouts tested, with the same optical length propagation. We will show that the IL variations of our setup are less than 0.05dB with respect to the IL variations of collimators alone.

Keywords: free-space optics, variable optical delay lines, optical cavity, auto-alignment

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Authors: Ramandeep Kaur, Tarsem Singh Dhillon, Rajinder Kumar Dhall, Ruma Devi

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French bean (Phaseolous vulgaris L.) is an economically potential legume vegetable grown at high altitude (>1000 ft.). More recently, its cultivation in Northern Indian plans is gaining popularity but there is severe reduction in its yield and quality due to low temperature during extreme winter conditions of December-January in open field conditions. Therefore, present study was undertaken to evaluate 29 indeterminate French bean genotypes for various yield and quality traits in poly-net house with the objective to identify best performing genotypes during winter conditions. The significant variation was observed among all the genotypes for all the studied traits. The green pod yield was significantly higher in genotype Lakshmi (992.33 g/plant) followed by Star-I (955.50 g/plant) and FBK-4 (911.17 g/plant). However, the genotypes FBK-10 (105.50 days) and Lakshmi (106.83 days) took least number of days to first harvest and were significantly better than all other genotypes (109.00-136.83 days). The maximum numbers of 10 pickings were recorded in genotype Lakshmi whereas maximum harvesting span as also observed in Lakshmi (60.50 days) which was significantly higher than all other genotypes (31.17-56.50 days). Regarding quality traits, maximum dry matter was observed in FBK-13 (13.87%), protein content in FBK-1 (9.67%), sugar content in FBK-5 (9.60%) and minimum fiber content in FBK-12 (0.69%). It is hereby concluded that high productivity and better quality of French bean (genotypes: Lakshmi, Star-I, FBK-4) was produced in poly-net house conditions of Punjab, India and these pods fetches premium price in the market as there is no availability of green pods at that time in high altitudes. Hence, there is a great scope of cultivation of indeterminate French bean under poly-net house conditions in Punjab.

Keywords: earliness, pod, protected environment, quality, yield

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Authors: K. Ebrahimi, S. Shahid, H. Dehban

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Climate variability can affect surface water quality. The objective of present study is to assess the impacts of climate variability on water quality of Gorganroud River, Iran, over the time period 1971 to 2011. To achieve this aim, climate variability and water quality variations were studied involving a newly developed drought index (MRDI) and hysteresis curves, respectively. The results show that climate variability significantly affected surface water quality over the time. The existence of yearly internal variation and hysteresis phenomenon for pH and EC parameters was observed. It was found that though drought affected pH considerably, it could not affect EC significantly.

Keywords: climate variability, hysteresis curves, multi drought index, water quality

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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