Search results for: genotype frequencies
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1084

Search results for: genotype frequencies

844 The Mechanical Response of a Composite Propellant under Harsh Conditions

Authors: Xin Tong, Jin-sheng Xu, Xiong Chen, Ya Zheng

Abstract:

The aim of this paper is to study the mechanical properties of HTPB (Hydroxyl-terminated polybutadiene) composite propellant under harsh conditions. It describes two tests involving uniaxial tensile tests of various strain rates (ranging from 0.0005 s-1 to 1.5 s-1), temperatures (ranging from 223 K to 343 K) and high-cycle fatigue tests under low-temperature (223 K, frequencies were set at 50, 100, 150 Hz) using DMA (Dynamic Mechanical Analyzer). To highlight the effect of small pre-strain on fatigue properties of HTPB propellant, quasi-static stretching was carried out before fatigue loading, and uniaxial tensile tests at constant strain rates were successively applied. The results reveal that flow stress of propellant increases with reduction in temperature and rise in strain rate, and the strain rate-temperature equivalence relationship could be described by TTSP (time-temperature superposition principle) incorporating a modified WLF equation. Moreover, the rate of performance degradations and damage accumulation of propellant during fatigue tests increased with increasing strain amplitude and loading frequencies, while initial quasi-static loading has a negative effect on fatigue properties by comparing stress-strain relations after fatigue tests.

Keywords: fatigue, HTPB propellant, tensile properties, time-temperature superposition principle

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843 A Comparative Study on ANN, ANFIS and SVM Methods for Computing Resonant Frequency of A-Shaped Compact Microstrip Antennas

Authors: Ahmet Kayabasi, Ali Akdagli

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In this study, three robust predicting methods, namely artificial neural network (ANN), adaptive neuro fuzzy inference system (ANFIS) and support vector machine (SVM) were used for computing the resonant frequency of A-shaped compact microstrip antennas (ACMAs) operating at UHF band. Firstly, the resonant frequencies of 144 ACMAs with various dimensions and electrical parameters were simulated with the help of IE3D™ based on method of moment (MoM). The ANN, ANFIS and SVM models for computing the resonant frequency were then built by considering the simulation data. 124 simulated ACMAs were utilized for training and the remaining 20 ACMAs were used for testing the ANN, ANFIS and SVM models. The performance of the ANN, ANFIS and SVM models are compared in the training and test process. The average percentage errors (APE) regarding the computed resonant frequencies for training of the ANN, ANFIS and SVM were obtained as 0.457%, 0.399% and 0.600%, respectively. The constructed models were then tested and APE values as 0.601% for ANN, 0.744% for ANFIS and 0.623% for SVM were achieved. The results obtained here show that ANN, ANFIS and SVM methods can be successfully applied to compute the resonant frequency of ACMAs, since they are useful and versatile methods that yield accurate results.

Keywords: a-shaped compact microstrip antenna, artificial neural network (ANN), adaptive neuro-fuzzy inference system (ANFIS), support vector machine (SVM)

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842 Application of the Extended Kantorovich Method to Size-Dependent Vibrational Analysis of Fully Clamped Rectangular Micro-Plates

Authors: Amir R. Askari, Masoud Tahani

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The objective of the present paper is to investigate the effect of size on the vibrational behavior of fully clamped rectangular micro-plates based on the modified couple stress theory (MCST). To this end, a size-dependent Kirchhoff plate model is considered and the equation of motion which accounts for the effect of residual and couple stress components is derived using the Hamilton's principle. The eigenvalue problem associated with the free vibrations of fully clamped micro-plates is extracted and solved analytically using the extended Kantorovich method (EKM). The present findings are compared and validated by available results in the literature and an excellent agreement between them is observed. A parametric study is also conducted to show the significant effects of couple stress components on natural frequencies of fully clamped micro-plates. It is found that the ratio of MCST natural frequencies to those obtained by the classical theory (CT) only depends on the Poisson's ratio of the plate and is totally independent of plate's aspect ratio for cases with no residual stresses.

Keywords: vibrational analysis, modified couple stress theory, fully clamped rectangular micro-plates, extended Kantorovich method.

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841 Free Vibration of Axially Functionally Graded Simply Supported Beams Using Differential Transformation Method

Authors: A. Selmi

Abstract:

Free vibration analysis of homogenous and axially functionally graded simply supported beams within the context of Euler-Bernoulli beam theory is presented in this paper. The material properties of the beams are assumed to obey the linear law distribution. The effective elastic modulus of the composite was predicted by using the rule of mixture. Here, the complexities which appear in solving differential equation of transverse vibration of composite beams which limit the analytical solution to some special cases are overcome using a relatively new approach called the Differential Transformation Method. This technique is applied for solving differential equation of transverse vibration of axially functionally graded beams. Natural frequencies and corresponding normalized mode shapes are calculated for different Young’s modulus ratios. MATLAB code is designed to solve the transformed differential equation of the beam. Comparison of the present results with the exact solutions proves the effectiveness, the accuracy, the simplicity, and computational stability of the differential transformation method. The effect of the Young’s modulus ratio on the normalized natural frequencies and mode shapes is found to be very important.

Keywords: differential transformation method, functionally graded material, mode shape, natural frequency

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840 Geo-Spatial Distribution of Radio Refractivity and the Influence of Fade Depth on Microwave Propagation Signals over Nigeria

Authors: Olalekan Lawrence Ojo

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Designing microwave terrestrial propagation networks requires a thorough evaluation of the severity of multipath fading, especially at frequencies below 10 GHz. In nations like Nigeria, without a large enough databases to support the existing empirical models, the mistakes in the prediction technique intended for the evaluation may be severe. The need for higher bandwidth for various satellite applications makes the investigation of the effects of radio refractivity, fading due to multipath, and Geoclimatic factors on satellite propagation links more important. One of the key elements to take into account for the best functioning of microwave frequencies is the clear air effects. This work has taken into account the geographical distribution of radio refractivity and fades depth over a number of stations in Nigeria. Data from five locations in Nigeria—Akure, Enugu, Jos, Minna, and Sokoto—based on five-year (2017–2021) measurement methods of atmospheric pressure, relative, and humidity temperature—at two levels (ground surface and 100 m heights)—are studied to deduced their effects on signals propagated through a µwave communication links. The assessments included considerations for µwave communication systems as well as the impacts of the dry and wet components of radio refractivity, the effects of the fade depth at various frequencies, and a 20 km link distance. The results demonstrate that the percentage occurrence of the dry terms dominated the radio refractivity constituent at the surface level, contributing a minimum of about 78% and a maximum of about 92%, while at heights of 100 meters, the percentage occurrence of the dry terms dominated the radio refractivity constituent, contributing a minimum of about 79% and a maximum of about 92%. The spatial distribution reveals that, regardless of height, the country's tropical rainforest (TRF) and freshwater swampy mangrove (FWSM) regions reported the greatest values of radio refractivity. The statistical estimate shows that fading values can differ by as much as 1.5 dB, especially near the TRF and FWSM coastlines, even during clear air conditions. The current findings will be helpful for budgeting Earth-space microwave links, particularly for the rollout of Nigeria's 5G and 6G projected microcellular networks.

Keywords: fade depth, geoclimatic factor, refractivity, refractivity gradient

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839 Parametric Analysis and Optimal Design of Functionally Graded Plates Using Particle Swarm Optimization Algorithm and a Hybrid Meshless Method

Authors: Foad Nazari, Seyed Mahmood Hosseini, Mohammad Hossein Abolbashari, Mohammad Hassan Abolbashari

Abstract:

The present study is concerned with the optimal design of functionally graded plates using particle swarm optimization (PSO) algorithm. In this study, meshless local Petrov-Galerkin (MLPG) method is employed to obtain the functionally graded (FG) plate’s natural frequencies. Effects of two parameters including thickness to height ratio and volume fraction index on the natural frequencies and total mass of plate are studied by using the MLPG results. Then the first natural frequency of the plate, for different conditions where MLPG data are not available, is predicted by an artificial neural network (ANN) approach which is trained by back-error propagation (BEP) technique. The ANN results show that the predicted data are in good agreement with the actual one. To maximize the first natural frequency and minimize the mass of FG plate simultaneously, the weighted sum optimization approach and PSO algorithm are used. However, the proposed optimization process of this study can provide the designers of FG plates with useful data.

Keywords: optimal design, natural frequency, FG plate, hybrid meshless method, MLPG method, ANN approach, particle swarm optimization

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838 Growth and Yield Potential of Quinoa genotypes on Salt Affected Soils

Authors: Shahzad M. A. Basra, Shahid Iqbal, Irfan Afzal, Hafeez-ur-Rehman

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Quinoa a facultative halophyte crop plant is a new introduction in Pakistan due to its superior nutritional profile and its abiotic stress tolerance, especially against salinity. Present study was conducted to explore halophytic behavior of quinoa. Four quinoa genotypes (A1, A2, A7 and A9) were evaluated against high salinity (control, 100, 200, 300 and 400 mM). Evaluation was made on the basis of ionic analysis (Na+, K+ and K+: Na+ ratio in shoot) and root- shoot fresh and dry weight at four leaf stage. Seedling growth i.e. fresh and dry weight of shoot and root increased by 100 mM salinity and then growth decreased gradually with increasing salinity level in all geno types. Mineral analysis indicated that A2 and A7 have more tolerant behavior having low Na+ and high K+ ¬concentration as compared to A1 and A9. Same geno types as above were also evaluated against high salinity (control, 10, 20, 30, and 40 dS m-1) in pot culture during 2012-13. It was found that increase in salinity up to 10 dS m-1 the plant height, stem diameter and yield related traits increased but decreased with further increase in salinity. Same trend was observed in ionic contents. Maximum grain yield was achieved by A7 (100 g plant-1) followed by A2 (82 g plant-1) at salinity level 10 dS m-1. Next phase was carried out through field settings by using salt tolerant geno types (A2 and A7) at Crop Physiology Research Area Farm (non saline soil as control)/ Proka Farm (salt affected with EC up to 15 dS m-1), University of Agriculture, Faisalabad and Soil Salinity Research Institute, Pindi Bhtiaan (SSRI) Farm (one normal as control and two salt affected fields with EC values up to 15 and 30 dS m-1) during 2013-14. Genotype A7 showed maximum growth and gave maximum yield (3200 kg ha-1) at Proka Farm which was statistically at par to the values of yield obtained on normal soils of Faisalabad. Geno type A7 also gave maximum yield 2800 kg ha-1 on normal field of Pindi bhtiaan followed by as obtained (2340) on salt problem field (15 dS m-1) of same location.

Keywords: quinoa, salinity, halophyte, genotype

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837 Vibration of a Beam on an Elastic Foundation Using the Variational Iteration Method

Authors: Desmond Adair, Kairat Ismailov, Martin Jaeger

Abstract:

Modelling of Timoshenko beams on elastic foundations has been widely used in the analysis of buildings, geotechnical problems, and, railway and aerospace structures. For the elastic foundation, the most widely used models are one-parameter mechanical models or two-parameter models to include continuity and cohesion of typical foundations, with the two-parameter usually considered the better of the two. Knowledge of free vibration characteristics of beams on an elastic foundation is considered necessary for optimal design solutions in many engineering applications, and in this work, the efficient and accurate variational iteration method is developed and used to calculate natural frequencies of a Timoshenko beam on a two-parameter foundation. The variational iteration method is a technique capable of dealing with some linear and non-linear problems in an easy and efficient way. The calculations are compared with those using a finite-element method and other analytical solutions, and it is shown that the results are accurate and are obtained efficiently. It is found that the effect of the presence of the two-parameter foundation is to increase the beam’s natural frequencies and this is thought to be because of the shear-layer stiffness, which has an effect on the elastic stiffness. By setting the two-parameter model’s stiffness parameter to zero, it is possible to obtain a one-parameter foundation model, and so, comparison between the two foundation models is also made.

Keywords: Timoshenko beam, variational iteration method, two-parameter elastic foundation model

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836 SAR and B₁ Considerations for Multi-Nuclear RF Body Coils

Authors: Ria Forner

Abstract:

Introduction: Due to increases in the SNR at 7T and above, it becomes more favourable to make use of X-nuclear imaging. Integrated body coils tuned to 120MHz for 31P, 79MHz for 23Na, and 75 MHz for 13C at 7T were simulated with a human male, female, or child body model to assess strategies of use for metabolic MR imaging in the body. Methods: B1 and SAR efficiencies in the heart, liver, spleen, and kidneys were assessed using numerical simulations over the three frequencies with phase shimming. Results: B1+ efficiency is highly variable over the different organs, particularly for the highest frequency; however, local SAR efficiency remains relatively constant over the frequencies in all subjects. Although the optimal phase settings vary, one generic phase setting can be identified for each frequency at which the penalty in B1+ is at a max of 10%. Discussion: The simulations provide practical strategies for power optimization, B1 management, and maintaining safety. As expected, the B1 field is similar at 75MHz and 79MHz, but reduced at 120MHz. However, the B1 remains relatively constant when normalised by the square root of the peak local SAR. This is in contradiction to generalized SAR considerations of 1H MRI at different field strengths, which is defined by global SAR instead. Conclusion: Although the B1 decreases with frequency, SAR efficiency remains constant throughout the investigated frequency range. It is possible to shim the body coil to obtain a maximum of 10% extra B1+ in a specific organ in a body when compared to a generic setting.

Keywords: birdcage, multi-nuclear, B1 shimming, 7 Tesla MRI, liver, kidneys, heart, spleen

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835 Haplotypes of the Human Leukocyte Antigen-G Different HIV-1 Groups from the Netherlands

Authors: A. Alyami, S. Christmas, K. Neeltje, G. Pollakis, B. Paxton, Z. Al-Bayati

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The Human leukocyte antigen-G (HLA-G) molecule plays an important role in immunomodulation. To date, 16 untranslated regions (UTR) HLA-G haplotypes have been previously defined by sequenced SNPs in the coding region. From these, UTR-1, UTR-2, UTR-3, UTR-4, UTR-5, UTR-6 and UTR-7 are the most frequent 3’UTR haplotypes at the global level. UTR-1 is associated with higher levels of soluble HLA-G and HLA-G expression, whereas UTR-5 and UTR-7 are linked with low levels of soluble HLA-G and HLA-G expression. Human immunodeficiency virus type 1 (HIV-1) infection results in the progressive loss of immune function in infected individuals. The virus escape mechanism typically includes T lymphocytes and NK cell recognition and lyses by classical HLA-A and B down-regulation, which has been associated with non-classical HLA-G molecule up-regulation, respectively. We evaluated the haplotypes of the HLA-G 3′ untranslated region frequencies observed in three HIV-1 groups from the Netherlands and their susceptibility to develop infection. The three groups are made up of mainly men who have sex with men (MSM), injection drug users (IDU) and a high-risk-seronegative (HRSN) group. DNA samples were amplified with published primers prior sequencing. According to our results, the low expresser frequencies show higher in HRSN compared to other groups. This is indicating that 3’UTR polymorphisms may be identified as potential prognostic biomarkers to determine susceptibility to HIV.

Keywords: Human leukocyte antigen-G (HLA-G) , men who have sex with men (MSM), injection drug users (IDU), high-risk-seronegative (HRSN) group, high-untranslated region (UTR)

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834 Design and Implementation of a 94 GHz CMOS Double-Balanced Up-Conversion Mixer for 94 GHz Imaging Radar Sensors

Authors: Yo-Sheng Lin, Run-Chi Liu, Chien-Chu Ji, Chih-Chung Chen, Chien-Chin Wang

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A W-band double-balanced mixer for direct up-conversion using standard 90 nm CMOS technology is reported. The mixer comprises an enhanced double-balanced Gilbert cell with PMOS negative resistance compensation for conversion gain (CG) enhancement and current injection for power consumption reduction and linearity improvement, a Marchand balun for converting the single LO input signal to differential signal, another Marchand balun for converting the differential RF output signal to single signal, and an output buffer amplifier for loading effect suppression, power consumption reduction and CG enhancement. The mixer consumes low power of 6.9 mW and achieves LO-port input reflection coefficient of -17.8~ -38.7 dB and RF-port input reflection coefficient of -16.8~ -27.9 dB for frequencies of 90~100 GHz. The mixer achieves maximum CG of 3.6 dB at 95 GHz, and CG of 2.1±1.5 dB for frequencies of 91.9~99.4 GHz. That is, the corresponding 3 dB CG bandwidth is 7.5 GHz. In addition, the mixer achieves LO-RF isolation of 36.8 dB at 94 GHz. To the authors’ knowledge, the CG, LO-RF isolation and power dissipation results are the best data ever reported for a 94 GHz CMOS/BiCMOS up-conversion mixer.

Keywords: CMOS, W-band, up-conversion mixer, conversion gain, negative resistance compensation, output buffer amplifier

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833 Association of 105A/C IL-18 Gene Single Nucleotide Polymorphism with House Dust Mite Allergy in an Atopic Filipino Population

Authors: Eisha Vienna M. Fernandez, Cristan Q. Cabanilla, Hiyasmin Lim, John Donnie A. Ramos

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Allergy is a multifactorial disease affecting a significant proportion of the population. It is developed through the interaction of allergens and the presence of certain polymorphisms in various susceptibility genes. In this study, the correlation of the 105A/C single nucleotide polymorphism (SNP) of the IL-18 gene and house dust mite-specific IgE among Filipino allergic and non-allergic population was investigated. Atopic status was defined by serum total IgE concentration of ≥100 IU/mL, while house dust mite allergy was defined by specific IgE value ≥ +1SD of IgE of nonatopic participants. Two hundred twenty match-paired Filipino cases and controls aged 6-60 were the subjects of this investigation. The level of total IgE and Specific IgE were measured using Enzyme-Linked Immunosorbent Assay (ELISA) while Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) analysis was used in the SNP detection. Sensitization profiles of the allergic patients revealed that 97.3% were sensitized to Blomia tropicalis, 40.0% to Dermatophagoides farinae, and 29.1% to Dermatophagoides pteronyssinus. Multiple sensitization to HDMs was also observed among the 47.27% of the atopic participants. Any of the allergy classes of the atopic triad were exhibited by the cases (allergic asthma: 48.18%; allergic rhinitis: 62.73%; atopic dermatitis: 19.09%), and two or all of these atopic states are concurrently occurring in 26.36% of the cases. A greater proportion of the atopic participants with allergic asthma and allergic rhinitis were sensitized to D. farinae, and D. pteronyssinus, while more of those with atopic dermatitis were sensitized to D. pteronyssinus than D. farinae. Results show that there is overrepresentation of the allele “A” of the 105A/C IL-18 gene SNP in both cases and control groups of the population. The genotype that predominate the population is the heterozygous “AC”, followed by the homozygous wild “AA”, and the homozygous variant “CC” being the least. The study confirmed a positive association between serum specific IgE against B. tropicalis and D. pteronyssinus and the allele “C” (Bt P=0.021, Dp P=0.027) and “AC” (Bt P=0.003, Dp P=0.026) genotype. Findings also revealed that the genotypes “AA” (OR:1.217; 95% CI: 0.701-2.113) and “CC” (OR, 3.5; 95% CI: 0.727-16.849) increase the risk of developing allergy. This indicates that the 105A/C IL-18 gene SNP is a candidate genetic marker for HDM allergy among Filipino patients.

Keywords: house dust mite allergy, interleukin-18 (IL-18), single nucleotide polymorphism,

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832 A Study of Interleukin-1β Genetic Polymorphisms in Gastric Carcinoma and Colorectal Carcinoma in Egyptian Patients

Authors: Mariam Khaled, Noha Farag, Ghada Mohamed Abdel Salam, Khaled Abu-Aisha, Mohamed El-Azizi

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Gastric and colorectal cancers are among the most frequent causes of cancer-associated mortalities in Africa. They have been considered as a global public health concern, as nearly one million new cases are reported per year. IL-1β is a pro-inflammatory cytokine-produced by activated macrophages and monocytes- and a member of the IL-1 family. The inactive IL-1β precursor is cleaved and activated by caspase-1 enzyme, which itself is activated by the assembly of intracellular structures defined as NLRP3 (Nod Like receptor P3) inflammasomes. Activated IL-1β stimulates the Interleukin-1 receptor type-1 (IL-1R1), which is responsible for the initiation of a signal transduction pathway leading to cell proliferation. It has been proven that the IL-1β gene is a highly polymorphic gene in which single nucleotide polymorphisms (SNPs) may affect its expression. It has been previously reported that SNPs including base transitions between C and T at positions, -511 (C-T; dbSNP: rs16944) and -31 (C-T; dbSNP: rs1143627), from the transcriptional start site, contribute to the pathogenesis of gastric and colorectal cancers by affecting IL-1β levels. Altered production of IL-1β due to such polymorphisms is suspected to stimulate an amplified inflammatory response and promote Epithelial Mesenchymal Transition leading to malignancy. Allele frequency distribution of the IL-1β-31 and -511 SNPs, in different populations, and their correlation to the incidence of gastric and colorectal cancers, has been intriguing to researchers worldwide. The current study aims to investigate allele distributions of the IL-1β SNPs among gastric and colorectal cancers Egyptian patients. In order to achieve to that, 89 Biopsy and surgical specimens from the antrum and corpus mucosa of chronic gastritis subjects and gastric and colorectal carcinoma patients was collected for DNA extraction followed by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR). The amplified PCR products of IL-1β-31C > T and IL-1β-511T > C were digested by incubation with the restriction endonuclease enzymes ALu1 and Ava1. Statistical analysis was carried out to determine the allele frequency distribution in the three studied groups. Also, the effect of the IL-1β -31 and -511 SNPs on nuclear factor binding was analyzed using Fluorescence Electrophoretic Mobility Shift Assay (EMSA), preceded by nuclear factor extraction from gastric and colorectal tissue samples and LPS stimulated monocytes. The results of this study showed that a significantly higher percentage of Egyptian gastric cancer patients have a homozygous CC genotype at the IL-1β-31 position and a heterozygous TC genotype at the IL-1β-511 position. Moreover, a significantly higher percentage of the colorectal cancer patients have a homozygous CC genotype at the IL-1β-31 and -511 positions as compared to the control group. In addition, the EMSA results showed that IL-1β-31C/T and IL-1β-511T/C SNPs do not affect nuclear factor binding. Results of this study suggest that the IL-1β-31 C/T and IL-1β-511 T/C may be correlated to the incidence of gastric cancer in Egyptian patients; however, similar findings couldn’t be proven in the colorectal cancer patients group for the IL-1β-511 T/C SNP. This is the first study to investigate IL-1β -31 and -511 SNPs in the Egyptian population.

Keywords: colorectal cancer, Egyptian patients, gastric cancer, interleukin-1β, single nucleotide polymorphisms

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831 Genetic Diversity of Norovirus Strains in Outpatient Children from Rural Communities of Vhembe District, South Africa, 2014-2015

Authors: Jean Pierre Kabue, Emma Meader, Afsatou Ndama Traore, Paul R. Hunter, Natasha Potgieter

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Norovirus is now considered the most common cause of outbreaks of nonbacterial gastroenteritis. Limited data are available for Norovirus strains in Africa, especially in rural and peri-urban areas. Despite the excessive burden of diarrhea disease in developing countries, Norovirus infections have been to date mostly reported in developed countries. There is a need to investigate intensively the role of viral agents associated with diarrhea in different settings in Africa continent. To determine the prevalence and genetic diversity of Norovirus strains circulating in the rural communities in the Limpopo Province, South Africa and investigate the genetic relationship between Norovirus strains, a cross-sectional study was performed on human stools collected from rural communities. Between July 2014 and April 2015, outpatient children under 5 years of age from rural communities of Vhembe District, South Africa, were recorded for the study. A total of 303 stool specimens were collected from those with diarrhea (n=253) and without (n=50) diarrhea. NoVs were identified using real-time one-step RT-PCR. Partial Sequence analyses were performed to genotype the strains. Phylogenetic analyses were performed to compare identified NoVs genotypes to the worldwide circulating strains. Norovirus detection rate was 41.1% (104/253) in children with diarrhea. There was no significant difference (OR=1.24; 95% CI 0.66-2.33) in Norovirus detection between symptomatic and asymptomatic children. Comparison of the median CT values for NoV in children with diarrhea and without diarrhea revealed significant statistical difference of estimated GII viral load from both groups, with a much higher viral burden in children with diarrhea. To our knowledge, this is the first study reporting on the differences in estimated viral load of GII and GI NoV positive cases and controls. GII.Pe (n=9) were the predominant genotypes followed by GII.Pe/GII.4 Sydney 2012 (n=8) suspected recombinant and GII.4 Sydney 2012 variants(n=7). Two unassigned GII.4 variants and an unusual RdRp genotype GII.P15 were found. With note, the rare GIIP15 identified in this study has a common ancestor with GIIP15 strain from Japan previously reported as GII/untypeable recombinant strain implicated in a gastroenteritis outbreak. To our knowledge, this is the first report of this unusual genotype in the African continent. Though not confirmed predictive of diarrhea disease in this study, the high detection rate of NoV is an indication of subsequent exposure of children from rural communities to enteric pathogens due to poor sanitation and hygiene practices. The results reveal that the difference between asymptomatic and symptomatic children with NoV may possibly be related to the NoV genogroups involved. The findings emphasize NoV genetic diversity and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An uncommon GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe District/South Africa. NoV surveillance is required to help to inform investigations into NoV evolution, and to support vaccine development programmes in Africa.

Keywords: asymptomatic, common, outpatients, norovirus genetic diversity, sporadic gastroenteritis, South African rural communities, symptomatic

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830 Studying the Dynamical Response of Nano-Microelectromechanical Devices for Nanomechanical Testing of Nanostructures

Authors: Mohammad Reza Zamani Kouhpanji

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Characterizing the fatigue and fracture properties of nanostructures is one of the most challenging tasks in nanoscience and nanotechnology due to lack of a MEMS/NEMS device for generating uniform cyclic loadings at high frequencies. Here, the dynamic response of a recently proposed MEMS/NEMS device under different inputs signals is completely investigated. This MEMS/NEMS device is designed and modeled based on the electromagnetic force induced between paired parallel wires carrying electrical currents, known as Ampere’s Force Law (AFL). Since this MEMS/NEMS device only uses two paired wires for actuation part and sensing part, it represents highly sensitive and linear response for nanostructures with any stiffness and shapes (single or arrays of nanowires, nanotubes, nanosheets or nanowalls). In addition to studying the maximum gains at different resonance frequencies of the MEMS/NEMS device, its dynamical responses are investigated for different inputs and nanostructure properties to demonstrate the capability, usability, and reliability of the device for wide range of nanostructures. This MEMS/NEMS device can be readily integrated into SEM/TEM instruments to provide real time study of the fatigue and fracture properties of nanostructures as well as their softening or hardening behaviors, and initiation and/or propagation of nanocracks in them.

Keywords: MEMS/NEMS devices, paired wire actuators and sensors, dynamical response, fatigue and fracture characterization, Ampere’s force law

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829 Screening of Wheat Wild Relatives as a Gene Pool for Improved Photosynthesis in Wheat Breeding

Authors: Amanda J. Burridge, Keith J. Edwards, Paul A. Wilkinson, Tom Batstone, Erik H. Murchie, Lorna McAusland, Ana Elizabete Carmo-Silva, Ivan Jauregui, Tracy Lawson, Silvere R. M. Vialet-Chabrand

Abstract:

The rate of genetic progress in wheat production must be improved to meet global food security targets. However, past selection for domestication traits has reduced the genetic variation in modern wheat cultivars, a fact that could severely limit the future rate of genetic gain. The genetic variation in agronomically important traits for the wild relatives and progenitors of wheat is far greater than that of the current domesticated cultivars, but transferring these traits into modern cultivars is not straightforward. Between the elite cultivars of wheat, photosynthetic capacity is a key trait for which there is limited variation. Early screening of wheat wild relative and progenitors has shown differences in photosynthetic capacity and efficiency not only between wild relative species but marked differences between the accessions of each species. By identifying wild relative accessions with improved photosynthetic traits and characterising the genetic variation responsible, it is possible to incorporate these traits into advanced breeding programmes by wide crossing and introgression programmes. To identify the potential variety of photosynthetic capacity and efficiency available in the secondary and tertiary genepool, a wide scale survey was carried out for over 600 accessions from 80 species including those from the genus Aegilops, Triticum, Thinopyrum, Elymus, and Secale. Genotype data were generated for each accession using a ‘Wheat Wild Relative’ Single Nucleotide Polymorphism (SNP) genotyping array composed of 35,000 SNP markers polymorphic between wild relatives and elite hexaploid wheat. This genotype data was combined with phenotypic measurements such as gas exchange (CO₂, H₂O), chlorophyll fluorescence, growth, morphology, and RuBisCO activity to identify potential breeding material with enhanced photosynthetic capacity and efficiency. The data and associated analysis tools presented here will prove useful to anyone interested in increasing the genetic diversity in hexaploid wheat or the application of complex genotyping data to plant breeding.

Keywords: wheat, wild relatives, pre-breeding, genomics, photosynthesis

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828 Influence of Genotype, Explant, and Hormone Treatment on Agrobacterium-Transformation Success in Salix Callus Culture

Authors: Lukas J. Evans, Danilo D. Fernando

Abstract:

Shrub willows (Salix spp.) have many characteristics which make them suitable for a variety of applications such as riparian zone buffers, environmental contaminant sequestration, living snow fences, and biofuel production. In some cases, these functions are limited due to physical or financial obstacles associated with the number of individuals needed to reasonably satisfy that purpose. One way to increase the efficiency of willows is to bioengineer them with the genetic improvements suitable for the desired use. To accomplish this goal, an optimized in vitro transformation protocol via Agrobacterium tumefaciens is necessary to reliably express genes of interest. Therefore, the aim of this study is to observe the influence of tissue culture with different willow cultivars, hormones, and explants on the percentage of calli expressing reporter gene green florescent protein (GFP) to find ideal transformation conditions. Each callus was produced from 1 month old open-pollinated seedlings of three Salix miyabeana cultivars (‘SX61’, ‘WT1’, and ‘WT2’) from three different explants (lamina, petiole, and internodes). Explants were cultured for 1 month on an MS media with different concentrations of 6-Benzylaminopurine (BAP) and 1-Naphthaleneacetic acid (NAA) (No hormones, 1 mg⁻¹L BAP only, 3 mg⁻¹L NAA only, 1 mg⁻¹L BAP and 3 mg⁻¹L NAA, and 3 mg⁻¹L BAP and 1 mg⁻¹L NAA) to produce a callus. Samples were then treated with Agrobacterium tumefaciens at an OD600 of 0.6-0.8 to insert the transgene GFP for 30 minutes, co-cultivated for 72 hours, and selected on the same media type they were cultured on with added 7.5 mg⁻¹L of Hygromycin for 1 week before GFP visualization under a UV dissecting scope. Percentage of GFP expressing calli as well as the average number of fluorescing GFP units per callus were recorded and results were evaluated through an ANOVA test (α = 0.05). The WT1 internode-derived calli on media with 3 mg-1L NAA+1 mg⁻¹L BAP and mg⁻¹L BAP alone produced a significantly higher percentage of GFP expressing calli than each other group (19.1% and 19.4%, respectively). Additionally, The WT1 internode group cultured with 3 mg⁻¹L NAA+1 mg⁻¹L BAP produced an average of 2.89 GFP units per callus while the group cultivated with 1 mg⁻¹L BAP produced an average of 0.84 GFP units per callus. In conclusion, genotype, explant choice, and hormones all play a significant role in increasing successful transformation in willows. Future studies to produce whole callus GFP expression and subsequent plantlet regeneration are necessary for a complete willow transformation protocol.

Keywords: agrobacterium, callus, Salix, tissue culture

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827 Determination of Phenolic Contents and Antioxidant Activities of Chenopodium quinoa Willd. Seed Extracts

Authors: Nilgün Öztürk, Hakan Sabahtin Ali, Hülya Tuba Kıyan

Abstract:

The genus Chenopodium belongs to Amaranthaceae, is represented by approximately 250 species in the world and 15 species and three subspecies in Turkey. Chenopodium species are traditionally used to treat chest and abdominal pain, shortness of breath, cough and neurological disorders. Chenopodium quinoa Willd. (Quinoa) is native to Andes region of South America (especially Peru and Bolivia) and cultivated in many countries include also Turkey in the world nowadays. The seeds of quinoa are rich in protein, and the phytochemical composition consists of antioxidant substances such as polyphenolic compounds, flavonoids, vitamins, and minerals; anticancer and neuroprotective compounds such as tocotrienols; anti-inflammatory compounds such as carotenoids and anthocyanins and also saponins and starch. Food products of quinoa such as quinoa cereal bar, pasta and cornflakes are used in the diet made during many disorders like obesity, cardiovascular disorder, hypertension and Celiac disease. Also quinoa seems to have antimicrobial, anti-inflammatory and cholesterol-lowering properties because of its bioactive compounds. In this present study, the aqueous ethanolic extracts of the seeds of three different coloured genotypes of quinoa were investigated for their antioxidant activities using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, ferrous ion-chelating effect, ferric-reducing antioxidant power, ABTS radical cation decolorization assays and total phenolic contents using Folin-Ciocalteu assay. Among the three genotypes of quinoa; the aqueous ethanolic extract of the red genotype had the highest total phenolic content (83.54 ± 2.12 mg gallic acid/100 g extract) whereas the extract of the white genotype had the lowest total phenolic content (70.66 ± 0.25 mg gallic acid/100 g). According to the antioxidant activity results; the extracts showed moderate reducing power effect whereas weak ABTS radical cation decolorization and ferrous ion-chelating effect and also too weak DPPH radical scavenging activity when compared to the positive standards.

Keywords: amaranthaceae, antioxidant activity, Chenopodium quinoa willd., total phenolic content

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826 Identification of Mx Gene Polymorphism in Indragiri Hulu duck by PCR-RFLP

Authors: Restu Misrianti

Abstract:

The amino acid variation of Asn (allele A) at position 631 in Mx gene was specific to positive antiviral to avian viral desease. This research was aimed at identifying polymorphism of Mx gene in duck using molecular technique. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique was used to select the genotype of AA, AG and GG. There were thirteen duck from Indragiri Hulu regency (Riau Province) used in this experiment. DNA amplification results showed that the Mx gene in duck is found in a 73 bp fragment. Mx gene in duck did not show any polymorphism. The frequency of the resistant allele (AA) was 0%, while the frequency of the susceptible allele (GG) was 100%.

Keywords: duck, Mx gene, PCR, RFLP

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825 Mackerel (Scomber Australasicus) Reproduction in Northeastern Taiwan

Authors: Sunarti Sinaga, Hsueh-Jung Lu, Jia-Rong Lin

Abstract:

Blue mackerel (Scomber australasicus) is a crucial target species for Taiwan coastal fisheries and has maintained its status as the highest-produced species. Timely measurement of spawning status is crucial for determining the correct management strategy for this species. The objective of this study was to determine size at maturity, fecundity, batch fecundity, and spawning frequency on the basis of samples collected from Nan-Fang-Ao fishing port in Yilan during the spawning season from 2017 to 2019. Histological sections indicated that the blue mackerel are multiple spawners. A higher percentage of female fish spawned at the peak of the gonadosomatic index. The 50% sizes at maturity were 32.02, 32.13, and 29.64 cm. Mean total fecundity (batch fecundity) was 165 (103), 229 (96), and 210 (68) oocytes per ovary-free weight (g) for 2017, 2018, and 2019, respectively; fecundity was determined through observation of postovulatory follicles (POFs). The spawning frequencies (spawning fraction) in 2017, 2018, and 2019 were 3–10 days (0.13), 4–14 days (0.08), and 4–12 days (0.08), respectively. The spawning frequencies determined through the 3 estimated methods, namely the sums of (a) hydrated and Day 0 POFs; (b) Day 1+ POFs, and (c) all data combined, were 1 spawning event per 8, 10, and 9 days, respectively. The reproduction of the blue mackerel was greater in 2017 than it was in 2018 or 2019, as indicated by the higher batch fecundity and shorter spawning seasons. Environmental factors should also be considered as a major factor influencing successful reproduction and the spawning season.

Keywords: scomber australasicus, spawning frequency, batch fecundity, fecundity

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824 Using Coupled Oscillators for Implementing Frequency Diverse Array

Authors: Maryam Hasheminasab, Ahmed Cheldavi, Ahmed Kishk

Abstract:

Frequency-diverse arrays (FDAs) have garnered significant attention from researchers due to their ability to combine frequency diversity with the inherent spatial diversity of an array. The introduction of frequency diversity in FDAs enables the generation of auto-scanning patterns that are range-dependent, which can have advantageous applications in communication and radar systems. However, the main challenge in implementing FDAs lies in determining the technique for distributing frequencies among the array elements. One approach to address this challenge is by utilizing coupled oscillators, which are a technique commonly employed in active microwave theory. Nevertheless, the limited stability range of coupled oscillators poses another obstacle to effectively utilizing this technique. In this paper, we explore the possibility of employing a coupled oscillator array in the mode lock state (MLS) for implementing frequency distribution in FDAs. Additionally, we propose and simulate the use of a digital phase-locked loop (DPLL) as a backup technique to stabilize the oscillators. Through simulations, we validate the functionality of this technique. This technique holds great promise for advancing the implementation of phased arrays and overcoming current scan rate and phase shifter limitations, especially in millimeter wave frequencies.

Keywords: angle-changing rate, auto scanning beam, pull-in range, hold-in range, locking range, mode locked state, frequency locked state

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823 Microwave Dielectric Properties and Microstructures of Nd(Ti₀.₅W₀.₅)O₄ Ceramics for Application in Wireless Gas Sensors

Authors: Yih-Chien Chen, Yue-Xuan Du, Min-Zhe Weng

Abstract:

Carbon monoxide is a substance produced by the incomplete combustion. It is toxic even at concentrations of less than 100ppm. Since it is colorless and odorless, it is difficult to detect. CO sensors have been developed using a variety of physical mechanisms, including semiconductor oxides, solid electrolytes, and organic semiconductors. Many works have focused on using semiconducting sensors composed of sensitive layers such as ZnO, TiO₂, and NiO with high sensitivity for gases. However, these sensors working at high temperatures increased their power consumption. On the other hand, the dielectric resonator (DR) is attractive for gas detection due to its large surface area and sensitivity for external environments. Materials that are to be employed in sensing devices must have a high-quality factor. Numerous researches into the fergusonite-type structure and related ceramic systems have explored. Extensive research into RENbO₄ ceramics has explored their potential application in resonators, filters, and antennas in modern communication systems, which are operated at microwave frequencies. Nd(Ti₀.₅W₀.₅)O₄ ceramics were synthesized herein using the conventional mixed-oxide method. The Nd(Ti₀.₅W₀.₅)O₄ ceramics were prepared using the conventional solid-state method. Dielectric constants (εᵣ) of 15.4-19.4 and quality factor (Q×f) of 3,600-11,100 GHz were obtained at sintering temperatures in the range 1425-1525°C for 4 h. The dielectric properties of the Nd(Ti₀.₅W₀.₅)O₄ ceramics at microwave frequencies were found to vary with the sintering temperature. For a further understanding of these microwave dielectric properties, they were analyzed by densification, X-ray diffraction (XRD), and by making microstructural observations.

Keywords: dielectric constant, dielectric resonators, sensors, quality factor

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822 A Broadband Tri-Cantilever Vibration Energy Harvester with Magnetic Oscillator

Authors: Xiaobo Rui, Zhoumo Zeng, Yibo Li

Abstract:

A novel tri-cantilever energy harvester with magnetic oscillator was presented, which could convert the ambient vibration into electrical energy to power the low-power devices such as wireless sensor networks. The most common way to harvest vibration energy is based on the use of linear resonant devices such as cantilever beam, since this structure creates the highest strain for a given force. The highest efficiency will be achieved when the resonance frequency of the harvester matches the vibration frequency. The limitation of the structure is the narrow effective bandwidth. To overcome this limitation, this article introduces a broadband tri-cantilever harvester with nonlinear stiffness. This energy harvester typically consists of three thin cantilever beams vertically arranged with Neodymium Magnets ( NdFeB)magnetics at its free end and a fixed base at the other end. The three cantilevers have different resonant frequencies by designed in different thicknesses. It is obviously that a similar advantage of multiple resonant frequencies as piezoelectric cantilevers array structure is built. To achieve broadband energy harvesting, magnetic interaction is used to introduce the nonlinear system stiffness to tune the resonant frequency to match the excitation. Since the three cantilever tips are all free and the magnetic force is distance dependent, the resonant frequencies will be complexly changed with the vertical vibration of the free end. Both model and experiment are built. The electromechanically coupled lumped-parameter model is presented. An electromechanical formulation and analytical expressions for the coupled nonlinear vibration response and voltage response are given. The entire structure is fabricated and mechanically attached to a electromagnetic shaker as a vibrating body via the fixed base, in order to couple the vibrations to the cantilever. The cantilevers are bonded with piezoelectric macro-fiber composite (MFC) materials (Model: M8514P2). The size of the cantilevers is 120*20mm2 and the thicknesses are separately 1mm, 0.8mm, 0.6mm. The prototype generator has a measured performance of 160.98 mW effective electrical power and 7.93 DC output voltage via the excitation level of 10m/s2. The 130% increase in the operating bandwidth is achieved. This device is promising to support low-power devices, peer-to-peer wireless nodes, and small-scale wireless sensor networks in ambient vibration environment.

Keywords: tri-cantilever, ambient vibration, energy harvesting, magnetic oscillator

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821 Study on the Post-Traumatic Stress Disorder and Its Psycho-Social-Genetic Risk Factors among Tibetan Alolescents in Heavily-Hit Area Three Years after Yushu Earthquake in Qinghai Province, China

Authors: Xiaolian Jiang, Dongling Liu, Kun Liu

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Aims: To examine the prevalence of POST-TRAUMATIC STRESS DISORDER (PTSD) symptoms among Tibetan adolescents in heavily-hit disaster area three years after Yushu earthquake, and to explore the interactions of the psycho-social-genetic risk factors. Methods: This was a three-stage study. Firstly, demographic variables,PTSD Checklist-Civilian Version (PCL-C),the Internality、Powerful other、Chance Scale,(IPC),Coping Style Scale(CSS),and the Social Support Appraisal(SSA)were used to explore the psychosocial factors of PTSD symptoms among adolescent survivors. PCL-C was used to examine the PTSD symptoms among 4072 Tibetan adolescents,and the Structured Clinical Interview for DSM-IV Disorders(SCID)was used by psychiatrists to make the diagnosis precisely. Secondly,a case-control trial was used to explore the relationship between PTSD and gene polymorphisms. 287adolescents diagnosed with PTSD were recruited in study group, and 280 adolescents without PTSD in control group. Polymerase chain reaction-restriction fragment length polymorphism technology(PCR-RFLP)was used to test gene polymorphisms. Thirdly,SPSS 22.0 was used to explore the interactions of the psycho-social-genetic risk factors of PTSD on the basis of the above results. Results and conclusions: 1.The prevalence of PTSD was 9.70%. 2.The predictive psychosocial factors of PTSD included earthquake exposure, support from others, imagine, abreact, tolerant, powerful others and family support. 3.Synergistic interactions between A1 gene of DRD2 TaqIA and the external locus of control, negative coping style, severe earthquake exposure were found. Antagonism interactions between A1 gene of DRD2 TaqIA and poor social support was found. Synergistic interactions between A1/A1 genotype and the external locus of control, negative coping style were found. Synergistic interactions between 12 gene of 5-HTTVNTR and the external locus of control, negative coping style, severe earthquake exposure were found. Synergistic interactions between 12/12 genotype and the external locus of control, negative coping style, severe earthquake exposure were also found.

Keywords: adolescents, earthquake, PTSD, risk factors

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820 Cleaning Performance of High-Frequency, High-Intensity 360 kHz Frequency Operating in Thickness Mode Transducers

Authors: R. Vetrimurugan, Terry Lim, M. J. Goodson, R. Nagarajan

Abstract:

This study investigates the cleaning performance of high intensity 360 kHz frequency on the removal of nano-dimensional and sub-micron particles from various surfaces, uniformity of the cleaning tank and run to run variation of cleaning process. The uniformity of the cleaning tank was measured by two different methods i.e 1. ppbTM meter and 2. Liquid Particle Counting (LPC) technique. In the second method, aluminium metal spacer components was placed at various locations of the cleaning tank (such as centre, top left corner, bottom left corner, top right corner, bottom right corner) and the resultant particles removed by 360 kHz frequency was measured. The result indicates that the energy was distributed more uniformly throughout the entire cleaning vessel even at the corners and edges of the tank when megasonic sweeping technology is applied. The result also shows that rinsing the parts with 360 kHz frequency at final rinse gives lower particle counts, hence higher cleaning efficiency as compared to other frequencies. When megasonic sweeping technology is applied each piezoelectric transducers will operate at their optimum resonant frequency and generates stronger acoustic cavitational force and higher acoustic streaming velocity. These combined forces are helping to enhance the particle removal and at the same time improve the overall cleaning performance. The multiple extractions study was also carried out for various frequencies to measure the cleaning potential and asymptote value.

Keywords: power distribution, megasonic sweeping, cavitation intensity, particle removal, laser particle counting, nano, submicron

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819 Magnetic and Optical Properties of GaFeMnN

Authors: A.Abbad, H.A.Bentounes, W.Benstaali

Abstract:

The full-potential linearized augmented plane wave method (FP-LAPW) within the Generalized Gradient Approximation (GGA) is used to calculate the magnetic and optical properties of quaternary GaFeMnN. The results show that the compound becomes magnetic and half metallic and there is an apparition of peaks at low frequencies for the optical properties.

Keywords: FP-LAPW, LSDA, magnetic moment, reflectivity

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818 Morphological Parameters and Selection of Turkish Edible Seed Pumpkins (Cucurbita pepo L.) Germplasm

Authors: Onder Turkmen, Musa Seymen, Sali Fidan, Mustafa Paksoy

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There is a requirement for registered edible seed pumpkin suitable for eating in Turkey. A total of 81 genotypes collected from the researchers in 2005 originated from Eskisehir, Konya, Nevsehir, Tekirdag, Sakarya, Kayseri and Kirsehir provinces were utilized. The used genetic materials were brought to S5 generation by the research groups among 2006 and 2010 years. In this research, S5 stage reached in the genotype given some of the morphological features, and selection of promising genotypes generated scale were made. Results showed that the A-1 (420), A-7 (410), A-8 (420), A-32 (420), B-17 (410), B-24 (410), B-25 (420), B-33 (400), C-24 (420), C-25 (410), C-26 (410) and C-30 (420) genotypes are expected to be promising varieties.

Keywords: candidate cultivar, edible seed pumpkin, morphologic parameters, selection

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817 Theoretical-Experimental Investigations on Free Vibration of Glass Fiber/Polyester Composite Conical Shells Containing Fluid

Authors: Tran Ich Thinh, Nguyen Manh Cuong

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Free vibrations of partial fluid-filled composite truncated conical shells are investigated using the Dynamic Stiffness Method (DSM) or Continuous Element Method (CEM) based on the First Order Shear Deformation Theory (FSDT) and non-viscous incompressible fluid equations. Numerical examples are given for analyzing natural frequencies and harmonic responses of clamped-free conical shells partially and completely filled with fluid. To compare with the theoretical results, detailed experimental results have been obtained on the free vibration of a clamped-free conical shells partially filled with water by using a multi-vibration measuring machine (DEWEBOOK-DASYLab 5.61.10). Three glass fiber/polyester composite truncated cones with the radius of the larger end 285 mm, thickness 2 mm, and the cone lengths along the generators are 285 mm, 427.5 mm and 570 mm with the semi-vertex angles 27, 14 and 9 degrees respectively were used, and the filling ratio of the contained water was 0, 0.25, 0.50, 0.75 and 1.0. The results calculated by proposed computational model for studied composite conical shells are in good agreement with experiments. Obtained results indicate that the fluid filling can reduce significantly the natural frequencies of composite conical shells. Parametric studies including circumferential wave number, fluid depth and cone angles are carried out.

Keywords: dynamic stiffness method, experimental study, free vibration, fluid-shell interaction, glass fiber/polyester composite conical shell

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816 Computational Investigation on Structural and Functional Impact of Oncogenes and Tumor Suppressor Genes on Cancer

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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815 Halogenated Methoxy- and Methyl-benzoic Acids: Joint Experimental and DFT Study For Molecular Structure, Vibrational Analysis, and Other Molecular Properties

Authors: Boda Sreenivas, Lyathakula Ravindranath, Kanugula Srishailam, Byru Venkatram Reddy

Abstract:

Extensive research into the optimized structure and molecular properties of 3-Flouro-2-methylbenzoicacid(FMB), 3-Chloro-2-methoxybenzoicacid (CMB), and 3-Bromo-2-methylbenzoicacid (BMB) was carried out using FT-IR, FT-Raman and UV-Visible spectra, as well as theoretically using the DFT approach with B3LYPfunctional in conjunction with 6-311++G(d,p) basis set. The optimized structure was determined by evaluating torsional scans about free rotation bonds. Structure parameters, harmonic vibrational frequencies, potential energy distribution(PED), and infrared and Raman intensities were computed. The computational results from the DFT approach, such asFT-IR, FT-Raman, and UV-Visible spectra, were compared with the experimental results and found good agreement. Observed and calculated frequencies agreed with an rms error of 8.42, 6.60, and 6.95 cm-1 for FMB, CMB, and BMB, respectively. Unambiguous vibrational assignments were made for all fundamentals using PED and eigenvectors. The electronic HOMO-LUMO, H-bonding, and strong conjugative interactions across different molecular entities are discussed using experimental and simulated Ultraviolet-Visible spectra. The title molecules' molecular properties such as dipole moment, mean polarizability, and first-order hyperpolarizability, were calculated to study their non-linear optical (NLO) behavior. The chemical reactivity descriptors and mapped electrostatic surface potential (MESP) were also evaluated. Natural bond orbital (NBO) analysis was used to examine the stability of molecules resulting from hyperconjugative interactions and charge delocalization.

Keywords: ftir/raman spectra, DFT, NLO, homo-lumo, NBO, halogenated benzoic acids

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