Search results for: genotype variations

Authors: S. Mohamed, D. Gonzalez, C. Sayada, P. Halfon

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Drug resistance mutations are routinely detected using standard Sanger sequencing, which does not detect minor variants with a frequency below 20%. The impact of detecting minor variants generated by ultra-deep sequencing (UDS) on HIV drug-resistance (DR) interpretations has not yet been studied. Fifty HIV-1 patients who experienced virological failure were included in this retrospective study. The HIV-1 UDS protocol allowed the detection and quantification of HIV-1 protease and reverse transcriptase variants related to genotypes A, B, C, E, F, and G. DeepChek®-HIV simplified DR interpretation software was used to compare Sanger sequencing and UDS. The total time required for the UDS protocol was found to be approximately three times longer than Sanger sequencing with equivalent reagent costs. UDS detected all of the mutations found by population sequencing and identified additional resistance variants in all patients. An analysis of DR revealed a total of 643 and 224 clinically relevant mutations by UDS and Sanger sequencing, respectively. Three resistance mutations with > 20% prevalence were detected solely by UDS: A98S (23%), E138A (21%) and V179I (25%). A significant difference in the DR interpretations for 19 antiretroviral drugs was observed between the UDS and Sanger sequencing methods. Y181C and T215Y were the most frequent mutations associated with interpretation differences. A combination of UDS and DeepChek® software for the interpretation of DR results would help clinicians provide suitable treatments. A cut-off of 1% allowed a better characterisation of the viral population by identifying additional resistance mutations and improving the DR interpretation.

Keywords: HIV-1, ultra-deep sequencing, Sanger sequencing, drug resistance

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Authors: Sakshi Dhumale, Madhushree C., Amba Shetty

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The effect of station density on the geostatistical prediction of groundwater levels is of critical importance to ensure accurate and reliable predictions. Monitoring station density directly impacts the accuracy and reliability of geostatistical predictions by influencing the model's ability to capture localized variations and small-scale features in groundwater levels. This is particularly crucial in regions with complex hydrogeological conditions and significant spatial heterogeneity. Insufficient station density can result in larger prediction uncertainties, as the model may struggle to adequately represent the spatial variability and correlation patterns of the data. On the other hand, an optimal distribution of monitoring stations enables effective coverage of the study area and captures the spatial variability of groundwater levels more comprehensively. In this study, we investigate the effect of station density on the predictive performance of groundwater levels using the geostatistical technique of Ordinary Kriging. The research utilizes groundwater level data collected from 121 observation wells within the semi-arid Berambadi watershed, gathered over a six-year period (2010-2015) from the Indian Institute of Science (IISc), Bengaluru. The dataset is partitioned into seven subsets representing varying sampling densities, ranging from 15% (12 wells) to 100% (121 wells) of the total well network. The results obtained from different monitoring networks are compared against the existing groundwater monitoring network established by the Central Ground Water Board (CGWB). The findings of this study demonstrate that higher station densities significantly enhance the accuracy of geostatistical predictions for groundwater levels. The increased number of monitoring stations enables improved interpolation accuracy and captures finer-scale variations in groundwater levels. These results shed light on the relationship between station density and the geostatistical prediction of groundwater levels, emphasizing the importance of appropriate station densities to ensure accurate and reliable predictions. The insights gained from this study have practical implications for designing and optimizing monitoring networks, facilitating effective groundwater level assessments, and enabling sustainable management of groundwater resources.

Keywords: station density, geostatistical prediction, groundwater levels, monitoring networks, interpolation accuracy, spatial variability

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Patrianef Darwis, Alexander Jayadi Utama, Raden Suhartono, D. Suryandari, Luluk Yunaini, Tom Ch Adriani

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Objective: Diabetic Foot Ulcer (DFU) is one of the complications of Type 2 Diabetes Mellitus (T2DM) that can lead to disability and death. Inadequate vascularization condition will affect healing process of DFU. Therefore, we investigated the expression of polymorphism TGF- β1 in the relation of the occurrence of DFU in T2DM. Methods: We designed a case-control study to investigate the polymorphism TGF- β1 gene 1800469 C > T and 1982073 C > T in T2DM in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. We used PCR techniques and compared the results in a group of T2DM patients with DFU as the case study and without DFU as the control group. Results: There were 203 patients, 102 patients with DFU and 101 patients control without DFU. 49,8% is male and 50,2% female with mean age about 56 years. Distribution of wild-type genotype TGF-B1 1800469 C > T wild type CC was found in 44,8%, the number of mutant heterozygote CT was 10,8% and mutant homozygote is 11,3%. Distribution of TGF-B1 1982073 C>T wild type CC was 32,5%, mutant heterozygote is 38,9% and mutant homozygote 25,1%. Conclusion: Distribution of alleles from TGF-B1 1800469 C > T is C 75% and T 25% and from TGF-B1 1982073 C > T is C53,8% and T 46,2%. In the other word polymorphism TGF- β1 plays a role in the occurrence and healing process of the DFU in T2DM patients.

Keywords: diabetic foot ulcers, diabetes mellitus, polymorphism, TGF-β1

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Authors: Wonil Nam, Xiang Ren, Inyoung Kim, Masoud Agah, Wei Zhou

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Despite its ultrasensitive detection capability, surface-enhanced Raman spectroscopy (SERS) faces challenges as a quantitative biochemical analysis tool due to the significant dependence of local field intensity in hotspots on nanoscale geometric variations of plasmonic nanostructures. Therefore, despite enormous progress in plasmonic nanoengineering of high-performance SERS devices, it is still challenging to quantitatively correlate the measured SERS signals with the actual molecule concentrations at hotspots. A significant effort has been devoted to developing SERS calibration methods by introducing internal standards. It has been achieved by placing Raman tags at plasmonic hotspots. Raman tags undergo similar SERS enhancement at the same hotspots, and ratiometric SERS signals for analytes of interest can be generated with reduced dependence on geometrical variations. However, using Raman tags still faces challenges for real-world applications, including spatial competition between the analyte and tags in hotspots, spectral interference, laser-induced degradation/desorption due to plasmon-enhanced photochemical/photothermal effects. We show that electronic Raman scattering (ERS) signals from metallic nanostructures at hotspots can serve as the internal calibration standard to enable quantitative SERS analysis and improve biostatistical analysis. We perform SERS with Au-SiO₂ multilayered metal-insulator-metal nano laminated plasmonic nanostructures. Since the ERS signal is proportional to the volume density of electron-hole occupation in hotspots, the ERS signals exponentially increase when the wavenumber is approaching the zero value. By a long-pass filter, generally used in backscattered SERS configurations, to chop the ERS background continuum, we can observe an ERS pseudo-peak, IERS. Both ERS and SERS processes experience the |E|⁴ local enhancements during the excitation and inelastic scattering transitions. We calibrated IMRS of 10 μM Rhodamine 6G in solution by IERS. The results show that ERS calibration generates a new analytical value, ISERS/IERS, insensitive to variations from different hotspots and thus can quantitatively reflect the molecular concentration information. Given the calibration capability of ERS signals, we performed label-free SERS analysis of living biological systems using four different breast normal and cancer cell lines cultured on nano-laminated SERS devices. 2D Raman mapping over 100 μm × 100 μm, containing several cells, was conducted. The SERS spectra were subsequently analyzed by multivariate analysis using partial least square discriminant analysis. Remarkably, after ERS calibration, MCF-10A and MCF-7 cells are further separated while the two triple-negative breast cancer cells (MDA-MB-231 and HCC-1806) are more overlapped, in good agreement with the well-known cancer categorization regarding the degree of malignancy. To assess the strength of ERS calibration, we further carried out a drug efficacy study using MDA-MB-231 and different concentrations of anti-cancer drug paclitaxel (PTX). After ERS calibration, we can more clearly segregate the control/low-dosage groups (0 and 1.5 nM), the middle-dosage group (5 nM), and the group treated with half-maximal inhibitory concentration (IC50, 15 nM). Therefore, we envision that ERS calibrated SERS can find crucial opportunities in label-free molecular profiling of complicated biological systems.

Keywords: cancer cell drug efficacy, plasmonics, surface-enhanced Raman spectroscopy (SERS), SERS calibration

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Authors: Irina S. Burashnikova, Dmitriy A. Sychev, Ruslan Y. Kazakov

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Сytochrome P450 CYP2D6 activity affects antipsychotic therapy safety. CYP2D6*4 polymorphism frequency varies among different ethnic groups. We studied CYP2D6*4 polymorphism frequency in Tatar and Russian schizophrenic patients and association of CYP2D6*4 polymorphism and extrapyramidal disorders (EPD) frequency in schizophrenic patients on haloperidol monotherapy in daily doses up to 20 mg. Results: Heterozygous CYP2D6*4 allele carrier frequency among Tatars was lower (23.8% vs 32.4% in Russians), but the differences did not reach statistical significance. CYP2D6*4 allele frequency among Tatars was also lower (11.9% vs 24.3% in Russians), but the difference was not quite significant (p=0.0592). Average daily haloperidol dose in the group without EPD was significantly higher than in the group with EPD (11.35±4.6 vs 13.87±3.3 mg, p=0.0252), but average daily haloperidol dose/weight ratios in the compared groups had no significant differences. Statistically significant association between EPD development and heterozygous CYP2D6*1/*4 genotype and CYP2D6*4 allele carrier frequency was revealed among all schizophrenic patients and among those of Tatar nationality. Further well designed pharmacogenetic studies in different Russian regions are needed to improve psychotropic therapy safety and to establish evidence-based indications for pharmacogenetic testing in clinical practice.

Keywords: antipsychotic, CYP2D6 polymorphism, ethnic differences of CYP2D6*4 allele frequency, extrapyramidal side effects/disorder, schizophrenia, pharmacogenetics, Russians, Tatars

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Authors: Sadeq Al Yaari, Muhammad Alkhunayn, Adham Al Yaari, Montaha Al Yaari, Ayman Al Yaari, Aayah Al Yaari, Sajedah Al Yaari, Fatehi Eissa

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Introduction: Like many dialects, the Arabic dialect of Yemen (ADY) exhibited utterance phonemic distinction- vowel deletion, lengthening, and insertion- that were investigated using speakers from different dialectal backgrounds, with particular focus on the difference typically developing and achieving speakers and those suffering linguistic problems make. Phonological variations were found to be inevitable, suggesting further investigation of consonants to see to what extent they are prone to such phonemic changes. This study investigates the patterns of consonant substitution in ADY by examining if there is a clear-cut line between normal and pathological consonants to decide which of these consonants is substituted more. Methods: A total of hundred and twenty nine Yemeni male participants (age= 6-13) were enrolled in this study. Participants were preassigned into two groups (Articulation disorders (AD) group= 42 and typically developing and achieving group (TD) = 70), each of which consists of five sub-groups in decided sociolinguistic classification. In a 45 minute-session, 180 pictures of commonly used verbs (4 pics/m.) were presented to participants who were asked to impulsively describe these verbs before their production was psychoneurolinguistically and statistically analyzed. Results: There was a pattern of consonant substitution in some dialects that participants from both groups have in common: Voiceless consonants (/t/, /ṣ/,/s/, /ḥ, /k/, /ʃ/, /f//, and /k/) in northern and eastern dialects; voiced consonants (/q/, /gh/, /Ʒ/, /g/,/ḍ/, /b/, and /d/) in southern, eastern, western and central dialects; and voiceless and voiced consonants(/t/, /f/, /Ø/, /ṣ/, /s/, /q/, /gh/, /Ʒ/, /g/,/ḍ/, and /b/) in southern dialect. Voiceless consonants (/t/, /ṣ/,/s/, /ḥ, /k/, /ʃ/, /f//, /Ø/and /k/) found to be substituted more by ADY speakers of both AD and TD groups followed by voiced consonants (/q/, /gh/, /Ʒ/, /g/,/ḍ/,/d/ /b/, and /ð/), nasals (/m/, /n/), mute (/h/), semi-vowels (/w/ and /j/) and laterals (/l/ and /r/). Unexpectedly, a short vowel (/æ/) and two long vowels (/u: and /a:/) were found to substitute consonants in ADY both by AD and TD participants. Conclusions: AD and TD participants of ADY substitute consonants in their dialectal speech. Consonant substitution processes cover not only consonants but extend to include monophthongs. The finding that speakers of ADY substitute consonants in multisyllabic words is probably due to the fact that the sociolinguistic factor plays a pivotal role in the problematic substitution of consonants in ADY speakers. Larger longitudinal studies are necessary to further investigate the effect of sociolinguistic background on phonological variations, notably sound change in the speech of Yemeni TD speakers compared to those with linguistic impairments.

Keywords: consonant substitution, Arabic dialect of Yemen, phonetics, phonology, syllables, articulation disorders

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Authors: Andrey Lebedev, Ilya Dmitrenok, JooYoung Lee, Leonard Johard

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Top-k shortest path routing problem is an extension of finding the shortest path in a given network. Shortest path is one of the most essential measures as it reveals the relations between two nodes in a network. However, in many real world networks, whose diameters are small, top-k shortest path is more interesting as it contains more information about the network topology. Many variations to compute top-k shortest paths have been studied. In this paper, we apply an efficient top-k shortest distance routing algorithm to the link prediction problem and test its efficacy. We compare the results with other base line and state-of-the-art methods as well as with the shortest path. Then, we also propose a top-k distance based graph matching algorithm.

Keywords: graph matching, link prediction, shortest path, similarity

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Authors: T. Manzur, S. Iffat, M. A. Noor

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In this paper, relationship between different properties of IC concrete and water cement ratio, obtained from a comprehensive experiment conducted on IC using local materials (Burnt clay chips- BC) is presented. In addition, saturated SAP was used as an IC material in some cases. Relationships have been developed through regression analysis. The focus of this analysis is on developing relationship between a dependent variable and an independent variable. Different percent replacements of BC and water cement ratios were used. Compressive strength, modulus of elasticity, water permeability and chloride permeability were tested and variations of these parameters were analyzed with respect to water cement ratio.

Keywords: compressive strength, concrete, curing, lightweight, aggregate, superabsorbent polymer, internal curing

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Authors: Alisha Akya, Afsaneh salami

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Background and Objective: Pseudomonas aeruginosa is an opportunistic pathogen associated with nosocomial infections. One of the major concerns for the treatment of P. aeruginosa infections is its resistant to a variety of antibiotics. The purpose of this study was to assess the dissemination of p. aeruginosa isolates obtained from major hospitals in Kermanshah, west of Iran. Materials and Methods: Antibiotic susceptibility testing was performed using the minimal inhibitory concentrations. Mettalo-beta-lactamase was investigated using the double disk diffusion (DDST) test and PCR. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE). Results: The 60 P. aeruginosa isolates, 30 (50%) were resistant to gentamicin, 38 (63/3%) to piperacilin, 42 (70%) to ceftazidime, and 45 (75%) to cefepime. Twenty-nine (48/3%) isolates were MBLs producer based on the DDST test. Five (8/3%) isolates were positive for VIM gene and 4 of them were from burn specimens. PFGE analysis among MBLs producers revealed 12 distinct genotype patterns. A pattern covering the highest number of strains was determined as the dominant clone. Conclusions: Our study showed that P. aeruginosa strains can be spread between patients in hospitals or acquired from different environmental sources. P. aeruginosa isolates were highly resistant to antibiotics and, therefore, the susceptibility of isolates to antibiotics should be tested before treatment. Given the clinical significance of MBLs producing isolates, identification of these organisms is essential in the hospitals in order to get a better therapeutic response and control of bacterial dissemination.

Keywords: clonal dissemination, mettalo-beta-lactamase, Pseudomonas aeruginosa, PFGE

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Authors: Zunnu Raen Akhtar, Haseeb Jan, Muhammad Latif, Ali Aziz, Ali Akash, Waleed Afzal Naveed, Muhammad Naveed Akhtar

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Wheat (Triticum aestivium) is main staple food crop of Pakistan. This crop is highly infested with aphids which cause the loss of yield. A study was carried out at Entomological Research Institute of Ayub Agriculture Research Institute Faisalabad during 2015-16. Eleven wheat genotypes (FSD- 08, v-11098, NIBGE gandum-3, shafaq 2006, v-13372, Punjab-2011, v-12304, 11C023, v-13005, v-13016, v-12120) were sown using the Randomized Complete Block Design in the research area of Entomological Research Institute Faisalabad during the year 2015-16. The aphid infestation per tiller on each genotype was observed from the first week of January till the third week of March maximum. The results reveal that shafaq 2006 and V-12120 were found more susceptible with 10.22 and 9.90 aphids per tiller and minimum infestation was observed on the Punjab-2011 and 11C023 i.e., 5.72 and 5.99 aphid per tiller respectively. When the peak season observations were analyzed, slight changes occur in the peak population of aphid among all wheat genotypes. The most susceptible genotypes were Shafaq 2006 and V-12304 with 18.63 and 18.23 aphids per tiller while the wheat genotypes 11C023 and Punjab 2011 received minimum aphid population which was 9.99 and 10.47 aphids per tiller and they considered more tolerant.

Keywords: Triticum aestivium, Schizaphis graminum, population, resistance

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Authors: Faheema Khan

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In order to investigate the influence of genetic background on salt tolerance in Soybean (Glycine max) ten soybean genotypes released/notified in India were selected. (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712). The 10-day-old seedlings were subjected to 0, 25, 50, 75, 100, 125, and 150 mM NaCl for 15 days. Plant growth, leaf osmotic adjustment, and RAPD analysis were studied. In comparison to control plants, the plant growth in all genotypes was decreased by salt stress, respectively. Salt stress decreased leaf osmotic potential in all genotypes however the maximum reduction was observed in genotype Pusa-24 followed by PK-416 and Pusa-20. The difference in osmotic adjustment between all the genotypes was correlated with the concentrations of ion examined such as Na+ and the leaf proline concentration. These results suggest that the genotypic variation for salt tolerance can be partially accounted for by plant physiological measures. The genetic polymorphisms between soybean genotypes differing in response to salt stress were characterized using 25 RAPD primers. These primers generated a total of 1640 amplification products, among which 1615 were found to be polymorphic. A very high degree of polymorphism (98.30%) was observed. UPGMA cluster analysis of genetic similarity indices grouped all the genotypes into two major clusters. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in soybean genotypes.

Keywords: glycine max, NaCl, RAPD, proteomics

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Authors: Hidefumi Kawakatsu, Dong Li, Kosuke Kato

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In Japan, meat-type chickens are mainly classified into three categories: (1) Broilers, (2) Branded chickens, and (3) Jidori (Free-range local traditional pedigree chickens). The Jidori chickens are certified by the Japanese Ministry of Agriculture, whilst, for the Branded chickens, there is no regulation with respect to their breed (genotype) or methods for rearing them. It is, therefore, relatively easy for poultry farmers to introduce Branded than Jidori chickens. The Branded chickens are normally fed a low-calorie diet with ingredients such as herbs, which lengthens their breeding period (compared with that of the Broilers) and increases their market value. In the field of inventory management, fast-growing animals such as broilers are categorised as ameliorating items. To the best of our knowledge, there are no previous studies that have explicitly considered smaller sized poultry farmers with limited breeding areas. This study develops an inventory model for a small sized poultry farmer that produces both the Broilers (Product 1) and the Branded chickens (Product 2) with different amelioration rates. The poultry farmer’s total profit per unit of time is formulated as a function of selling prices by using a price-dependent demand function. The existence of a unique optimal selling price for each product, which maximises the total profit, established. It has also been confirmed through numerical examples that, when the breeding area is fixed, the total profit could increase if the poultry farmer reduced the product quantity of Product 1 to introduce Product 2.

Keywords: amelioration, deterioration, small sized poultry farmers, optimal price

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Authors: Nivedita Paul

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Marriages in India are part and parcel of kinship and cultural practices. Marriage practices differ in India because of cross-regional diversities in social relations which itself has evolved as a result of causal relationship between space and culture. As the place is important for the formation of culture and other social structures, therefore there is regional differentiation in cultural practices and marital customs. Based on the cultural practices some scholars have divided India into North and South kinship regions where women in the North get married early and have lesser autonomy compared to women in the South where marriages are mostly consanguineous. But, the emergence of new modes and alternative strategies such as matrimonial advertisements becoming popular, as well as the increase in women’s literacy and work force participation, matchmaking process in India has changed to some extent. The present study uses data from Indian Human Development Survey II (2011-12) which is a nationally representative multitopic survey that covers 41,554 households. Currently married women of age group 15-49 in their first marriage; whose year of marriage is from the 1970s to 2000s have been taken for the study. Based on spouse selection experiences, the sample of women has been divided into three marriage categories-self, semi and family arranged. Women in self-arranged or love marriage is the sole decision maker in choosing the partner, in semi-arranged marriage or arranged marriage with consent both parents and women together take the decision, whereas in family arranged or arranged marriage without consent only parents take the decision. The main aim of the study is to show the spatial and regional variations in spouse selection decision making. The basis for regionalization has been taken from Irawati Karve’s pioneering work on kinship studies in India called Kinship Organization in India. India is divided into four kinship regions-North, Central, South and East. Since this work was formulated in 1953, some of the states have experienced changes due to modernization; hence these have been regrouped. After mapping spouse selection patterns using GIS software, it is found that the northern region has mostly family arranged marriages (around 64.6%), the central zone shows a mixed pattern since family arranged marriages are less than north but more than south and semi-arranged marriages are more than north but less than south. The southern zone has the dominance of semi-arranged marriages (around 55%) whereas the eastern zone has more of semi-arranged marriage (around 53%) but there is also a high percentage of self-arranged marriage (around 42%). Thus, arranged marriage is the dominant form of marriage in all four regions, but with a difference in the degree of the involvement of the female and her parents and relatives.

Keywords: spouse selection, consent, kinship, regional pattern

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Authors: Shalini Bahel, Maalti Puri, Sukhleen Bindra Narang

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Ceramic samples of (Pb0.55Ca0.45) (Fe0.5Nb0.5)O3 and (Pb0.45Ca0.55)(Fe0.5Nb0.5)O3 were synthesized by columbite precursor method and characterized for structural and dielectric properties. Both the synthesized samples have perovskite structure with tetragonal symmetry. The variations in relative permittivity and loss tangent were measured as a function of frequency at room temperature. Both the relative permittivity and loss tangent decreased with increase in frequency. A reasonably high value of relative permittivity of 63.46, loss tangent of 0.0067 at 15 MHz and temperature coefficient of relative permittivity of -82 ppm/˚C was obtained for (Pb0.45Ca0.55) (Fe0.5Nb0.5) O3.

Keywords: loss tangent, perovskite, relative permittivity, X-ray diffraction

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Authors: Benalia Nadia, Bensiali Nadia, Zerzouri Noura

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This paper presents an analysis of the effects of parameters np and nq for exponential load on the transmission line voltage profile, transferred power and transmission losses for different shunt compensation size. For different values for np and nq in which active and reactive power vary with it is terminal voltages as in exponential form, variations of the load voltage for different sizes of shunt capacitors are simulated with a simple two-bus power system using Matlab SimPowerSystems Toolbox. It is observed that the compensation level is significantly affected by the voltage sensitivities of loads.

Keywords: static load model, shunt compensation, transmission system, exponentiel load model

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

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Gastric cancer (GC) has high morbidity and fatality rate in various countries and is still one of the most frequent and deadly diseases. Novel mitogenic and motogenic Gastrokine1 (GKN1) and Gastrokine 2 (GKN2) genes that are highly expressed in the normal stomach epithelium and plays an important role in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. Significant loss of copy number and mRNA transcript of GKN1 and GKN2 gene expression were frequently observed in all types of gastric cancer. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age were investigated with gene expression analysis and mutation screening by monetering RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of inactivation of gastrokines. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age or cancer type of patients. Reduced of gastrokine genes seems to occur at the initial steps of cancer development. In order to understand the investigation between gastric cancer and diagnostic biomarker; further analysis is necessary.

Keywords: gastric cancer, diagnostic biomarker, nucleotide sequencing, semi-quantitative RT-PCR

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Authors: Imren Kutlu, Nurdilek Gulmezoglu

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Triticale (Triticosecale Wittmack) is a man-made crop developed by crossing wheat (Triticum L.) and rye (Secale cereale L.). Triticale has until now been used mostly for animal feed; however, it can be consumed by humans in the form of biscuits, cookies, and unleavened bread. Moreover, one of the reasons for the development of triticale is that it is more efficient in nutrient deficient soil than wheat cultivars. After nitrogen fertilizer, phosphorus (P) is the most used fertilizer for crop production because P fixation occurs highly when it is applied the soil. The aim of the present study was to evaluate P uptake of winter triticale genotypes under different P fertilizer rates in different growth stages. The experiment was conducted in Eskisehir, Central Anatolia, Turkey. Treatments consisted of five triticale lines and one triticale cultivars (Samursortu) with four rates of P fertilization (0, 30, 60 and 120 kg P2O5 ha⁻¹). Phosphorus uptake of triticale genotypes in tillering, heading, as well as grain and straw at harvest stage and yield of grain and straw were determined. The results showed that a P rate of 60 kg/ha and the TCL-25 genotype produced the highest yields of straw and grain at harvest. Phosphorus uptake was the highest in tillering stage, and it decreased towards to harvest time. Phosphorus uptake of all growth stage increased as P rates raised and the application of 120 kg/ha P₂O₅ had the highest P uptake. Phosphorus uptake of genotypes was found differently. The regression analyses indicated that P uptake at tillering stage was the most effective on grain yield. These results will provide useful information to triticale growers about suitable phosphorus fertilization for both forage and food usage.

Keywords: grain yield, growth stage, phosphorus fertilization, phosphorus uptake, triticale

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Authors: Tshipeng Mwenze, Charles Okujeni, Abdi Siad, Russel Bailie, Dirk Frei, Marcelene Voigt, Petrus Le Roux

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The Platreef is a platinum group element (PGE) deposit in the northern limb of the Bushveld Igneous Complex (BIC) which was emplaced as a series of mafic and ultramafic sills between the Main Zone (MZ) and the country rocks. The PGE mineralisation in the Platreef is hosted in different rock types, and its distribution and style vary with depth and along strike. This study contributes towards understanding the processes involved in the genesis of the Platreef. Twenty-four Platreef (2 harzburgites, 4 olivine pyroxenites, 17 feldspathic pyroxenites and 1 gabbronorite) and few MZ (1 gabbronorite and 1 leucogabbronorite) quarter core samples were collected from four drill cores (e.g., TN754, TN200, SS339, and OY482) and analysed for whole-rock Sr-Nd isotope data. The results show positive ɛNd values (+3.53 to +7.51) for harzburgites suggesting their parental magmas derived from the depleted Mantle. The remaining Platreef rocks have negative ɛNd values (-2.91 to -22.88) and show significant variations in Sr-Nd isotopic compositions. The first group of Platreef samples has relatively high isotopic compositions (ɛNd= -2.91 to -5.68; ⁸⁷Sr/⁸⁶Sri= 0.709177 - 0.711998). The second group of Platreef samples has Sr ratios (⁸⁷Sr/⁸⁶Sri= 0.709816-0.712106) overlapping with samples of the first group but slightly lower ɛNd values (-7.44 to -8.39). Lastly, the third group of Platreef samples has low ɛNd values (-10.82 to -14.32) and low Sr ratios (⁸⁷Sr/⁸⁶Sri= 0.707545-0.710042) than those from samples of the two Platreef groups mentioned above. There is, however, a Platreef sample with ɛNd value (-5.26) in range with the Platreef samples of the first group, but its Sr ratio (0.707281) is the lowest even when compared to samples of the third Platreef group. There are also five other Platreef samples which have either anomalous ɛNd or Sr ratios which make it difficult to assess their isotopic compositions relative to other samples. These isotopic variations for the Platreef samples indicate both multiple sources and multiple magma chambers where varying crustal contamination styles have operated during the evolution of these magmas prior their emplacements into the Platreef setting as sills. Furthermore, the MZ rocks have different Sr-Nd isotopic compositions (For OY482 gabbronorite [ɛNd= +0.65; ⁸⁷Sr/⁸⁶Sri= 0.711746]; for TN754 leucogabbronorite [ɛNd= -7.44; ⁸⁷Sr/⁸⁶Sri= 0.709322]) which do not only indicate different MZ magma chambers, but also different magmas from those of the Platreef. Although the Platreef is still considered a single stratigraphic unit in the northern limb of the BIC, its genesis involved multiple magmatic processes which evolved independently from each other.

Keywords: crustal contamination styles, magma chambers, magma sources, multiple sills emplacement

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Authors: Chiung-Man Tsai, Chia-Jui Weng

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Leptin (LEP) and leptin receptor (LEPR) both play a crucial role in the mediation of physiological reactions and carcinogenesis and may serve as a candidate biomarker of oral cancer. The present case-control study aimed to examine the effects of single nucleotide polymorphisms (SNPs) of LEP -2548 G/A (rs7799039), LEPR K109R (rs1137100), and LEPR Q223R (rs1137101) with or without interacting to environmental carcinogens on the risk for oral squamous cell carcinoma (OSCC). The SNPs of three genetic allele, from 567 patients with oral cancer and 560 healthy controls in Taiwan were analyzed. All of The three genetic polymorphisms exhibited insignificant (P > .05) effects on the risk to have oral cancer. However, the patients with polymorphic allele of LEP -2548 have a significant low risk for the development of clinical stage (A/G, AOR = 0.670, 95% CI = 0.454–0.988, P < .05; A/G+G/G, AOR = 0.676, 95% CI = 0.467–0.978, P < .05) compared to patients with ancestral homozygous A/A genotype. Additionally, an interesting result was found that the impact of LEP -2548 G/A SNP on oral carcinogenesis in subjects without tobacco consumption (A/G, AOR=2.078, 95% CI: 1.161-3.720, p=0.014; A/G+G/G, AOR=2.002, 95% CI: 1.143-3.505, p=0.015) is higher than subjects with tobacco consumption. These results suggest that the genetic polymorphism of LEP -2548 G/A (rs7799039), LEPR K109R (rs1137100), and LEPR Q223R (rs1137101) were not associated with the susceptibility of oral cancer; SNP in LEP -2548 G/A showed a poor clinicopathological development of oral cancer; Population without tobacco consumption and with polymorphic LEP -2548 G/A gene may significantly increase the risk to have oral cancer.

Keywords: carcinogen, leptin, leptin receptor, oral squamous cell carcinoma, single nucleotide polymorphism

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Authors: Daniil Karzanov

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This paper studies the effect of quarterly earnings reports on the stock price. The profitability of the stock is modeled by geometric Brownian diffusion and the Constant Elasticity of Variance model. We fit several variations of stochastic differential equations to the pre-and after-report period using the Maximum Likelihood Estimation and Grid Search of parameters method. By examining the change in the model parameters after reports’ publication, the study reveals that the reports have enough evidence to be a structural breakpoint, meaning that all the forecast models exploited are not applicable for forecasting and should be refitted shortly.

Keywords: stock market, earnings reports, financial time series, structural breaks, stochastic differential equations

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Authors: Hailekiros Tadesse Tekle, Yemane Tsehaye, Fetien Abay

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Barley (Hordeum vulgare L.) is one of the most important cereal crops in the world, grown for the poor farmers in Tigray with low yield production. The purpose of this research was to estimate the performance of 166 barley genotypes against the quantitative traits with detailed analysis of the variance component, heritability, genetic advance, and genetic usefulness parameters. The finding of ANOVA was highly significant variation (p ≤ 0:01) for all the genotypes. We found significant differences in coefficient of variance (CV of 15%) for 5 traits out of the 12 quantitative traits. The topmost broad sense heritability (H2) was recorded for seeds per spike (98.8%), followed by thousand seed weight (96.5%) with 79.16% and 56.25%, respectively, of GAM. The traits with H2 ≥ 60% and GA/GAM ≥ 20% suggested the least influenced by the environment, governed by the additive genes and direct selection for improvement of such beneficial traits for the studied genotypes. Hence, the 20 outstanding recombinant inbred lines (RIL) barley genotypes performing early maturity, high yield, and 1000 seed weight traits simultaneously were the top ranked group barley genotypes out of the 166 genotypes. These are; G5, G25, G33, G118, G36, G123, G28, G34, G14, G10, G3, G13, G11, G32, G8, G39, G23, G30, G37, and G26. They were early in maturity, high TSW and GYP (TSW ≥ 55 g, GYP ≥ 15.22 g/plant, and DTM below 106 days). In general, the 166 genotypes were classified as high (group 1), medium (group 2), and low yield production (group 3) genotypes in terms of yield and yield component trait analysis by clustering; and genotype parameter analysis such as the heritability, genetic advance, and genetic usefulness traits in this investigation.

Keywords: barley, clustering, genetic advance, heritability, usefulness, variability, yield

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Authors: Mehdi Nasr Esfahani, Abdal-Rasool Gholamalian, Abdelfattah A. Dababat

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Wheat, Triticum aestivum L. is one of the most important and strategic crops in the human diet. Several diseases threaten this particular crop. Common root rot disease of wheat by a fungal agent, Bipolaris sorokiniana is one of the important diseases, causing considerable losses worldwide. Resistant sources are the only feasible and effective method of control for managing diseases. In this study, the response of 33 domestic and exotic wheat genotypes, including cultivars and promising lines were screened to B. sorokiniana at greenhouse and field conditions, based on five scoring scale indexes of 0 to 100 severity percentage. The screening was continued on resistant wheat genotypes and repeated several times to confirm the greenhouse and field results. Statistical and cluster analysis of data was performed using SAS and SPSS software, respectively. The results showed that, the response of wheat genotypes to the disease in the greenhouse and field conditions was highly significant. The highest rate of common root rot disease infection, B. sorokiniana in the greenhouse and field, was of CVS. Karkheh and Beck Cross-Roshan with 60.83% and 59.16% disease severity respectively, and the lowest one were in cv. Alvand with 18.33%, followed by cv. Baharan with 19.16% disease severity, with a highly significant difference respectively. The remaining wheat genotypes were located in between these two highest and lowest infected groups to B. sorokiniana significantly. There was a high correlation coefficient between the related statistical groups and cluster analysis.

Keywords: wheat, rot, root, crown, fungus, genotype, resistance

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Authors: R. Saini, R. Lal

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The effect of non-homogeneity on the free transverse vibration of thin rectangular plates of bilinearly varying thickness has been analyzed using generalized differential quadrature (GDQ) method. The non-homogeneity of the plate material is assumed to arise due to linear variations in Young’s modulus and density of the plate material with the in-plane coordinates x and y. Numerical results have been computed for fully clamped and fully simply supported boundary conditions. The solution procedure by means of GDQ method has been implemented in a MATLAB code. The effect of various plate parameters has been investigated for the first three modes of vibration. A comparison of results with those available in literature has been presented.

Keywords: rectangular, non-homogeneous, bilinear thickness, generalized differential quadrature (GDQ)

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Authors: Shengyong Zhang, Mike Mikulich

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Vibration is a crucial limiting consideration in the analysis and design of airplane wing structures to avoid disastrous failures due to the propagation of existing cracks in the material. In this paper, we build CAD models of aircraft wings to capture the design intent with configurations. Subsequent FEA vibration analysis is performed to study the natural vibration properties and impulsive responses of the resulting user-defined wing models. This study reveals the variations of the wing’s vibration characteristics with respect to changes in its structural configurations. Integrating CAD modelling and FEA vibration analysis enables designers to improve wing architectures for implementing design requirements in the preliminary design stage.

Keywords: aircraft wing, CAD modelling, FEA, vibration analysis

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Authors: Bayoumy Mohamed, Khaled Alam El-Din

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In the present study, 24 years of gridded sea level anomalies (SLA) from satellite altimetry and sea surface temperature (SST) from advanced very-high-resolution radiometer (AVHRR) daily data (1993-2016) are used. These data have been used to investigate the sea level rising and warming rates of SST, and their spatial distribution in the Mediterranean Sea. The results revealed that there is a significant sea level rise in the Mediterranean Sea of 2.86 ± 0.45 mm/year together with a significant warming of 0.037 ± 0.007 °C/year. The high spatial correlation between sea level and SST variations suggests that at least part of the sea level change reported during the period of study was due to heating of surface layers. This indicated that the steric effect had a significant influence on sea level change in the Mediterranean Sea.

Keywords: altimetry, AVHRR, Mediterranean Sea, sea level and SST changes, trend analysis

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Authors: Murali Munisamy, Gauthaman Karunakaran, Mubarak Al-Gahtany, Vivekanandhan Subbiah, M. Manjari Tripati

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Background: Sodium valproate is a widely prescribed broad-spectrum anti-epileptic drug. It shows high inter-individual variability in pharmacokinetics and pharmacodynamics and has a narrow therapeutic range. We evaluated the effects of polymorphic uridine diphosphate glucuronosyltransferase (UGT1A9) metabolizing enzyme on the pharmacokinetics of sodium valproate in the patients with epilepsy who showed toxicity to therapy. Methods: Genotype analysis of the patients was made with polymerase chain–restriction fragment length polymorphism (RFLP) with sequencing. Plasma drug concentrations were measured with reversed phase high-performance liquid chromatography (HPLC) and concentration–time data were analyzed by using a non-compartmental approach. Results: The results of this study suggested a significant genotypic as well as allelic association with valproic acid toxicity for UGT1A9 polymorphic enzymes. The elimination half-life (t 1/2=40.2 h) of valproic acid was longer and the clearance rate (CL=937 ml/h) was lower in the poor metabolizers group of UGT1A9 polymorphism who showed toxicity than in the intermediate metabolizers group (t1/2=35.5 h, CL=1042 ml/h) or the extensive metabolizers group (t1/2=26. h, CL=1,302 ml/h). Conclusion: Our findings suggest that the UGT1A9 genetic polymorphism plays a significant role in the steady state concentration of sodium valproate, and it thereby has an impact on the toxicity of the sodium valproate used in the patients with epilepsy.

Keywords: UGT1A9, sodium valporate, pharmacogenetics, polymorphism

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Authors: Nada Jasim Habeeb, Rana Saad Mohammed, Muntaha Khudair Abbass

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For more efficient and fast video summarization, this paper presents a surveillance video summarization method. The presented method works to improve video summarization technique. This method depends on temporal differencing to extract most important data from large video stream. This method uses histogram differencing and Sum Conditional Variance which is robust against to illumination variations in order to extract motion objects. The experimental results showed that the presented method gives better output compared with temporal differencing based summarization techniques.

Keywords: temporal differencing, video summarization, histogram differencing, sum conditional variance

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Authors: Salah Menouar, Sara Hassoul

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The dynamic of time-dependent three coupled oscillators is studied through an approach based on decoupling of them using the unitary transformation method. From a first unitary transformation, the Hamiltonian of the complicated original system is transformed to an equal but a simple one associated with the three coupled oscillators of which masses are unity. Finally, we diagonalize the matrix representation of the transformed hamiltonian by using a unitary matrix. The diagonalized Hamiltonian is just the same as the Hamiltonian of three simple oscillators. Through these procedures, the coupled oscillatory subsystems are completely decoupled. From this uncouplement, we can develop complete dynamics of the whole system in an easy way by just examining each oscillator independently. Such a development of the mechanical theory can be done regardless of the complication of the parameters' variations.

Keywords: schrödinger equation, hamiltonian, time-dependent three coupled oscillators, unitary transformation

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Authors: John Davodi, Maryam Davodi-Far

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The human body is the most elaborate of all machines and technologies on Earth, while the human mind is the interdependent source that expels and absorbs the five senses: touch, smell, sight, sound, and taste. Meditation is an ancient form of mind power that has many variations. In fact, those who practice meditation may bring about a positive change in their five senses, depending on the aim of the practitioner. This paper examines the research related to meditation and its effects on individuals suffering from chronic pain. Moreover, consideration is given to whether perceptions of pain can be changed by the practice of meditation as well as whether meditation can have a noticeable and long-term positive effect on the human body. Lastly, the paper examines the type of meditation that is best suited to minimize pain sensations for those who suffer from chronic pain.

Keywords: meditation, pain, relaxation, suffering

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Authors: Nafisa Banu

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The present study is an attempt to analyze the regional disparities in the level of education in West Bengal. The data based on secondary sources obtained from a census of India. The study is divided into four sections. The first section presents introductions, objectives and brief descriptions of the study area, second part discuss the methodology and data base, while third and fourth comprise the empirical results, interpretation, and conclusion respectively. For showing the level of educational development, 8 indicators have been selected and Z- score and composite score techniques have been applied. The present study finds out there are large variations of educational level due to various historical, economical, socio-cultural factors of the study area.

Keywords: education, regional disparity, literacy rate, Z-score, composite score

Procedia PDF Downloads 321