Search results for: genotype frequencies

Authors: Yan Torres, Fernanda Simoes, Francisco Petrucci-Fonseca, Freddie-Jeanne Richard

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The non-invasive samples are an alternative of collecting genetic samples directly. Non-invasive samples are collected without the manipulation of the animal (e.g., scats, feathers and hairs). Nevertheless, the use of non-invasive samples has some limitations. The main issue is degraded DNA, leading to poorer extraction efficiency and genotyping. Those errors delayed for some years a widespread use of non-invasive genetic information. Possibilities to limit genotyping errors can be done using analysis methods that can assimilate the errors and singularities of non-invasive samples. Genotype matching and population estimation algorithms can be highlighted as important analysis tools that have been adapted to deal with those errors. Although, this recent development of analysis methods there is still a lack of empirical performance comparison of them. A comparison of methods with dataset different in size and structure can be useful for future studies since non-invasive samples are a powerful tool for getting information specially for endangered and rare populations. To compare the analysis methods, four different datasets used were obtained from the Dryad digital repository were used. Three different matching algorithms (Cervus, Colony and Error Tolerant Likelihood Matching - ETLM) are used for matching genotypes and two different ones for population estimation (Capwire and BayesN). The three matching algorithms showed different patterns of results. The ETLM produced less number of unique individuals and recaptures. A similarity in the matched genotypes between Colony and Cervus was observed. That is not a surprise since the similarity between those methods on the likelihood pairwise and clustering algorithms. The matching of ETLM showed almost no similarity with the genotypes that were matched with the other methods. The different cluster algorithm system and error model of ETLM seems to lead to a more criterious selection, although the processing time and interface friendly of ETLM were the worst between the compared methods. The population estimators performed differently regarding the datasets. There was a consensus between the different estimators only for the one dataset. The BayesN showed higher and lower estimations when compared with Capwire. The BayesN does not consider the total number of recaptures like Capwire only the recapture events. So, this makes the estimator sensitive to data heterogeneity. Heterogeneity in the sense means different capture rates between individuals. In those examples, the tolerance for homogeneity seems to be crucial for BayesN work properly. Both methods are user-friendly and have reasonable processing time. An amplified analysis with simulated genotype data can clarify the sensibility of the algorithms. The present comparison of the matching methods indicates that Colony seems to be more appropriated for general use considering a time/interface/robustness balance. The heterogeneity of the recaptures affected strongly the BayesN estimations, leading to over and underestimations population numbers. Capwire is then advisable to general use since it performs better in a wide range of situations.

Keywords: algorithms, genetics, matching, population

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Authors: M. Chňapek, M. Tomka, R. Peroutková, Z. Gálová

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Processes of plant breeding, testing and licensing of new varieties, patent protection in seed production, relations in trade and protection of copyright are dependent on identification, differentiation and characterization of plant genotypes. Therefore, we focused our research on utilization of wheat storage proteins as genetic markers suitable not only for differentiation of individual genotypes, but also for identification and characterization of their considerable properties. We analyzed a collection of 102 genotypes of bread wheat (Triticum aestivum L.), 41 genotypes of spelt wheat (Triticum spelta L.), and 35 genotypes of durum wheat (Triticum durum Desf.), in this study. Our results show, that genotypes of bread wheat and durum wheat were homogenous and single line, but spelt wheat genotypes were heterogenous. We observed variability of HMW-GS composition according to environmental factors and level of breeding and predict technological quality on the basis of Glu-score calculation.

Keywords: genotype identification, HMW-GS, wheat quality, polymorphism

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Authors: Arpita Mondal, Aurobinda Routray, Sreeraj Puravankara, Rajashree Biswas

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The most difficult part of designing a battery management system (BMS) is battery modeling. A good battery model can capture the dynamics which helps in energy management, by accurate model-based state estimation algorithms. So far the most suitable and fruitful model is the equivalent circuit model (ECM). However, in real-time applications, the model parameters are time-varying, changes with current, temperature, state of charge (SOC), and aging of the battery and this make a great impact on the performance of the model. Therefore, to increase the equivalent circuit model performance, the parameter estimation has been carried out in the frequency domain. The battery is a very complex system, which is associated with various chemical reactions and heat generation. Therefore, it’s very difficult to select the optimal model structure. As we know, if the model order is increased, the model accuracy will be improved automatically. However, the higher order model will face the tendency of over-parameterization and unfavorable prediction capability, while the model complexity will increase enormously. In the time domain, it becomes difficult to solve higher order differential equations as the model order increases. This problem can be resolved by frequency domain analysis, where the overall computational problems due to ill-conditioning reduce. In the frequency domain, several dominating frequencies can be found in the input as well as output data. The selective frequency domain estimation has been carried out, first by estimating the frequencies of the input and output by subspace decomposition, then by choosing the specific bands from the most dominating to the least, while carrying out the least-square, recursive least square and Kalman Filter based parameter estimation. In this paper, a second order battery model consisting of three resistors, two capacitors, and one SOC controlled voltage source has been chosen. For model identification and validation hybrid pulse power characterization (HPPC) tests have been carried out on a 2.6 Ah LiFePO₄ battery.

Keywords: equivalent circuit model, frequency estimation, parameter estimation, subspace decomposition

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

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Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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Authors: Fitri Rahmi Fadhilah, Edhyana Sahiratmadja, Ani Melani Maskoen, Ratu Safitri, Supartini Syarif, Herman Susanto

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Cervical cancer is the second most common cancer in women after breast cancer. In Indonesia, the incidence of cervical cancer cases is estimated at 25-40 per 100,000 women per year. Human papillomavirus (HPV) infection is a major cause of cervical cancer, and HPV-16 is the most common genotype that infects the cervical tissue. The major late protein L1 may be associated with infectivity and pathogenicity and its variation can be used to classify HPV isolates. The aim of this study was to determine the phylogenetic tree of HPV 16 L1 gene from cervical cancer patient isolates in Bandung. After confirming HPV-16 by Linear Array Genotyping Test, L1 gene was amplified using specific primers and subject for sequencing. Phylogenetic analysis revealed that HPV 16 from Bandung was in the subgroup of Asia and East Asia, showing the close host-agent relationship among the Asian type.

Keywords: L1 HPV 16, cervical cancer, bandung, phylogenetic

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Authors: Mohammad Yusuf, Qazi Fariduddin

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The main aim of this study was to explore the different cultivars of Vigna radiata on basis of photosynthesis, antioxidants and proline to assess Ni-sensitive and Ni-tolerant cultivar. Seeds of five different cultivars were sown in soil amended with different levels of Ni (0, 50, 100, or 150 mg kg 1). At 30 d stage, plants were harvested to assess the various parameters. The Ni treatment diminished growth, leaf water potential, chlorophyll content and net photosynthesis along with nitrate reductase and carbonic anhydrase activities in the concentration dependent manner whereas, it enhanced proline content and various antioxidant enzymes. The varieties T-44 found least affected, whereas PDM-139 experienced maximum damage at 150 mg kg-1 of Ni. Moreover, T-44 possessed maximum activity of antioxidant enzymes and proline content at all the levels of metal whereas PDM-139 possessed minimum values. Therefore, T-44 and PDM-139 were established as the most resistant and sensitive varieties, respectively.

Keywords: Vigna radiata, antioxidants, nickel, photosynthesis, proline

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Authors: Byl Farney Cunha Junior

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In this work the dynamic three-dimensional analysis of a 47-story building located in Goiania city when subjected to wind loads generated using both the Wind Brazilian code, NBR6123 (ABNT, 1988) and the Synthetic-Wind method is realized. To model the frames three different methodologies are used: the shear building model and both bi and three-dimensional finite element models. To start the analysis, a plane frame is initially studied to validate the shear building model and, in order to compare the results of natural frequencies and displacements at the top of the structure the same plane frame was modeled using the finite element method through the SAP2000 V10 software. The same steps were applied to an idealized 20-story spacial frame that helps in the presentation of the stiffness correction process applied to columns. Based on these models the two methods used to generate the Wind loads are presented: a discrete model proposed in the Wind Brazilian code, NBR6123 (ABNT, 1988) and the Synthetic-Wind method. The method uses the Davenport spectrum which is divided into a variety of frequencies to generate the temporal series of loads. Finally, the 47- story building was analyzed using both the three-dimensional finite element method through the SAP2000 V10 software and the shear building model. The models were loaded with Wind load generated by the Wind code NBR6123 (ABNT, 1988) and by the Synthetic-Wind method considering different wind directions. The displacements and internal forces in columns and beams were compared and a comparative study considering a situation of a full elevated reservoir is realized. As can be observed the displacements obtained by the SAP2000 V10 model are greater when loaded with NBR6123 (ABNT, 1988) wind load related to the permanent phase of the structure’s response.

Keywords: finite element method, synthetic wind, tall buildings, shear building

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Authors: Hayder Raad Hafuze, Munqith Saleem Dawood, Jamal Abdul Jabbar

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The effect of using both ultrasounds with laser in medical imaging of the biological tissue has been studied in this paper. Different wave lengths of incident laser light (405 nm, 532 nm, 650 nm, 808 nm and 1064 nm) were used with different ultrasound frequencies (1MHz and 3.3MHz). The results showed that, the change of acoustic intensity enhance the laser penetration of the tissue for different thickness. The existence of the ideal Raman-Nath diffraction pattern were investigated in terms of phase delay and incident angle.

Keywords: tissue, laser, ultrasound, effect, imaging

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Authors: S. Sokel, M. Kale

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Norovirus (NoV) infection is effective and contagious in humans and many animals such as calves, pigs, dogs, cats, monkeys. There is not enough evidence about the zoonotic transmission of NoV between humans and animals. However, the fact that contamination of foods and environment by animal/human waste happens in indirect way leads to consideration of the agent as a zoonotic character. In our study, we aim to search the presence of NoV infection, which is a major public health problem, in possessed dogs showing diarrhea symptoms, to detect its genotype and to study nutrition and life conditions. We searched the existence of human NoV GI, GII and GIV in the stool of 128 pet dogs in Burdur Province with diarrhoea in various sex, age and breed by using Real-Time PCR method. Human NoV GII was found in only 5 of the 128 dog stool samples (3.91%). In the study, it was determined that the owners of the dogs with NoV GII are middle aged or elderly people most of whom are male and that there were no children in their houses. As these dogs are treated like the owner’s child, it is assumed that they could be transmitted with NoV GII as a result of close interaction with their owner.

Keywords: dog, human, norovirus, Real-Time PCR, stool

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Authors: Vivek Nair

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The objective of this research is to find out happiness determinants in MBA student life. To figure out the factors influencing happiness in life is sorted by their personal profiles. This paper used survey method to collect data. The survey was mainly conducted among Management Students and is based on three hypothesis viz. Family relationship, Friendship and God as a source of happiness, and whether happiness is manageable and controllable. The statistics used for interpreting the results included the frequencies, percentages, and z test analysis. The findings revealed that family relationships and friendship have the same effect on individual happiness.

Keywords: happiness, family, MBA students, friends

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Authors: L. Tonia, I. Daglis, W. Kurth

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The sound of the universe creates an affinity with the sounds of music. The analysis of the sound of space focuses on the existence of a tone material, the microstructure and macrostructure, and the form of the sound through the signals recorded during the flight of the spacecraft Van Allen Probes and Cassini’s mission. The sound becomes from the frequencies that belong to electromagnetic waves. Plasma Wave Science Instrument and Electric and Magnetic Field Instrument Suite and Integrated Science (EMFISIS) recorded the signals from space. A transformation of that signals to audio gave the opportunity to study and analyze the sound. Due to the fact that the musical tone pitch has a frequency and every electromagnetic wave produces a frequency too, the creation of a musical score, which appears as the sound of space, can give information about the form, the symmetry, and the harmony of the sound. The conversion of space radio emissions to audio provides a number of tone pitches corresponding to the original frequencies. Through the process of these sounds, we have the opportunity to present a music score that “composed” from space. In this score, we can see some basic features associated with the music form, the structure, the tone center of music material, the construction and deconstruction of the sound. The structure, which was built through a harmonic world, includes tone centers, major and minor scales, sequences of chords, and types of cadences. The form of the sound represents the symmetry of a spiral movement not only in micro-structural but also to macro-structural shape. Multiple glissando sounds in linear and polyphonic process of the sound, founded in magnetic fields around Earth, Saturn, and Jupiter, but also a spiral movement appeared on the spectrogram of the sound. Whistles, Auroral Kilometric Radiations, and Chorus emissions reveal movements similar to musical excerpts of works by contemporary composers like Sofia Gubaidulina, Iannis Xenakis, EinojuhamiRautavara.

Keywords: space sound analysis, spiral, space music, analysis

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Authors: A. Bortkiewcz, A. Dudarewicz, P. Małecki, M. Kłaczyński, T. Wszołek, Małgorzata Pawlaczyk-Łuszczyńska

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Low-frequency noise (LFN) has been recognized as a special environmental pollutant. It is usually considered a broadband noise with the dominant content of low frequencies from 10 Hz to 250 Hz. A growing body of data shows that LFN differs in nature from other environmental noises, which are at comparable levels but not dominated by low-frequency components. The primary and most frequent adverse effect of LFN exposure is annoyance. Moreover, some recent investigations showed that LFN at relatively low A-weighted sound pressure levels (40−45 dB) occurring in office-like areas could adversely affect the mental performance, especially of high-sensitive subjects. It is well documented that high-frequency noise disturbs various types of human functions; however, there is very little data on the impact of LFN on well-being and health, including the cardiovascular system. Heart rate variability (HRV) is a sensitive marker of autonomic regulation of the circulatory system. Walker and co-workers found that LFN has a significantly more negative impact on cardiovascular response than exposure to high-frequency noise and that changes in HRV parameters resulting from LFN exposure tend to persist over time. The negative reactions of the cardiovascular system in response to LFN generated by wind turbines (20-200 Hz) were confirmed by Chiu. The scientific aim of the study is to assess the relationship between the spectral-temporal characteristics of LFN and the activity of the autonomic nervous system, considering the subjective assessment of annoyance, sensitivity to this type of noise, and cognitive and general health status. The study will be conducted in 20 male students in a special, acoustically prepared, constantly supervised room. Each person will be tested 4 times (4 sessions), under conditions of non-exposure (sham) and exposure to noise of wind turbines recorded at a distance of 250 meters from the turbine with different frequencies and frequency ranges: acoustic band 20 Hz-20 kHz, infrasound band 5-20 Hz, acoustic band + infrasound band. The order of sessions of the experiment will be randomly selected. Each session will last 1 h. There will be a 2-3 days break between sessions to exclude the possibility of the earlier session influencing the results of the next one. Before the first exposure, a questionnaire will be conducted on noise sensitivity, general health status using the GHQ questionnaire, hearing organ status and sociodemographic data. Before each of the 4 exposures, subjects will complete a brief questionnaire on their mood and sleep quality the night before the test. After the test, the subjects will be asked about any discomfort and subjective symptoms during the exposure. Before the test begins, Holter ECG monitoring equipment will be installed. HRV will be analyzed from the ECG recordings, including time and frequency domain parameters. The tests will always be performed in the morning (9-12) to avoid the influence of diurnal rhythm on HRV results. Students will perform psychological tests 15 minutes before the end of the test (Vienna Test System).

Keywords: neurovegetative control, heart rate variability (HRV), cognitive processes, low frequency noise

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: Mohamed dammak

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Great attention has been paid to the design and synthesis of novel organic-inorganic compounds in recent decades because of their structural variety and the large diversity of atomic arrangements. In this work, the structure for the novel dimethyl aminopyridine tetrachlorocobaltate (C₇H₁₁N₂)₂CoCl₄ prepared by the slow evaporation method at room temperature has been successfully discussed. The X-ray diffraction results indicate that the hybrid material has a triclinic structure with a P space group and features a 0D structure containing isolated distorted [CoCl₄]2- tetrahedra interposed between [C7H11N²⁻]+ cations forming planes perpendicular to the c axis at z = 0 and z = ½. The effect of the synthesis conditions and the reactants used, the interactions between the cationic planes, and the isolated [CoCl4]2- tetrahedra are employing N-H...Cl and C-H…Cl hydrogen bonding contacts. The inspection of the Hirshfeld surface analysis helps to discuss the strength of hydrogen bonds and to quantify the inter-contacts. A phase transition was discovered by thermal analysis at 390 K, and comprehensive dielectric research was reported, showing a good agreement with thermal data. Impedance spectroscopy measurements were used to study the electrical and dielectric characteristics over a wide range of frequencies and temperatures, 40 Hz–10 MHz and 313–483 K, respectively. The Nyquist plot (Z" versus Z') from the complex impedance spectrum revealed semicircular arcs described by a Cole-Cole model. An electrical circuit consisting of a link of grain and grain boundary elements is employed. The real and imaginary parts of dielectric permittivity, as well as tg(δ) of (C₇H₁₁N₂)₂CoCl₄ at different frequencies, reveal a distribution of relaxation times. The presence of grain and grain boundaries is confirmed by the modulus investigations. Electric and dielectric analyses highlight the good protonic conduction of this material.

Keywords: organic-inorganic, phase transitions, complex impedance, protonic conduction, dielectric analysis

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Authors: St. Subaedah, A. Takdir, Netty, D. Hidrawati

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Maize development at the rainfed lowland after rice is often confronted with the occurrence of drought stress at the time of entering the generative phase, which will cause be hampered crop production. Consequently, in the utilization of the rainfed lowland areas optimally, an effort that can be done using the varieties of early maturity to minimize crop failures due to its short rainy season. The aim of this research was evaluating the potential yield of genotypes of candidates of maize early maturity in the rainfed lowland areas. The study was conducted during May to August 2016 at South Sulawesi, Indonesia. The study used randomized block design to compare 12 treatments and consists of 8 genotypes namely CH1, CH2, CH3, CH4, CH5, CH6, CH7, CH8 and the use of four varieties, namely Bima 3, Bima 7, Lamuru and Gumarang. The results showed that genotype of CH2, CH3, CH5, CH 6, CH7 and CH8 harvesting has less than 90 days. There are two genotypes namely genotypes of CH7 and CH8 that have a fairly high production respectively of 7.16 tons / ha and 8.11 tons/ ha and significantly not different from the superior varieties Bima3.

Keywords: evaluation, early maturity, maize, yield potential

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Authors: Salem A. Abdalla Bozrayda, Abulgasem M. Hubara

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The use of commercial poultry breeds in Libya may result in large economic losses because genotypes selected in temperate climates may respond differently to other climate conditions and management. Therefore three commercial breeds (Hypeco, Avian, and Shaver) were evaluated in two regions. The data were obtained from weekly records of three parental flocks for each breed at Ghout El-sultan and Tawargha region. Feed Hen Housed (FHH), Hen Housed Egg Production (HHEP) Mortility % were the studied traits. Statistical model include location, year, month, age and breed. Hypeco produced more HHEP 68.6 with Less FHH 22.9 kg but with higher mortility 8.5 % than Avian and shaver breeds. The breeds exhibited different responses to the different months in Libya. In conclusion, the differences, which exhibited between the breeds in traits studied, indicate that genotype x environment must be considered when select breed to perform under Libyan conditions.

Keywords: hypeco avian shaver, feed hen housed, hen housed egg production, mortility, Libya

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Authors: Samia Ait Ali Yahia

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The rock paintings of Grande Kabylia contain a good number of Libyan inscriptions. Of the 54 sites discovered, 23 have inscriptions painted in red ocher. We find them in rock shelters, on blocks of sandstone in the northern part of Kabylia. Our job is to collect as many cave paintings as possible with Libyan inscriptions. Then we will make an analysis on the epigraphic level, the different forms of the characters and their frequencies. The other purpose of this research is to bring out the different characters used in these paintings and compare them with those of the Libyan steles of Grande Kabylia.

Keywords: Grande Kabylia, Libyan inscriptions, Libyan stele, rock paintings

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Authors: Yusuf Ulaş Kabukçu, Si̇nan Çeli̇k, Onur Salan, Mai̇de Altuntaş, Mert Can Dalkiran, Gökseni̇n Bozdağ, Metehan Bulut, Fati̇h Yaman

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This study presents a more compact implementation of the 2.4GHz MIT Coffee Can Doppler Radar for 2.6GHz operating frequency. The main difference of our prototype depends on the use of microstrip antennas which makes it possible to transport with a small robotic vehicle. We have designed our radar system with two different channels: Tx and Rx. The system mainly consists of Voltage Controlled Oscillator (VCO) source, low noise amplifiers, microstrip antennas, splitter, mixer, low pass filter, and necessary RF connectors with cables. The two microstrip antennas, one is element for transmitter and the other one is array for receiver channel, was designed, fabricated and verified by experiments. The system has two operation modes: speed detection and range detection. If the switch of the operation mode is ‘Off’, only CW signal transmitted for speed measurement. When the switch is ‘On’, CW is frequency-modulated and range detection is possible. In speed detection mode, high frequency (2.6 GHz) is generated by a VCO, and then amplified to reach a reasonable level of transmit power. Before transmitting the amplified signal through a microstrip patch antenna, a splitter used in order to compare the frequencies of transmitted and received signals. Half of amplified signal (LO) is forwarded to a mixer, which helps us to compare the frequencies of transmitted and received (RF) and has the IF output, or in other words information of Doppler frequency. Then, IF output is filtered and amplified to process the signal digitally. Filtered and amplified signal showing Doppler frequency is used as an input of audio input of a computer. After getting this data Doppler frequency is shown as a speed change on a figure via Matlab script. According to experimental field measurements the accuracy of speed measurement is approximately %90. In range detection mode, a chirp signal is used to form a FM chirp. This FM chirp helps to determine the range of the target since only Doppler frequency measured with CW is not enough for range detection. Such a FMCW Doppler radar may be used in border security of the countries since it is capable of both speed and range detection.

Keywords: doppler radar, FMCW, range detection, speed detection

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Authors: Saad M. Howladar, Mike Dennett

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The effect of salinity (0-200 mMNaCl) on wheat growth (leaf and tiller numbers, and fresh and dry weights) underseed soaking (6 and 24 hs) insalicylic acid (SA) was investigated. The impact of salinity was less pronounced in salt tolerant cultivars (Sakha 93 and S24) than Paragon and S24. Chlorophyll content was increased as a response to salinity stress. It was raised in 100 mMNaCl more than 200 mMNaCl. The same trend was found in 24 hs soaking, except chlorophyll content in Paragon and S24 under 200 mMNaCl was more than 100 mMNaCl. SA application induced a positive effect on growth parameters in some cultivars, particularly Paragon under saline and non-saline condition. Soaking for 6 hs was more effective than 24 hs soaking, especially in Paragon and Sakha 93. SA supply caused a slight effect on chlorophyll content but this was not significant and there was no significant difference between both soaking hs. The effect of SA on growth parameters and chlorophyll content depends on cultivar genotype and SA concentration.

Keywords: salinity, salicylic acid, growth parameters, chlorophyll content, wheat cultivars

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Authors: M. G. Gopisankar, A. Surendiran, M. Hemachandren

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The dose requirement of warfarin to achieve target INR range varies in patients with prosthetic heart valve. This variation in is affected by both genetic and non-genetic factors. Earlier studies have identified role of CYP2C9 and VKORC1 genetic polymorphisms on warfarin dose requirement. Warfarin being a substrate for drug transporter, P-glycoprotein coded by ABCB1 gene, may also be influenced by its genetic polymorphisms. This study was aimed to study the effect of single nucleotide polymorphism (SNP), ABCB1 2677G > T on warfarin maintenance dose requirement in patients with steady-state International Normalized Ratio (INR). The median dose requirement was significantly different between the genotype groups GG vs. GT (35 ± 20; 42.5 ± 18, p < 0.05), GG vs. TT (35 ± 20; 41.25 ± 25, p<0.05). There was no significant difference between GT vs. TT. In conclusion, patients with variant allele require a higher weekly maintenance dose of warfarin compared to patients without variant allele.

Keywords: warfarin pharamcogenetics, pharmacogenomics of warfarin, ABCB1 and warfarin, pglycoprotein and warfarin

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Authors: M. F. Miah, A. Chakrabarty

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Two popular and highly valued fish, Stinging catfish (Heteropneustes fossilis) and Asian catfish (Clarias batrachus) are considered for observing genetic enhancement. Cross breeding was performed considering wild and farmed fish through inducing agent. Five RAPD markers were used to assess genetic diversity among parents and offspring of these two catfish for evaluating genetic enhancement in F1 generation. Considering different genetic data such as banding pattern of DNA, polymorphic loci, polymorphic information content (PIC), inter individual pair wise similarity, Nei genetic similarity, genetic distance, phylogenetic relationships, allele frequency, genotype frequency, intra locus gene diversity and average gene diversity of parents and offspring of these two fish were analyzed and finally in both cases higher genetic diversity was found in F1 generation than the parents.

Keywords: Heteropneustes fossilis, Clarias batrachus, cross breeding, genetic enhancement

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Authors: Jianguo Huang, Hong Cai, Bin Dong, Jifang Tao, Aiqun Liu, Dim-Lee Kwong, Yuandong Gu

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We developed a miniaturized tunable optomechanical oscillator based on the nanoelectromechanical systems (NEMS) technology, and its frequencies can be electrostatically tuned by as much as 10%. By taking both advantages of optical and electrical spring, the oscillator achieves a high tuning sensitivity without resorting to mechanical tension. In particular, the proposed high-Q optical cavity design greatly enhances the system sensitivity, making it extremely sensitive to the small motional signal.

Keywords: nanoelectromechanical systems (NEMS), nanotechnology, optical force, oscillator

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Authors: Fumiya Sugino, Naohiro Nakamura, Yuji Miyazu

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In earthquake resistant design of buildings, evaluation of vibration characteristics is important. In recent years, due to the increment of super high-rise buildings, the evaluation of response is important for not only the first mode but also higher modes. The knowledge of vibration characteristics in buildings is mostly limited to the first mode and the knowledge of higher modes is still insufficient. In this paper, using earthquake observation records of a SRC building by applying frequency filter to ARX model, characteristics of first and second modes were studied. First, we studied the change of the eigen frequency and the damping ratio during the 3.11 earthquake. The eigen frequency gradually decreases from the time of earthquake occurrence, and it is almost stable after about 150 seconds have passed. At this time, the decreasing rates of the 1st and 2nd eigen frequencies are both about 0.7. Although the damping ratio has more large error than the eigen frequency, both the 1st and 2nd damping ratio are 3 to 5%. Also, there is a strong correlation between the 1st and 2nd eigen frequency, and the regression line is y=3.17x. In the damping ratio, the regression line is y=0.90x. Therefore 1st and 2nd damping ratios are approximately the same degree. Next, we study the eigen frequency and damping ratio from 1998 after 3.11 earthquakes, the final year is 2014. In all the considered earthquakes, they are connected in order of occurrence respectively. The eigen frequency slowly declined from immediately after completion, and tend to stabilize after several years. Although it has declined greatly after the 3.11 earthquake. Both the decresing rate of the 1st and 2nd eigen frequencies until about 7 years later are about 0.8. For the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1% and the 2nd increases by less than 1%. For the eigen frequency, there is a strong correlation between the 1st and 2nd, and the regression line is y=3.17x. For the damping ratio, the regression line is y=1.01x. Therefore, it can be said that the 1st and 2nd damping ratio is approximately the same degree. Based on the above results, changes in eigen frequency and damping ratio are summarized as follows. In the long-term study of the eigen frequency, both the 1st and 2nd gradually declined from immediately after completion, and tended to stabilize after a few years. Further it declined after the 3.11 earthquake. In addition, there is a strong correlation between the 1st and 2nd, and the declining time and the decreasing rate are the same degree. In the long-term study of the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1%, the 2nd increases by less than 1%. Also, the 1st and 2nd are approximately the same degree.

Keywords: eigenfrequency, damping ratio, ARX model, earthquake observation records

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Authors: Oyvind Nordvik, Peder O. L. Heggdal, Jonas Brannstrom, Flemming Vassbotn, Anne Kari Aarstad, Hans Jorgen Aarstad

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Background: Hearing Loss (HL) is a condition that may affect people in all stages of life, but the prevalence increases with age, mostly because of age-related HL, generally referred to as presbyacusis. As human speech is related to relatively high frequencies, even a limited hearing loss at high frequencies may cause impaired speech intelligibility. Being diagnosed with, treated for and living with a chronic condition such as HL, must for many be a disabling and stressful condition that put ones coping resources to test. Stress is a natural part of life and most people will experience stressful events or periods. Chronic diseases, such as HL, are risk factor for distress in individuals, causing anxiety and lowered mood. How an individual cope with HL may be closely connected to the level of distress he or she is experiencing and to personality, which can be defined as those characteristics of a person that account for consistent patterns of feelings, thinking, and behavior. Thus, as to distress in life, such as illness or disease, available coping strategies may be more important than the challenge itself. The same line of arguments applies to level of experienced health-related quality of life (HRQoL). Aim: The aim of this study was to investigate the relationship between distress, HRQoL, reported hearing loss, personality and coping in patients with HL. Method: 158 adult (aged 18-78 years) patients with HL, referred for hearing aid (HA) fitting at Haukeland University Hospital in western Norway, participated in the study. Both first-time users, as well as patients referred for HA renewals were included. First-time users had been pre-examined by an ENT-specialist. The questionnaires were answered before the actual HA fitting procedure. The pure-tone average (PTA; frequencies 0.5, 1, 2, and 4 kHz) was determined for each ear. The Eysenck personality inventory, neuroticism and lie scales, the Theoretically Originated Measure of the Cognitive Activation Theory of Stress (TOMCATS) measuring active coping, hopelessness and helplessness, as well as distress (General Health Questionnaire (GHQ) - 12 items) and the EORTC Quality of Life Questionnaire general part were answered. In addition, we used a revised and shortened version of the Abbreviated Profile of Hearing Aid Benefit (APHAB) as a measure of patient-reported hearing loss. Results: Significant correlations were determined between APHAB (weak), HRQoL scores (strong), distress scores (strong) on the one side and personality and choice of coping scores on the other side. As measured by stepwise regression analyses, the distress and HRQoL scores were scored secondary to the obtained personality and coping scores. The APHAB scores were as determined by regression analyses scored secondary to PTA (best ear), level of neuroticism and lie score. Conclusion: We found that reported employed coping style, distress/HRQoL and personality are closely connected to each other in this patient group. Patient-reported HL was associated to hearing level and personality. There is need for further investigations on these questions, and how these associations may influence the clinical context.

Keywords: coping, distress, hearing loss, personality

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Authors: Foad Alzoughool

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Conflicting studies on the association between the rs5219 polymorphism and type 2 diabetes, some studies have confirmed a strong relationship between this variant and type2 diabetes, on the other hand, many studies denied the existence of this association. This study aimed to provide evidence about whether the rs5219 polymorphism has or hasn't a role as a risk factor for diabetes and meta-analysis to investigate the role of the control age group in the association. Genotyping of the rs5219 polymorphism was performed in a cohort of 266 healthy elderly subjects with a mean age (60.2 ± 5.1) with no history of diabetes (HbA1c < 6%) using standard Sanger sequencing methods. Lys/Lys alleles were detected in 20 persons (7.5%), Lys/Glu alleles in 96 persons (36.1%), and Glu/Glu in 150 persons (56.4%). The genotype distribution was consistent with Hardy–Weinberg equilibrium (P =0.7). Meta-analysis notably indicates no association between rs5219 polymorphism and type 2 diabetes in all studies used the younger age of the control group compared to the patient's age. In conclusion, our study sheds light on the importance of age factor among the control group recruited in case-control studies.

Keywords: Type 2 diabetes, rs5219 polymorphism, E23K, KCNJ11 gene

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Authors: Bharath Anantharamaiah, Tomas Bouda, Elke Deckers, Stijn Jonckheere, Wim Desmet, Juan J. Garcia

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Automotive tyres are gaining importance recently in terms of their noise emission, not only with respect to reduction in noise, but also their perception and detection. Tyres exhibit a mechanical noise generation mechanism up to 1 kHz. However, owing to the fact that tyre is a composite of several materials, it has been difficult to model it using finite elements to predict noise at high frequencies. The currently available FE models have a reliability of about 500 Hz, the limit which, however, is not enough to perceive the roughness or sharpness of noise from tyre. These noise components are important in order to alert pedestrians on the street about passing by slow, especially electric vehicles. In order to model tyre noise behaviour up to 1 kHz, its dynamic behaviour must be accurately developed up to a 1 kHz limit using finite elements. Materials play a vital role in modelling the dynamic tyre behaviour precisely. Since tyre is a composition of several components, their precise definition in finite element simulations is necessary. However, during the tyre manufacturing process, these components are subjected to various pressures and temperatures, due to which these properties could change. Hence, material definitions are better described based on the tyre responses. In this work, the hyperelasticity of tyre component rubbers is calibrated, using the design of experiments technique from the tyre characteristic responses that are measured on a stiffness measurement machine. The viscoelasticity of rubbers are defined by the Prony series for rubbers, which are determined from the loss factor relationship between the loss and storage moduli, assuming that the rubbers are excited within the linear viscoelasticity ranges. These values of loss factor are measured and theoretically expressed as a function of rubber shore hardness or hyperelasticities. From the results of the work, there exists a good correlation between test and simulation vibrational transfer function up to 1 kHz. The model also allows flexibility, i.e., the frequency limit can also be extended, if required, by calibrating the Prony parameters of rubbers corresponding to the frequency of interest. As future work, these tyre models are used for noise generation at high frequencies and thus for tyre noise perception.

Keywords: tyre dynamics, rubber materials, prony series, hyperelasticity

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Authors: Rohit Shrivastava, Stefan Luding

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A mechanical wave is propagation of vibration with transfer of energy and momentum. Studying the energy as well as spectral energy characteristics of a propagating wave through disordered granular media can assist in understanding the overall properties of wave propagation through inhomogeneous materials like soil. The study of these properties is aimed at modeling wave propagation for oil, mineral or gas exploration (seismic prospecting) or non-destructive testing for the study of internal structure of solids. The study of Energy content (Kinetic, Potential and Total Energy) of a pulse propagating through an idealized one-dimensional discrete particle system like a mass disordered granular chain can assist in understanding the energy attenuation due to disorder as a function of propagation distance. The spectral analysis of the energy signal can assist in understanding dispersion as well as attenuation due to scattering in different frequencies (scattering attenuation). The selection of one-dimensional granular chain also helps in studying only the P-wave attributes of the wave and removing the influence of shear or rotational waves. Granular chains with different mass distributions have been studied, by randomly selecting masses from normal, binary and uniform distributions and the standard deviation of the distribution is considered as the disorder parameter, higher standard deviation means higher disorder and lower standard deviation means lower disorder. For obtaining macroscopic/continuum properties, ensemble averaging has been used. Interpreting information from a Total Energy signal turned out to be much easier in comparison to displacement, velocity or acceleration signals of the wave, hence, indicating a better analysis method for wave propagation through granular materials. Increasing disorder leads to faster attenuation of the signal and decreases the Energy of higher frequency signals transmitted, but at the same time the energy of spatially localized high frequencies also increases. An ordered granular chain exhibits ballistic propagation of energy whereas, a disordered granular chain exhibits diffusive like propagation, which eventually becomes localized at long periods of time.

Keywords: discrete elements, energy attenuation, mass disorder, granular chain, spectral energy, wave propagation

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Authors: Md Monir Hossain, Anne Staples, Kuya Takami, Tomonari Furukawa

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Tire noise has a significant impact on ride quality and vehicle interior comfort, even at low frequency. Reduction of tire noise is especially important due to strict state and federal environmental regulations. The primary sources of tire noise are the low frequency structure-borne noise and the noise that originates from the release of trapped air between the tire tread and road surface during each revolution of the tire. The frequency response of the tire changes at low and high frequency. At low frequency, the tension and bending moment become dominant, while the internal structure and local deformation become dominant at higher frequencies. Here, we analyze tire response in terms of deformation and rolling velocity at low revolution frequency. An Abaqus FEA finite element model is used to calculate the static and dynamic response of a rolling tire under different rolling conditions. The natural frequencies and mode shapes of a deformed tire are calculated with the FEA package where the subspace-based steady state dynamic analysis calculates dynamic response of tire subjected to harmonic excitation. The analysis was conducted on the dynamic response at the road (contact point of tire and road surface) and side nodes of a static and rolling tire when the tire was excited with 200 N vertical load for a frequency ranging from 20 to 200 Hz. The results show that frequency has little effect on tire deformation up to 80 Hz. But between 80 and 200 Hz, the radial and lateral components of displacement of the road and side nodes exhibited significant oscillation. For the static analysis, the fluctuation was sharp and frequent and decreased with frequency. In contrast, the fluctuation was periodic in nature for the dynamic response of the rolling tire. In addition to the dynamic analysis, a steady state rolling analysis was also performed on the tire traveling at ground velocity with a constant angular motion. The purpose of the computation was to demonstrate the effect of rotating motion on deformation and rolling velocity with respect to a fixed Newtonian reference point. The analysis showed a significant variation in deformation and rolling velocity due to centrifugal and Coriolis acceleration with respect to a fixed Newtonian point on ground.

Keywords: natural frequency, rotational motion, steady state rolling, subspace-based steady state dynamic analysis

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Authors: Farrah Putri Salmanida, Mei-Li Wu, Rika Wahyuningtyas, Wen-Bin Chung, Hso-Chi Chaung, Ko-Tung Chang

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Within the field of immunotherapy, oncolytic virotherapy (OVT) employs dual approaches that directly eliminate tumor cells while preserving healthy ones and indirectly reprogram the tumor microenvironment (TME) to elicit antitumor responses. Within the TME, tumor associated macrophages (TAMs) manifest characteristics akin to those of anti-inflammatory M2 macrophages, thus earning the designation of M2-like TAMs. In prior research, two antigens denoted as A1 (g6Ld10T) and A3 (ORF6L5), derived from a complete sequence of ORF5 with partial sequence of ORF6 in Porcine Reproductive and Respiratory Syndrome Virus Genotype 2 (PRRSV-2), demonstrated the capacity to repolarize M2-type porcine alveolar macrophages (PAMs) into M1 phenotypes. In this study, we sought for utilizing OVT strategies by introducing A1 or A3 on TAMs to endow them with the anti-tumor traits of M1 macrophages while retaining their capacity to target cancer cells. Upon exposing human THP-1-derived M2 macrophages to a cross-species test with 2 µg/ml of either A1 or A3 for 24 hours, real time PCR revealed that A3, but not A1, treated cells exhibited upregulated gene expressions of M1 markers (CCR7, IL-1ß, CCL2, Cox2, CD80). These cells reacted to virus-derived antigen, as evidenced by increased expression of pattern-recognition receptors TLR3, TLR7, and TLR9, subsequently providing feedback in the form of type I interferon responses like IFNAR1, IFN-ß, IRF3, IRF7, OAS1, Mx1, and ISG15. Through an MTT assay, only after 15 µg/ml of A3 treatment could the cell viability decrease, with a predicted IC50 of 16.96 µg/ml. Interestingly, A3 caused dose-dependent toxicity to a rat C6 glial cancer cell line even at doses as low as 2.5 µg/ml and reached its IC50 at 9.419 µg/ml. Using Annexin V/7AAD staining and PCR test, we deduced that a significant proportion of C6 cells were undergoing the early apoptosis phase predominantly through the intrinsic apoptosis cascade involving Bcl-2 family proteins. Following this stage, we conducted a test on A3’s repolarization ability, which revealed a significant rise in M1 gene expression markers, such as TNF, CD80, and IL-1ß, in M2-like TAMs generated in vitro from murine RAW264.7 macrophages grown with conditioned medium of 4T1 breast cancer cells. This was corroborated by the results of transcriptome analysis, which revealed that the primary subset among the top 10 to top 30 significantly upregulated differentially expressed genes (DEGs) dominantly consisted of M1 macrophages profiles, including Ccl3, Ccl4, Csf3, TNF, Bcl6b, Stc1, and Dusp2. Our findings unveiled the remarkable potential of the PRRSV-derived antigen A3 to repolarize macrophages while also being capable of selectively inducing apoptosis in cancerous cells. While further in vivo study is needed for A3, it holds promise as an adjuvant by its dual effects in cancer therapy modalities.

Keywords: cancer cell apoptosis, interferon responses, macrophage repolarization, recombinant protein

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