Search results for: simple sequence repeats

Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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A simple adaptive voice activity detector (VAD) is implemented using Gabor and gammatone atomic decomposition of speech for high Gaussian noise environments. Matching pursuit is used for atomic decomposition, and is shown to achieve optimal speech detection capability at high data compression rates for low signal to noise ratios. The most active dictionary elements found by matching pursuit are used for the signal reconstruction so that the algorithm adapts to the individual speakers dominant time-frequency characteristics. Speech has a high peak to average ratio enabling matching pursuit greedy heuristic of highest inner products to isolate high energy speech components in high noise environments. Gabor and gammatone atoms are both investigated with identical logarithmically spaced center frequencies, and similar bandwidths. The algorithm performs equally well for both Gabor and gammatone atoms with no significant statistical differences. The algorithm achieves 70% accuracy at a 0 dB SNR, 90% accuracy at a 5 dB SNR and 98% accuracy at a 20dB SNR using 30dB SNR as a reference for voice activity.

Keywords: atomic decomposition, gabor, gammatone, matching pursuit, voice activity detection

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Authors: Louise H. Gracioso, Marcela P.G. Baltazar, Ingrid R. Avanzi, Bruno Karolski, Luciana J. Gimenes, Claudio O. Nascimento, Elen A. Perpetuo

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Introduction: Higher copper concentrations promote a selection pressure on organisms such as plants, fungi and bacteria, which allows surviving only the resistant organisms to the contaminated site. This selective pressure keeps only the organisms most resistant to a specific condition and subsequently increases their bioremediation potential. Despite the bacteria importance for biosphere maintenance, it is estimated that only a small fraction living microbial species has been described and characterized. Due to the molecular biology development, tools based on analysis 16S ribosomal RNA or another specific gene are making a new scenario for the characterization studies and identification of microorganisms in the environment. News identification of microorganisms methods have also emerged like Biotyper (MALDI / TOF), this method mass spectrometry is subject to the recognition of spectroscopic patterns of conserved and features proteins for different microbial species. In view of this, this study aimed to isolate bacteria resistant to copper present in a Copper Processing Area (Sossego Mine, Canaan, PA) and identifies them in two different methods: Recent (spectrometry mass) and conventional. This work aimed to use them for a future bioremediation of this Mining. Material and Methods: Samples were collected at fifteen different sites of five periods of times. Microorganisms were isolated from mining wastes by culture enrichment technique; this procedure was repeated 4 times. The isolates were inoculated into MJS medium containing different concentrations of chloride copper (1mM, 2.5mM, 5mM, 7.5mM and 10 mM) and incubated in plates for 72 h at 28 ºC. These isolates were subjected to mass spectrometry identification methods (Biotyper – MALDI/TOF) and 16S gene sequencing. Results: A total of 105 strains were isolated in this area, bacterial identification by mass spectrometry method (MALDI/TOF) achieved 74% agreement with the conventional identification method (16S), 31% have been unsuccessful in MALDI-TOF and 2% did not obtain identification sequence the 16S. These results show that Biotyper can be a very useful tool in the identification of bacteria isolated from environmental samples, since it has a better value for money (cheap and simple sample preparation and MALDI plates are reusable). Furthermore, this technique is more rentable because it saves time and has a high performance (the mass spectra are compared to the database and it takes less than 2 minutes per sample).

Keywords: copper mining area, bioremediation, microorganisms, identification, MALDI/TOF, RNA 16S

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Authors: A. Kyprianou, A. Tjirkallis

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Condition monitoring of structures in service is very important as it provides information about the risk of damage development. One of the essential constituents of structural condition monitoring is the damage detection methodology. In the context of condition monitoring of in service structures a damage detection methodology analyses data obtained from the structure while it is in operation. Usually, this means that the data could be affected by operational and environmental conditions in a way that could mask the effects of a possible damage on the data. This, depending on the damage detection methodology, could lead to either false alarms or miss existing damages. In this article a damage detection methodology that is based on the Spatio-temporal continuous wavelet transform (SPT-CWT) analysis of a sequence of experimental time responses of a cantilever beam is proposed. The cantilever is subjected to white and pink noise excitation to simulate different operating conditions. In addition, in order to simulate changing environmental conditions, the cantilever is subjected to heating by a heat gun. The response of the cantilever beam is measured by a high-speed camera. Edges are extracted from the series of images of the beam response captured by the camera. Subsequent processing of the edges gives a series of time responses on 439 points on the beam. This sequence is then analyzed using the SPT-CWT to identify damage. The algorithm proposed was able to clearly identify damage under any condition when the structure was excited by white noise force. In addition, in the case of white noise excitation, the analysis could also reveal the position of the heat gun when it was used to heat the structure. The analysis could identify the different operating conditions i.e. between responses due to white noise excitation and responses due to pink noise excitation. During the pink noise excitation whereas damage and changing temperature were identified it was not possible to clearly identify the effect of damage from that of temperature. The methodology proposed in this article for damage detection enables the separation the damage effect from that due to temperature and excitation on data obtained from measurements of a cantilever beam. This methodology does not require information about the apriori state of the structure.

Keywords: spatiotemporal continuous wavelet transform, damage detection, data normalization, varying temperature

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Authors: Salman Akrokayan

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Synthetic cDNA (ScDNA) of granulocyte colony-stimulating factor (G-CSF) was constructed using a DNA synthesizer with the aim to increase its expression level. 5' end of the ScDNA of G-CSF coding region was modified by decreasing the GC content without altering the predicted amino acids sequence. The identity of the resulting protein from ScDNA was confirmed by the highly specific enzyme-linked immunosorbent assay. In conclusion, a synthetic G-CSF cDNA in combination with the recombinant DNA protocol offers a rapid and reliable strategy for synthesizing the target protein. However, the commercial utilization of this methodology requires rigorous validation and quality control.

Keywords: synthetic cDNA, recombinant G-CSF, cloning, gene expression

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Duaa Mughal, Syeda Areeba Nadeem, Shakil Ahmed, Ishtiaq Ahmed Khan

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The identification of porcine DNA in Halal food items is critical to ensuring compliance with dietary restrictions and religious beliefs. In Islam, Porcine is prohibited as clearly mentioned in Quran (Surah Al-Baqrah, Ayat 173). The purpose of this study was to compare two DNA extraction procedures for detecting 0.001% of porcine DNA in processed Halal food sample mixtures containing chicken, camel, veal, turkey and goat meat using the TaqMan Real-Time PCR technology. In this research, two different commercial kit protocols were compared. The processed sample mixtures were prepared by spiking known concentration of porcine DNA to non-porcine food matrices. Afterwards, TaqMan Real-Time PCR technique was used to target a particular porcine gene from the extracted DNA samples, which was quantified after extraction. The results of the amplification were evaluated for sensitivity, specificity, and reproducibility. The results of the study demonstrated that two DNA extraction techniques can detect 0.01% of porcine DNA in mixture of Halal food samples. However, as compared to the alternative approach, Eurofins| GeneScan GeneSpin DNA Isolation kit showed more effective sensitivity and specificity. Furthermore, the commercial kit-based approach showed great repeatability with minimal variance across repeats. Quantification of DNA was done by using fluorometric assay. In conclusion, the comparison of DNA extraction methods for detecting porcine DNA in Halal food sample mixes using the TaqMan Real-Time PCR technology reveals that the commercial kit-based approach outperforms the other methods in terms of sensitivity, specificity, and repeatability. This research helps to promote the development of reliable and standardized techniques for detecting porcine DNA in Halal food items, religious conformity and assuring nutritional.

Keywords: real time PCR (qPCR), DNA extraction, porcine DNA, halal food authentication, religious conformity

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Authors: Parvin Samadi Pakchin, Reza Saber, Hossein Ghanbari, Yadollah Omidi

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Ovarian cancer is one of the leading cause of mortality among the gynecological malignancies, and it remains the one of the most prevalent cancer in females worldwide. Tumor markers are biochemical molecules in blood or tissues which can indicates cancers occurrence in the human body. So, the sensitive and specific detection of cancer markers typically recruited for diagnosing and evaluating cancers. Recently extensive research efforts are underway to achieve a simple, inexpensive and accurate device for detection of cancer biomarkers. Compared with conventional immunoassay techniques, electrochemical immunosensors are of great interest, because they are specific, simple, inexpensive, easy to handling and miniaturization. Moreover, in the past decade nanotechnology has played a crucial role in the development of biosensors. In this study, a signal-off electrochemical immunosensor for the detection of CA125 antigen has been developed using chitosan-gold nanoparticles (CS-AuNP) and multi-wall carbon nanotubes (MWCNT) composites. Toluidine blue (TB) is used as redox probe which is immobilized on the electrode surface. CS-AuNP is synthesized by a simple one step method that HAuCl4 is reduced by NH2 groups of chitosan. The CS-AuNP-MWCNT modified electrode has shown excellent electrochemical performance compared with bare Au electrode. MWCNTs and AuNPs increased electrochemical conductivity and accelerate electrons transfer between solution and electrode surface while excessive amine groups on chitosan lead to the effective loading of the biological material (CA125 antibody) and TB on the electrode surface. The electrochemical, immobilization and sensing properties CS-AuNP-MWCNT-TB modified electrodes are characterized by cyclic voltammetry, electrochemical impedance spectroscopy, differential pulse voltammetry and square wave voltammetry with Fe(CN)63−/4−as an electrochemical redox indicator.

Keywords: signal-off electrochemical biosensor, CA125, ovarian cancer, chitosan-gold nanoparticles

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Authors: Benjamin Lee Warren

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Many problems exist in additive number theory which is essential to determine the primes that are the sum of two elements from a given single-variable polynomial sequence, and most of them are unattackable in the present day. Here, we determine solutions for this problem to a few certain sequences (certain binomial coefficients and power sums) using only elementary algebra and some algebraic factoring methods (as well as Euclid’s Lemma and Faulhaber’s Formula). In particular, we show that there are finitely many primes as sums of two of these types of elements. Several cases are fully illustrated, and bounds are presented for the cases not fully illustrated.

Keywords: binomial coefficients, power sums, primes, algebra

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: globular protein, modulating function, white noise, winding probability

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Authors: Kyoungok Jung, Chang Hong Bak, Gyeong Cheon Jo, Jin-Baek Kim

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Nanostructured arrays have drawn extensive attention because of their unique properties resulting from nanoscale features. However, it is difficult to achieve uniform and freestanding 1D nanostrcutures over a large area. Here, a simple and novel method was developed for fabrication of universal nanoporous templates for high-density nanostructure arrays, by combining self-assembly of a Si-containing block copolymer with a bilayer lithography system. We introduced a dually responsive photoresist bottom layer into which the nanopatterns of block copolymer are transferred by oxygen reactive ion etching. Because the dually responsive layer becomes cross-linked by heating, it can be used as a hard template during the etching process. It becomes soluble again by chain scission upon exposure to light. Therefore, it can be easily removed by the lift-off process. The template was applicable to the various conducting substrates due to the compatibility of the photoresist with a wide range of substrates and was used in electrodeposition for well-aligned and high-density inorganic and organic nanoarrays. We successfully obtained vertically aligned and highly ordered gold nanorods and polypyrrole dots on the substrate without aggregation, and these arrays did not collapse after removing the dually responsive templates by the simple lift-off process.

Keywords: block copolymer, dually responsive, nanostructure, photoresist

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Authors: Mina Mortazavi, Pezhman Sharafi

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Cold-formed steel sections are popular construction materials as structural or non-structural elements. The objective of this paper is to propose an optimisation method for open cross sections targeting the maximum nominal axial strength. The cross sections considered in the optimisation process should all meet a determined critical global buckling load to be considered as a candidate for optimisation process. The maximum dimensions of the cross section are fixed and limited into a predefined rectangular area. The optimisation process is repeated for different available coil thicknesses of 1 mm, 2.5 mm and 3 mm to determine the optimum thickness according to the cross section buckling behaviour. A simple-simple boundary is assumed as end conditions. The number of folds is limited to 20 folds to prevent extra complicated sections. The global buckling load is considered as Euler load and is determined according to the moment of inertia of the cross-section with a constant length. The critical buckling loads are obtained using Finite Strip Method. The results of the optimisation analysis are provided, and the optimum cross-section within the considered range is determined.

Keywords: shape optimisation, buckling, cold formed steel, finite strip method

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Authors: Abdul Hakim Chikho

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Calculating the ultimate load of a column in a sway framed structure involves, in the currently used design method, the calculation of the column effective length and utilizing the interaction formulas or tables. Therefore, no allowance is usually made for the effects of the presence of semi rigid connections or the presence of infill panels. In this paper, a new and simple design procedure is recommend to calculate the ultimate load of a framed Column allowing for the presence of rotational end restraints, semi rigid connections, the column end moments resulted from the applied vertical and horizontal loading and infill panels in real steel structure. In order to verify the accuracy of the recommended method to predict good and safe estimations of framed column ultimate loads, several examples have been solved utilizing the recommended procedure, and the results were compared to those obtained using a second order computer program, and good correlation had been obtained. Therefore, the accuracy of the proposed method to predict the Behaviour of practical steel columns in framed structures has been verified.

Keywords: column ultimate load, semi rigid connections, steel column, infill panel, steel structure

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Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

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Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity

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Authors: Rajkumar Ghosh

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Jhakri Thrust (JT), Sarahan Thrust (ST), and Chaura Thrust (CT) are the three OOST along Jakhri-Chaura segment along the Sutlej river valley in Himachal Pradesh. CT is deciphered only by Apatite Fission Track dating. Such geochronological information is not currently accessible for the Jhakri and Sarahan thrusts. JT was additionally validated as OOST without any dating. The described rock types include ductile sheared gneisses and upper greenschist-amphibolite facies metamorphosed schists. Locally, the Munsiari (Jutogh) Thrust is referred to as the JT. Brittle shear, the JT, borders the research area's southern and ductile shear, the CT, and its northern margins. The JT has a 50° western dip and is south-westward verging. It is 15–17 km deep. A progressive rise in strain towards the JT zone based on microstructural tests was observed by previous researchers. The high-temperature ranges of the MCT root zone are cited in the current work as supportive evidence for the ductile nature of the OOST. In Himachal Pradesh, the lithological boundaries for OOST are not set. In contrast, the Sarahan thrust is NW-SE striking and 50-80 m wide. ST and CT are probably equivalent and marked by a sheared biotite-chlorite matrix with a top-to-SE kinematic indicator. It is inferred from cross-section balancing that the CT is folded with this anticlinorium. These thrust systems consist of several branches, some of which are still active. The thrust system exhibits complex internal geometry consisting of box folds, boudins, scar folds, crenulation cleavages, kink folds, and tension gashes. Box folds are observed on the hanging wall of the Chaura thrust. The ductile signature of CT represents steepen downward of the thrust. After the STDSU stopped deformation, out-of-sequence thrust was initiated in some sections of the Higher Himalaya. A part of GHC and part of the LH is thrust southwestward along the Jutogh Thrust/Munsiari Thrust/JT as also the Jutogh Nappe. The CT is concealed beneath Jutogh Thrust sheet hence the basal part of GHC is unexposed to the surface in Sutlej River section. Fieldwork and micro-structural studies of the Greater Himalayan Crystalline (GHC) along the Sutlej section reveal (a) initial top-to-SW sense of ductile shearing (CT); (b) brittle-ductile extension (ST); and (c) uniform top-to-SW sense of brittle shearing (JT). A group of samples of schistose rock from Jutogh Group of Greater Himalayan Crystalline and Quartzite from Rampur Group of Lesser Himalayan Crystalline were analyzed. No such physiographic transition in that area is to determine a break in the landscape due to OOST. OOSTs from GHC are interpreted mainly from geochronological studies to date, but proper field evidence is missing. Apart from minimal documentation in geological mapping for OOST, there exists a lack of suitable exposure of rock to generalize the features of OOST in the field in NW Higher Himalaya. Multiple sets of thrust planes may be activated within this zone or a zone along which OOST is engaged.

Keywords: out-of-sequence thrust, main central thrust, grain boundary migration, South Tibetan detachment system, Jakhri Thrust, Sarahan Thrust, Chaura Thrust, higher Himalaya, greater Himalayan crystalline

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Authors: Assia Amri, Naima Layachi, Ali Ladjama

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The characterization of some Algerian honey was carried out on the basis of their physico-chemical properties: moisture,hydroxy methyl furfural, diastase activity, pH,free, total and lactonic acidity, electrical conductivity, minerals and proline content. Studied samples are found to be low in moisture and therefore safe from fermentation, low in HMF level and high in diastase activity. Additionally the diastase activity and the HMF content are widely recognized parameters indicating the freshness of honey. Phenolic compounds present in honey are classified into two groups - simple phenols and polyphenols. The simple phenols in honey are various phenol acids, but polyphenols are various flavonoids and flavonides. The aim of our work was to determine antioxidant properties of various Algerian honey samples–the total phenol content, total flavonoids content, as well as honey anti radical activity.The quality of honey samples differs on account of various factors such as season, packaging and processing conditions, floral source, geographical origin and storage period. It is important that precautions should be taken to ensure standardization and rationalization of beekeeping techniques, manufacturing procedures and storing processes to improve honey quality.

Keywords: honey, physico-chemical characterization, phenolic coumpound, HMF, diastase activity

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Authors: Salman Obaidoon, Mohamed Hassan, Omer Bakather

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As environmental regulations increase, the need for a clean and inexpensive energy is becoming necessary these days using an available raw material with high efficiency and low emissions of toxic gases. This paper presents a study on modifying a gas turbine power plant fired by diesel, which is located in Saudi Arabia in order to increase the efficiency and capacity of the station as well as decrease the rate of emissions. The studied power plant consists of 30 units with different capacities and total net power is 1470 MW. The study was conducted on unit number 25 (GT-25) which produces 72.3 MW with 29.5% efficiency. In the beginning, the unit was modeled and simulated by using WinSim Design II software. In this step, actual unit data were used in order to test the validity of the model. The net power and efficiency obtained from software were 76.4 MW and 32.2% respectively. A difference of about 6% was found in the simulated power plant compared to the actual station which means that the model is valid. After the validation of the model, the simple gas turbine power plant was converted to a combined cycle power plant (CCPP). In this case, the exhausted gas released from the gas turbine was introduced to a heat recovery steam generator (HRSG), which consists of three heat exchangers: an economizer, an evaporator and a superheater. In this proposed model, many scenarios were conducted in order to get the optimal operating conditions. The net power of CCPP was increased to 116.4 MW while the overall efficiency of the unit was reached to 49.02%, consuming the same amount of fuel for the gas turbine power plant. For the purpose of comparing the rate of emissions of carbon dioxide on each model. It was found that the rate of CO₂ emissions was decreased from 15.94 kg/s to 9.22 kg/s by using the combined cycle power model as a result of reducing of the amount of diesel from 5.08 kg/s to 2.94 kg/s needed to produce 76.5 MW. The results indicate that the rate of emissions of carbon dioxide was decreased by 42.133% in CCPP compared to the simple gas turbine power plant.

Keywords: combined cycle power plant, efficiency, heat recovery steam generator, simulation, validation, WinSim design II software

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Authors: Rosa Figueroa, Christopher Flores

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Text categorization is the problem of assigning a new document to a set of predetermined categories, on the basis of a training set of free-text data that contains documents whose category membership is known. To train a classification model, it is necessary to extract characteristics in the form of tokens that facilitate the learning and classification process. In text categorization, the feature extraction process involves the use of word sequences also known as N-grams. In general, it is expected that documents belonging to the same category share similar features. The Smith-Waterman (SW) algorithm is a dynamic programming algorithm that performs a local sequence alignment in order to determine similar regions between two strings or protein sequences. This work explores the use of SW algorithm as an alternative to feature extraction in text categorization. The dataset used for this purpose, contains 2,610 annotated documents with the classes Obese/Non-Obese. This dataset was represented in a matrix form using the Bag of Word approach. The score selected to represent the occurrence of the tokens in each document was the term frequency-inverse document frequency (TF-IDF). In order to extract features for classification, four experiments were conducted: the first experiment used SW to extract features, the second one used unigrams (single word), the third one used bigrams (two word sequence) and the last experiment used a combination of unigrams and bigrams to extract features for classification. To test the effectiveness of the extracted feature set for the four experiments, a Support Vector Machine (SVM) classifier was tuned using 20% of the dataset. The remaining 80% of the dataset together with 5-Fold Cross Validation were used to evaluate and compare the performance of the four experiments of feature extraction. Results from the tuning process suggest that SW performs better than the N-gram based feature extraction. These results were confirmed by using the remaining 80% of the dataset, where SW performed the best (accuracy = 97.10%, weighted average F-measure = 97.07%). The second best was obtained by the combination of unigrams-bigrams (accuracy = 96.04, weighted average F-measure = 95.97) closely followed by the bigrams (accuracy = 94.56%, weighted average F-measure = 94.46%) and finally unigrams (accuracy = 92.96%, weighted average F-measure = 92.90%).

Keywords: comorbidities, machine learning, obesity, Smith-Waterman algorithm

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Authors: Jaehyung An, Sungjoo Lee

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Patent documents constitute an up-to-date and reliable source of knowledge for reflecting technological advance, so patent analysis has been widely used for identification of technological trends and formulation of technology strategies. But, identifying technological information from patent data entails some limitations such as, high cost, complexity, and inconsistency because it rely on the expert’ knowledge. To overcome these limitations, researchers have applied to a quantitative analysis based on the keyword technique. By using this method, you can include a technological implication, particularly patent documents, or extract a keyword that indicates the important contents. However, it only uses the simple-counting method by keyword frequency, so it cannot take into account the sematic relationship with the keywords and sematic information such as, how the technologies are used in their technology area and how the technologies affect the other technologies. To automatically analyze unstructured technological information in patents to extract the semantic information, it should be transformed into an abstracted form that includes the technological key concepts. Specific sentence structure ‘SAO’ (subject, action, object) is newly emerged by representing ‘key concepts’ and can be extracted by NLP (Natural language processor). An SAO structure can be organized in a problem-solution format if the action-object (AO) states that the problem and subject (S) form the solution. In this paper, we propose the new methodology that can extract the SAO structure through technical elements extracting rules. Although sentence structures in the patents text have a unique format, prior studies have depended on general NLP (Natural language processor) applied to the common documents such as newspaper, research paper, and twitter mentions, so it cannot take into account the specific sentence structure types of the patent documents. To overcome this limitation, we identified a unique form of the patent sentences and defined the SAO structures in the patents text data. There are four types of technical elements that consist of technology adoption purpose, application area, tool for technology, and technical components. These four types of sentence structures from patents have their own specific word structure by location or sequence of the part of speech at each sentence. Finally, we developed algorithms for extracting SAOs and this result offer insight for the technology innovation process by providing different perspectives of technology.

Keywords: NLP, patent analysis, SAO, semantic-analysis

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Authors: M. Gogniashvili, I. Maisaia, A. Kotorashvili, N. Kotaria, T. Beridze

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Three types of plasmon (A, B and G) is typical for genus Triticum. In polyploid species - Triticum turgidum L. and Triticum aestivum L. plasmon B is detected. In the forthcoming paper, complete nucleotide sequence of chloroplast DNA of 11 representatives of Georgian wheat polyploid species, carrying plasmon B was determined. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. All contigs were aligned to the reference chloroplast genome sequence using BLASTN. For detection of SNPs and Indels and phylogeny tree construction computer programs Mafft and Blast were used. Using Triticum aestivum L. subsp. macha (Dekapr. & Menabde) Mackey var. paleocolchicum Dekapr. et Menabde as a reference, 5 SNPs can be identified in chloroplast DNA of Georgian endemic polyploid wheat. The number of noncoding substitutions is 2, coding substitutions - 3. In comparison with reference DNA two - 38 bp and 56 bp inversions were observed in paleocolchicum subspecies. There were six 1 bp indels detected in Georgian polyploid wheats, all of them at microsatellite stretches. The phylogeny tree shows that subspecies macha, carthlicum and paleocolchicum occupy different positions. According to the simplified scheme based on SNP and indel data, the ancestral, female parent of the all studied polyploid wheat is unknown X predecesor, from which four lines were formed. 1 SNP and two inversions (38 bp and 56 bp) caused the formation of subsp. paleocolchicum. Three other lines are macha, durum and carthlicum lines. Macha line is further divided into two sublines (M_1 and M_4). Carthlicum line includes subsp.carthlicum and T.aestivum - C_1 - C_2 - A_1. One of the central question of wheat domestication is which people(s) participated in wheat domestication? It is proposed that the predecessors of Georgian peoples (Proto-Kartvelians) must be placed, on the evidence of archaic lexical and toponymic data, in the mountainous regions of the western and central part of the Little Caucasus (the Transcaucasian foothills) at least 4,000 years ago. One of the possibility to explain the ‘wheat puzzle’ is that Kartvelian speakers brought domesticated wheat species and subspecis from Fertile Crescent further north to South Caucasus.

Keywords: chloroplast DNA, sequencing, SNP, triticum

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Authors: Minjung Kim, Hyunkoo Kang, Jinkoo Kim

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In this study, a seismic retrofit scheme for a reinforced concrete shear wall structure using steel slit dampers was presented. The stiffness and the strength of the slit damper used in the retrofit were verified by cyclic loading test. A genetic algorithm was applied to find out the optimum location of the slit dampers. The effects of the slit dampers on the seismic retrofit of the model were compared with those of jacketing shear walls. The seismic performance of the model structure with optimally positioned slit dampers was evaluated by nonlinear static and dynamic analyses. Based on the analysis results, the simple procedure for determining required damping ratio using capacity spectrum method along with the damper distribution pattern proportional to the inter-story drifts was validated. The analysis results showed that the seismic retrofit of the model structure using the slit dampers was more economical than the jacketing of the shear walls and that the capacity spectrum method combined with the simple damper distribution pattern led to satisfactory damper distribution pattern compatible with the solution obtained from the genetic algorithm.

Keywords: seismic retrofit, slit dampers, genetic algorithm, jacketing, capacity spectrum method

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Authors: Krishnendra Shekhawat

Abstract:

Given a graph G = (V, E), a rectangular dual of G represents the vertices of G by a set of interior-disjoint rectangles such that two rectangles touch if and only if there is an edge between the two corresponding vertices in G. Rectangular duals do not exist for every graph, so we can define maximal rectangular duals. A maximal rectangular dual is a rectangular dual of a graph G such that there exists no graph G ′ with a rectangular dual where G is a subgraph of G ′. In this paper, we enumerate all maximal rectangular duals (or, to be precise, the corresponding planar graphs) up to six nodes and presents a necessary condition for the existence of a rectangular dual. This work allegedly has applications in integrated circuit design and architectural floor plans.

Keywords: adjacency, degree sequence, dual graph, rectangular dual

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Authors: Narayan Moger, Divya B., Preethi Jambagi, Krishnaveni C. K., Apsana M. R., B. R. Patil, Basvaraj Bagewadi

Abstract:

Salinity is one of the major threats to world food security. Considering the requirement for salt tolerant crop plants in the present study was undertaken to clone and transferred the salt tolerant ectA gene from marine ecosystem into agriculture crop system to impart salinity tolerance. Ectoine is the compatible solute which accumulates in the cell membrane, is known to be involved in salt tolerance activity in most of the Halophiles. The present situation is insisting to development of salt tolerant transgenic lines to combat abiotic stress. In this background, the investigation was conducted to develop transgenic tomato lines by cloning and transferring of ectA gene is an ectoine derivative capable of enzymatic action for the production of acetyl-diaminobutyric acid. The gene ectA is involved in maintaining the osmotic balance of plants. The PCR amplified ectA gene (579bp) was cloned into T/A cloning vector (pTZ57R/T). The construct pDBJ26 containing ectA gene was sequenced by using gene specific forward and reverse primers. Sequence was analyzed using BLAST algorithm to check similarity of ectA gene with other isolates. Highest homology of 99.66 per cent was found with ectA gene sequences of isolates Halomonas elongata with the available sequence information in NCBI database. The ectA gene was further sub cloned into pRI101-AN plant expression vector and transferred into E. coli DH5α for its maintenance. Further pDNM27 was mobilized into A. tumefaciens LBA4404 through tri-parental mating system. The recombinant Agrobacterium containing pDNM27 was transferred into tomato plants through In planta plant transformation method. Out of 300 seedlings, co-cultivated only twenty-seven plants were able to well establish under the greenhouse condition. Among twenty-seven transformants only twelve plants showed amplification with gene specific primers. Further work must be extended to evaluate the transformants at T1 and T2 generations for ectoine accumulation, salinity tolerance, plant growth and development and yield.

Keywords: salinity, computable solutes, ectA, transgenic, in planta transformation

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Authors: Cristian Chacha, David Asiain, Jesús Ponce de León, José Ramón Beltrán

Abstract:

This work explores and characterizes the behavior of the AFE AD5941 in impedance measurement using an embedded algorithm with a constant current AC source. The main aim of this research is to improve the exact measurement of impedance values for their application in EDA-focused wearable devices. Through comprehensive study and characterization, it has been observed that employing a measurement sequence with a constant current source produces results with increased dispersion but higher accuracy. As a result, this approach leads to a more accurate system for impedance measurement.

Keywords: EDA, constant current AC source, wearable, precision, accuracy, impedance

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

Abstract:

Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Chisomo Patrick Kumbuyo, Katsuyuki Shimizu, Hiroshi Yasuda, Yoshinobu Kitamura

Abstract:

This study deals with a way of predicting Malawi rainfall from global sea surface temperature (SST) using a simple multiple regression model. Monthly rainfall data from nine stations in Malawi grouped into two zones on the basis of inter-station rainfall correlations were used in the study. Zone 1 consisted of Karonga and Nkhatabay stations, located in northern Malawi; and Zone 2 consisted of Bolero, located in northern Malawi; Kasungu, Dedza, Salima, located in central Malawi; Mangochi, Makoka and Ngabu stations located in southern Malawi. Links between Malawi rainfall and SST based on statistical correlations were evaluated and significant results selected as predictors for the regression models. The predictors for Zone 1 model were identified from the Atlantic, Indian and Pacific oceans while those for Zone 2 were identified from the Pacific Ocean. The correlation between the fit of predicted and observed rainfall values of the models were satisfactory with r=0.81 and 0.54 for Zone 1 and 2 respectively (significant at less than 99.99%). The results of the models are in agreement with other findings that suggest that SST anomalies in the Atlantic, Indian and Pacific oceans have an influence on the rainfall patterns of Southern Africa.

Keywords: Malawi rainfall, forecast model, predictors, SST

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Authors: Rana Zeina

Abstract:

Objective: The association between Sensory problems and cognitive abilities has been studied in individuals with Autism Spectrum Disorders (ASDs). In this study, we used a neuropsychological test to evaluate memory and attention in ASDs children with sensory problems compared to the ASDs children without sensory problems. Methods: Four visual memory tests of Cambridge Neuropsychological Test Automated Battery (CANTAB) including Big/Little Circle (BLC), Simple Reaction Time (SRT), Intra/Extra Dimensional Set Shift (IED), Spatial Recognition Memory (SRM), were administered to 14 ASDs children with sensory problems compared to 13 ASDs without sensory problems aged 3 to 12 with IQ of above 70. Results: ASDs Individuals with sensory problems performed worse than the ASDs group without sensory problems on comprehension, learning, reversal and simple reaction time tasks, and no significant difference between the two groups was recorded in terms of the visual memory and visual comprehension tasks. Conclusion: The findings of this study suggest that ASDs children with sensory problems are facing deficits in learning, comprehension, reversal, and speed of response to stimuli.

Keywords: visual memory, attention, autism spectrum disorders, CANTAB eclipse

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Authors: Carlos Cuenca, Diego Sarzosa

Abstract:

Ductile fracture occurs by the mechanism of void nucleation, void growth and coalescence. Potential sites for initiation are second phase particles or non-metallic inclusions. Modelling of ductile damage at the microscopic level is very difficult and complex task for engineers. Therefore, conservative predictions of ductile failure using simple models are necessary during the design and optimization of critical structures like pressure vessels and pipelines. Nowadays, it is well known that the initiation phase is strongly influenced by the stress triaxiality and plastic deformation at the microscopic level. Thus, a simple model used to study the ductile failure under multiaxial stress condition is the Stress Modified Critical Strain (SMCS) approach. Ductile rupture has been study for a structural steel under different stress triaxiality conditions using the SMCS method. Experimental tests are carried out to characterize the relation between stress triaxiality and equivalent plastic strain by notched round bars. After calibration of the plasticity and damage properties, predictions are made for low constraint bending specimens with and without side grooves. Stress/strain fields evolution are compared between the different geometries. Advantages and disadvantages of the SMCS methodology are discussed.

Keywords: damage, SMSC, SEB, steel, failure

Procedia PDF Downloads 297

Authors: Rowan Moore, Kai Scheffler, Eugen Damoc, Jennifer Sutton, Aaron Bailey, Stephane Houel, Simon Cubbon, Jonathan Josephs

Abstract:

Purpose: MS analysis of monoclonal antibodies (mAbs) at the protein and peptide levels is critical during development and production of biopharmaceuticals. The compositions of current generation therapeutic proteins are often complex due to various modifications which may affect efficacy. Intact proteins analyzed by MS are detected in higher charge states that also provide more complexity in mass spectra. Protein analysis in native or native-like conditions with zero or minimal organic solvent and neutral or weakly acidic pH decreases charge state value resulting in mAb detection at higher m/z ranges with more spatial resolution. Methods: Three commercially available mAbs were used for all experiments. Intact proteins were desalted online using size exclusion chromatography (SEC) or reversed phase chromatography coupled on-line with a mass spectrometer. For streamlined use of the LC- MS platform we used a single SEC column and alternately selected specific mobile phases to perform separations in either denaturing or native-like conditions: buffer A (20 % ACN, 0.1 % FA) with Buffer B (100 mM ammonium acetate). For peptide analysis mAbs were proteolytically digested with and without prior reduction and alkylation. The mass spectrometer used for all experiments was a commercially available Thermo Scientific™ hybrid Quadrupole-Orbitrap™ mass spectrometer, equipped with the new BioPharma option which includes a new High Mass Range (HMR) mode that allows for improved high mass transmission and mass detection up to 8000 m/z. Results: We have analyzed the profiles of three mAbs under reducing and native conditions by direct infusion with offline desalting and with on-line desalting via size exclusion and reversed phase type columns. The presence of high salt under denaturing conditions was found to influence the observed charge state envelope and impact mass accuracy after spectral deconvolution. The significantly lower charge states observed under native conditions improves the spatial resolution of protein signals and has significant benefits for the analysis of antibody mixtures, e.g. lysine variants, degradants or sequence variants. This type of analysis requires the detection of masses beyond the standard mass range ranging up to 6000 m/z requiring the extended capabilities available in the new HMR mode. We have compared each antibody sample that was analyzed individually with mixtures in various relative concentrations. For this type of analysis, we observed that apparent native structures persist and ESI is benefited by the addition of low amounts of acetonitrile and formic acid in combination with the ammonium acetate-buffered mobile phase. For analyses on the peptide level we analyzed reduced/alkylated, and non-reduced proteolytic digests of the individual antibodies separated via reversed phase chromatography aiming to retrieve as much information as possible regarding sequence coverage, disulfide bridges, post-translational modifications such as various glycans, sequence variants, and their relative quantification. All data acquired were submitted to a single software package for analysis aiming to obtain a complete picture of the molecules analyzed. Here we demonstrate the capabilities of the mass spectrometer to fully characterize homogeneous and heterogeneous therapeutic proteins on one single platform. Conclusion: Full characterization of heterogeneous intact protein mixtures by improved mass separation on a quadrupole-Orbitrap™ mass spectrometer with extended capabilities has been demonstrated.

Keywords: disulfide bond analysis, intact analysis, native analysis, mass spectrometry, monoclonal antibodies, peptide mapping, post-translational modifications, sequence variants, size exclusion chromatography, therapeutic protein analysis, UHPLC

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Authors: Darius Diogo Barreto, Ajeet Kumar, Sushma Santapuri

Abstract:

We present an axisymmetric variational formulation for coupled extension-torsion-inflation deformation in magnetoelastomeric thin tubes when both azimuthal and axial magnetic fields are applied. The tube's material is assumed to have a preferred magnetization direction which imparts helical magnetic anisotropy to the tube. We have also derived the expressions of the first derivative of free energy per unit tube's undeformed length with respect to various imposed strain parameters. On applying the thin tube limit, the two nonlinear ordinary differential equations to obtain the in-plane radial displacement and radial component of the Lagrangian magnetic field get converted into a set of three simple algebraic equations. This allows us to obtain simple analytical expressions in terms of the applied magnetic field, magnetization direction, and magnetoelastic constants, which tell us how these parameters can be tuned to generate positive/negative Poisson's effect in such tubes. We consider both torsionally constrained and torsionally relaxed stretching of the tube. The study can be useful in designing magnetoelastic tubular actuators.

Keywords: nonlinear magnetoelasticity, extension-torsion coupling, negative Poisson's effect, helical anisotropy, thin tube

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Authors: Lara Dutil-Fafard, Caroline Rhéaume, Patrick Archambault, Daniel Lafond, Neal W. Pollock

Abstract:

Improving resources for medical autonomy of astronauts in prolonged space missions, such as a Mars mission, requires not only technology development, but also decision-making support systems. The Advanced Crew Medical System - Medical Condition Requirements study, funded by the Canadian Space Agency, aimed to create knowledge content and a scenario-based query capability to support medical autonomy of astronauts. The key objective of this study was to create a prototype tool for identifying medical infrastructure requirements in terms of medical knowledge, skills and materials. A multicriteria decision-making method was used to prioritize the highest risk medical events anticipated in a long-term space mission. Starting with those medical conditions, event sequence diagrams (ESDs) were created in the form of decision trees where the entry point is the diagnosis and the end points are the predicted outcomes (full recovery, partial recovery, or death/severe incapacitation). The ESD formalism was adapted to characterize and compare possible outcomes of medical conditions as a function of available medical knowledge, skills, and supplies in a given mission scenario. An extensive literature review was performed and summarized in a medical condition database. A PostgreSQL relational database was created to allow query-based evaluation of health outcome metrics with different medical infrastructure scenarios. Critical decision points, skill and medical supply requirements, and probable health outcomes were compared across chosen scenarios. The three medical conditions with the highest risk rank were acute coronary syndrome, sepsis, and stroke. Our efforts demonstrate the utility of this approach and provide insight into the effort required to develop appropriate content for the range of medical conditions that may arise.

Keywords: decision support system, event-sequence diagram, exploration mission, medical autonomy, scenario-based queries, space medicine

Procedia PDF Downloads 127