Search results for: as-recorded seismic sequences

Authors: Sarah Devi Silvian, Hanna Shobrina Iqomatul Haq, Fara Cholidatun Nabila, Agustin Krisna Wardani

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Bacteria ability to survive in antibiotic is controlled by the presence of gene that encodes the antibiotic resistance protein. The instability of the antibiotic resistance gene can be observed by exposing the bacteria under the lethal dose of antibiotic. Low concentration of antibiotic can induce mutation, which may take a role in bacterial adaptation through the antibiotic concentration. Lactobacillus casei FNCC 0090 is one of the probiotic bacteria that has an ability to survive in tetracycline by expressing the tetM gene. The aims of this study are to observe the possibilities of mutation happened in L.casei FNCC 0090 by exposing in sub-lethal dose of tetracycline and also observing the instability of the tetM gene by comparing the sequence between the wild type and mutant. L.casei FNCC 0090 has a lethal dose in 60 µg/ml, low concentration is applied to induce the mutation, the range from 10 µg/ml, 15 µg/ml, 30 µg/ml, 45 µg/ml, and 50 µg/ml. L.casei FNCC 0090 is exposed to the low concentration from lowest to the highest concentration to induce the adaptation. Plasmid is isolated from the highest concentration culture which is 50 µg/ml by using modified alkali lysis method with the addition of lysozyme. The tetM gene is isolated by using PCR (Polymerase Chain Reaction) method, then PCR amplicon is purified and sequenced. Sequencing is done on both samples, wild type and mutant. Both sequences are compared and the mutations can be traced in the presence of nucleotides changes. The changing of the nucleotides means that the tetM gene is instable.

Keywords: L. casei FNCC 0090, probiotic, tetM, tetracycline

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Authors: Lal Hussain, Wajid Aziz, Imtiaz Ahmed Awan, Sharjeel Saeed

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Multiscale entropy analysis (MSE) is a useful technique recently developed to quantify the dynamics of physiological signals at different time scales. This study is aimed at investigating the electroencephalogram (EEG) signals to analyze the background activity of alcoholic and control subjects by inspecting various coarse-grained sequences formed at different time scales. EEG recordings of alcoholic and control subjects were taken from the publically available machine learning repository of University of California (UCI) acquired using 64 electrodes. The MSE analysis was performed on the EEG data acquired from all the electrodes of alcoholic and control subjects. Mann-Whitney rank test was used to find significant differences between the groups and result were considered statistically significant for p-values<0.05. The area under receiver operator curve was computed to find the degree separation between the groups. The mean ranks of MSE values at all the times scales for all electrodes were higher control subject as compared to alcoholic subjects. Higher mean ranks represent higher complexity and vice versa. The finding indicated that EEG signals acquired through electrodes C3, C4, F3, F7, F8, O1, O2, P3, T7 showed significant differences between alcoholic and control subjects at time scales 1 to 5. Moreover, all electrodes exhibit significance level at different time scales. Likewise, the highest accuracy and separation was obtained at the central region (C3 and C4), front polar regions (P3, O1, F3, F7, F8 and T8) while other electrodes such asFp1, Fp2, P4 and F4 shows no significant results.

Keywords: electroencephalogram (EEG), multiscale sample entropy (MSE), Mann-Whitney test (MMT), Receiver Operator Curve (ROC), complexity analysis

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Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

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Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

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Authors: Jayashree S. Bhat, Megha Mohan

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Play is any activity spontaneously chosen, inherently motivated, and personally directed. There is a wide range of literature and research supporting the concept of play in promoting healthy development in young children. Modern children are experiencing nurture that has more structure and adult involvement than previous generations and free, unstructured, and child directed play is under peril. Play behaviors serve as a reflection of a child’s cultural and ethnic background and can be an index of a child’s development. The influence and impact of culture in children’s play is diverse. The culturally variable dimensions of play includes the choice of objects, the involvement of specific play partners, the amount of child initiations of social pretend play with caregivers along with its the components, and sequences and specific themes involved during play. India is a country well known for its cultural diversity. In this study, a cross sectional study design with convenient sampling was adopted. The mother child free play interaction was video clipped at their residence among typically developing children between 12 to 24 months in an urban city from South India. It was ascertained that all the children were first born and mothers were unemployed belonging to middle socioeconomic status. The video clippings were coded and analysed using SPSS software version 17. The results revealed interesting behaviors demonstrated by the mother as well as the child during the play interaction. The results high light the need for focusing on the play behaviors of children during their developmental assessment, especially so for children with challenges.

Keywords: culture, free play, interaction, typically developing

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Authors: Nazanin Amanat, Alison Tayler, Steve Whyard

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While chemical insecticides effectively control many insect pests, they also harm many non-target species. Double-stranded RNA (dsRNA) pesticides, in contrast, can be designed to target unique gene sequences and thus act in a species-specific manner. DsRNA insecticides do not, however, work equally well for all insects, and for some species that are considered refractory to dsRNA, a primary factor affecting efficacy is the relative ease by which dsRNA can enter a target cell’s cytoplasm. In this study, we are examining how different structured dsRNAs (linear, hairpin, and paperclip) can enter mosquito and lepidopteran cells, as they represent dsRNA-sensitive and refractory species, respectively. To determine how the dsRNAs enter the cells, we are using chemical inhibitors and RNA interference (RNAi)-mediated knockdown of key proteins associated with different endocytosis processes. Understanding how different dsRNAs enter cells will ultimately help in the design of molecules that overcome refractoriness to RNAi or develop resistance to dsRNA-based insecticides. To date, we have conducted chemical inhibitor experiments on both cell lines and have evidence that linear dsRNAs enter the cells using clathrin-mediated endocytosis, while the paperclip dsRNAs (pcRNAs) can enter both species’ cells in a clathrin-independent manner to induce RNAi. An alternative uptake mechanism for the pcRNAs has been tentatively identified, and the outcomes of our RNAi-mediated knockdown experiments, which should provide corroborative evidence of our initial findings, will be discussed.

Keywords: dsRNA, RNAi, uptake, insecticides, dipteran, lepidopteran

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Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck, Jason Stanley, Leroy Whilby

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major threat to fruit and vegetable industries in the United States. The establishment of pest fruit fly in the agricultural industries and produce severe ecological and economic impacts on agricultural diversification and trade. Detection and identification of these agricultural pests in a timely manner will facilitate the possibility of eradication from newly invaded areas. Identification of larval stages to species level is difficult, but is required to determine pest loads and their pathways into the United States. The aim of this study is the New World genus, Anastrepha which includes pests of major economic importance. Mitochondrial cytochrome c oxidase I (COI) gene sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level. During phylogenetics analysis numerous nuclear mitochondrial pseudogenes (numts) were discovered in different specimens. The numts are nonfunctional copies of the mtDNA present in the nucleus and are easily coamplified with the mitochondrial COI gene copy by using conserved universal primers. This is problematic for DNA Barcoding, which attempts to characterize all living organisms by using the COI gene. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed.

Keywords: tephritid, Anastrepha fraterculus, COI, numts

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Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

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The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

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Authors: Zhang Lei, Zhao Qingrong, Wang Chen, Zhang Sufang, Zhang Hanguo

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Larch is the main afforestation and timber tree species in Northeast China, and drought is one of the main factors limiting the growth of Larch and other organisms in Northeast China. In order to further explore the mechanism of Larch drought resistance, PEG was used to simulate drought stress. The full-length sequencing of Larch embryogenic callus under PEG simulated drought stress was carried out by combining Illumina-Hiseq and SMRT-seq. A total of 20.3Gb clean reads and 786492 CCS reads were obtained from the second and third generation sequencing. The de-redundant transcript sequences were predicted by lncRNA, 2083 lncRNAs were obtained, and the target genes were predicted, and a total of 2712 target genes were obtained. The de-redundant transcripts were further screened, and 1654 differentially expressed genes (DEGs )were obtained. Among them, different DEGs respond to drought stress in different ways, such as oxidation-reduction process, starch and sucrose metabolism, plant hormone pathway, carbon metabolism, lignin catabolic/biosynthetic process and so on. This study provides basic full-length sequencing data for the study of Larch drought resistance, and excavates a large number of DEGs in response to drought stress, which helps us to further understand the function of Larch drought resistance genes and provides a reference for in-depth analysis of the molecular mechanism of Larch drought resistance.

Keywords: larch, drought stress, full-length transcriptome sequencing, differentially expressed genes

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Authors: S. A. Anuar, N. H. Hamid, M. H. Hashim, S. M. D. Salleh

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This paper present the experimental work on the seismic performance of double unit tunnel form building (TFB) subjected to in-plane lateral cyclic loading. A one third scale of 3-storey double unit of TFB is tested at ±0.01%, ±0.1%, ±0.25%, ±0.5%, ±0.75% and ±1.0% drifts until the structure achieves its strength degradation. After that, the TFB is repaired and retrofitted using additional shear wall, steel angle and CFRP sheet. A similar testing approach is applied to the specimen after repair and retrofit. The crack patterns, lateral strength, stiffness, ductility and equivalent viscous damping (EVD) were analyzed and compared before and after repair and retrofit. The result indicates that the lateral strength increases by 22 in pushing direction and 27% in pulling direction. Moreover, the stiffness and ductility obtained before and after retrofit increase tremendously by 87.87% and 39.66%, respectively. Meanwhile, the energy absorption measured by equivalent viscous damping obtained after retrofit increase by 12.34% in pulling direction. It can be concluded that the proposed retrofit method is capable to increase the lateral strength capacity, stiffness and energy absorption of double unit TFB.

Keywords: tunnel form building, in-plane lateral cyclic loading, crack pattern, lateral strength, stiffness, ductility, equivalent viscous damping, repair and retrofit

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Issam Aouari, Abdelmalek Abdelhamid

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For seismologists, the characterization of seismic demand should include the amplitude and duration of strong shaking in the system. The duration of ground shaking is one of the key parameters in earthquake resistant design of structures. This paper proposes a nonlinear statistical model to estimate earthquake ground motion duration in soft soils using multiple seismicity indicators. Three definitions of ground motion duration proposed by literature have been applied. With a comparative study, we select the most significant definition to use for predict the duration. A stochastic model is presented for the McCann and Shah Method using nonlinear regression analysis based on a data set for moment magnitude, source to site distance and site conditions. The data set applied is taken from PEER strong motion databank and contains shallow earthquakes from different regions in the world; America, Turkey, London, China, Italy, Chili, Mexico...etc. Main emphasis is placed on soft site condition. The predictive relationship has been developed based on 600 records and three input indicators. Results have been compared with others published models. It has been found that the proposed model can predict earthquake ground motion duration in soft soils for different regions and sites conditions.

Keywords: duration, earthquake, prediction, regression, soft soil

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Authors: Aymen Arfaoui, Abdelkader Soumaya, Ali Kadri, Noureddine Ben Ayed

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The Tunisian dorsal backland is located on the Eastern Atlas side of the Maghrebides (North Africa). The analysis of collected field data in the Rouas and Ruissate mountains area allowed us to develop new interpretations for its structural framework. Our kinematic analysis of fault-slip data reveals the presence of an extensional tectonic regime with NE-SW Shmin, characterizing the Mesozoic times. In addition, geophysical data shows that the synsedimentary normal faulting is accompanied by thickness variations of sedimentary sequences and Triassic salt movements. Then, after the Eurasia-Africa plate’s convergence during the Eocene, compressive tectonic deformations affected and reactivated the inherited NW-SE and N-S trending normal faults as dextral strike-slip and reverse faults, respectively. This tectonic inversion, with compression to the transpressional tectonic regime and NW-SE SHmax, continued during the successive shortening phases of the upper Miocene and Quaternary. The geometry of the Rouas and Ruissate belt is expressed as a fault propagation fold, affecting Jurassic and Cretaceous deposits. The Triassic evaporates constitute the decollement levels, facilitating the detachment and deformation of the sedimentary cover. The backland of this thrust belt is defined by NNE-SSW trending imbrication features that are controlled by a basement N-S fault.

Keywords: Tunisian dorsal backland, fault slip data; synsedimentary faults, tectonic inversion, decollement level, fault propagation fold

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Authors: Nicolae Daniel Stoica, Ion Mierlus Mazilu

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This work is one of numerical research and aims to address the issue of the design of new buildings in a 3D location of existing buildings. In today's continuous development and congestion of urban centers is a big question about the influence of the new buildings on an already existent vicinity site. Thus, in this study, we tried to focus on how existent buildings may be affected by any newly constructed buildings and in how far this influence is really decreased. The problem of modeling the influence of interaction between buildings is not simple in any area in the world, and neither in Romania. Unfortunately, most often the designers not done calculations that can determine how close to reality these 3D influences nor the simplified method and the more superior methods. In the most literature making a "shield" (the pilots or molded walls) is absolutely sufficient to stop the influence between the buildings, and so often the soil under the structure is ignored in the calculation models. The main causes for which the soil is neglected in the analysis are related to the complexity modeling of interaction between soil and structure. In this paper, based on a new simple but efficient methodology we tried to determine for a lot of study cases the influence, in terms of assessing the interaction land structure on the behavior of structures that influence a new building on an existing one. The study covers additional subsidence that may occur during the execution of new works and after its completion. It also highlighted the efforts diagrams and deflections in the soil for both the original case and the final stage. This is necessary to see to what extent the expected impact of the new building on existing areas.

Keywords: soil, structure, interaction, piles, earthquakes

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Authors: Y. Kumru, K. Enhos, H. Köymen

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In this paper, we report the experimental results on using complementary Golay coded signals at 7.5 MHz to detect breast microcalcifications of 50 µm size. Simulations using complementary Golay coded signals show perfect consistence with the experimental results, confirming the improved signal to noise ratio for complementary Golay coded signals. For improving the success on detecting the microcalcifications, orthogonal complementary Golay sequences having cross-correlation for minimum interference are used as coded signals and compared to tone burst pulse of equal energy in terms of resolution under weak signal conditions. The measurements are conducted using an experimental ultrasound research scanner, Digital Phased Array System (DiPhAS) having 256 channels, a phased array transducer with 7.5 MHz center frequency and the results obtained through experiments are validated by Field-II simulation software. In addition, to investigate the superiority of coded signals in terms of resolution, multipurpose tissue equivalent phantom containing series of monofilament nylon targets, 240 µm in diameter, and cyst-like objects with attenuation of 0.5 dB/[MHz x cm] is used in the experiments. We obtained ultrasound images of monofilament nylon targets for the evaluation of resolution. Simulation and experimental results show that it is possible to differentiate closely positioned small targets with increased success by using coded excitation in very weak signal conditions.

Keywords: coded excitation, complementary golay codes, DiPhAS, medical ultrasound

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Authors: Jean-Pierre Dubois, Jihad S. Daba, H. Karam, J. Abdallah

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Tsunami early detection and warning systems have proved to be of ultimate importance, especially after the destructive tsunami that hit Japan in March 2012. Such systems are crucial to inform the authorities of any risk of a tsunami and of the degree of its danger in order to make the right decision and notify the public of the actions they need to take to save their lives. The purpose of this research is to enhance existing tsunami detection and warning systems. We first propose an automated and miniaturized model of an early tsunami detection and warning system. The model for the operation of a tsunami warning system is simulated using the data acquisition toolbox of Matlab and measurements acquired from specified internet pages due to the lack of the required real-life sensors, both seismic and hydrologic, and building a graphical user interface for the system. In the second phase of this work, we implement various satellite image filtering schemes to enhance the acquired synthetic aperture radar images of the tsunami affected region that are masked by speckle noise. This enables us to conduct a post-tsunami damage extent study and calculate the percentage damage. We conclude by proposing improvements to the existing telecommunication infrastructure of existing warning tsunami systems using a migration to IP-based networks and fiber optics links.

Keywords: detection, GIS, GSN, GTS, GPS, speckle noise, synthetic aperture radar, tsunami, wiener filter

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Authors: Seyed Sadegh Naseralavi, Sadegh Balaghi, Ehsan Khojastehfar

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Time history dynamic analysis of structures is considered as an exact method while being computationally intensive. Filtration of earthquake strong ground motions applying wavelet transform is an approach towards reduction of computational efforts, particularly in optimization of structures against seismic effects. Wavelet transforms are categorized into continuum and discrete transforms. Since earthquake strong ground motion is a discrete function, the discrete wavelet transform is applied in the present paper. Wavelet transform reduces analysis time by filtration of non-effective frequencies of strong ground motion. Filtration process may be repeated several times while the approximation induces more errors. In this paper, strong ground motion of earthquake has been filtered once applying each wavelet. Strong ground motion of Northridge earthquake is filtered applying various wavelets and dynamic analysis of sampled shear and moment frames is implemented. The error, regarding application of each wavelet, is computed based on comparison of dynamic response of sampled structures with exact responses. Exact responses are computed by dynamic analysis of structures applying non-filtered strong ground motion.

Keywords: wavelet transform, computational error, computational duration, strong ground motion data

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Authors: Muhammad Fiaz Qamar, Ahmad Faraz, Muhammad Arfan Zaman, Kazim Ali, Waleed Akram

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Babesiosis is reflected as the most important disease of cattle that are transmitted by arthropods. In Pakistan, its prevalence is up to 29% in the cattle and buffalo population in different regions. Cattle show a long lasting and durable immunity by giving an infection of B.bovis, B. bigemina, or Babesiadivergens. this is used in cattle to immunize them in a few countries as anti-babesiosis vaccine. Development of frozen vaccine allows for complete testing after production of each batch, However, once thawed, its reduced its shelf life, frozen vaccines are more difficult to transport as well as expensive to produce as compared to chilled vaccine. The contamination of blood derived vaccine has the potential risk that makes pre-production and post-production quality control necessary. For the trail master seed production of whole blood frozen bivalent Babesia(Babesiabovis and Babesiabigemina), 100 blood samples of Babesial positive suspected cattle was taken and processed for separation microscopic detection and rectification by PCR. Vaccine passages were done to reduce the parasitaemiasis in live calves. After 8 passages, parasitemia of Babesia reduced from 80% to 15%. Infected donor calf’s blood was taken by jugular cannulation by using preservative free lithium heparin as an anticoagulant (5 International Units IU heparin/ml blood). In lab, parasite containing blood was mixed in equal volumes with 3 M glycerol in PBS supplemented with 5 mM glucose (final concentration of glycerol 1.5 M) at 37°C. The mixture was then equilibrized at 37°C for 30 minutes and were dispensed in required containers (e.g., 5 ml cryovials).

Keywords: distribution, babesia, primer sequences, PCV

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Authors: Mun Yee Chan, Sin Ming Goh, Lisa Gaik Ai Ong

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Approximately 10,000 different types of dyes and pigments are being used in various industrial applications yearly, which include the textile and printing industries. However, these dyes are difficult to degrade naturally once they enter the aquatic system. Their high persistency in natural environment poses a potential health hazard to all form of life. Hence, there is a need for alternative dye removal strategy in the environment via bioremediation. In this study, fungi laccase is investigated via commercial agar dyes plates and submerged fermentation to explore the application of fungi laccase in textile dye wastewater treatment. Two locally isolated basidiomycetes were screened for laccase activity using media added with commercial dyes such as 2, 2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), guaiacol and Remazol Brillant Blue R (RBBR). Isolate TBB3 (1.70±0.06) and EL2 (1.78±0.08) gave the highest results for ABTS plates with the appearance of greenish halo on around the isolates. Submerged fermentation performed on Isolate TBB3 with the productivity 3.9067 U/ml/day, whereas the laccase activity for Isolate EL2 was much lower (0.2097 U/ml/day). As isolate TBB3 showed higher laccase production, it was subjected to molecular characterization by DNA isolation, PCR amplification and sequencing of ITS region of nuclear ribosomal DNA. After being compared with other sequences in National Center for Biotechnology Information (NCBI database), isolate TBB3 is probably from species Trametes hirsutei. Further research work can be performed on this isolate by upscale the production of laccase in order to meet the demands of the requirement for higher enzyme titer for the bioremediation of textile dyes.

Keywords: bioremediation, dyes, fermentation, laccase

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Authors: Sofia Hartati

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This research is aimed at describing training in early childhood education program empirically, describing teachers ability to plan lessons empirically, and acquiring empirical data as well as analyzing the influence of guided and independent training toward teachers competence in planning early childhood learning program. The method used is an experiment. It collected data with a population of 76 early childhood educators in Tunjung Teja Sub District area through random sampling technique and grouped into two namely 38 people in an experiment class and 38 people in a controlled class. The technique used for data collections is a test. The result of the research shows that there is a significant influence between training for guided educators toward Teachers Ability toward Planning Early Childhood Learning Program. Guided training has been proven to improve the ability to comprehend planning a learning program. The ability to comprehend planning a learning program owned by teachers of early childhood program comprises of 1) determining the characteristics and competence of students prior to learning; 2) formulating the objective of the learning; 3) selecting materials and its sequences; 4) selecting teaching methods; 5) determining the means or learning media; 6) selecting evaluation strategy as a part of teachers pedagogic competence. The result of this research describes a difference in the competence level of teachers who have joined guided training which is relatively higher than the teachers who joined the independent training. Guided training is one of an effective way to improve the knowledge and competence of early childhood educators.

Keywords: competence, planning, teachers, training

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Authors: Babak Dizangian, Mohammad Reza Ghasemi, Akram Ghalandari

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Moment frames have considerable ductility against cyclic lateral loads and displacements; however, if this feature causes the relative displacement to exceed the permissible limit, it can impose unfavorable hysteretic behavior on the frame. Therefore, adding a bracing system with the capability of preserving the capacity of high energy absorption and controlling displacements without a considerable increase in the stiffness is quite important. This paper investigates the retrofitting of a single storey steel moment frame through a delayed wire-rope bracing system using a middle steel plate. In this model, the steel plate lies where the wire ropes meet, and the model geometry is such that the cables are continuously under tension so that they can take the most advantage of the inherent potential they have in tolerating tensile stress. Using the steel plate also reduces the system stiffness considerably compared to cross bracing systems and preserves the ductile frame’s energy absorption capacity. In this research, the software models of delayed wire-rope bracing system have been studied, validated, and compared with other researchers’ laboratory test results.

Keywords: cyclic loading, delayed wire rope bracing, ductile moment frame, energy absorption, hysteresis curve

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Authors: Abdull Halim

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The Standard Penetration Test (SPT-N) is the most common in situ test for soil investigations. The Shearing Seismic Standard Penetration Test (SSPT-N), on the other hand, is a new method using shearing wave with propagation exponent equation between the shearing wave, Vs., and hardness, N values without any need for borehole data. Due to the fast and accurate results that can be obtained, the SSPT has found many applications such as in the field rectification buried pipe line, the acid tank settlement and foundation design analyses, and the quality control assessment. Many geotechnical regimes and properties have attempted to correlate both the SSPT and the SPT-N values. Various foundation design methods have been developed based on the outcomes of these tests. Hence, it is pertinent to correlate these tests so that either one of the test can be used in the absence of the other, especially for preliminary evaluation and design purposes. The primary purpose of this study was to investigate the relationship between the SSPT-N and SPT-N values for different types of cohesive soil in Peninsular Malaysia. Data were collected from four different sites, and the correlations were established between the hardness N values, principal stress-strain Mohr circle curve, cohesion, friction angle and vertical effective stress. A positive exponent relationship was found between the shearing wave, sVs., and the hardness N values of the soil. In general, the SSPT-N value was slightly lower than the SPT-N value due to the upper limit boundary of the soil layer.

Keywords: InsituSoil determination; shearing wave; hardness; correlation, SSPT-N, SPT-N

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Authors: Hedi Dghim, Ahmed El-Naggar, Istvan Erlich

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Power electronic converters are being introduced in low voltage (LV) grids at an increasingly rapid rate due to the growing adoption of power electronic-based home appliances in residential grid. Photovoltaic (PV) systems are considered one of the potential installed renewable energy sources in distribution power systems. This trend has led to high distortion in the supply voltage which consequently produces harmonic currents in the network and causes an inherent voltage unbalance. In order to investigate the effect of harmonic distortions, a case study of a typical LV grid configuration with high penetration of 3-phase and 1-phase rooftop mounted PV from southern Germany was first considered. Electromagnetic transient (EMT) simulations were then carried out under the MATLAB/Simulink environment which contain detailed models for power electronic-based loads, ohmic-based loads as well as 1- and 3-phase PV. Note that, the switching patterns of the power electronic circuits were considered in this study. Measurements were eventually performed to analyze the distortion levels when PV operating under different solar irradiance. The characteristics of the load-side harmonic impedances were analyzed, and their harmonic contributions were evaluated for different distortion levels. The effect of the high penetration of PV on the harmonic distortion of both positive and negative sequences was also investigated. The simulation results are presented based on case studies. The current distortion levels are in agreement with relevant standards, otherwise the Total Harmonic Distortion (THD) increases under low PV power generation due to its inverse relation with the fundamental current.

Keywords: harmonic distortion analysis, power quality, PV systems, residential distribution system

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Authors: Alvaro Jose Cordova, Hsuan Teh Hu

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The use of concrete masonry constructions in developing countries has become very frequent, especially for domestic purpose. Most of them with asymmetric wall configurations in plan resulting in significant torsional actions when subjected to seismic loads. The study consisted on the finding of a material model for hollow unreinforced concrete masonry and a validation with experimental data found in literature. Numerical simulations were performed to 20 buildings with variations in wall distributions and heights. Results were analyzed by inspection and with a non-linear static method. The findings revealed that eccentricities as well as structure rigidities have a strong influence on the overall response of concrete masonry buildings. In addition, slab rotations depicted more accurate information about the torsional behavior than maximum versus average displacement ratios. The failure modes in low buildings were characterized by high tensile strains in the first floor. Whereas in tall buildings these strains were lowered significantly by higher compression stresses due to a higher self-weight. These tall buildings developed multiple plastic hinges along the height. Finally, the non-linear static analysis exposed a brittle response for all masonry assemblies. This type of behavior is undesired in any construction and the need for a material model for reinforced masonry is pointed out.

Keywords: concrete damaged plasticity, concrete masonry, macro-modeling, nonlinear static analysis, torsional capacity

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Authors: Muhammad Shahzad Iqbal, Zobia Sarwar, Salah-ud-Din

Abstract:

Tomato spotted wilt virus (TSWV) belongs to the genus Tospoviruses (family Bunyaviridae). It is one of the most devastating pathogens of tomato (Solanum Lycopersicum) and heavily damages the crop yield each year around the globe. In this study, we retrieved 329 mature miRNA sequences from two microRNA databases (miRBase and miRSoldb) and checked the putative target sites in the downloaded-genome sequence of TSWV. A consensus of three miRNA target prediction tools (RNA22, miRanda and psRNATarget) was used to screen the false-positive microRNAs targeting sites in the TSWV genome. These tools calculated different target sites by calculating minimum free energy (mfe), site-complementarity, minimum folding energy and other microRNA-mRNA binding factors. R language was used to plot the predicted target-site data. All the genes having possible target sites for different miRNAs were screened by building a consensus table. Out of these 329 mature miRNAs predicted by three algorithms, only eight miRNAs met all the criteria/threshold specifications. MC-Fold and MC-Sym were used to predict three-dimensional structures of miRNAs and further analyzed in USCF chimera to visualize the structural and conformational changes before and after microRNA-mRNA interactions. The results of the current study show that the predicted eight miRNAs could further be evaluated by in vitro experiments to develop TSWV-resistant transgenic tomato plants in the future.

Keywords: tomato spotted wild virus (TSWV), Solanum lycopersicum, plant virus, miRNAs, microRNA target prediction, mRNA

Procedia PDF Downloads 135

Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

Abstract:

Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Siamak Epackachi, Andrew S. Whittaker, Amit H. Varma

Abstract:

An experimental program on steel-plate concrete (SC) composite shear walls was executed in the NEES laboratory at the University at Buffalo. Four large-size specimens were tested under displacement-controlled cyclic loading. The design variables considered in the testing program included wall thickness, reinforcement ratio, and faceplate slenderness ratio. The aspect ratio (height-to-length) of the four walls was 1.0. Each SC wall was installed on top of a re-usable foundation block. A bolted baseplate to RC foundation connection was used for all four walls. The walls were identified to be flexure-critical. This paper presents the damage to SC walls at different drift ratios, the cyclic force-displacement relationships, energy dissipation and equivalent viscous damping ratios, the strain and stress fields in the steel faceplates and the contribution of the steel faceplates to the total shear load, the variation of vertical strain in the steel faceplates along the length of the wall, near the base, at different drift ratios, the contributions of shear, flexure, and base rotation to the total lateral displacement, the displacement ductility of the SC walls, and the cyclic secant stiffness of the four SC walls.

Keywords: steel-plate composite shear wall, safety-related nuclear structure, flexure-critical wall, cyclic loading

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Authors: Subzar Ahmad Bhat, Saraswati Setia, V. K.Sehgal

Abstract:

During the past earthquakes, open ground storey buildings have performed poorly due to the soft storey defect. Indian Standard IS 1893:2002 allows analysis of open ground storey buildings without considering infill stiffness but with a multiplication factor 2.5 in compensation for the stiffness discontinuity. Therefore, the aim of this paper is to check the applicability of the multiplication factor of 2.5 and study behaviour of the structure after the application of the multiplication factor. For this purpose, study is performed on models considering infill stiffness using SAP 2000 (Version 14) by linear static analysis and response spectrum analysis. Total seven models are analysed and designed for the range of multiplication factor ranging from 1.25 to 2.5. The value of multiplication factor equal to 2.5 has been found on the higher side, resulting in increased dimension and percentage of reinforcement without significant enhancement beyond a certain multiplication factor. When the building with OGS is designed for values of MF higher than 1.25 considering infill stiffness soft storey effect shifts from ground storey to first storey. For the analysis of the OGS structure best way to analysis the structure is to analyse it as the frame with stiffness and strength of the infill taken into account. The provision of infill walls in the upper storeys enhances the performance of the structure in terms of displacement and storey drift controls.

Keywords: open ground storey, multiplication factor, IS 1893:2002 provisions, static analysis, response spectrum analysis, infill stiffness, equivalent strut

Procedia PDF Downloads 375

Authors: Z. Okay, M. Kalkan Erdoğan, M. Şahin, M. Saçak

Abstract:

Polyacrylonitrile (PAN) is one of the most common and cheap fiber-forming polymers because of its high strength and high abrasion resistance properties. The result of alkaline hydrolysis of PAN fiber could be formed the products with conjugated sequences of –C=N–, acrylamide, sodium acrylate, and amidine. In this study, PAN fiber was hydrolyzed in a solution of sodium hydroxide, and this hydrolyzed PAN (HPAN) fiber was used to prepare conductive composite fiber by silver particles. The electrically conductive PAN fiber has the usage potential to produce variety of materials such as antistatic materials, life jackets and static charge reducing products. We monitored the change in the weight loss values of the PAN fiber with hydrolysis time. It was observed that a 60 % of weight loss was obtained in the fiber weight after 7h hydrolysis under the investigated conditions, but the fiber lost its fibrous structure. The hydrolysis time of 5h was found to be suitable in terms of preserving its fibrous structure. The change in the conductivity values of the composite with the preparation conditions such as hydrolysis time, silver ion concentration was studied. PAN fibers with different degrees of hydrolysis were treated with aqueous solutions containing different concentrations of silver ions by continuous stirring at 20 oC for 30 min, and the composite having the maximum conductivity of 2 S/cm could be prepared. The antibacterial property of the conductive HPAN fibers participated silver was also investigated. While the hydrolysis of the PAN fiber was characterized with FTIR and SEM techniques, the silver reduction process of the HPAN fiber was investigated with SEM and TGA-DTA techniques. The SEM micrographs showed that the surface of HPAN fiber was rougher and much more corroded than that of the PAN fiber. Composite, Conducting polymer, Fiber, Polyacrylonitrile.

Keywords: composite, conducting polymer, fiber, polyacrylonitrile

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Authors: Keyur Raval, Steffen Krohn, Bruno Moerschbacher

Abstract:

Chitin, the biopolymer of the N-acetylglucosamine, is the most abundant biopolymer on the planet after cellulose. Industrially, chitin is isolated and purified from the shell residues of shrimps. A deacetylated derivative of chitin i.e. chitosan has more market value and applications owing to it solubility and overall cationic charge compared to the parent polymer. This deacetylation on an industrial scale is performed chemically using alkalis like sodium hydroxide. This reaction not only is hazardous to the environment owing to negative impact on the marine ecosystem. A greener option to this process is the enzymatic process. In nature, the naïve chitin is converted to chitosan by chitin deacetylase (CDA). This enzymatic conversion on the industrial scale is however hampered by the crystallinity of chitin. Thus, this enzymatic action requires the substrate i.e. chitin to be soluble which is technically difficult and an energy consuming process. We in this project wanted to address this shortcoming of CDA. In lieu of this, we have modeled a fusion protein with CDA and an auxiliary protein. The main interest being to increase the accessibility of the enzyme towards crystalline chitin. A similar fusion work with chitinases had improved the catalytic ability towards insoluble chitin. In the first step, suitable partners were searched through the protein data bank (PDB) wherein the domain architecture were sought. The next step was to create the models of the fused product using various in silico techniques. The models were created by MODELLER and evaluated for properties such as the energy or the impairment of the binding sites. A fusion PCR has been designed based on the linker sequences generated by MODELLER and would be tested for its activity towards insoluble chitin.

Keywords: chitin deacetylase, modeling, chitin binding domain, chitinases

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Authors: H. Aldewachi, M. Hines, M. McCulloch, N. Woodroofe, P. Gardiner

Abstract:

DPP-IV is an enzyme whose expression is affected in a variety of diseases, therefore, has been identified as possible diagnostic or prognostic marker for various tumours, immunological, inflammatory, neuroendocrine, and viral diseases. Recently, DPP-IV enzyme has been identified as a novel target for type II diabetes treatment where the enzyme is involved. There is, therefore, a need to develop sensitive and specific methods that can be easily deployed for the screening of the enzyme either as a tool for drug screening or disease marker in biological samples. A variety of assays have been introduced for the determination of DPP-IV enzyme activity using chromogenic and fluorogenic substrates, nevertheless these assays either lack the required sensitivity especially in inhibited enzyme samples or displays low water solubility implying difficulty for use in vivo samples in addition to labour and time-consuming sample preparation. In this study, novel strategies based on exploiting the high extinction coefficient of gold nanoparticles (GNPs) are investigated in order to develop fast, specific and reliable enzymatic assay by investigating synthetic peptide sequences containing a DPP IV cleavage site and coupling them to GNPs. The DPP IV could be detected by colorimetric response of peptide capped GNPs (P-GNPS) that could be monitored by a UV-visible spectrophotometer or even naked eyes, and the detection limit could reach 0.01 unit/ml. The P-GNPs, when subjected to DPP IV, showed excellent selectivity compared to other proteins (thrombin and human serum albumin) , which led to prominent colour change. This provided a simple and effective colorimetric sensor for on-site and real-time detection of DPP IV.

Keywords: gold nanoparticles, synthetic peptides, colorimetric detection, DPP-IV enzyme

Procedia PDF Downloads 289