Search results for: as-recorded seismic sequences

Authors: Mohammad W. Dewan, Jahangir Alam, Khurshida Sharmin

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Synthetic fibers (carbon, glass, aramid, etc.) are generally utilized to make composite materials for better mechanical and thermal properties. However, they are expensive and non-biodegradable. In the perspective of Bangladesh, jute fibers are available, inexpensive, and comprising good mechanical properties. The improved properties (i.e., low cost, low density, eco-friendly) of natural fibers have made them a promising reinforcement in hybrid composites without sacrificing mechanical properties. In this study, jute and e-glass fiber reinforced hybrid composite materials are fabricated utilizing hand lay-up followed by a compression molding technique. Room temperature cured two-part epoxy resin is used as a matrix. Approximate 6-7 mm thick composite panels are fabricated utilizing 17 layers of woven glass and jute fibers with different fiber layering sequences- only jute, only glass, glass, and jute alternatively (g/j/g/j---) and 4 glass - 9 jute – 4 glass (4g-9j-4g). The fabricated composite panels are analyzed through fiber volume calculation, tensile test, bending test, and water absorption test. The hybridization of jute and glass fiber results in better tensile, bending, and water absorption properties than only jute fiber-reinforced composites, but inferior properties as compared to only glass fiber reinforced composites. Among different fiber layering sequences, 4g-9j-4g fibers layering sequence resulted in better tensile, bending, and water absorption properties. The effect of chemical treatment on the woven jute fiber and chopped glass microfiber infusion are also investigated in this study. Chemically treated jute fiber and 2 wt. % chopped glass microfiber infused hybrid composite shows about 12% improvements in flexural strength as compared to untreated and no micro-fiber infused hybrid composite panel. However, fiber chemical treatment and micro-filler do not have a significant effect on tensile strength.

Keywords: compression molding, chemical treatment, hybrid composites, mechanical properties

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Authors: Carlos H. Cuadra, Nobuhiro Shimoi

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Application of piezoelectric sensors to detect structural damage due to seismic action on building structures is investigated. Plate-type piezoelectric sensor was developed and proposed for this task. A film-type piezoelectric sheet was attached on a steel plate and covered by a layer of glass. A special glue is used to fix the glass. This glue is a silicone that requires the application of ultraviolet rays for its hardening. Then, the steel plate was set up at a steel column-beam joint of a test specimen that was subjected to bending moment when test specimen is subjected to monotonic load and cyclic load. The structural behavior of test specimen during cyclic loading was verified using a finite element model, and it was found good agreement between both results on load-displacement characteristics. The cross section of steel elements (beam and column) is a box section of 100 mm×100 mm with a thin of 6 mm. This steel section is specified by the Japanese Industrial Standards as carbon steel square tube for general structure (STKR400). The column and beam elements are jointed perpendicularly using a fillet welding. The resulting test specimen has a T shape. When large deformation occurs the glass plate of the sensor device cracks and at that instant, the piezoelectric material emits a voltage signal which would be the indicator of a certain level of deformation or damage. Applicability of this piezoelectric sensor to detect structural damages was verified; however, additional analysis and experimental tests are required to establish standard parameters of the sensor system.

Keywords: piezoelectric sensor, static cyclic test, steel structure, seismic damages

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Authors: M. Eskandarighadi, C. R. McGann

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It is observed from past experiences of earthquakes that local site conditions can significantly affect the strong ground motion characteristics experience at the site. One-dimensional seismic site response analysis is the most common approach for investigating site response. This approach assumes that soil is homogeneous and infinitely extended in the horizontal direction. Therefore, tying side boundaries together is one way to model this behavior, as the wave passage is assumed to be only vertical. However, 1D analysis cannot capture the 2D nature of wave propagation, soil heterogeneity, and 2D soil profile with features such as inclined layer boundaries. In contrast, 2D seismic site response modeling can consider all of the mentioned factors to better understand local site effects on strong ground motions. 2D wave propagation and considering that the soil profile on the two sides of the model may not be identical clarifies the importance of a boundary condition on each side that can minimize the unwanted reflections from the edges of the model and input appropriate loading conditions. Ideally, the model size should be sufficiently large to minimize the wave reflection, however, due to computational limitations, increasing the model size is impractical in some cases. Another approach is to employ free-field boundary conditions that take into account the free-field motion that would exist far from the model domain and apply this to the sides of the model. This research focuses on implementing free-field boundary conditions in OpenSees for 2D site response analysisComparisons are made between 1D models and 2D models with various boundary conditions, and details and limitations of the developed free-field boundary modeling approach are discussed.

Keywords: boundary condition, free-field, opensees, site response analysis, wave propagation

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Authors: Judith Mogouong, Philippe Constant, Robert Lavallee, Claude Guertin

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The emerald ash borer (EAB) is an exotic wood borer insect native from China, which is associated with important environmental and economic damages in North America. Beetles are known to be vectors of microbial communities related to their adaptive capacities. It is now established that environmental stress factors may induce physiological events on the host trees, such as phytochemical changes. Consequently, that may affect the establishment comportment of herbivorous insect. Considering the number of insects collected on ash trees (insects’ density) as an abiotic factor related to stress damage, the aim of our study was to explore the dynamic of EAB gut microbial community genome (microbiome) when facing that factor and to monitor its diversity. Insects were trapped using specific green Lindgren© traps. A gradient of the captured insect population along the St. Lawrence River was used to create three levels of insects’ density (low, intermediate, and high). After dissection, total DNA extracted from insect guts of each level has been sent for amplicon sequencing of bacterial 16S rRNA gene and fungal ITS2 region. The composition of microbial communities among sample appeared largely diversified with the Simpson index significantly different across the three levels of density for bacteria. Add to that; bacteria were represented by seven phyla and twelve classes, whereas fungi were represented by two phyla and seven known classes. Using principal coordinate analysis (PCoA) based on Bray Curtis distances of 16S rRNA sequences, we observed a significant variation between the structure of the bacterial communities depending on insects’ density. Moreover, the analysis showed significant correlations between some bacterial taxa and the three classes of insects’ density. This study is the first to present a complete overview of the bacterial and fungal communities associated with the gut of EAB base on culture-independent methods, and to correlate those communities with a potential stress factor of the host trees.

Keywords: gut microbiome, DNA, 16S rRNA sequences, emerald ash borer

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Authors: Henry Munoz, Muhammad Mohsan, Takashi Kiyota

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Strength and deformability characteristics of a liquefiable sand deposit including the development of earthquake-induced shear stress and shear strain as well as soil softening via the progressive degradation of shear modulus were studied via shaking table experiments. To do so, a model of a liquefiable sand deposit was constructed and densely instrumented where accelerations, pressures, and displacements at different locations were continuously monitored. Furthermore, the confinement effects on the strength and deformation characteristics of the liquefiable sand deposit due to an external surcharge by placing a heavy concrete slab (i.e. the model of an actual structural rigid pavement) on the ground surface were examined. The results indicate that as the number of seismic-loading cycles increases, the sand deposit softens progressively as large shear strains take place in different sand elements. Liquefaction state is reached after the combined effects of the progressive degradation of the initial shear modulus associated with the continuous decrease in the mean principal stress, and the buildup of the excess of pore pressure takes place in the sand deposit. Finally, the confinement effects given by a concrete slab placed on the surface of the sand deposit resulted in a favorable increasing in the initial shear modulus, an increase in the mean principal stress and a decrease in the softening rate (i.e. the decreasing rate in shear modulus) of the sand, thus making the onset of liquefaction to take place at a later stage. This is, only after the sand deposit having a concrete slab experienced a higher number of seismic loading cycles liquefaction took place, in contrast to an ordinary sand deposit having no concrete slab.

Keywords: liquefaction, shear modulus degradation, shaking table, earthquake

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Authors: Abdel-Monem Sayed Mohamed

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Lake Aswan is one of the largest man-made reservoirs in the world. The reservoir began to fill in 1964 and the level rose gradually, with annual irrigation cycles, until it reached a maximum water level of 181.5 m in November 1999, with a capacity of 160 km3. The filling of such large reservoir changes the stress system either through increasing vertical compressional stress by loading and/or increased pore pressure through the decrease of the effective normal stress. The resulted effect on fault zones changes stability depending strongly on the orientation of pre-existing stress and geometry of the reservoir/fault system. The main earthquake occurred on November 14, 1981, with magnitude 5.5. This event occurred after 17 years of the reservoir began to fill, along the active part of the Kalabsha fault and located not far from the High Dam. Numerous of small earthquakes follow this earthquake and continue till now. For this reason, 13 seismograph stations (radio-telemetry network short-period seismometers) were installed around the northern part of Lake Aswan. The main purpose of the network is to monitor the earthquake activity continuously within Aswan region. The data described here are obtained from the continuous record of earthquake activity and lake-water level variation through the period from 1982 to 2015. The seismicity is concentrated in the Kalabsha area, where there is an intersection of the easterly trending Kalabsha fault with the northerly trending faults. The earthquake foci are distributed in two seismic zones, shallow and deep in the crust. Shallow events have focal depths of less than 12 km while deep events extend from 12 to 28 km. Correlation between the seismicity and the water level variation in the lake provides great suggestion to distinguish the micro-earthquakes, particularly, those in shallow seismic zone in the reservoir–triggered seismicity category. The water loading is one factor from several factors, as an activating medium in triggering earthquakes. The common factors for all cases of induced seismicity seem to be the presence of specific geological conditions, the tectonic setting and water loading. The role of the water loading is as a supplementary source of earthquake events. So, the earthquake activity in the area originated tectonically (ML ≥ 4) and the water factor works as an activating medium in triggering small earthquakes (ML ≤ 3). Study of the inducing seismicity from the water level variation in Aswan Lake is of great importance and play great roles necessity for the safety of the High Dam body and its economic resources.

Keywords: Aswan lake, Aswan seismic network, seismicity, water level variation

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Authors: Nemat Sokhandan Bashir

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Threats from viruses to agricultural crops could be even larger than the losses caused by the other pathogens because, in many cases, the viral infection is latent but crucial from an epidemic point of view. Wild vegetation can be a source of many viruses that eventually find their destiny in crop plants. Although often asymptomatic in wild plants due to adaptation, they can potentially cause serious losses in crops. Therefore, exploring viruses in wild vegetation is very important. Recently, omics have been quite useful for exploring plant viruses from various plant sources, especially wild vegetation. For instance, we have discovered viruses such as Ambrossia asymptomatic virus I (AAV-1) through the application of metagenomics from Oklahoma Prairie Reserve. Accordingly, extracts from randomly-sampled plants are subjected to high speed and ultracentrifugation to separated virus-like particles (VLP), then nucleic acids in the form of DNA or RNA are extracted from such VLPs by treatment with phenol—chloroform and subsequent precipitation by ethanol. The nucleic acid preparations are separately treated with RNAse or DNAse in order to determine the genome component of VLPs. In the case of RNAs, the complementary cDNAs are synthesized before submitting to DNA sequencing. However, for VLPs with DNA contents, the procedure would be relatively straightforward without making cDNA. Because the length of the nucleic acid content of VPLs can be different, various strategies are employed to achieve sequencing. Techniques similar to so-called "chromosome walking" may be used to achieve sequences of long segments. When the nucleotide sequence data were obtained, they were subjected to BLAST analysis to determine the most related previously reported virus sequences. In one case, we determined that the novel virus was AAV-l because the sequence comparison and analysis revealed that the reads were the closest to the Indian citrus ringspot virus (ICRSV). AAV—l had an RNA genome with 7408 nucleotides in length and contained six open reading frames (ORFs). Based on phylogenies inferred from the replicase and coat protein ORFs of the virus, it was placed in the genus Mandarivirus.

Keywords: wild, plant, novel, metagenomics

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Authors: Jefriza, Habibah Lateh, Saumi Syahreza

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The 2016 Mw 6.5 Pidie Jaya earthquake is one of the biggest disasters that has occurred in Aceh within the last five years. This earthquake has caused severe damage to many infrastructures such as schools, hospitals, mosques, and houses in the district of Pidie Jaya and surrounding areas. Earthquakes commonly occur in Aceh Province due to the Aceh-Sumatra is located in the convergent boundaries of the Sunda Plate subducted beneath the Indo-Australian Plate. This convergence is responsible for the intensification of seismicity in this region. The plates are tilted at a speed of 63 mm per year and the right lateral component is accommodated by strike- slip faulting within Sumatra, mainly along the great Sumatran fault. This paper presents preliminary findings of InSAR study aimed at investigating the co-seismic surface deformation pattern in Pidie Jaya, Aceh-Indonesia. Coseismic surface deformation is rapid displacement that occurs at the time of an earthquake. Coseismic displacement mapping is required to study the behavior of seismic faults. InSAR is a powerful tool for measuring Earth surface deformation to a precision of a few centimetres. In this study, two radar images of the same area but at two different times are required to detect changes in the Earth’s surface. The ascending and descending Sentinel-1A (S1A) synthetic aperture radar (SAR) data and Sentinels application platform (SNAP) toolbox were used to generate SAR interferogram image. In order to visualize the InSAR interferometric, the S1A from both master (26 Nov 2016) and slave data-sets (26 Dec 2016) were utilized as the main data source for mapping the coseismic surface deformation. The results show that the fringes of phase difference have appeared in the border region as a result of the movement that was detected with interferometric technique. On the other hand, the dominant fringes pattern also appears near the coastal area, this is consistent with the field investigations two days after the earthquake. However, the study has also limitations of resolution and atmospheric artefacts in SAR interferograms. The atmospheric artefacts are caused by changes in the atmospheric refractive index of the medium, as a result, has limitation to produce coherence image. Low coherence will be affected the result in creating fringes (movement can be detected by fringes). The spatial resolution of the Sentinel satellite has not been sufficient for studying land surface deformation in this area. Further studies will also be investigated using both ALOS and TerraSAR-X. ALOS and TerraSAR-X improved the spatial resolution of SAR satellite.

Keywords: earthquake, InSAR, interferometric, Sentinel-1A

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Authors: Vikrant Gupta, Amrit Goswami

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The fixed income market forms the basis of the modern financial market. All other assets in financial markets derive their value from the bond market. Owing to its over-the-counter nature, corporate bonds have relatively less data publicly available and thus is researched upon far less compared to Equities. Bond price prediction is a complex financial time series forecasting problem and is considered very crucial in the domain of finance. The bond prices are highly volatile and full of noise which makes it very difficult for traditional statistical time-series models to capture the complexity in series patterns which leads to inefficient forecasts. To overcome the inefficiencies of statistical models, various machine learning techniques were initially used in the literature for more accurate forecasting of time-series. However, simple machine learning methods such as linear regression, support vectors, random forests fail to provide efficient results when tested on highly complex sequences such as stock prices and bond prices. hence to capture these intricate sequence patterns, various deep learning-based methodologies have been discussed in the literature. In this study, a recurrent neural network-based deep learning model using long short term networks for prediction of corporate bond prices has been discussed. Long Short Term networks (LSTM) have been widely used in the literature for various sequence learning tasks in various domains such as machine translation, speech recognition, etc. In recent years, various studies have discussed the effectiveness of LSTMs in forecasting complex time-series sequences and have shown promising results when compared to other methodologies. LSTMs are a special kind of recurrent neural networks which are capable of learning long term dependencies due to its memory function which traditional neural networks fail to capture. In this study, a simple LSTM, Stacked LSTM and a Masked LSTM based model has been discussed with respect to varying input sequences (three days, seven days and 14 days). In order to facilitate faster learning and to gradually decompose the complexity of bond price sequence, an Empirical Mode Decomposition (EMD) has been used, which has resulted in accuracy improvement of the standalone LSTM model. With a variety of Technical Indicators and EMD decomposed time series, Masked LSTM outperformed the other two counterparts in terms of prediction accuracy. To benchmark the proposed model, the results have been compared with traditional time series models (ARIMA), shallow neural networks and above discussed three different LSTM models. In summary, our results show that the use of LSTM models provide more accurate results and should be explored more within the asset management industry.

Keywords: bond prices, long short-term memory, time series forecasting, empirical mode decomposition

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Authors: M. D. Nirmani, K. L. N. Perera, G. H. Galhena

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Dengue has become one of the most important arbo-viral disease in all tropical and subtropical regions of the world. Aedes aegypti, is the principal vector of the virus, vary in both epidemiological and behavioral characteristics, which could be finely measured through DNA sequence comparison at their population level. Such knowledge in the population differences can assist in implementation of effective vector control strategies allowing to make estimates of the gene flow and adaptive genomic changes, which are important predictors of the spread of Wolbachia infection or insecticide resistance. As such, this study was undertaken to investigate the phylogenetic relationships of Ae. aegypti from Galle and Colombo, Sri Lanka, based on the ribosomal protein region which spans between two exons, in order to understand the geographical distribution of genetically distinct mosquito clades and its impact on mosquito control measures. A 320bp DNA region spanning from 681-930 bp, corresponding to the ribosomal protein, was sequenced in 62 Ae. aegypti larvae collected from Galle (N=30) and Colombo (N=32), Sri Lanka. The sequences were aligned using ClustalW and the haplotypes were determined with DnaSP 5.10. Phylogenetic relationships among haplotypes were constructed using the maximum likelihood method under Tamura 3 parameter model in MEGA 7.0.14 including three previously reported sequences of Australian (N=2) and Brazilian (N=1) Ae. aegypti. The bootstrap support was calculated using 1000 replicates and the tree was rooted using Aedes notoscriptus (GenBank accession No. KJ194101). Among all sequences, nineteen different haplotypes were found among which five haplotypes were shared between 80% of mosquitoes in the two populations. Seven haplotypes were unique to each of the population. Phylogenetic tree revealed two basal clades and a single derived clade. All observed haplotypes of the two Ae. aegypti populations were distributed in all the three clades, indicating a lack of genetic differentiation between populations. The Brazilian Ae. aegypti haplotype and one of the Australian haplotypes were grouped together with the Sri Lankan basal haplotype in the same basal clade, whereas the other Australian haplotype was found in the derived clade. Phylogram showed that Galle and Colombo Ae. aegypti populations are highly related to each other despite the large geographic distance (129 Km) indicating a substantial genetic similarity between them. This may have probably arisen from passive migration assisted by human travelling and trade through both land and water as the two areas are bordered by the sea. In addition, studied Sri Lankan mosquito populations were closely related to Australian and Brazilian samples. Probably this might have caused by shipping industry between the three countries as all of them are fully or partially enclosed by sea. For example, illegal fishing boats migrating to Australia by sea is perhaps a good mean of transportation of all life stages of mosquitoes from Sri Lanka. These findings indicate that extensive mosquito migrations occur between populations not only within the country, but also among other countries in the world which might be a main barrier to the successful vector control measures.

Keywords: Aedes aegypti, dengue control, extensive mosquito migration, haplotypes, phylogeny, ribosomal protein

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Authors: F. Longo, G. Granello, G. Tecchio, F. Da Porto

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Unreinforced masonry (URM) infill walls are widely used throughout the world, also in seismic prone regions, as partitions in reinforced concrete building frames. Even if they do not represent structural elements, they can dramatically affect both strength and stiffness of RC structures by acting as a diagonal strut, modifying shear and displacements distribution along the building height, with uncertain consequences on structural safety. In the last decades, many refined models have been developed to describe infill walls effect on frame structural behaviour, but generally restricted to in-plane actions. Only very recently some new approaches were implemented to consider in-plane/out-of-plane interaction of URM infill walls in progressive collapse simulations. In the present work, a particularly promising macro-model was adopted for the progressive collapse analysis of infilled RC frames. The model allows to consider the bi-directional interaction in terms of displacement and strength capacity for URM infills, and to remove the infill contribution when the URM wall is supposed to fail during the analysis process. The model was calibrated on experimental data regarding two different URM panels thickness, modelling with particular care the post-critic softening branch. A frame specimen set representing the most common Italian structures was built considering two main normative approaches: a traditional design philosophy, corresponding to structures erected between 50’s-80’s basically designed to support vertical loads, and a seismic design philosophy, corresponding to current criteria that take into account horizontal actions. Non-Linear Static analyses were carried out on the specimen set and some preliminary evaluations were drawn in terms of different performance exhibited by the RC frame when the contemporary effect of the out-of-plane damage is considered for the URM infill.

Keywords: infill Panels macromodels, in plane-out of plane interaction, RC frames, URM infills

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Authors: Harunori Kawabe, Hideyuki Aoshima, Koji Murakami, Minoru Kawakami, Yuka Nakano, David D. Ordinario, C. W. Crawford, Iri Sato-Baran

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With the recent advances in gene editing technologies allowing the rewriting of genetic sequences, additional market growth in the global floriculture market beyond previous trends is anticipated through increasingly sophisticated plant breeding techniques. As a prerequisite for gene editing, the gene sequence of the target plant must first be identified. This necessitates the genetic analysis of plants with unknown gene sequences, the extraction of RNA, and comprehensive expression analysis. Consequently, a technology capable of consistently and effectively extracting high-purity DNA and RNA from plants is of paramount importance. Although model plants, such as Arabidopsis and tobacco, have established methods for DNA and RNA extraction, floricultural species such as roses present unique challenges. Different techniques to extract DNA and RNA from various floricultural species were investigated. Upon sampling and grinding the petals of several floricultural species, it was observed that nucleic acid extraction from the ground petal solutions of low viscosity was straightforward; solutions of high viscosity presented a significant challenge. It is postulated that the presence of substantial quantities of polysaccharides and polyphenols in the plant tissue was responsible for the inhibition of nucleic acid extraction. Consequently, attempts were made to extract high-purity DNA and RNA by improving the CTAB method and combining it with commercially available nucleic acid extraction kits. The quality of the total extracted DNA and RNA was evaluated using standard methods. Finally, the effectiveness of the extraction method was assessed by determining whether it was possible to create a library that could be applied as a suitable template for a next-generation sequencer. In conclusion, a method was developed for consistent and accurate nucleic acid extraction from high-viscosity floricultural samples. These results demonstrate improved techniques for DNA and RNA extraction from flowers, help facilitate gene editing of floricultural species and expand the boundaries of research and commercial opportunities.

Keywords: floriculture, gene editing, next-generation sequencing, nucleic acid extraction

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Authors: Pranab Kumar Das

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Vulnerability assessment of buildings with irregularity in the vertical direction has been carried out in this study. The constructions of vertically irregular buildings are increasing in the context of fast urbanization in the developing countries including India. During two reconnaissance based survey performed after Nepal earthquake 2015 and Imphal (India) earthquake 2016, it has been observed that so many structures are damaged due to the vertically irregular configuration. These irregular buildings are necessary to perform safely during seismic excitation. Therefore, it is very urgent demand to point out the actual vulnerability of the irregular structure. So that remedial measures can be taken for protecting those structures during natural hazard as like earthquake. This assessment will be very helpful for India and as well as for the other developing countries. A sufficient number of research has been contributed to the vulnerability of plan asymmetric buildings. In the field of vertically irregular buildings, the effort has not been forwarded much to find out their vulnerability during an earthquake. Irregularity in vertical direction may be caused due to irregular distribution of mass, stiffness and geometrically irregular configuration. Detailed analysis of such structures, particularly non-linear/ push over analysis for performance based design seems to be challenging one. The present paper considered a number of models of irregular structures. Building models made of both reinforced concrete and brick masonry are considered for the sake of generality. The analyses are performed with both help of finite element method and computational method.The study, as a whole, may help to arrive at a reasonably good estimate, insight for fundamental and other natural periods of such vertically irregular structures. The ductility demand, storey drift, and seismic response study help to identify the location of critical stress concentration. Summarily, this paper is a humble step for understanding the vulnerability and framing up the guidelines for vertically irregular structures.

Keywords: ductility, stress concentration, vertically irregular structure, vulnerability

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Authors: Okolie Pius Ifeanyi, Emerenini Emilymary Chima

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Aims: The study investigated the diversity and identities of Lactic Acid Bacteria (LAB) isolated from different fresh fruits using Molecular Nested PCR analysis and the efficacy of cell free supernatants from Lactic Acid Bacteria (LAB) isolated from fresh fruits for in vitro control of some tomato pathogens. Study Design: Nested PCR approach was used in this study employing universal 16S rRNA gene primers in the first round PCR and LAB specific Primers in the second round PCR with the view of generating specific Nested PCR products for the LAB diversity present in the samples. The inhibitory potentials of supernatant obtained from LAB isolates of fruits origin that were molecularly characterized were investigated against some tomato phytopathogens using agar-well method with the view to develop biological agents for some tomato disease causing organisms. Methodology: Gram positive, catalase negative strains of LAB were isolated from fresh fruits on Man Rogosa and Sharpe agar (Lab M) using streaking method. Isolates obtained were molecularly characterized by means of genomic DNA extraction kit (Norgen Biotek, Canada) method. Standard methods were used for Nested Polymerase Chain Reaction (PCR) amplification targeting the 16S rRNA gene using universal 16S rRNA gene and LAB specific primers, agarose gel electrophoresis, purification and sequencing of generated Nested PCR products (Macrogen Inc., USA). The partial sequences obtained were identified by blasting in the non-redundant nucleotide database of National Center for Biotechnology Information (NCBI). The antimicrobial activities of characterized LAB against some tomato phytopathogenic bacteria which include (Xanthomonas campestries, Erwinia caratovora, and Pseudomonas syringae) were obtained by using the agar well diffusion method. Results: The partial sequences obtained were deposited in the database of National Centre for Biotechnology Information (NCBI). Isolates were identified based upon the sequences as Weissella cibaria (4, 18.18%), Weissella confusa (3, 13.64%), Leuconostoc paramensenteroides (1, 4.55%), Lactobacillus plantarum (8, 36.36%), Lactobacillus paraplantarum (1, 4.55%) and Lactobacillus pentosus (1, 4.55%). The cell free supernatants of LAB from fresh fruits origin (Weissella cibaria, Weissella confusa, Leuconostoc paramensenteroides, Lactobacillus plantarum, Lactobacillus paraplantarum and Lactobacillus pentosus) can inhibits these bacteria by creating clear zones of inhibition around the wells containing cell free supernatants of the above mentioned strains of lactic acid bacteria. Conclusion: This study shows that potentially LAB can be quickly characterized by molecular methods to specie level by nested PCR analysis of the bacteria isolate genomic DNA using universal 16S rRNA primers and LAB specific primer. Tomato disease causing organisms can be most likely biologically controlled by using extracts from LAB. This finding will reduce the potential hazard from the use of chemical herbicides on plant.

Keywords: nested pcr, molecular characterization, 16s rRNA gene, lactic acid bacteria

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Authors: Iyabode A. Kehinde, Joshua O. Oyekanmi, Jumoke T. Abimbola, Olajumoke E. Ayanda

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African yam bean (AYB), (Sphenostylis stenocarpa) is a leguminous crop that provides nutritionally rich seeds, tubers and leaves for human consumption. AYB potentials as an important food security crop is yet to be realized and thus classified as underutilized crop. Underutilization of the crop has been partly associated with scarce information on the incidence and characterization of fungal endophytes infecting vascular parts of AYB. Accurate and robust detection of these endophytic fungi is essential for diagnosis, modeling, surveillance and protection of germplasm (seed) health. This work aimed at isolating and identifying fungal endophytes associated with leaves, stems and roots of AYB in Ogun State, Nigeria. This study investigated both cultural and molecular properties of endophytic fungi in AYB for its characterization and diversity. Fungal endophytes were isolated and culturally identified. DNA extraction, PCR amplification using ITS primers and analyses of nucleotide sequences of ribosomal DNA fragments were conducted on selected isolates. BLAST analysis was conducted on consensus nucleotide sequences of 28 out of 30 isolates and results showed similar homology with genera of Rhizopus, Cunninghamella, Fusarium, Aspergillus, Penicillium, Alternaria, Diaporthe, Nigrospora, Purpureocillium, Corynespora, Magnaporthe, Macrophomina, Curvularia, Acrocalymma, Talaromyces and Simplicillium. Slight similarity was found with endophytes associated with soybean. Phylogenetic analysis by maximum likelihood method showed high diversity among the general. These organisms have high economic importance in crop improvement. For an instance, Purpureocillium lilacinum showed high potential in control of root rot caused by nematodes in tomatoes. Though some can be pathogens, but many of the fungal endophytes have beneficial attributes to plant in host health, uptake of nutrients, disease suppression, and host immunity.

Keywords: molecular characterization, African Yam Bean, fungal endophyte, plant parts

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Authors: M. Inmaculada Alvarez-Fernández, Celestino González-Nicieza, M. Belén Prendes-Gero, Fernando López-Gayarre

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Among many factors affecting the stability of mining excavations, rock-bursts and tremors play a special role. These dynamic loads occur practically always and have different sources of generation. The most important of them is the commonly used mining technique, which disintegrates a certain area of the rock mass not only in the area of the planned mining, but also creates waves that significantly exceed this area affecting the structural elements. In this work it is analysed the consequences of dynamic loads over the structural elements in an underground room and pillar mine to avoid roof instabilities. With this end, dynamic loads were evaluated through in situ and laboratory tests and simulated with numerical modelling. Initially, the geotechnical characterization of all materials was carried out by mean of large-scale tests. Then, drill holes were done on the roof of the mine and were monitored to determine possible discontinuities in it. Three seismic stations and a triaxial accelerometer were employed to measure the vibrations from blasting tests, establish the dynamic behaviour of roof and pillars and develop the transmission laws. At last, computer simulations by FLAC3D software were done to check the effect of vibrations on the stability of the roofs. The study shows that in-situ tests have a greater reliability than laboratory samples because of eliminating the effect of heterogeneities, that the pillars work decreasing the amplitude of the vibration around them, and that the tensile strength of a beam and depending on its span is overcome with waves in phase and delayed. The obtained transmission law allows designing a blasting which guarantees safety and prevents the risk of future failures.

Keywords: dynamic modelling, long term instability risks, room and pillar, seismic collapse

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Authors: L. Pavithra, R. Sharmila, Shivani Sridhar

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Columns severe structural damage needs proportioning a significant portion of earthquake energy can be dissipated yielding in the beams. Presence of axial load along with cyclic loading has a significant influence on column. The objective of this paper is to present the analytical results of columns subjected to biaxial cyclic loading.

Keywords: RC column, Seismic behaviour, cyclic behaviour, biaxial testing, ductile behaviour

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Juan S. Mantilla, Peter Thomson

Abstract:

Seismic events may result in discomfort on occupants of the buildings, structural damage or even buildings collapse. Traditional design aims to reduce dynamic response of structures by increasing stiffness, thus increasing the construction costs and the design forces. Structural control systems arise as an alternative to reduce these dynamic responses. A commonly used control systems in buildings are the passive friction dampers, which adds energy dissipation through damping mechanisms induced by sliding friction between their surfaces. Passive friction dampers are usually implemented on the diagonal of braced buildings, but such devices have the disadvantage that are optimal for a range of sliding force and out of that range its efficiency decreases. The above implies that each passive friction damper is designed, built and commercialized for a specific sliding/clamping force, in which the damper shift from a locked state to a slip state, where dissipates energy through friction. The risk of having a variation in the efficiency of the device according to the sliding force is that the dynamic properties of the building can change as result of many factor, even damage caused by a seismic event. In this case the expected forces in the building can change and thus considerably reduce the efficiency of the damper (that is designed for a specific sliding force). It is also evident than when a seismic event occurs the forces in each floor varies in the time what means that the damper's efficiency is not the best at all times. Semi-Active Friction devices adapt its sliding force trying to maintain its motion in the slipping phase as much as possible, because of this, the effectiveness of the device depends on the control strategy used. This paper deals with the development and performance evaluation of a low cost Semiactive Variable Friction Damper (SAVFD) in reduced scale to reduce vibrations of structures subject to earthquakes. The SAVFD consist in a (1) hydraulic brake adapted to (2) a servomotor which is controlled with an (3) Arduino board and acquires accelerations or displacement from (4) sensors in the immediately upper and lower floors and a (5) power supply that can be a pair of common batteries. A test structure, based on a Benchmark structure for structural control, was design and constructed. The SAVFD and the structure are experimentally characterized. A numerical model of the structure and the SAVFD is developed based on the dynamic characterization. Decentralized control algorithms were modeled and later tested experimentally using shaking table test using earthquake and frequency chirp signals. The controlled structure with the SAVFD achieved reductions greater than 80% in relative displacements and accelerations in comparison to the uncontrolled structure.

Keywords: earthquake response, friction damper, semiactive control, shaking table

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Authors: German Hernandez-Alonso, Antonio Lazcano, Arturo Becerra

Abstract:

Until today, viruses remain controversial and poorly understood; about their origin, this problem represents an enigma and one of the great challenges for the contemporary biology. Three main theories have tried to explain the origin of viruses: regressive evolution, escaped host gene, and pre-cellular origin. Under the perspective of the escaped host gene theory, it can be assumed a cellular origin of viral components, like protein RNA-binding domains. These universal distributed RNA-binding domains are related to the RNA metabolism processes, including transcription, processing, and modification of transcripts, translation, RNA degradation and its regulation. In the case of viruses, these domains are present in important viral proteins like helicases, nucleases, polymerases, capsid proteins or regulation factors. Therefore, they are implicated in the replicative cycle and parasitic processes of viruses. That is why it is possible to think that those domains present low levels of divergence due to selective pressures. For these reasons, the main goal for this project is to create a catalogue of the RNA-binding domains found in all the available viral proteomes, using bioinformatics tools in order to analyze its evolutionary process, and thus shed light on the general virus evolution. ProDom database was used to obtain larger than six thousand RNA-binding domain families that belong to the three cellular domains of life and some viral groups. From the sequences of these families, protein profiles were created using HMMER 3.1 tools in order to find distant homologous within greater than four thousand viral proteomes available in GenBank. Once accomplished the analysis, almost three thousand hits were obtained in the viral proteomes. The homologous sequences were found in proteomes of the principal Baltimore viral groups, showing interesting distribution patterns that can contribute to understand the evolution of viruses and their host-virus interactions. Presence of cellular RNA-binding domains within virus proteomes seem to be explained by closed interactions between viruses and their hosts. Recruitment of these domains is advantageous for the viral fitness, allowing viruses to be adapted to the host cellular environment.

Keywords: bioinformatics tools, distant homology, RNA-binding domains, viral evolution

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Authors: Reza Hedayati, Meysam Jahanbakhshi

Abstract:

In this work, Fracture Mechanics is used to predict crack propagation in the adhesive joining aluminum and composite plates. Three types of loadings and two types of glass-epoxy composite sequences: [0/90]2s and [0/45/-45/90]s are considered for the composite plate. Therefore, 2*3=6 cases are considered and their results are compared. The debonding initiation load, complete debonding load, crack face profile and load-displacement diagram have been compared for the six cases.

Keywords: adhesive joint, debonding, fracture, LEFM, APDL

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Authors: Jyoti Bharti, Navneet Manjhi, M. K.Gupta, Bimi Jain

Abstract:

A reliable gait features are required to extract the gait sequences from an images. In this paper suggested a simple method for gait identification which is based on moments. Moment values are extracted on different number of frames of gray scale and silhouette images of CASIA database. These moment values are considered as feature values. Fuzzy logic and nearest neighbour classifier are used for classification. Both achieved higher recognition.

Keywords: gait, fuzzy logic, nearest neighbour, recognition rate, moments

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Authors: Arwin Malabanan, Carl Chester Ragudo, Jerome Tadiosa, John Dee Mangoba, Eric Augustus Tingatinga, Romeo Eliezer Longalong

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Concrete hollow blocks (CHB) are the most commonly used masonry block for walls in residential houses, school buildings and public buildings in the Philippines. During the recent 2013 Bohol earthquake (Mw 7.2), it has been proven that CHB walls are very vulnerable to severe external action like strong ground motion. In this paper, a numerical model of CHB structures is proposed, and seismic behavior of CHB houses is presented. In modeling, the Rigid Body Spring-Discrete Element method (RBS-DEM)) is used wherein masonry blocks are discretized into rigid elements and connected by nonlinear springs at preselected contact points. The shear and normal stiffness of springs are derived from the material properties of CHB unit incorporating the grout and mortar fillings through the volumetric transformation of the dimension using material ratio. Numerical models of reinforced and unreinforced walls are first subjected to linearly-increasing in plane loading to observe the different failure mechanisms. These wall models are then assembled to form typical model masonry houses and then subjected to the El Centro and Pacoima earthquake records. Numerical simulations show that the elastic, failure and collapse behavior of the model houses agree well with shaking table tests results. The effectiveness of the method in replicating failure patterns will serve as a basis for the improvement of the design and provides a good basis of strengthening the structure.

Keywords: concrete hollow blocks, discrete element method, earthquake, rigid body spring model

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Authors: Reza Hedayati, Meysam Jahanbakhshi

Abstract:

In this work, Fracture Mechanics is used to predict crack propagation in the adhesive jointing aluminum and composite plates. Three types of loadings and two types of glass-epoxy composite sequences: [0/90]2s and [0/45/-45/90]s are considered for the composite plate. Therefore 2*3=6 cases are considered and their results are compared. The debonding initiation load, complete debonding load, crack face profile and load-displacement diagram have been compared for the six cases.

Keywords: fracture, adhesive joint, debonding, APDL, LEFM

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Authors: Benjamin Lee Warren

Abstract:

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: Vivian A. Panes, Raymond John S. Rebong, Miel Q. Diaz

Abstract:

Moringa oleifera Lam. is known mainly for its high nutritional value and medicinal properties contributing to its popular reputation as a 'miracle plant' in the tropical climates where it usually grows. The main objective of this study is to discover the genes and gene products involved in abiotic stress-induced activity that may impact the M. oleifera Lam. mature seeds as well as their corresponding functions. In this study, RNA-sequencing and de novo transcriptome assembly were performed using two assemblers, Trinity and Oases, which produced 177,417 and 120,818 contigs respectively. These transcripts were then subjected to various bioinformatics tools such as Blast2GO, UniProt, KEGG, and COG for gene annotation and the analysis of relevant metabolic pathways. Furthermore, FPKM analysis was performed to identify gene expression levels. The sequences were filtered according to the 'response to stress' GO term since this study dealt with stress response. Clustered Orthologous Groups (COG) showed that the highest frequencies of stress response gene functions were those of cytoskeleton which make up approximately 14% and 23% of stress-related sequences under Trinity and Oases respectively, recombination, repair and replication at 11% and 14% respectively, carbohydrate transport and metabolism at 23% and 9% respectively and defense mechanisms 16% and 12% respectively. KEGG pathway analysis determined the most abundant stress-response genes in the phenylpropanoid biosynthesis at counts of 187 and 166 pathways for Oases and Trinity respectively, purine metabolism at 123 and 230 pathways, and biosynthesis of antibiotics at 105 and 102. Unique and cumulative GO term counts revealed that majority of the stress response genes belonged to the category of cellular response to stress at cumulative counts of 1,487 to 2,187 for Oases and Trinity respectively, defense response at 754 and 1,255, and response to heat at 213 and 208, response to water deprivation at 229 and 228, and oxidative stress at 508 and 488. Lastly, FPKM was used to determine the levels of expression of each stress response gene. The most upregulated gene encodes for thiamine thiazole synthase chloroplastic-like enzyme which plays a significant role in DNA damage tolerance. Data analysis implies that M. oleifera stress response genes are directed towards the effects of climate change more than other stresses indicating the potential of M. oleifera for cultivation in harsh environments because it is resistant to climate change, pathogens, and foreign invaders.

Keywords: stress response, genes, Moringa oleifera, transcriptomics

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Authors: Rosa Figueroa, Christopher Flores

Abstract:

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: 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: Shiv Jyoti Pandey, Shveta Puri, G. M. Bhat, Neha Raina

Abstract:

The Jammu and Kashmir (J&K) region of Northwest Himalaya has a long history of earthquake activity which falls within Seismic Zones IV and V. To know the crustal structure beneath this region, we utilized teleseismic receiver function method. This paper presents the results of the analyses of the teleseismic earthquake waves recorded by 10 seismic observatories installed in the vicinity of major thrusts and faults. The teleseismic waves at epicentral distance between 30o and 90o with moment magnitudes greater than or equal to 5.5 that contains large amount of information about the crust and upper mantle structure directly beneath a receiver has been used. The receiver function (RF) technique has been widely applied to investigate crustal structures using P-to-S converted (Ps) phases from velocity discontinuities. The arrival time of the Ps, PpPs and PpSs+ PsPs converted and reverberated phases from the Moho can be combined to constrain the mean crustal thickness and Vp/Vs ratio. Over 500 receiver functions from 10 broadband stations located in the Jammu & Kashmir region of Northwest Himalaya were analyzed. With the help of H-K stacking method, we determined the crustal thickness (H) and average crustal Vp/Vs ratio (K) in this region. We also used Neighbourhood algorithm technique to verify our results. The receiver function results for these stations show that the crustal thickness under Jammu & Kashmir ranges from 45.0 to 53.6 km with an average value of 50.01 km. The Vp/Vs ratio varies from 1.63 to 1.99 with an average value of 1.784 which corresponds to an average Poisson’s ratio of 0.266 with a range from 0.198 to 0.331. High Poisson’s ratios under some stations may be related to partial melting in the crust near the uppermost mantle. The crustal structure model developed from this study can be used to refine the velocity model used in the precise epicenter location in the region, thereby increasing the knowledge to understand current seismicity in the region.

Keywords: H-K stacking, Poisson’s ratios, receiver function, teleseismic

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