Search results for: switching sequences

Authors: Dwi Arisandi Wijaya, Ernawati Arifin Giri-Rachman, Neni Nurainy

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Typhoid fever disease can be prevented by using a polysaccharide-based vaccine Vi which is a virulence factor of S.typhi. To produce high yield Vi polysaccharide from bacteria, it is important to know the biosynthesis of Vi polysaccharide and the regulators involved. In the In vivo condition, S. typhi faces different osmolarity, and the bacterial two-component system OmpR-EnvZ, regulate by up and down Capsular Vi polysaccharide biosynthesis. A high yielded Vi Polysaccharide strain, S. typhi strain C6524 used to study the effect of media osmolarity on Vi polysaccharide biosynthesis and the osmoregulation pattern of S. typhi strain C6524. The methods were performed by grown S. typhi strain C6524 grown on medium with 50 mM, 100 mM, and 150 mM osmolarity with the batch system. Vi polysaccharide concentration was measured by ELISA method. For further investigation of the osmoregulation pattern of strain C6524, the osmoregulator gene, OmpR, has been isolated and sequenced using the specific primer of the OmpR gene. Nucleotide sequence analysis is done with BLAST and Lallign. Amino Acid sequence analysis is done with Prosite and Multiple Sequence Alignment. The results of cultivation showed the average content of polysaccharide Vi for 50 mM, 100 mM, and 150 mM osmolarities 11.49 μg/mL, 12.06 μg/mL, and 14.53 μg/mL respectively. Analysis using Anova stated that the osmolarity treatment of 150 mM significantly affects Vi content. Analysis of nucleotide sequences shows 100% identity between S. typhi strain C6524 and Ty2. Analysis of amino acid sequences shows that the OmpR response regulator protein of the C6524 strain also has a α4-β5-α5 motif which is important for the regulatory activation system when phosphorylation occurs by domain kinase. This indicates that the regulator osmolarity response of S. typhi strain C6524 has no difference with the response regulator owned by S. typhi strain Ty2. A high Vi response rate in the 150 mM osmolarity treatment requires further research for RcsB-RcsC, another two-component system involved in Vi Biosynthesis.

Keywords: osmoregulator, OmpR, Salmonella, Vi polysaccharide

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Authors: Hanieh Mohammadi, Sarah Fraser, Anil Nigam, Frederic Lesage, Louis Bherer

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A chronically higher cerebral pulsatility is thought to damage cerebral microcirculation, leading to cognitive decline in older adults. Although it is widely known that regular physical activity is linked to improvement in some cognitive domains, including executive functions, the mediating role of cerebral pulsatility on this link remains to be elucidated. This study assessed the impact of 6 months of regular physical activity upon changes in an optical index of cerebral pulsatility and the role of physical activity for the improvement of executive functions. 27 older adults (aged 57-79, 66.7% women) with cardiovascular risk factors (CVRF) were enrolled in the study. The participants completed the behavioral Stroop test, which was extracted from the Delis-Kaplan executive functions system battery at baseline (T0) and after 6 months (T6) of physical activity. Near-infrared spectroscopy (NIRS) was applied for an innovative approach to indexing cerebral pulsatility in the brain microcirculation at T0 and T6. The participants were at standing rest while a NIRS device recorded hemodynamics data from frontal and motor cortex subregions at T0 and T6. The cerebral pulsatility index of interest was cerebral pulse amplitude, which was extracted from the pulsatile component of NIRS data. Our data indicated that 6 months of physical activity was associated with a reduction in the response time for the executive functions, including inhibition (T0: 56.33± 18.2 to T6: 53.33± 15.7,p= 0.038)and Switching(T0: 63.05± 5.68 to T6: 57.96 ±7.19,p< 0.001) conditions of the Stroop test. Also, physical activity was associated with a reduction in cerebral pulse amplitude (T0: 0.62± 0.05 to T6: 0.55± 0.08, p < 0.001). Notably, cerebral pulse amplitude was a significant mediator of the link between physical activity and response to the Stroop test for both inhibition (β=0.33 (0.61,0.23),p< 0.05)and switching (β=0.42 (0.69,0.11),p <0.01) conditions. This study suggests that regular physical activity may support cognitive functions through the improvement of cerebral pulsatility in older adults with CVRF.

Keywords: near-infrared spectroscopy, cerebral pulsatility, physical activity, cardiovascular risk factors, executive functions

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Authors: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Min L. Stewart, Patrick Johnston

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Predictive coding has been proposed as a general explanatory framework for understanding the neural mechanisms of perception. As such, an underweighting of perceptual priors has been hypothesised to underpin a range of differences in inferential and sensory processing in autism spectrum disorders. However, empirical evidence to support this has not been well established. The present study uses an electroencephalography paradigm involving changes of facial identity and person category (actors etc.) to explore how levels of autistic traits (AT) affect predictive coding at multiple stages in the visual processing hierarchy. The study uses a rapid serial presentation of faces, with hierarchically structured sequences involving both periodic and aperiodic repetitions of different stimulus attributes (i.e., person identity and person category) in order to induce contextual expectations relating to these attributes. It investigates two main predictions: (1) significantly larger and late neural responses to change of expected visual sequences in high-relative to low-AT, and (2) significantly reduced neural responses to violations of contextually induced expectation in high- relative to low-AT. Preliminary frequency analysis data comparing high and low-AT show greater and later event-related-potentials (ERPs) in occipitotemporal areas and prefrontal areas in high-AT than in low-AT for periodic changes of facial identity and person category but smaller ERPs over the same areas in response to aperiodic changes of identity and category. The research advances our understanding of how abnormalities in predictive coding might underpin aberrant perceptual experience in autism spectrum. This is the first stage of a research project that will inform clinical practitioners in developing better diagnostic tests and interventions for people with autism.

Keywords: hierarchical visual processing, face processing, perceptual hierarchy, prediction error, predictive coding

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Authors: Othman E. Othman, Agnés Germot, Daniel Petit, Abderrahman Maftah

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Threats to the biodiversity are increasing due to the loss of genetic diversity within the species utilized in agriculture. Due to the progressive substitution of the less productive, locally adapted and native breeds by highly productive breeds, the number of threatened breeds is increased. In these conditions, it is more strategically important than ever to preserve as much the farm animal diversity as possible, to ensure a prompt and proper response to the needs of future generations. Mitochondrial (mtDNA) sequencing has been used to explain the origins of many modern domestic livestock species. Studies based on sequencing of sheep mitochondrial DNA showed that there are five maternal lineages in the world for domestic sheep breeds; A, B, C, D and E. Because of the eastern location of Egypt in the Mediterranean basin and the presence of fat-tailed sheep breeds- character quite common in Turkey and Syria- where genotypes that seem quite primitive, the phylogenetic studies of Egyptian sheep breeds become particularly attractive. We aimed in this work to clarify the genetic affinities, biodiversity and phylogeny of five Egyptian sheep breeds using cytochrome B sequencing. Blood samples were collected from 63 animals belonging to the five tested breeds; Barki, Rahmani, Ossimi, Saidi and Sohagi. The total DNA was extracted and the specific primer allowed the conventional PCR amplification of the cytochrome B region of mtDNA (approximately 1272 bp). PCR amplified products were purified and sequenced. The alignment of Sixty-three samples was done using BioEdit software. DnaSP 5.00 software was used to identify the sequence variation and polymorphic sites in the aligned sequences. The result showed that the presence of 34 polymorphic sites leading to the formation of 18 haplotypes. The haplotype diversity in five tested breeds ranged from 0.676 in Rahmani breed to 0.894 in Sohagi breed. The genetic distances (D) and the average number of pairwise differences (Dxy) between breeds were estimated. The lowest distance was observed between Rahmani and Saidi (D: 1.674 and Dxy: 0.00150) while the highest distance was observed between Ossimi and Sohagi (D: 5.233 and Dxy: 0.00475). Neighbour-joining (Phylogeny) tree was constructed using Mega 5.0 software. The sequences of the 63 analyzed samples were aligned with references sequences of different haplogroups. The phylogeny result showed the presence of three haplogroups (HapA, HapB and HapC) in the 63 examined samples. The other two haplogroups described in literature (HapD and HapE) were not found. The result showed that 50 out of 63 tested animals cluster with haplogroup B (79.37%) whereas 7 tested animals cluster with haplogroup A (11.11%) and 6 animals cluster with haplogroup C (9.52%). In conclusion, the phylogenetic reconstructions showed that the majority of Egyptian sheep breeds belonging to haplogroup B which is the dominant haplogroup in Eastern Mediterranean countries like Syria and Turkey. Some individuals are belonging to haplogroups A and C, suggesting that the crosses were done with other breeds for characteristic selection for growth and wool quality.

Keywords: cytochrome B, diversity, phylogheny, Egyptian sheep breeds

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Authors: D. Rama Krishna, Y. Pandu Rangaiah

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This paper presents the design of multiband reconfigurable antenna using PIN diodes for four iterations and all the four iterations have been validated by measuring return loss and pattern measurements of developed prototype antenna. The simulated and experimental data have demonstrated the concepts of a multiband reconfigurable antenna by switching OFF and ON of PIN diodes for multiple band frequencies. The technique has taken the advantage of a different number of radiating lengths with the use of PIN diode switches, each configuration resonating at multiband frequencies.

Keywords: frequency reconfigurable, meandered line multiband antenna, PIN diode, multiband frequencies

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

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Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase– pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed- specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization

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Authors: Yi Hu, Chun-Chi Lin, Shau-En Yeh, Shin Lee

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In this study, p–n heterojunctions with La0.5Sr0.5CoO3 (LSCO) and W-doped VO2 thin films were fabricated by the radio frequency (r.f.) magnetron sputtering technique and sol-gel process, respectively. The thickness of VO2 and LSCO thin films are about 40 nm and 400 nm, respectively. Good crystalline match between LSCO and VO2 films was observed from the SEM. The built-in voltages for the junction are about 1.1 V and 2.3 V for the sample in the metallic and insulating state, respectively. The sample can undergo the current induced MIT during applying field when the sample was heated at 40 and 50ºC. This is in agreement with the value obtained from the difference in the work functions of LSCO and VO2. The band structure of the heterojunction was proposed based on the results of analysis.

Keywords: hetrojection, Mott transition, switching , VO2

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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: 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: Rakesh Krishna, Abhishek Poddar

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The paper discusses the work carried out on the implementation of control techniques like Digital Pulse Width Modulation (PWM) and Digital Pulse Fired control(PFC). These techniques are often used in devices like inverters, battery chargers, DC-to-DC converters can also be implemented on household devices like heaters. The advantage being the control and improved life span of device. In case of batteries using these techniques are known to increase the life span of battery in mobiles and other hand-held devices. 8051 microcontroller is used to implement these methods.Thyristors are used for switching operations.

Keywords: PWM, SVM, PFC, bidirectional inverters, snubber

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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: Wondmnew Derebe Yohannis

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Farming irrigation plays a crucial role in rural development strategies, impacting both annual household income and livelihood. This research aims to evaluate the factors influencing irrigation participation and assess the impact of small-scale irrigation on rural households' annual income. The study collected data from 287 farmers in the Dahana district of northern Ethiopia. The research investigates the driving forces behind farmers' decisions to adopt small-scale irrigation and its effect on annual income gain. The findings reveal that several factors positively influence the probability of adoption, including access to credit, cultivated land size, livestock holding, extension contact, and the education level of the household head. Conversely, the distance to local markets and water schemes negatively affects the likelihood of adoption. To understand the differences in annual income between farm households that adopted irrigation and those that did not, a simultaneous equations model with endogenous switching regression is estimated. This accounts for the heterogeneity in the adoption decision and unobservable characteristics of farmers and their farms. The analysis compares the expected income gain under actual and counterfactual scenarios, considering whether the farm household adopted irrigation or not. The study reveals that the group of farm households that adopted irrigation has distinct characteristics compared to those that did not adopt it. Furthermore, the research demonstrates that the adoption of irrigation practices leads to an increase in annual income. Interestingly, the impact of small-scale irrigation on annual income is greater for the farm households that actually adopted irrigation compared to those in the counterfactual scenario where they did not adopt. Based on the findings, the researcher concludes that small-scale irrigation is a practical solution for meeting household financial needs in the study area. It is recommended that investments in small-scale irrigation continue to further improve the livelihoods of rural farming communities by enhancing annual income gains.

Keywords: small-scale irrigation, income, rural farm households, endogenous switching regression, user, non-user

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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: Vishal H. Shukla, Sanjay B. Deshmukh

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Traffic engineering, at its center, is the ability of moving traffic approximately so that traffic from a congested link is moved onto the unused capacity on another link. Traffic Engineering ensures the best possible use of the resources. Now to support traffic engineering in the today’s network, Multiprotocol Label Switching (MPLS) is being used which is very helpful for reliable packets delivery in an ongoing internet services. Here a topology is been implemented on GNS3 to focus on the analysis of the communication take place from one site to other through the ISP. The comparison is made between the IP network & MPLS network based on Bandwidth & Jitter which are one of the performance parameters using JPERF simulator.

Keywords: GNS3, JPERF, MPLS, traffic engineering, VMware

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Authors: Joseph Bertrand Iboum Kissaaka, Charles Fonyuy Ngum Tchioben, Paul Gustave Fowe Kwetche, Jeannette Ngo Elogan Ntem, Joseph Binyet Njebakal, Ribert Yvan Makosso-Tchapi, François Mvondo Owono, Marie Joseph Ntamak-Nida

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Located in the Gulf of Guinea, the Kribi-Campo sub-basin belongs to the Aptian salt basins along the West African Margin. In this paper, we investigated the tectono-stratigraphic architecture of the basin, focusing on the role of salt tectonics and strike-slip faults along the Kribi Fracture Zone with implications for reservoir prediction. Using 2D seismic data and well data interpreted through sequence stratigraphy with integrated seismic attributes analysis with Python Programming and unsupervised Machine Learning, at least six second-order sequences, indicating three main stages of tectono-stratigraphic evolution, were determined: pre-salt syn-rift, post-salt rift climax and post-rift stages. The pre-salt syn-rift stage with KTS1 tectonosequence (Barremian-Aptian) reveals a transform rifting along NE-SW transfer faults associated with N-S to NNE-SSW syn-rift longitudinal faults bounding a NW-SE half-graben filled with alluvial to lacustrine-fan delta deposits. The post-salt rift-climax stage (Lower to Upper Cretaceous) includes two second-order tectonosequences (KTS2 and KTS3) associated with the salt tectonics and Campo High uplift. During the rift-climax stage, the growth of salt diapirs developed syncline withdrawal basins filled by early forced regression, mid transgressive and late normal regressive systems tracts. The early rift climax underlines some fine-grained hangingwall fans or delta deposits and coarse-grained fans from the footwall of fault scarps. The post-rift stage (Paleogene to Neogene) contains at least three main tectonosequences KTS4, KTS5 and KTS6-7. The first one developed some turbiditic lobe complexes considered as mass transport complexes and feeder channel-lobe complexes cutting the unstable shelf edge of the Campo High. The last two developed submarine Channel Complexes associated with lobes towards the southern part and braided delta to tidal channels towards the northern part of the Kribi-Campo sub-basin. The reservoir distribution in the Kribi-Campo sub-basin reveals some channels, fan lobes reservoirs and stacked channels reaching up to the polygonal fault systems.

Keywords: tectono-stratigraphic architecture, Kribi-Campo sub-basin, machine learning, pre-salt sequences, post-salt sequences

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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: 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: B. H. Lee

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Nowadays, a grid-connected photovoltaic (PV) inverter is adopted in various places like as home, factory, because grid-connected PV inverter can reduce total power consumption by supplying electricity from PV array. In this paper, design and implementation of a 300 W grid-connected PV inverter are described. It is implemented with TI Piccolo DSP core and operated at 100 kHz switching frequency in order to reduce harmonic contents. The maximum operating input voltage is up to 45 V. The characteristics of the designed system that include maximum power point tracking (MPPT), single operation and battery charging are verified by simulation and experimental results.

Keywords: design, grid-connected, implementation, photovoltaic

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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: Nada Poropat Jeletic, Gordana Hrzica

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Bilingual conversational corpora represent a meaningful and the most comprehensive data source for investigating the genuine contact phenomena in non-monitored bi-lingual speech productions. They can be particularly useful for bilingual research since some features of bilingual interaction can hardly be accessed with more traditional methodologies (e.g., elicitation tasks). The method of language sampling provides the resources for describing language interaction in a bilingual community and/or in bilingual situations (e.g. code-switching, amount of languages used, number of languages used, etc.). To capture these phenomena in genuine communication situations, such sampling should be as close as possible to spontaneous communication. Bilingual spoken corpus design is methodologically demanding. Therefore this paper aims at describing the methodological challenges that apply to the corpus design of the conversational corpus design of the Istrian Istrovenetian-Croatian Bilingual Corpus. Croatian is the first official language of the Croatian-Italian officially bilingual Istria County, while Istrovenetian is a diatopic subvariety of Venetian, a longlasting lingua franca in the Istrian peninsula, the mother tongue of the members of the Italian National Community in Istria and the primary code of informal everyday communication among the Istrian Italophone population. Within the CLARIN infrastructure, TalkBank is being used, as it provides relevant procedures for designing and analyzing bilingual corpora. Furthermore, it allows public availability allows for easy replication of studies and cumulative progress as a research community builds up around the corpus, while the tools developed within the field of corpus linguistics enable easy retrieval and analysis of information. The method of language sampling employed is kept at the level of spontaneous communication, in order to maximise the naturalness of the collected conversational data. All speakers have provided written informed consent in which they agree to be recorded at a random point within the period of one month after signing the consent. Participants are administered a background questionnaire providing information about the socioeconomic status and the exposure and language usage in the participants social networks. Recording data are being transcribed, phonologically adapted within a standard-sized orthographic form, coded and segmented (speech streams are being segmented into communication units based on syntactic criteria) and are being marked following the CHAT transcription system and its associated CLAN suite of programmes within the TalkBank toolkit. The corpus consists of transcribed sound recordings of 36 bilingual speakers, while the target is to publish the whole corpus by the end of 2020, by sampling spontaneous conversations among approximately 100 speakers from all the bilingual areas of Istria for ensuring representativeness (the participants are being recruited across three generations of native bilingual speakers in all the bilingual areas of the peninsula). Conversational corpora are still rare in TalkBank, so the Corpus will contribute to BilingBank as a highly relevant and scientifically reliable resource for an internationally established and active research community. The impact of the research of communities with societal bilingualism will contribute to the growing body of research on bilingualism and multilingualism, especially regarding topics of language dominance, language attrition and loss, interference and code-switching etc.

Keywords: conversational corpora, bilingual corpora, code-switching, language sampling, corpus design methodology

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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: German Hernandez-Alonso, Antonio Lazcano, Arturo Becerra

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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

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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: Anukwu John Uchenn, Nwamba, Helen Ogochukwu, Achikanu Cosmas, Chiaha Emiliana

Abstract:

The continuous decline in biodiversity is worrisome. This decline is predominant in fish population. Although taxonomy has been an age-long field of science, there are still undiscovered members of species and new species are waiting to be uncovered. The failure of traditional taxonomic method to address this issue has resulted to the adoption of a molecular approach-DNA barcoding. It was proposed that DNA barcoding using mitochondrion cytochrome oxidase subunit I (COI) gene has the capability to serve as a barcode for fishes. The aim of this study was to use DNA barcoding in the identification of fish species in Imo River, Rivers State. A total of eight (8) fish samples were collected and used for this study. Quick DNA Miniprep Plus kit (D4068, Zymo Research) was used for the DNA extraction which was followed by PCR amplification and sequencing. BLAST result shows correlation between the sequence queried and the biological sequences with the NCBI database. The names of the samples, percentage ID, predicted organisms and GenBank Accession numbers were clearly identified. A total of 16 sequences (all > 600bp) belonging to 7 species, 7 genera, 7 families and 4 orders were validated and submitted to the NCBI database. Each nucleotide peak was represented by a single colour with various percentage occurrences. Four (50%) out of the 8 original samples analyzed corresponded with the predicted organisms from BLAST result. Pairwise sequence alignment showed different consensus positions and a total of 11 mutations found in Chrysichthys nigrodigitatus (n=4), Oreochromis niloticus (n=2) and Clarias gariepinus (n=5). The whole mutations were substitution (transition and transversion) with no deletion and insertion. However, the transition mutation (n=6) was more in number compared to the transversion (n=5) mutation. There were a total of 834 positions in the final dataset. This work will facilitate more research in other keys areas such as identification of mislabeled fish products, illegal trading of endangered species and effective tracking of fish biodiversity.

Keywords: DNA barcoding, Imo river, phylogenetic tree, pairwise DNA alignment

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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

Procedia PDF Downloads 104