Search results for: primer sequences

Authors: Hyun-Koo Kim, Yong-Hun Kim, Soo-Young Suk, Ju H. Park, Ho-Youl Jung

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This paper presents an effective speed hump detection process at the day-time. we focus only on round types of speed humps in the day-time dynamic road environment. The proposed speed hump detection scheme consists mainly of two process as stereo matching and speed hump detection process. Our proposed process focuses to speed hump detection process. Speed hump detection process consist of noise reduction step, data fusion step, and speed hemp detection step. The proposed system is tested on Intel Core CPU with 2.80 GHz and 4 GB RAM tested in the urban road environments. The frame rate of test videos is 30 frames per second and the size of each frame of grabbed image sequences is 1280 pixels by 670 pixels. Using object-marked sequences acquired with an on-vehicle camera, we recorded speed humps and non-speed humps samples. Result of the tests, our proposed method can be applied in real-time systems by computation time is 13 ms. For instance; our proposed method reaches 96.1 %.

Keywords: data fusion, round types speed hump, speed hump detection, surface filter

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Authors: Alexander Vandesompele, Joni Dambre

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The diversity in dendritic arborization, as first illustrated by Santiago Ramon y Cajal, has always suggested a role for dendrites in the functionality of neurons. In the past decades, thanks to new recording techniques and optical stimulation methods, it has become clear that dendrites are not merely passive electrical components. They are observed to integrate inputs in a non-linear fashion and actively participate in computations. Regardless, in simulations of neural networks dendritic structure and functionality are often overlooked. Especially in a machine learning context, when designing artificial neural networks, point neuron models such as the leaky-integrate-and-fire (LIF) model are dominant. These models mimic the integration of inputs at the neuron soma, and ignore the existence of dendrites. In this work, the LIF point neuron model is extended with a simple form of dendritic computation. This gives the LIF neuron increased capacity to discriminate spatiotemporal input sequences, a dendritic functionality as observed in another study. Simulations of the spiking neurons are performed using the Bindsnet framework. In the common LIF model, incoming synapses are independent. Here, we introduce a dependency between incoming synapses such that the post-synaptic impact of a spike is not only determined by the weight of the synapse, but also by the activity of other synapses. This is a form of short term plasticity where synapses are potentiated or depressed by the preceding activity of neighbouring synapses. This is a straightforward way to prevent inputs from simply summing linearly at the soma. To implement this, each pair of synapses on a neuron is assigned a variable,representing the synaptic relation. This variable determines the magnitude ofthe short term plasticity. These variables can be chosen randomly or, more interestingly, can be learned using a form of Hebbian learning. We use Spike-Time-Dependent-Plasticity (STDP), commonly used to learn synaptic strength magnitudes. If all neurons in a layer receive the same input, they tend to learn the same through STDP. Adding inhibitory connections between the neurons creates a winner-take-all (WTA) network. This causes the different neurons to learn different input sequences. To illustrate the impact of the proposed dendritic mechanism, even without learning, we attach five input neurons to two output neurons. One output neuron isa regular LIF neuron, the other output neuron is a LIF neuron with dendritic relationships. Then, the five input neurons are allowed to fire in a particular order. The membrane potentials are reset and subsequently the five input neurons are fired in the reversed order. As the regular LIF neuron linearly integrates its inputs at the soma, the membrane potential response to both sequences is similar in magnitude. In the other output neuron, due to the dendritic mechanism, the membrane potential response is different for both sequences. Hence, the dendritic mechanism improves the neuron’s capacity for discriminating spa-tiotemporal sequences. Dendritic computations improve LIF neurons even if the relationships between synapses are established randomly. Ideally however, a learning rule is used to improve the dendritic relationships based on input data. It is possible to learn synaptic strength with STDP, to make a neuron more sensitive to its input. Similarly, it is possible to learn dendritic relationships with STDP, to make the neuron more sensitive to spatiotemporal input sequences. Feeding structured data to a WTA network with dendritic computation leads to a significantly higher number of discriminated input patterns. Without the dendritic computation, output neurons are less specific and may, for instance, be activated by a sequence in reverse order.

Keywords: dendritic computation, spiking neural networks, point neuron model

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Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

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Authors: Shonak Bansal, Prince Jain, Arun Kumar Singh, Neena Gupta

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Recently nature–inspired algorithms have widespread use throughout the tough and time consuming multi–objective scientific and engineering design optimization problems. In this paper, we present extended forms of firefly algorithm to find optimal Golomb ruler (OGR) sequences. The OGRs have their one of the major application as unequally spaced channel–allocation algorithm in optical wavelength division multiplexing (WDM) systems in order to minimize the adverse four–wave mixing (FWM) crosstalk effect. The simulation results conclude that the proposed optimization algorithm has superior performance compared to the existing conventional computing and nature–inspired optimization algorithms to find OGRs in terms of ruler length, total optical channel bandwidth and computation time.

Keywords: channel allocation, conventional computing, four–wave mixing, nature–inspired algorithm, optimal Golomb ruler, lévy flight distribution, optimization, improved multi–objective firefly algorithms, Pareto optimal

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Authors: Dorcas Ropo Abejide, Olamide Ahmed Falusi, Oladipupo Abdulazeez Yusuf Daudu, Bolaji Zuluqurineen Salihu, Muhammad Liman Muhammad

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This study evaluated the morpho-agronomic response of twenty-four (24) Nigerian Bambara groundnut landraces to water stress and genetic diversity of some selected accessions using SSR markers. The studies were carried out in the botanical garden of the Department of Plant Biology, Federal University of Technology, Minna, Niger State, Nigeria in a randomized complete block design using three replicates. Molecular analysis using SSR primers was carried out at the International Institute of Tropical Agriculture (IITA) Ibadan in order to characterize ten selected accessions comprising the seven most drought tolerant and three most susceptible accessions from the 24 accessions evaluated. Results revealed that water stress decreased morpho-agronomic traits such as plant height, leaf area, number of leaves per plant, seed yield, etc. A total of 22 alleles were detected by the SSR markers used with a mean number of 4 allelles. SSR markers MBamCO₃₃, Primer 65, and G358B2-D15 each detected 4 allelles, while Primer 3FR and 4FR detected 5 allelles each. The study revealed significantly high polymorphisms in 10 Loci. The mean value of polymorpic information content was 0.6997, implying the usefulness of the primers used in identifying genetic similarities and differences among the Bambara groundnut genotypes. The SSR analysis revealed a comparable pattern between genetic diversity and drought tolerance of the genotypes. The UPGMA dendrogram showed that at a genetic distance of 0.1, the accessions were grouped into three groups according to their level of tolerance to drought. The two most drought-tolerant accessions were grouped together, and the 5th and 6th most drought-tolerant accessions were also grouped together. This suggests that the genotypes grouped together may be genetically close, may possess similar genes, or have a common origin. The degree of genetic variants obtained from this profiling could be useful in Bambara groundnut breeding for drought tolerance. The identified drought tolerant Bambara groundnut landraces are important genetic resources for drought stress tolerance breeding programme of Bambara groundnut. The genotypes are also useful for germplasm conservation and global implications.

Keywords: Bambara groundnut, genetic diversity, germplasm, SSR markers, water stress

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Authors: Kyung Jin Kim, Jiwon Kwak, Jae-Hoon Lee, Soo Suk Lee

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MicroRNAs (miRNA) are a class of endogenous, single-stranded, small, and non-protein coding RNA molecules typically 20-25 nucleotides long. They are thought to regulate the expression of other genes in a broad range by binding to 3’- untranslated regions (3’-UTRs) of specific mRNAs. The detection of miRNAs is very important for understanding of the function of these molecules and in the diagnosis of variety of human diseases. However, detection of miRNAs is very challenging because of their short length and high sequence similarities within miRNA families. So, a simple-to-use, low-cost, and highly sensitive method for the detection of miRNAs is desirable. In this study, we demonstrate a novel bi-directional extension (BDE) assay. In the first step, a specific linear RT primer is hybridized to 6-10 base pairs from the 3’-end of a target miRNA molecule and then reverse transcribed to generate a cDNA strand. After reverse transcription, the cDNA was hybridized to the 3’-end which is BDE sequence; it played role as the PCR template. The PCR template was amplified in an SYBR green-based quantitative real-time PCR. To prove the concept, we used human brain total RNA. It could be detected quantitatively in the range of seven orders of magnitude with excellent linearity and reproducibility. To evaluate the performance of BDE assay, we contrasted sensitivity and specificity of the BDE assay against a commercially available poly (A) tailing method using miRNAs for let-7e extracted from A549 human epithelial lung cancer cells. The BDE assay displayed good performance compared with a poly (A) tailing method in terms of specificity and sensitivity; the CT values differed by 2.5 and the melting curve showed a sharper than poly (A) tailing methods. We have demonstrated an innovative, cost-effective BDE assay that allows improved sensitivity and specificity in detection of miRNAs. Dynamic range of the SYBR green-based RT-qPCR for miR-145 could be represented quantitatively over a range of 7 orders of magnitude from 0.1 pg to 1.0 μg of human brain total RNA. Finally, the BDE assay for detection of miRNA species such as let-7e shows good performance compared with a poly (A) tailing method in terms of specificity and sensitivity. Thus BDE proves a simple, low cost, and highly sensitive assay for various miRNAs and should provide significant contributions in research on miRNA biology and application of disease diagnostics with miRNAs as targets.

Keywords: bi-directional extension (BDE), microRNA (miRNA), poly (A) tailing assay, reverse transcription, RT-qPCR

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Authors: Vo Thi Hai Quan

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Nam Con Son sedimentary basin is one of the very important oil and gas basins in offshore Vietnam. Hai Thach field of block 05-2 contains mostly gas accumulations in fine-grained, sand/mud-rich turbidite system, which was deposited in a turbidite channel and fan environment. Major Upper Miocene reservoir of HT-3X lies above a well-developed unconformity. The main objectives of this study are to reconstruct depositional environment and to assess the reservoir quality using data from 14 meters of core samples and digital wireline data of the well HT-3X. The wireline log and core data showed that the vertical sequences of representative facies of the well mainly range from Tb to Te divisions of Bouma sequences with predominance of Tb and Tc compared to Td and Te divisions. Sediments in this well were deposited in a submarine fan association with very fine to fine-grained, homogeneous sandstones that have high porosity and permeability, high- density turbidity currents with longer transport route from the sediment source to the basin, indicating good quality of reservoir. Sediments are comprised mainly of the following sedimentary structures: massive, laminated sandstones, convoluted bedding, laminated ripples, cross-laminated ripples, deformed sandstones, contorted bedding.

Keywords: Hai Thach field, Miocene sand, turbidite, wireline data

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Authors: Daruliza Kernain, Shaharum Shamsuddin, See Too Wei Cun

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CTCF is a unique, highly conserved and ubiquitously expressed 11 zinc finger (ZF) transcriptional factor with multiple target sites. It is able to bind to various target sequences to perform different regulatory roles including promoter activation or repression, creating hormone-responsive gene silencing element, and functional block of enhancer-promoter interactions. The binding of CTCF to the essential binding site is through the combination of different ZF domain. On the other hand, BORIS for brother of the regulator of imprinted sites, which expressed only in the testis and certain cancer cell line is homology to CTCF 11 ZF domains. Since both transcriptional factors share the same ZF domains hence there is a possibility for both to bind to the same target sequences. In this study, the interaction of these two proteins to multi-functional Y-box DNA/RNA-binding factor, YB-1 was determined. The protein-protein interaction between CTCF/YB-1 and BORIS/YB-1 were discovered by Co-immuno-precipitation (CO-IP) technique through reciprocal experiment from RGBM total cell lysate. The results showed that both CTCF and BORIS were able to interact with YB-1 in Glioma RGBM cell line. To the best of our knowledge, this is the first findings demonstrating the ability of BORIS and YB-1 to form a complex in vivo.

Keywords: immunoprecipitation, CTCF/BORIS/YB-1, transcription factor, molecular medicine

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Authors: Vivek Verma, Sanjeev Kumar

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This study presents a novel quantum image encryption algorithm, using a 3D chaotic map and controlled qubit-level scrambling operations. The newly proposed 3D-BNM chaotic map effectively reduces the degradation of chaotic dynamics resulting from the finite word length effect. It facilitates the generation of highly unpredictable random sequences and enhances chaotic performance. The system’s efficacy is additionally enhanced by the inclusion of a SHA-256 hash function. Initially, classical plain images are converted into their quantum equivalents using the Novel Enhanced Quantum Representation (NEQR) model. The Generalized Quantum Arnold Transformation (GQAT) is then applied to disrupt the coordinate information of the quantum image. Subsequently, to diffuse the pixel values of the scrambled image, XOR operations are performed using pseudorandom sequences generated by the 3D-BNM chaotic map. Furthermore, to enhance the randomness and reduce the correlation among the pixels in the resulting cipher image, a controlled qubit-level scrambling operation is employed. The encryption process utilizes fundamental quantum gates such as C-NOT and CCNOT. Both theoretical and numerical simulations validate the effectiveness of the proposed algorithm against various statistical and differential attacks. Moreover, the proposed encryption algorithm operates with low computational complexity.

Keywords: 3D Chaotic map, SHA-256, quantum image encryption, Qubit level scrambling, NEQR

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Authors: Lana Burmistrova

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Introduction: The influence of visual impairments on several cognitive processes used in the music learning process is an increasingly important area in special education and cognitive musicology. Many children have several visual impairments due to the refractive errors and irreversible inhibitors. However, based on the compensatory neuroplasticity and functional reorganization, congenitally blind (CB) and early blind (EB) individuals use several areas of the occipital lobe to perceive and process auditory and tactile information. CB individuals have greater memory capacity, memory reliability, and less false memory mechanisms are used while executing several tasks, they have better working memory (WM) and short-term memory (STM). Blind individuals use several strategies while executing tactile and working memory n-back tasks: verbalization strategy (mental recall), tactile strategy (tactile recall) and combined strategies. Methods and design: The aim of the pilot study was to substantiate similar tendencies while executing attention, memory and combined auditory tasks in blind and sighted individuals constructed for this study, and to investigate attention, memory and combined mechanisms used in the music learning process. For this study eight (n=8) blind and eight (n=8) sighted individuals aged 13-20 were chosen. All respondents had more than five years music performance and music learning experience. In the attention task, all respondents had to identify pitch changes in tonal and randomized melodic pairs. The memory task was based on the mismatch negativity (MMN) proportion theory: 80 percent standard (not changed) and 20 percent deviant (changed) stimuli (sequences). Every sequence was named (na-na, ra-ra, za-za) and several items (pencil, spoon, tealight) were assigned for each sequence. Respondents had to recall the sequences, to associate them with the item and to detect possible changes. While executing the combined task, all respondents had to focus attention on the pitch changes and had to detect and describe these during the recall. Results and conclusion: The results support specific features in CB and EB, and similarities between late blind (LB) and sighted individuals. While executing attention and memory tasks, it was possible to observe the tendency in CB and EB by using more precise execution tactics and usage of more advanced periodic memory, while focusing on auditory and tactile stimuli. While executing memory and combined tasks, CB and EB individuals used passive working memory to recall standard sequences, active working memory to recall deviant sequences and combined strategies. Based on the observation results, assessment of blind respondents and recording specifics, following attention and memory correlations were identified: reflective attention and STM, reflective attention and periodic memory, auditory attention and WM, tactile attention and WM, auditory tactile attention and STM. The results and the summary of findings highlight the attention and memory features used in the music learning process in the context of blindness, and the tendency of the several attention and memory types correlated based on the task, strategy and individual features.

Keywords: attention, blindness, memory, music learning, strategy

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Authors: Konstantin S. Vainutis, Mark E. Andreev, Anastasia N. Voronova, Mikhail Yu. Shchelkanov

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Introduction: The trematodes from the family Cyclocoelidae (cyclocoelids) belong to the superfamily Echinostomatoidea infecting air sacs and trachea of wild birds. At present, the family Cyclocoelidae comprises nine valid genera in three subfamilies: Cyclocoelinae (type taxon), Haematotrephinae, and Typhlocoelinae. To our best knowledge, in this study, molecular genetic methods were used for the first time for studying cyclocoelids from the Russian Far East. Here we provide the data on the morphology and phylogeny of cyclocoelids from gadwall from the Russian Far East. The morphological and genetic data obtained for cyclocoelids indicated the necessity to revise the previously proposed classification within the family Cyclocoelidae. Objectives: The first objective was performing the morphological study of cyclocoelids found in M. strepera from the Russian Far East. The second objective is to reconstruct the phylogenetic relationships of the studied trematodes with other cyclocoelids using the 28S gene. Material and methods: During the field studies in the Khasansky district of the Primorsky region, 21 cyclocoelids were recovered from the air sacs of a single gadwall Mareca strepera. Seven samples of cyclocoelids were overstained in alum carmine, dehydrated in a graded ethanol series, cleared in clove oil, and mounted in Canada balsam. Genomic DNA was extracted from four cyclocoelids using the alkaline lysis method HotShot. The 28S rDNA fragment was amplified using the forward primer Digl2 and the reverse primer 1500R. Results: According to morphological features (ovary intratesticular, forming a triangle with the testes), the studied worms belong to the subfamily Cyclocoelinae Stossich, 1902. In particular, the highest morphological similarity was observed in relation to the trematodes of the genus Cyclocoelum Brandes, 1892 – genital pores are pharyngeal. However, the genetic analysis has shown significant discrepancies between the trematodes studied regarding the genus Cyclocoelum. On the phylogenetic tree, these trematodes took the sister position in relation to the genus Morishitium (previously considered in the subfamily Szidatitrematinae). Conclusion: Based on the results of the morphological and genetic studies, cyclocoelids isolated from Mareca strepera are suggested to be described in the previously unknown genus and differentiated from the type genus Cyclocoelum of the type subfamily Cyclocoelinae. Considering the available molecular data, including described cyclocoelids, the family Cyclocoelidae comprises ten valid genera in the three subfamilies mentioned above.

Keywords: new species, trematoda, phylogeny, cyclocoelidae

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Authors: Asma'u Mahe, Abdullahi A. Imam, Adamu J. Alhassan, Nasiru Abdullahi, Sadiya A. Bichi, Nura Lawal, Kamaluddeen Babagana

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Malaria is a disease with global health significance. It is caused by parasites and transmitted by Anopheles mosquitoes. Increase in insecticide resistance threatens the disease vector control. The strength of selection pressure acting on a mosquito population in relation to insecticide resistance can be assess by determining the genetic diversity of a fragment spanning exon- 20 of IIS6 of the voltage gated sodium channel (VGSC). Larval samples reared to adulthood were identified and kdr (knock down resistance) profile was determined. The DNA sequences were used to assess the patterns of genetic differentiation by determining the levels of genetic variability between the Anopheles mosquitoes. Genetic differentiation of the Anopheles mosquitoes based on a portion of the voltage gated sodium channel gene was obtained. Polymorphisms were detected; sequence variation and analysis were presented as a phylogenetic tree. Phylogenetic tree of VGSC haplotypes was constructed for samples of the Anopheles mosquitoes using the maximum likelihood method in MEGA 6.0 software. DNA sequences were edited using BioEdit sequence editor. The edited sequences were aligned with reference sequence (Kisumu strain). Analyses were performed as contained in dnaSP 5.10. Results of genetic parameters of polymorphism and haplotype reconstruction were presented in count. Twenty sequences were used for the analysis. Regions selected were 1- 576, invariable (monomorphic) sites were 460 while variable (polymorphic) sites were 5 giving the number of total mutations observed in this study. Mutations obtained from the study were at codon 105: TTC- Phenylalanine replaces TCC- Serine, codon 513: TAG- Termination replaces TTG- Leucine, codon 153, 300 and 553 mutations were non-synonymous. From the constructed phylogenetic tree, some groups were shown to be closer with Exon20Gambiae Kisumu (Reference strain) having some genetic distance, while 5-Exon20Gambiae-F I13.ab1, 18-Exon20Gambiae-F C17.ab1, and 2-Exon20Gambiae-F C13.ab1 clustered together genetically differentiated away from others. Mutations observed in this study can be attributed to the high insecticide resistance profile recorded in the study areas. Haplotype networks of pattern of genetic variability and polymorphism for the fragment of the VGSC sequences of sampled Anopheles mosquitoes revealed low haplotypes for the present study. Haplotypes are set of closely linked DNA variation on X-chromosome. Haplotypes were scaled accordingly to reflect their respective frequencies. Low haplotype number, four VGSC-1014F haplotypes were observed in this study. A positive association was previously established between low haplotype number of VGSC diversity and pyrethroid resistance through kdr mechanism. Significant values at (P < 0.05) of Tajima D and Fu and Li D’ were observed for some of the results indicating possible signature of positive selection on the fragment of VGSC in the study. This is the first report of VGSC-1014F in the study site. Based on the results, the mutation was present in low frequencies. However, the roles played by the observed mutations need further investigation. Mutations, environmental factors among others can affect genetic diversity. The study area has recorded increase in insecticide resistance that can affect vector control in the area. This finding might affect the efforts made against malaria. Sequences were deposited in GenBank for Accession Number.

Keywords: anopheles mosquitoes, insecticide resistance, kdr, malaria, voltage gated sodium channel

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Authors: Selen Unaldi, Emmanuel Richaud, Matthieu Gervais, Laurent Berthe

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Aircrafts are painted with several layers to guarantee their protection from external attacks. For aluminum AA 2024-T3 (metallic structural part of the plane), a protective primer is applied to ensure its corrosion protection. On top of this layer, the top coat is applied for aesthetic aspects. During the lifetime of an aircraft, top coat stripping has an essential role which should be operated as an average of every four years. However, since conventional stripping processes create hazardous disposals and need long hours of labor work, alternative methods have been investigated. Amongst them, laser stripping appears as one of the most promising techniques not only because of the reasons mentioned above but also its controllable and monitorable aspects. The application of a laser beam from the coated side provides stripping, but the depth of the process should be well controlled in order to prevent damage to a substrate and the anticorrosion primer. Apart from that, thermal effects should be taken into account on the painted layers. As an alternative, we worked on developing a process that includes the usage of shock wave propagation to create the stripping via mechanical effects with the application of the beam from the substrate side (back face) of the samples. Laser stripping was applied on thickness-specified samples with a thickness deviation of 10-20%. First, the stripping threshold is determined as a function of power density which is the first flight off of the top coats. After obtaining threshold values, the same power densities were applied to specimens to create large stripping zones with a spot overlap of 10-40%. Layer characteristics were determined on specimens in terms of physicochemical properties and thickness range both before and after laser stripping in order to validate the substrate material health and coating properties. The substrate health is monitored by measuring the roughness of the laser-impacted zones and free surface energy tests (both before and after laser stripping). Also, Hugoniot Elastic Limit (HEL) is determined from VISAR diagnostic on AA 2024-T3 substrates (for the back face surface deformations). In addition, the coating properties are investigated as a function of adhesion levels and anticorrosion properties (neutral salt spray test). The influence of polyurethane top-coat thickness is studied in order to verify the laser stripping process window for industrial aircraft applications.

Keywords: aircraft coatings, laser stripping, laser adhesion tests, epoxy, polyurethane

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Authors: M. Vivodík, Ž. Balážová, Z. Gálová

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The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.

Keywords: dendrogram, polymorphism, RAPD technique, Ricinus communis L.

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Authors: Tapiwa Brine Mutsauri

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The MEROPS system is an information resource for proteases that classifies them into clans according to their catalytic type. Within the Plant kingdom, cysteine ​​proteases are one of the best known, as they are the catalytic type on which the first studies on plant proteases were focused. Plant cysteine ​​proteases have a similar mechanism of action to serine proteases, and some are known to have activity on factors of the blood coagulation cascade, such as a potent antithrombotic effect, and also cause increased fibrinolysis. Of a few plant cysteine ​​proteases, the three-dimensional structure is known, so a method of interest to be able to predict their potential activity on the factors of the coagulation cascade would be to know their structure. Phylogenetics is the study of the evolutionary relationships between biological entities, often species, individuals, or genes (which can be called taxa). It is essential to identify the evolutionary position and the possible distribution of these enzymes in the plant kingdom, particularly those that act on coagulation factors. Bioinformatic tools, such as Clustal Omega / Jalview and Mega6, can be used to create phylogenetic trees. From the results of the alignment, it can be seen that although there is a certain degree of conservation (Conservation) and consensus (Consensus) among the eleven sequences, the functionally important motifs (those corresponding to the active site), the degree of conservation and consensus is very low. We could then infer that although activity on coagulation is reported for these enzymes, linked to their structural and mechanistic similarity with serine proteases, this activity may not have a direct or primary relationship with the proteolytic activity associated with their common, poorly conserved active site in this case. This ultimately could be related to modifications in the reaction mechanism of several of the enzymes studied, which would require more detailed study. Also, below, we will deal with factors that may have a greater influence on this result. The results of this work enrich the understanding of how species (and molecular sequences in general) evolve. Through phylogenetics, we learn not only how sequences came to be the way they are today but also the general principles that allow us to predict how they will change in the future. For pharmaceutical sciences, phylogenetic selection of biologically related species can help identify closely related members of a species with compounds of pharmacological importance, such as plant cysteine ​​proteases, in addition to identifying structural features that may influence their pharmacological activity and which can be valuable for drug design.

Keywords: computational simulation, proteases, coagulation, bioinformatics

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Authors: Margareta Rahayuningsih, Nugroho Edi K., Siti Alimah

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Wreathed Hornbill (Rhyticeros undulatus) is the one of hornbill species (Family: Bucerotidae) that found on Mount Ungaran. In the preservation or planning in situ conservation of Wreathed Hornbill require the habitat condition data. The objective of the research was to determine the land cover change on Mount Ungaran using satellite image data and GIS. Based on the land cover data on 1999-2009 the research showed that the primer forest on Mount Ungaran was decreased almost 50%, while the seconder forest, tea and coffee plantation, and the settlement were increased.

Keywords: GIS, Mount Ungaran, threatened habitat, Wreathed Hornbill (Rhyticeros undulatus)

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Authors: Mark Osborn

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Clustered, regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. Commercially available reagents were integrated into a CRISPR/Cas9-based lateral flow assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences with single-base specificity. This approach requires minimal equipment and represents a simplified platform for field-based deployment. A rapid, multiplex fluorescence CRISPR/Cas9 nuclease cleavage assay capable of detecting and differentiating SARS-CoV-2, influenza A and B, and respiratory syncytial virus in a single reaction was also developed. These findings provide proof of principle for CRISPR/Cas9 point-of-care diagnosis that can detect specific SARS-CoV-2 strain(s). Further, Cas9 cleavage allows for a scalable fluorescent platform for identifying respiratory viral pathogens with overlapping symptomology. Collectively, this approach is a facile platform for diagnostics with broad application to user-defined sequence interrogation and detection.

Keywords: CRISPR/Cas9, lateral flow assay, SARS-Co-V2, single-nucleotide resolution

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Authors: Bin Liu

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MicroRNAs (miRNAs) are small non-coding RNA molecules, functioning in transcriptional and post-transcriptional regulation of gene expression. The discrimination of the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops) is necessary for the understanding of miRNAs’ role in the control of cell life and death. Since both their small size and sequence specificity, it cannot be based on sequence information alone but requires structure information about the miRNA precursor to get satisfactory performance. Kmers are convenient and widely used features for modeling the properties of miRNAs and other biological sequences. However, Kmers suffer from the inherent limitation that if the parameter K is increased to incorporate long range effects, some certain Kmer will appear rarely or even not appear, as a consequence, most Kmers absent and a few present once. Thus, the statistical learning approaches using Kmers as features become susceptible to noisy data once K becomes large. In this study, we proposed a Gapped k-mer approach to overcome the disadvantages of Kmers, and applied this method to the field of miRNA prediction. Combined with the structure status composition, a classifier called imiRNA-GSSC was proposed. We show that compared to the original imiRNA-kmer and alternative approaches. Trained on human miRNA precursors, this predictor can achieve an accuracy of 82.34 for predicting 4022 pre-miRNA precursors from eleven species.

Keywords: gapped k-mer, imiRNA-GSSC, microRNA precursor, support vector machine

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Authors: M. Nakkuntod, S. Srinarang, K.W. Hilu

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Water lily (Nymphaea L.) is the largest genus of Nymphaeaceae. This family is composed of six genera (Nuphar, Ondinea, Euryale, Victoria, Barclaya, Nymphaea). Its members are nearly worldwide in tropical and temperate regions. The classification of some species in Nymphaea is ambiguous due to high variation in leaf and flower parts such as leaf margin, stamen appendage. Therefore, the phylogenetic relationships based on 18S rDNA were constructed to delimit this genus. DNAs of 52 specimens belonging to water lily family were extracted using modified conventional method containing cetyltrimethyl ammonium bromide (CTAB). The results showed that the amplified fragment is about 1600 base pairs in size. After analysis, the aligned sequences presented 9.36% for variable characters comprising 2.66% of parsimonious informative sites and 6.70% of singleton sites. Moreover, there are 6 regions of 1-2 base(s) for insertion/deletion. The phylogenetic trees based on maximum parsimony and maximum likelihood with high bootstrap support indicated that genus Nymphaea was a paraphyletic group because of Ondinea, Victoria and Euryale disruption. Within genus Nymphaea, subgenus Nymphaea is a basal lineage group which cooperated with Euryale and Victoria. The other four subgenera, namely Lotos, Hydrocallis, Brachyceras and Anecphya were included the same large clade which Ondinea was placed within Anecphya clade due to geographical sharing.

Keywords: nrDNA, phylogeny, taxonomy, waterlily

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Authors: Yuan-Hsiang Chang, Pin-Chi Lin, Li-Der Jeng

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Advance in techniques of image and video processing has enabled the development of intelligent video surveillance systems. This study was aimed to automatically detect moving human objects and to analyze events of dual human interaction in a surveillance scene. Our system was developed in four major steps: image preprocessing, human object detection, human object tracking, and motion trajectory analysis. The adaptive background subtraction and image processing techniques were used to detect and track moving human objects. To solve the occlusion problem during the interaction, the Kalman filter was used to retain a complete trajectory for each human object. Finally, the motion trajectory analysis was developed to distinguish between the interaction and non-interaction events based on derivatives of trajectories related to the speed of the moving objects. Using a database of 60 video sequences, our system could achieve the classification accuracy of 80% in interaction events and 95% in non-interaction events, respectively. In summary, we have explored the idea to investigate a system for the automatic classification of events for interaction and non-interaction events using surveillance cameras. Ultimately, this system could be incorporated in an intelligent surveillance system for the detection and/or classification of abnormal or criminal events (e.g., theft, snatch, fighting, etc.).

Keywords: motion detection, motion tracking, trajectory analysis, video surveillance

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Authors: Almas Rajguru, Archana Kamath, Rachana Singh

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The study aims to determine the depositional facies, high-resolution sequence stratigraphy, and diagenetic processes of Early Oligocene carbonates in N & N-W of Heera, Mumbai Offshore. Foraminiferal assemblage and microfacies from cores of Well A, B, C, D and E are indicative of facies association related to four depositional environments, i.e., restricted inner lagoons-tidal flats, shallow open lagoons, high energy carbonate bars-shoal complex and deeper mid-ramps of a westerly dipping homoclinal carbonate ramp. Two high-frequency (4th Order) depositional sequences bounded by sequence boundary, DS1 and DS2, displaying hierarchical stacking patterns, are identified and correlated across wells. Vadose zone diagenesis effect during short diastem/ subaerial exposure has rendered good porosity due to dissolution in HST carbonates and occasionally affected underlying TST sediments (Well D, C and E). On mapping and correlating the sequences, the presence of thin carbonate bars that can be potential reservoirs are envisaged along NW-SE direction, towards north and south of Wells E, D and C. A more pronounced development of these bars in the same orientation can be anticipated towards the west of the study area.

Keywords: sequence stratigraphy, depositional facies, diagenesis petrography, early Oligocene, Mumbai offshore

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Authors: Muhammad Fiaz Qamar, Uzma Mehreen, Muhammad Arfan Zaman, Kazim Ali

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Ovine Theileriosis is a world-wide concern, especially in tropical and subtropical areas, due to having tick abundance that has received less awareness in different developed and developing areas due to less worth of sheep, low to the middle level of infection in different small ruminants herd. Across Asia, the prevalence reports have been conducted to provide equivalent calculation of flock and animal level prevalence of Theileriosisin animals. It is a challenge for veterinarians to timely diagnosis & control of Theileriosis and famers because of the nature of the organism and inadequacy of restricted plans to control. All most work is based upon the development of such a technique which should be farmer-friendly, less expensive, and easy to perform into the field. By the timely diagnosis of this disease will decrease the irrational use of the drugs, and other plan was to determine the prevalence of Theileriosis in District Jhang by using the conventional method, PCR and qPCR, and LAMP. We quantify the molecular epidemiology of T.lestoquardiin sheep from Jhang districts, Punjab, Pakistan. In this study, we concluded that the overall prevalence of Theileriosis was (32/350*100= 9.1%) in sheep by using Giemsa staining technique, whereas (48/350*100= 13%) is observed by using PCR technique (56/350*100=16%) in qPCR and the LAMP technique have shown up to this much prevalence percentage (60/350*100= 17.1%). The specificity and sensitivity also calculated in comparison with the PCR and LAMP technique. Means more positive results have been shown when the diagnosis has been done with the help of LAMP. And there is little bit of difference between the positive results of PCR and qPCR, and the least positive animals was by using Giemsa staining technique/conventional method. If we talk about the specificity and sensitivity of the LAMP as compared to PCR, The cross tabulation shows that the results of sensitivity of LAMP counted was 94.4%, and specificity of LAMP counted was 78%. Advances in scientific field must be upon reality based ideas which can lessen the gaps and hurdles in the way of scientific research; the lamp is one of such techniques which have done wonders in adding value and helping human at large. It is such a great biological diagnostic tools and has helped a lot in the proper diagnosis and treatment of certain diseases. Other methods for diagnosis, such as culture techniques and serological techniques, have exposed humans with great danger. However, with the help of molecular diagnostic technique like LAMP, exposure to such pathogens is being avoided in the current era Most prompt and tentative diagnosis can be made using LAMP. Other techniques like PCR has many disadvantages when compared to LAMP as PCR is a relatively expensive, time consuming, and very complicated procedure while LAMP is relatively cheap, easy to perform, less time consuming, and more accurate. LAMP technique has removed hurdles in the way of scientific research and molecular diagnostics, making it approachable to poor and developing countries.

Keywords: distribution, thelaria, LAMP, primer sequences, PCR

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Authors: Mohammad Reza Dawoudi

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With the increasing rate of patients suffering from chronic pain, several methods for evaluating of chronic pain are suggested. Motion of morbid has been defined as the rate of pine and it is linked with various co-morbid conditions. This study provides a summary of procedure useful to statistics performing direct behavioral observation in hospital settings. We describe the need for and usefulness of comprehensive “morbid motions” observations; provide a primer on the identification, definition, and assessment of morbid behaviors; and outline and discuss specific statistical procedures, including formulating referral motions, describing and conducting the observation. We also provide practical devices for observing and analyzing the obtained information into a report that guides clinical intervention.

Keywords: assessing pain, DNA modeling, image matching technique, pain scale

Procedia PDF Downloads 413

Authors: Javeria Ahmad, Ayesha Maryam, Zahid Rizwan, Nadeem Nasir, Yasir Nawab, Hafiz Shehbaz Ahmad

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Mitigation of electromagnetic interference (EMI) through thin, lightweight, and cost-effective materials is critical for electronic appliances as well as human health. The present research work discusses the design of composites that are suitable to minimize EMI through various stacking sequences. The carbon fibers reinforced composite structures impregnated with dielectric (MWCNTs) and magnetic nanofillers (Fe₂O₃) were developed to investigate their microwave absorption properties. The composite structure comprising a single type of nanofillers, each of MWCNTs & Fe₂O₃, was developed, and then their layers were stacked over each other with various stacking sequences to investigate the best stacking sequence, which presents good microwave absorption characteristics. A vector network analyzer (VNA) was used to analyze the microwave absorption properties of these developed composite structures. The composite structures impregnated with the layers of a dielectric nanofiller and sandwiched between the layers of a magnetic nanofiller show the highest EMI shielding value of 59 dB and a dielectric conductivity of 35 S/cm in the frequency range of 0.1 to 13.6 GHz. The results also demonstrate that the microwave absorption properties of the developed composite structures were dominant over reflection properties. The absence of an external peak in X-ray diffraction (XRD), marked the purity of the added nanofillers.

Keywords: nanocomposites, microwave absorption, EMI shielding, skin depth, reflection loss

Procedia PDF Downloads 52

Authors: Muna A. Eissawi, Safaa Abed Elfataah, Haytham Hago, Fatima E Abukunna, Ibtisam Amin Goreish, Nahid Gornas

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The study examined and analyzed the genetic diversity of DRB1locus of exon 2 of major histocompatibility complex of Sudanese desert sheep using PCR-RFLP and DNA sequencing. Five hundred samples belonging to five ecotypes of Desert Sudanese sheep (Abrag (Ab), Ashgar (Ash), Hamari (H), Kabashi (K) and Watish (W) were included. Amplification of exon 2 of the DRB1 gene yielded (300bp) amplified product in different ecotypes. Nine different digestion patterns corresponding to Five distinct alleles were observed with Rsa1 digestion. Genotype (ag) was the most common among all ecotypes, with a percentage comprised (40.4 %). The Hardy-Weinberg equilibrium (HWE) test showed that the studied ecotypes have significantly deviated from the theoretical proportions of Rsa1 patterns; probability values of the Chi-square test for HWE for MHC-DRB1 gene in SDS were 0.00 in all ecotypes. The constructed phylogenetic tree revealed the relation of 22 Sudanese isolates with each other and showed the shared sequences with 47 published foreign sequences randomly selected from different geographic regions. The results of this study highlight the effect of heterozygosity of MHC genes of the Desert sheep of Sudan which may clarify some of genetic back ground of their disease resistance and adaptation to environment.

Keywords: desert sheep, MHC, Ovar-DRB1, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

Procedia PDF Downloads 78

Authors: Daniel Vargas-Herrera, Ivette Caldelas, Fernando Brambila-Paz, Rodrigo Montufar-Chaveznava

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In this paper, we present a virtual reality application for neurorehabilitation. This application was developed using the Unity SDK integrating the Oculus Rift and Leap Motion devices. Essentially, it consists of three stages according to the kind of rehabilitation to carry on: ocular rehabilitation, head/neck rehabilitation, and eye-hand coordination. We build three scenes for each task; for ocular and head/neck rehabilitation, there are different objects moving in the field of view and extended field of view of the user according to some patterns relative to the therapy. In the third stage the user must try to touch with the hand some objects guided by its view. We report the primer results of the use of the application with healthy people.

Keywords: virtual reality, interactive technologies, video games, neurorehabilitation

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Authors: Syed Bilawal Ali Shah

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The investigation of the hydrocarbon source rock potential of Eocene-Paleocene formations of Potwar Basin, part of Upper Indus Basin Pakistan, was done using geochemical and petrological techniques. Analysis was performed on forty-five core-cutting samples from two wells. The sequences analysed are Sakesar, Lockhart and Patala formations of Potwar Basin. Patala Formation is one of Potwar Basin's major petroleum-bearing source rocks. The Lockhart Formation samples VR (%Ro) and Tmax data indicate that the formation is early mature to immature for petroleum generation for hydrocarbon generation; samples from the Patala and Sakesar formations, however, have a peak oil generation window and an early maturity (oil window). With 3.37 weight percent mean TOC and HI levels up to 498 mg HC/g TOC, the source rock characteristics of the Sakesar and Patala formations generally exhibit good to very strong petroleum generative potential. The majority of sediments representing Lockhart Formation have 1.5 wt.% mean TOC having fair to good potential with HI values ranging between 203-498 mg HC/g TOC. 1. The analysed sediments of all formations possess primarily mixed Type II/III and Type III kerogen. Analysed sediments indicate that both the Sakesar and Patala formations can possess good oil-generation potential and may act as an oil source rock in the Potwar Basin.

Keywords: Potwar Basin, Patala Shale, Rock-Eval pyrolysis, Indus Basin, VR %Ro

Procedia PDF Downloads 90

Authors: Diego Santibañez Oyarce, Fernanda Bravo Cornejo, Camilo Cerda Sarabia, Belén Díaz Díaz, Esteban Gómez Terán, Hugo Osses Prado, Raúl Caulier-Cisterna, Jorge Vergara-Quezada, Ana Moya-Beltrán

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The advent of high-throughput sequencing technologies has revolutionized genomics, generating vast amounts of genetic data that challenge traditional bioinformatics methods. Machine learning addresses these challenges by leveraging computational power to identify patterns and extract information from large datasets. However, biological sequence data, being symbolic and non-numeric, must be converted into numerical formats for machine learning algorithms to process effectively. So far, some encoding methods, such as one-hot encoding or k-mers, have been explored. This work proposes additional approaches for encoding DNA sequences in order to compare them with existing techniques and determine if they can provide improvements or if current methods offer superior results. Data from the 16S rRNA gene, a universal marker, was used to analyze eight bacterial groups that are significant in the pulmonary environment and have clinical implications. The bacterial genes included in this analysis are Prevotella, Abiotrophia, Acidovorax, Streptococcus, Neisseria, Veillonella, Mycobacterium, and Megasphaera. These data were downloaded from the NCBI database in Genbank file format, followed by a syntactic analysis to selectively extract relevant information from each file. For data encoding, a sequence normalization process was carried out as the first step. From approximately 22,000 initial data points, a subset was generated for testing purposes. Specifically, 55 sequences from each bacterial group met the length criteria, resulting in an initial sample of approximately 440 sequences. The sequences were encoded using different methods, including one-hot encoding, k-mers, Fourier transform, and Wavelet transform. Various machine learning algorithms, such as support vector machines, random forests, and neural networks, were trained to evaluate these encoding methods. The performance of these models was assessed using multiple metrics, including the confusion matrix, ROC curve, and F1 Score, providing a comprehensive evaluation of their classification capabilities. The results show that accuracies between encoding methods vary by up to approximately 15%, with the Fourier transform obtaining the best results for the evaluated machine learning algorithms. These findings, supported by the detailed analysis using the confusion matrix, ROC curve, and F1 Score, provide valuable insights into the effectiveness of different encoding methods and machine learning algorithms for genomic data analysis, potentially improving the accuracy and efficiency of bacterial classification and related genomic studies.

Keywords: DNA encoding, machine learning, Fourier transform, Fourier transformation

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Jeisson Alejandro Triana, Maria Fernanda Quiceno Vallejo, Patricia del Portillo, Juan Manuel Anzola

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Most of the known antimicrobials so far discovered are secondary metabolites. The potential for new natural products of this category increases as new microbial genomes and metagenomes are being sequenced. Despite the advances, there is no systematic way to interrogate metagenomic clones for their potential to contain clusters of genes related to these pathways. Here we analyzed 52 biosynthetic pathways from the AntiSMASH database at the protein domain level in order to identify domains of high specificity and sensitivity with respect to specific biosynthetic pathways. These domains turned out to have various degrees of divergence at the DNA level. We propose PCR assays targetting such domains in-silico and corroborated one by Sanger sequencing.

Keywords: bioinformatic, anti smash, antibiotics, secondary metabolites, natural products, protein domains

Procedia PDF Downloads 181