Search results for: target sequencing

Authors: Mohd Ritzman Abdul Karim, Zhaohui Huang

Abstract:

A current focus in seismic engineering practice is the development of seismic design approach that focuses on the performance-based design. Performance-based design aims to design the structures to achieve specified performance based on the damage limit states. This damage limit is more restrictive limit than life safety and needs to be carefully estimated to avoid damage in piers due to failure in transverse reinforcement. In this paper, a different perspective of damage limit states has been explored by integrating two damage control material limit state, concrete and reinforcement by introduced parameters such as expected yield stress of transverse reinforcement where peak tension strain prior to bar buckling is introduced in a recent study. The different perspective of damage limit states with modified yield displacement and the modified plastic-hinge length is used in order to predict damage-control target displacement for reinforced concreate (RC) bridge pier. Three-dimensional (3D) finite element (FE) model has been developed for estimating damage target displacement to validate proposed damage limit states. The result from 3D FE analysis was validated with experimental study found in the literature. The validated model then was applied to predict the damage target displacement for RC bridge pier and to validate the proposed study. The tensile strain on reinforcement and compression on concrete were used to determine the predicted damage target displacement and compared with the proposed study. The result shows that the proposed damage limit states were efficient in predicting damage-control target displacement consistent with FE simulations.

Keywords: damage-control target displacement, damage limit states, reinforced concrete bridge pier, yield displacement

Procedia PDF Downloads 123

Authors: Aseel Zibin, Abdel Rahman Altakhaineh

Abstract:

This study analyses 30 cartoons depicting THE DEAL OF THE CENTURY as envisaged by two Jordanian cartoonists, namely, EmadHajjaj and Osama Hajjaj. Conceptual Blending Theory (CBT) and Multimodal Metaphor Theory (MMT) are adopted as a theoretical framework to interpret the metaphors and metonymies used in the target cartoons. The results reveal that the target domain THE DEAL OF THE CENTURY was conceptualized mainly through layered metaphors that have metonymic basis and event metaphors\allegories. Specifically, 6 groups were identified: OBJECT or a situation involving OBJECTS, situations involving HUMANS\HYBRIDS of HUMANS and OBJECTS, an ANIMAL OR situation involving an ANIMAL, hybrids of WEAPONS and humans, and event metaphors used to build a story\allegory. The target domain was also depicted via event metaphors used to build a story; some of which are embedded in the Jordanian culture, while others could be perceivable cross-culturally. The results also demonstrate that the most widely used configurations to construe the metaphors was the pictorial source–verbal target in line with Lan and Zuo (2016); the motivation was probably the greater conceptual density and concreteness of visual representation since the target is better captured verbally because of its abstractness. The use of cross-modal mappings of this type was attributed to the abstractness of the target domain, THE DEAL OF THE CENTURY, which makes it more construable via verbal cues rather than visual ones. In contrast, the source domains used were mainly concrete and thus perceivable pictorially rather than verbally.

Keywords: semiotics, cognitive semantics, metaphor, culture, blending, cartoon

Procedia PDF Downloads 116

Authors: Yo-Seph Byun, Gyu-Phil Lee, Young-Bin Park, Gye-Chun Cho, Seong-Won Lee

Abstract:

In Korea, a study on Limit State Design (LSD) for underground structures is being conducted in order to perform more effective design. In this study, as a result of MCS (Monte-Carlo Simulation) technique, failure probabilities of the structure during normal and earthquake are estimated in reliability analysis. Target reliability indexes are determined depending on load combinations for underground structure, and then, design variables such as load and material factors in LSD are decided. As a result, through the research in order to determine more reliable design variables, a specification of LSD for underground structures is able to be developed.

Keywords: design variable, limit state design, target reliability index, underground structure

Procedia PDF Downloads 246

Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

Abstract:

In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

Procedia PDF Downloads 299

Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

Abstract:

Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

Procedia PDF Downloads 250

Authors: Boukerch Haroun, Luo Qing Sheng, Li Hua Shi, Boukraa Sebti

Abstract:

In this paper we present the design and the implementation of a target tracking system where the target is set to be a moving person in a video sequence. The system can be applied easily as a vision system for mobile robot. The system is composed of two major parts the first is the detection of the person in the video frame using the SVM learning machine based on the “HOG” descriptors. The second part is the tracking of a moving person it’s done by using a combination of the Kalman filter and a modified version of the Camshift tracking algorithm by adding the target motion feature to the color feature, the experimental results had shown that the new algorithm had overcame the traditional Camshift algorithm in robustness and in case of occlusion.

Keywords: camshift algorithm, computer vision, Kalman filter, object tracking

Procedia PDF Downloads 418

Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

Abstract:

Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

Procedia PDF Downloads 159

Authors: Surajit Bhattacharya, Daniel Veltri, Atit A. Patel, Daniel N. Cox

Abstract:

miRNAs have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel tool in R, Intra-miR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithms, using statistical methods including Pearson and Distance Correlation on microarray data, to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using Drosophila melanogaster as a model organism for bioinformatics analyses and functional validation. A number of putative targets were obtained which were also validated using qRT-PCR analysis. Additional features of the tool include downloadable text files containing GO analysis from DAVID and Pubmed links of literature related to gene sets. Moreover, we are constructing interaction maps of intragenic miRNAs, using both micro array and RNA-seq data, focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development.

Keywords: miRNA, miRNA:mRNA target prediction, statistical methods, miRNA:mRNA interaction network

Procedia PDF Downloads 472

Authors: D. Hammad, D. P. Tonge

Abstract:

Rheumatoid arthritis (RA) is a disabling and common autoimmune disease during which the body's immune system attacks healthy tissues. This results in complicated and long-lasting actions being carried out by the immune system, which typically only occurs when the immune system encounters a foreign object. In the case of RA, the disease affects millions of people and causes joint inflammation, ultimately leading to the destruction of cartilage and bone. Interestingly, the disease mechanism still remains unclear. It is likely that RA occurs as a result of a complex interplay of genetic and environmental factors including an imbalance in the microorganism population inside our body. The human microbiome or microbiota is an extensive community of microorganisms in and on the bodies of animals, which comprises bacteria, fungi, viruses, and protozoa. Recently, the development of molecular techniques to characterize entire bacterial communities has renewed interest in the involvement of the microbiome in the development and progression of RA. We believe that an imbalance in some of the specific bacterial species in the gut, mouth and other sites may lead to atopobiosis; the translocation of these organisms into the blood, and that this may lead to changes in immune system status. The aim of this study was, therefore, to characterize the microbiome of RA serum samples in comparison to healthy control subjects using 16S rRNA gene amplification and sequencing. Serum samples were obtained from healthy control volunteers and from patients with RA both prior to, and following treatment. The bacterial community present in each sample was identified utilizing V4 region 16S rRNA amplification and sequencing. Bacterial identification, to the lowest taxonomic rank, was performed using a range of bioinformatics tools. Significantly, the proportions of the Lachnospiraceae, Ruminococcaceae, and Halmonadaceae families were significantly increased in the serum of RA patients compared with healthy control serum. Furthermore, the abundance of Bacteroides and Lachnospiraceae nk4a136_group, Lachnospiraceae_UGC-001, RuminococcaceaeUCG-014, Rumnococcus-1, and Shewanella was also raised in the serum of RA patients relative to healthy control serum. These data support the notion of a blood microbiome and reveal RA-associated changes that may have significant implications for biomarker development and may present much-needed opportunities for novel therapeutic development.

Keywords: blood microbiome, gut and oral bacteria, Rheumatoid arthritis, 16S rRNA gene sequencing

Procedia PDF Downloads 99

Authors: Yanwen Li, Shuguo Xie

Abstract:

In electromagnetic imaging, because of the diffraction limited system, the pixel values could change slowly near the edge of the image targets and they also change with the location in the same target. Using traditional digital image segmentation methods to segment electromagnetic gradient images could result in lots of errors because of this change in pixel values. To address this issue, this paper proposes a novel image segmentation and extraction algorithm based on Mean-Shift and dictionary learning. Firstly, the preliminary segmentation results from adaptive bandwidth Mean-Shift algorithm are expanded, merged and extracted. Then the overlap rate of the extracted image block is detected before determining a segmentation region with a single complete target. Last, the gradient edge of the extracted targets is recovered and reconstructed by using a dictionary-learning algorithm, while the final segmentation results are obtained which are very close to the gradient target in the original image. Both the experimental results and the simulated results show that the segmentation results are very accurate. The Dice coefficients are improved by 70% to 80% compared with the Mean-Shift only method.

Keywords: gradient image, segmentation and extract, mean-shift algorithm, dictionary iearning

Procedia PDF Downloads 238

Authors: Amir Mukhtar, Dr. Likun Xia

Abstract:

An improved, robust and efficient visual target tracking algorithm using particle filtering is proposed. Particle filtering has been proven very successful in estimating non-Gaussian and non-linear problems. In this paper, the particle filter is used with color feature to estimate the target state with time. Color distributions are applied as this feature is scale and rotational invariant, shows robustness to partial occlusion and computationally efficient. The performance is made more robust by choosing the different (YIQ) color scheme. Tracking is performed by comparison of chrominance histograms of target and candidate positions (particles). Color based particle filter tracking often leads to inaccurate results when light intensity changes during a video stream. Furthermore, background subtraction technique is used for size estimation of the target. The qualitative evaluation of proposed algorithm is performed on several real-world videos. The experimental results demonstrate that the improved algorithm can track the moving objects very well under illumination changes, occlusion and moving background.

Keywords: tracking, particle filter, histogram, corner points, occlusion, illumination

Procedia PDF Downloads 354

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

Abstract:

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

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

Procedia PDF Downloads 120

Authors: Guilherme Gorgulho, Carlos Roberto Camello Lima

Abstract:

Due to the competitive market in which companies are currently engaged, the constant changes require companies to react quickly regarding the variability of demand and process. The changes are caused by customers, or by demand fluctuations or variations of products, or the need to serve customers within agreed delivery taking into account the continuous search for quality and competitive prices in products. These changes end up influencing directly or indirectly the activities of the Planning and Production Control (PPC), which does business in strategic, tactical and operational levels of production systems. One area of concern for organizations is in the short term (operational level), because this planning stage any error or divergence will cause waste and impact on the delivery of products on time to customers. Thus, this study aims to optimize the efficiency of production scheduling, using different sequencing strategies in an automotive company. Seeking to aim the proposed objective, we used the computer simulation in conjunction with lean manufacturing to build and validate the current model, and subsequently the creation of future scenarios.

Keywords: computational simulation, lean manufacturing, production scheduling, sequencing strategies

Procedia PDF Downloads 243

Authors: D. S. V. Barbieri, R. R. Gomes, G. D. Santos, P. F. Herkert, M. Moreira, E. S. Trindade, V. A. Vicente

Abstract:

The importance of yeast infections has increased in recent decades. The monitoring of Candida yeasts has been relevant in the study of groups and populations. This research evaluated 31 Candida spp. isolates from oral microbiota of 12 Brazilian schoolchildren coinfected with Streptococcus mutans. The isolates were evaluated for their ability to form biofilm in vitro and molecularly characterized based on the sequencing of intergenic spacer regions ITS1-5,8S-ITS2 and variable domains of the large subunit (D1/D2) regions of the rDNA, as well as ABC system genotyping. The sequencing confirmed 26 lineages of Candida albicans, three Candida tropicalis, one Candida guillhermondii and one Candida glabrata. Genetic variability and differences on in biofilm formation were observed among Candida yeasts lineages. At least one Candida strain from each caries activity child was C.albicans genotype A or Candida non-albicans. C. tropicalis was associated with highest cavities rates. These results indicate that the presence of C. albicans genotype A or multi-colonization by non albicans species seem to be associates to the potentialization of caries risk.

Keywords: biofilm, Candida albicans, oral microbiota, caries

Procedia PDF Downloads 484

Authors: Aishik Deb, Rituparna Sinha

Abstract:

We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

Procedia PDF Downloads 102

Authors: Hesham Abdin, Mohamed Zakaria, Talaat Abd-Elmonaem, Alaa El-Din Sayed Hafez

Abstract:

Kalman filter algorithm is an estimator known as the workhorse of estimation. It has an important application in missile guidance, especially in lack of accurate data of the target due to noise or uncertainty. In this paper, a Kalman filter is used as a tracking filter in a simulated target-interceptor scenario with noise. It estimates the position, velocity, and acceleration of the target in the presence of noise. These estimations are needed for both proportional navigation and differential geometry guidance laws. A Kalman filter has a good performance at low noise, but a large noise causes considerable errors leads to performance degradation. Therefore, a new technique is required to overcome this defect using tuning factors to tune a Kalman filter to adapt increasing of noise. The values of the tuning factors are between 0.8 and 1.2, they have a specific value for the first half of range and a different value for the second half. they are multiplied by the estimated values. These factors have its optimum values and are altered with the change of the target heading. A genetic algorithm updates these selections to increase the maximum effective range which was previously reduced by noise. The results show that the selected factors have other benefits such as decreasing the minimum effective range that was increased earlier due to noise. In addition to, the selected factors decrease the miss distance for all ranges of this direction of the target, and expand the effective range which leads to increase probability of kill.

Keywords: proportional navigation, differential geometry, Kalman filter, genetic algorithm

Procedia PDF Downloads 483

Authors: Seyedmahdi Mousavihashemi

Abstract:

One of the most important subjects of interest in researches is 'improving' which result in various algorithms. In so many geometrical problems we are faced with target functions which should be optimized. In group practices, all the functions’ cooperation lead to convergence. In the study, the optimization algorithm of dense particles is used. Usage of the algorithm improves the given performance norms. The results reveal that usage of swarm algorithm for reinforced particles in designing state feedback improves the given performance norm and in optimized designing of multi-target state feedback controlling, the network will maintain its bearing structure. The results also show that PSO is usable for optimization of state feedback controllers.

Keywords: multi-objective, enhanced, feedback, optimization, algorithm, particle, design

Procedia PDF Downloads 468

Authors: X. Laurent, M. A. Estevez, P. Mari-Beffa

Abstract:

A focus of recent research is to understand the role of our own response goals in the selection of information that will be encoded in episodic memory. For example, if we respond to a target in the presence of distractors, an important aspect under study is whether the distractor and the target share a common response (compatible) or not (incompatible). Some studies have found that compatible objects tend to be groups together and stored in episodic memory, whereas others found that targets in the presence of incompatible distractors are remembered better. Our current research seems to support both views. We used a Tulving-based definition of episodic memory to differentiate memory from episodic and non-episodic traces. In this task, participants first had to classify a blue object as human or animal (target) which appeared in the presence of a green one (distractor) that could belong to the same category of the target (compatible), to the opposite (incompatible) or to an irrelevant one (neutral). Later they had to report the identity (What), location (Where) and time (When) of both target objects (which had been previously responded to) and distractors (which had been ignored). Episodic memory was inferred when the three scene properties (identity, location and time) were correct. The measure of non-episodic memory consisted of those trials in which the identity was correctly remembered, but not the location or time. Our results showed that episodic memory for compatible stimuli is significantly superior to incompatible ones. In sharp contrast, non-episodic measures found superior memory for targets in the presence of incompatible distractors. Our results demonstrate that response compatibility affects the encoding of episodic and non-episodic memory traces in different ways.

Keywords: episodic memory, action systems, compatible response, what-where-when task

Procedia PDF Downloads 143

Authors: Iman Farasat, Howard M. Salis

Abstract:

The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

Procedia PDF Downloads 377

Authors: Ivayla Trifonova, Naoum Jamous, Holger Schrödl

Abstract:

A good web design is a prerequisite for a successful business nowadays, especially since the internet is the most common way for people to inform themselves. Web design includes the optical composition, the structure, and the user guidance of websites. The importance of each website leads to the question if there is a way to measure its usefulness. The aim of this paper is to suggest a methodology for the evaluation of web design. The desired outcome is to have an evaluation that is concentrated on a specific website and its target group.

Keywords: evaluation methodology, factor analysis, target group, web design

Procedia PDF Downloads 601

Authors: Emanuele Peggi

Abstract:

The regulation of competitive takeover bids is one of the most problematic issues of any legislation on takeovers since it concerns a particular type of market, that of corporate control, whose peculiar characteristic is that companies represent "assets" unique of their kind, for each of which there will be a relevant market characterized by the presence of different subjects interested in acquiring control. Firstly, this work aims to analyze, from a comparative point of view, the regulation of takeover bids in competitive scenarios, characterized by the presence of multiple takeover bids for the same target company, and contribute to the debate on the impact that various solutions adopted in some legal systems examined (Italy, UK, and USA) have had on the efficiency of the market for corporate control. Secondly, the different auction models identified by the economic literature and their possible applications to corporate acquisitions in competitive scenarios will be examined, as well as the consequences that the application of each of them causes on the efficiency of the market for corporate control and the interests of the target shareholders. The scope is to study the possibility of attributing to the management of the target company the power to design the auction in order to better protect the interests of shareholders through the adoption of ad hoc models according to the specific context. and in particular on the ground of their assessment of the buyer's risk profile.

Keywords: takeovers, auction theory, shareholders, target company

Procedia PDF Downloads 148

Authors: Maryam Zafar, Sajida Rasheed, Imran Hashmi

Abstract:

Water as an environmental reservoir is reported to act as a habitat and transmission route to microaerophilic bacteria such as Heliobacter pylori. It has been studied that in biofilms are the predominant dwellings for the bacteria to grow in water and protective reservoir for numerous pathogens by protecting them against harsh conditions, such as shear stress, low carbon concentration and less than optimal temperature. In this study, influence of these and many other parameters was studied on H. pylori in stagnant and moving water biofilms both in surface and underground aquatic reservoirs. H. pylori were recovered from pipe of different materials such as Polyvinyl Chloride, Polypropylene and Galvanized iron pipe cross sections from an urban water distribution network. Biofilm swabbed from inner cross section was examined by molecular biology methods coupled with gene sequencing and H. pylori 16S rRNA peptide nucleic acid probe showing positive results for H. pylori presence. Studies showed that pipe material affect growth of biofilm which in turn provide additional survival mechanism for pathogens like H. pylori causing public health concerns.

Keywords: biofilm, gene sequencing, heliobacter pylori, pipe materials

Procedia PDF Downloads 330

Authors: Seokbeen Lim, KyeongSeok Sim, DaKyeong Shin, Gilwon Yoon

Abstract:

Event-related potential (ERP) is one of the useful tools for investigating cognitive reactions. In this study, the potential of ERP components detected after auditory and visual stimuli was examined. Subjects were asked to respond upon stimuli that were of three categories; Target, Non-Target and Standard stimuli. The ERP after stimulus was measured. In the experiment of visual evoked potentials (VEPs), the subjects were asked to gaze at a center point on the monitor screen where the stimuli were provided by the reversal pattern of the checkerboard. In consequence of the VEP experiments, we observed consistent reactions. Each peak voltage could be measured when the ensemble average was applied. Visual stimuli had smaller amplitude and a longer latency compared to that of auditory stimuli. The amplitude was the highest with Target and the smallest with Standard in both stimuli.

Keywords: auditory stimulus, EEG, event related potential, oddball task, visual stimulus

Procedia PDF Downloads 256

Authors: Abu Salim Mustafa

Abstract:

Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing

Procedia PDF Downloads 346

Authors: Ziv Kassner, Gal Ribak

Abstract:

Members of the Odonata order (dragonflies and damselflies) stand out for their maneuverability and superb flight control, which allow them to catch flying prey in the air. These outstanding aerial abilities were fine-tuned during millions of years of an evolutionary arms race between Odonata and their prey, providing an attractive research model for studying the relationship between sensory input – and aerodynamic output in a flying insect. The ability to catch a maneuvering target in air is interesting not just for insect behavioral ecology and neuroethology but also for designing small and efficient robotic air vehicles. While the aerial prey interception of dragonflies (suborder: Anisoptera) have been studied before, little is known about how damselflies (suborder: Zygoptera) intercept prey. Here, high-speed cameras (filming at 1000 frames per second) were used to explore how damselflies catch unpredictable targets that move through air. Blue-tailed damselflies - Ischnura elegans (family: Coenagrionidae) were introduced to a flight arena and filmed while landing on moving targets that were oscillated harmonically. The insects succeeded in capturing targets that were moved with an amplitude of 6 cm and frequencies of 0-2.5 Hz (fastest mean target speed of 0.3 m s⁻¹) and targets that were moved in 1 Hz (an average speed of 0.3 m s⁻¹) but with an amplitude of 15 cm. To land on stationary or slow targets, damselflies either flew directly to the target, or flew sideways, up to a point in which the target was fixed in the center of the field of view, followed by direct flight path towards the target. As the target moved in increased frequency, damselflies demonstrated an ability to track the targets while flying sideways and minimizing the changes of their body direction on the yaw axis. This was likely an attempt to keep the targets at the center of the visual field while minimizing rotational optic flow of the surrounding visual panorama. Stabilizing rotational optic flow helps in estimation of the velocity and distance of the target. These results illustrate how dynamic visual information is used by damselflies to guide them towards a maneuvering target, enabling the superb aerial hunting abilities of these insects. They also exemplifies the plasticity of the damselfly flight apparatus which enables flight in any direction, irrespective of the direction of the body.

Keywords: bio-mechanics, insect flight, target fixation, tracking and interception

Procedia PDF Downloads 128

Authors: A. Delimitsou, C. Gouedard, E. Konstanta, A. Koletis, S. Patera, E. Manou, K. Spaho, S. Murray

Abstract:

Background: There remains a lack of International Standard Control Reference materials for Next Generation Sequencing-based approaches or device calibration. We have designed and validated dsDNA biomimetic reference materials for targeted such approaches incorporating proprietary motifs (patent pending) for device/test calibration. They enable internal single-sample calibration, alleviating sample comparisons to pooled historical population-based data assembly or statistical modelling approaches. We have validated such an approach for BRCA Copy Number Variation analytics using iQRS™-CNVSUITE versus Mixed Ligation-dependent Probe Amplification. Methods: Standard BRCA Copy Number Variation analysis was compared between mixed ligation-dependent probe amplification and next generation sequencing using a cohort of 198 breast/ovarian cancer patients. Next generation sequencing based copy number variation analysis of samples spiked with iQRS™ dsDNA biomimetics were analysed using proprietary CNVSUITE software. Mixed ligation-dependent probe amplification analyses were performed on an ABI-3130 Sequencer and analysed with Coffalyser software. Results: Concordance of BRCA – copy number variation events for mixed ligation-dependent probe amplification and CNVSUITE indicated an overall sensitivity of 99.88% and specificity of 100% for iQRS™-CNVSUITE. The negative predictive value of iQRS-CNVSUITE™ for BRCA was 100%, allowing for accurate exclusion of any event. The positive predictive value was 99.88%, with no discrepancy between mixed ligation-dependent probe amplification and iQRS™-CNVSUITE. For device calibration purposes, precision was 100%, spiking of patient DNA demonstrated linearity to 1% (±2.5%) and range from 100 copies. Traditional training was supplemented by predefining the calibrator to sample cut-off (lock-down) for amplicon gain or loss based upon a relative ratio threshold, following training of iQRS™-CNVSUITE using spiked iQRS™ calibrator and control mocks. BRCA copy number variation analysis using iQRS™-CNVSUITE™ was successfully validated and ISO15189 accredited and now enters CE-IVD performance evaluation. Conclusions: The inclusion of a reference control competitor (iQRS™ dsDNA mimetic) to next generation sequencing-based sequencing offers a more robust sample-independent approach for the assessment of copy number variation events compared to mixed ligation-dependent probe amplification. The approach simplifies data analyses, improves independent sample data analyses, and allows for direct comparison to an internal reference control for sample-specific quantification. Our iQRS™ biomimetic reference materials allow for single sample copy number variation analytics and further decentralisation of diagnostics to single patient sample assessment.

Keywords: validation, diagnostics, oncology, copy number variation, reference material, calibration

Procedia PDF Downloads 45

Authors: Mohammad Tarek Al Muallim, Ozhan Duzenli, Ceyhun Ilguy

Abstract:

Passive sonar is a method for detecting acoustic signals in the ocean. It detects the acoustic signals emanating from external sources. With passive sonar, we can determine the bearing of the target only, no information about the range of the target. Target Motion Analysis (TMA) is a process to estimate the position and speed of a target using passive sonar information. Since bearing is the only available information, the TMA technique called Bearing-only TMA. Many TMA techniques have been developed. However, until now, there is not a very effective method that could be used to always track an unknown target and extract its moving trace. In this work, a design of effective Bearing-only TMA Algorithm is done. The measured bearing angles are very noisy. Moreover, for multi-beam sonar, the measurements is quantized due to the sonar beam width. To deal with this, modified gain extended Kalman filter algorithm is used. The algorithm is fine-tuned, and many modules are added to improve the performance. A special validation gate module is used to insure stability of the algorithm. Many indicators of the performance and confidence level measurement are designed and tested. A new method to detect if the target is maneuvering is proposed. Moreover, a reactive optimal observer maneuver based on bearing measurements is proposed, which insure converging to the right solution all of the times. To test the performance of the proposed TMA algorithm a simulation is done with a MATLAB program. The simulator program tries to model a discrete scenario for an observer and a target. The simulator takes into consideration all the practical aspects of the problem such as a smooth transition in the speed, a circular turn of the ship, noisy measurements, and a quantized bearing measurement come for multi-beam sonar. The tests are done for a lot of given test scenarios. For all the tests, full tracking is achieved within 10 minutes with very little error. The range estimation error was less than 5%, speed error less than 5% and heading error less than 2 degree. For the online performance estimator, it is mostly aligned with the real performance. The range estimation confidence level gives a value equal to 90% when the range error less than 10%. The experiments show that the proposed TMA algorithm is very robust and has low estimation error. However, the converging time of the algorithm is needed to be improved.

Keywords: target motion analysis, Kalman filter, passive sonar, bearing-only tracking

Procedia PDF Downloads 367

Authors: Hongquan Zhang

Abstract:

Inspired by endogenous protein motors, researchers have constructed various synthetic DNA motors based on the specificity and predictability of Watson-Crick base pairing. However, the application of DNA motors to signal amplification and biosensing is limited because of low mobility and difficulty in real-time monitoring of the walking process. The objective of our work was to construct a new type of DNA motor termed target-triggered DNA motors that can walk for hundreds of steps in response to a single target binding event. To improve the mobility and processivity of DNA motors, we used gold nanoparticles (AuNPs) as scaffolds to build high-density, three-dimensional tracks. Hundreds of track strands are conjugated to a single AuNP. To enable DNA motors to respond to specific protein and nucleic acid targets, we adapted the binding-induced DNA assembly into the design of the target-triggered DNA motors. In response to the binding of specific target molecules, DNA motors are activated to autonomously walk along AuNP, which is powered by a nicking endonuclease or DNAzyme-catalyzed cleavage of track strands. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of DNA motors in real time. The motors can translate a single binding event into the generation of hundreds of oligonucleotides from a single nanoparticle. The motors have been applied to amplify the detection of proteins and nucleic acids in test tubes and live cells. The motors were able to detect low pM concentrations of specific protein and nucleic acid targets in homogeneous solutions without the need for separation. Target-triggered DNA motors are significant for broadening applications of DNA motors to molecular sensing, cell imagining, molecular interaction monitoring, and controlled delivery and release of therapeutics.

Keywords: biosensing, DNA motors, gold nanoparticles, signal amplification

Procedia PDF Downloads 50

Authors: Homer Hermes De Dios, Dewoowoogen Baclayon

Abstract:

The community assemblages of reef fishes was conducted in ten marine sanctuaries and ten non-marine sanctuary areas in Sogod Bay, Southern Leyte, Philippines from 2014-2015. A total of 223 species belonging to 39 families of reef fishes in Sogod Bay were recorded. Family Pomacentridae (e.g. damsel fishes) has the highest number of species (42), followed by Labridae or wrasses (27), Chaetodonthidae or butterfly fish (22), Scaridae or parrotfishes (17), and Acanthuridae (surgeonfishes) and Pomacanthidae (angelfishes) both with 10 species. Two of the recorded fish species were included in the IUCN Red List, wherein one is near threatened (Chlorurus bowersi) and the other is endangered species (Cheilinus undulatus). The mean total fish biomass (target + indicator + major or other fish) in MPA was significantly higher (13,468 g/500m2 or equivalent to 26.94 mt/km2) than Non-MPA with 7,408 g/500m2 or 15,216mt/km2 in Non-MPA. The mean total fish biomass in MPAs in Sogod Bay can be categorized as high (21-40 mt/km2) with minimal fishing and medium or slightly moderately fished (11-20 mt/km2) in Non-MPAs. The mean (±SE) biomass of target fishes was significantly higher in MPA than Non-MPA and differ significantly across two depths. The target fish biomass was significantly higher in Limasawa Marine Sanctuary (13,569 g/500m2) followed by Lungsodaan Marine Sanctuary in Padre Burgos (11,884 g/500m2) and the lowest was found in San Isidro (735 g/500m2). The mean total fish density (target + indicator + major or other fish) did not differ between Marine Protected area (607.912 fishes/500m2 or 1215.824 fishes/1000m2) and 525.937 fishes/500m2 in non-Marine Protected Area and can be categorized as moderate (667-2267mt/km2). The mean density of target fishes was significantly (p=0.022) higher in deeper areas (12-15m) than in shallow areas but did not differ significantly between MPAs and Non-MPA. No significant difference of the biomass and density for indicator and other fishes in MPAs and Non-MPAs.

Keywords: abundance, density, species richness, target fish, coral reef management

Procedia PDF Downloads 285

Authors: Jingyuan Hu, Zhandong Liu

Abstract:

CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

Procedia PDF Downloads 17