Search results for: 16S rDNA sequence analysis

Authors: Carmel Sofer, Dan Vilenchik, Ron Dotsch, Galia Avidan

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Studies investigating emotional facial expressions typically reveal consensus among observes regarding the meaning of basic expressions, whose number ranges between 6 to 15 emotional states. Given this limited number of discrete expressions, how is it that the human vocabulary of emotional states is so rich? The present study argues that perceivers use sequences of these discrete expressions as the basis for a much richer vocabulary of emotional states. Such mechanisms, in which a relatively small number of basic components is expanded to a much larger number of possible combinations of meanings, exist in other human communications modalities, such as spoken language and music. In these modalities, letters and notes, which serve as basic components of spoken language and music respectively, are temporally linked, resulting in the richness of expressions. In the current study, in each trial participants were presented with sequences of two images containing facial expression in different combinations sampled out of the eight static basic expressions (total 64; 8X8). In each trial, using single word participants were required to judge the 'state of mind' portrayed by the person whose face was presented. Utilizing word embedding methods (Global Vectors for Word Representation), employed in the field of Natural Language Processing, and relying on machine learning computational methods, it was found that the perceived meanings of the sequences of facial expressions were a weighted average of the single expressions comprising them, resulting in 22 new emotional states, in addition to the eight, classic basic expressions. An interaction between the first and the second expression in each sequence indicated that every single facial expression modulated the effect of the other facial expression thus leading to a different interpretation ascribed to the sequence as a whole. These findings suggest that the vocabulary of emotional states conveyed by facial expressions is not restricted to the (small) number of discrete facial expressions. Rather, the vocabulary is rich, as it results from combinations of these expressions. In addition, present research suggests that using word embedding in social perception studies, can be a powerful, accurate and efficient tool, to capture explicit and implicit perceptions and intentions. Acknowledgment: The study was supported by a grant from the Ministry of Defense in Israel to GA and CS. CS is also supported by the ABC initiative in Ben-Gurion University of the Negev.

Keywords: Glove, face perception, facial expression perception. , facial expression production, machine learning, word embedding, word2vec

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Authors: Bimali Sanjeevani Weerakoon, Toshiaki Osuga, Takehisa Konishi

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Magnetic Resonance Imaging Contrast Agents (MRI-CM) are significant in the clinical and biological imaging as they have the ability to alter the normal tissue contrast, thereby affecting the signal intensity to enhance the visibility and detectability of images. Superparamagnetic Iron Oxide (SPIO) nanoparticles, coated with dextran or carboxydextran are currently available for clinical MR imaging of the liver. Most SPIO contrast agents are T2 shortening agents and Resovist (Ferucarbotran) is one of a clinically tested, organ-specific, SPIO agent which has a low molecular carboxydextran coating. The enhancement effect of Resovist depends on its relaxivity which in turn depends on factors like magnetic field strength, concentrations, nanoparticle properties, pH and temperature. Therefore, this study was conducted to investigate the impact of field strength and different contrast concentrations on enhancement effects of Resovist. The study explored the MRI signal intensity of Resovist in the physiological range of plasma from T2-weighted spin echo sequence at three magnetic field strengths: 0.47 T (r1=15, r2=101), 1.5 T (r1=7.4, r2=95), and 3 T (r1=3.3, r2=160) and the range of contrast concentrations by a mathematical simulation. Relaxivities of r1 and r2 (L mmol-1 Sec-1) were obtained from a previous study and the selected concentrations were 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, and 3.0 mmol/L. T2-weighted images were simulated using TR/TE ratio as 2000 ms /100 ms. According to the reference literature, with increasing magnetic field strengths, the r1 relaxivity tends to decrease while the r2 did not show any systematic relationship with the selected field strengths. In parallel, this study results revealed that the signal intensity of Resovist at lower concentrations tends to increase than the higher concentrations. The highest reported signal intensity was observed in the low field strength of 0.47 T. The maximum signal intensities for 0.47 T, 1.5 T and 3 T were found at the concentration levels of 0.05, 0.06 and 0.05 mmol/L, respectively. Furthermore, it was revealed that, the concentrations higher than the above, the signal intensity was decreased exponentially. An inverse relationship can be found between the field strength and T2 relaxation time, whereas, the field strength was increased, T2 relaxation time was decreased accordingly. However, resulted T2 relaxation time was not significantly different between 0.47 T and 1.5 T in this study. Moreover, a linear correlation of transverse relaxation rates (1/T2, s–1) with the concentrations of Resovist can be observed. According to these results, it can conclude that the concentration of SPIO nanoparticle contrast agents and the field strengths of MRI are two important parameters which can affect the signal intensity of T2-weighted SE sequence. Therefore, when MR imaging those two parameters should be considered prudently.

Keywords: Concentration, resovist, field strength, relaxivity, signal intensity

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Authors: Pushpendra Kumar, Sanjeev Kumar, R. Balasubramanian

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Estimation of optical flow from a sequence of images using variational methods is one of the most successful approach. Discontinuity between different motions is one of the challenging problem in flow estimation. In this paper, we design a new anisotropic diffusion operator, which is able to provide smooth flow over a region and efficiently preserve discontinuity in optical flow. This operator is designed on the basis of intensity differences of the pixels and isotropic operator using exponential function. The combination of these are used to control the propagation of flow. Experimental results on the different datasets verify the robustness and accuracy of the algorithm and also validate the effect of anisotropic operator in the discontinuity preserving.

Keywords: optical flow, variational methods, computer vision, anisotropic operator

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Authors: Ladznar S. Laja, Rosalio G. Artes, Jr.

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This paper introduced a graph polynomial relating convexity concepts. A graph polynomial is a polynomial representing a graph given some parameters. On the other hand, a subgraph H of a graph G is said to be convex in G if for every pair of vertices in H, every shortest path with these end-vertices lies entirely in H. We define the convex subgraph polynomial of a graph G to be the generating function of the sequence of the numbers of convex subgraphs of G of cardinalities ranging from zero to the order of G. This graph polynomial is monic since G itself is convex. The convex index which counts the number of convex subgraphs of G of all orders is just the evaluation of this polynomial at 1. Relationships relating algebraic properties of convex subgraphs polynomial with graph theoretic concepts are established.

Keywords: convex subgraph, convex index, generating function, polynomial ring

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Authors: Zhan Haiyang, Zhang Lei, Ning Juan

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This paper presents a configuration software solution in Linux, which is used for the control of space environment simulator. After introducing the structure and basic principle, it is said that the developing of QT software frame and the dynamic data exchanging between PLC and computer. The OPC driver in Linux is also developed. This driver realizes many-to-many communication between hardware devices and SCADA software. Moreover, an algorithm named “Scan PRI” is put forward. This algorithm is much more optimizable and efficient compared with "Scan in sequence" in Windows. This software has been used in practical project. It has a good control effect and can achieve the expected goal.

Keywords: Linux OS, configuration software, OPC Server driver, MYSQL database

Procedia PDF Downloads 282

Authors: Elif Tugce Aksun Tumerkan, Chris Lowe, Hannah Krupa

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Fluorescent proteins are self-sufficient in forming chromophores with a visible wavelength from 3 amino acids sequence within their own polypeptide structure. This chromophore – a molecule that absorbs a photon of light and exhibits an energy transition equal to the energy of the absorbed photon. Fluorescent proteins (FPs) consisted of a chain of 238 amino acid residues and composed of 11 beta strands shaped in a cylinder surrounding an alpha helix structure. A better understanding of the system of the chromospheres and the increasing advance in protein engineering in recent years, the properties of FPs offers the potential for new applications. They have used sensors and probes in molecular biology and cell-based research that giving a chance to observe these FPs tagged cell localization, structural variation and movement. For clarifying functional uses of fluorescent proteins, electrophoretic properties of these proteins are one of the most important parameters. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is used for determining electrophoretic properties commonly. While there are many techniques are used for determining the functionality of protein-based research, SDS-PAGE analysis can only provide a molecular level assessment of the proteolytic fragments. Before SDS-PAGE analysis, fluorescent proteins need to successfully purified. Due to directly purification of the target, FPs is difficult from the animal, gene expression is commonly used which must be done by transformation with the plasmid. Furthermore, used gel within electrophoresis and staining agents properties have a key role. In this review, the different factors that have the impact on the electrophoretic properties of fluorescent proteins explored. Fluorescent protein separation and purification are the essential steps before electrophoresis that should be done very carefully. For protein purification, gene expression process and following steps have a significant function. For successful gene expression, the properties of selected bacteria for expression, used plasmid are essential. Each bacteria has own characteristics which are very sensitive to gene expression, also used procedure is the important factor for fluorescent protein expression. Another important factors are gel formula and used staining agents. Gel formula has an effect on the specific proteins mobilization and staining with correct agents is a key step for visualization of electrophoretic bands of protein. Visuality of proteins can be changed depending on staining reagents. Apparently, this review has emphasized that gene expression and purification have a stronger effect than electrophoresis protocol and staining agents.

Keywords: cell biology, gene expression, staining agents, SDS-page

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Authors: Simon Espigolé, Igor Shalyminov, Helen Hastie

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Deep machine learning techniques including deep neural networks (DNN) have been used to model language and dialogue for conversational agents to perform tasks, such as giving technical support and also for general chit-chat. They have been shown to be capable of generating long, diverse and coherent sentences in end-to-end dialogue systems and natural language generation. However, these systems tend to imitate the training data and will only generate the concepts and language within the scope of what they have been trained on. This work explores how deep neural networks can be used in a task that would normally require human creativity, whereby the human would read the movie description and/or watch the movie and come up with a compelling, interesting movie title. This task differs from simple summarization in that the movie title may not necessarily be derivable from the content or semantics of the movie description. Here, we train a type of DNN called a sequence-to-sequence model (seq2seq) that takes as input a short textual movie description and some information on e.g. genre of the movie. It then learns to output a movie title. The idea is that the DNN will learn certain techniques and approaches that the human movie titler may deploy that may not be immediately obvious to the human-eye. To give an example of a generated movie title, for the movie synopsis: ‘A hitman concludes his legacy with one more job, only to discover he may be the one getting hit.’; the original, true title is ‘The Driver’ and the one generated by the model is ‘The Masquerade’. A human evaluation was conducted where the DNN output was compared to the true human-generated title, as well as a number of baselines, on three 5-point Likert scales: ‘creativity’, ‘naturalness’ and ‘suitability’. Subjects were also asked which of the two systems they preferred. The scores of the DNN model were comparable to the scores of the human-generated movie title, with means m=3.11, m=3.12, respectively. There is room for improvement in these models as they were rated significantly less ‘natural’ and ‘suitable’ when compared to the human title. In addition, the human-generated title was preferred overall 58% of the time when pitted against the DNN model. These results, however, are encouraging given the comparison with a highly-considered, well-crafted human-generated movie title. Movie titles go through a rigorous process of assessment by experts and focus groups, who have watched the movie. This process is in place due to the large amount of money at stake and the importance of creating an effective title that captures the audiences’ attention. Our work shows progress towards automating this process, which in turn may lead to a better understanding of creativity itself.

Keywords: creativity, deep machine learning, natural language generation, movies

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Authors: Jia Xue, Frederica G. Lamar, Siyu Lin, Jennifer G. Lamori, Samendra Sherchan

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Brackish water samples from Lake Pontchartrain in Louisiana were assessed for the presence of pathogenic amoeba Naegleria fowleri, which causes primary amoebic meningoencephalitis (PAM). In our study, quantitative polymerase chain reaction (qPCR) methods were used to determine N. fowleri, E. coli, and Enterococcus in water collected from Lake Pontchartrain. A total of 158 water samples were analyzed over the 10-month sampling period. Statistically significant positive correlation between water temperature and N. fowleri concentration was observed. N. fowleri target sequence was detected at 35.4% (56/158) of the water samples from ten sites around the Lake ranged from 11.6 GC/100 ml water to 457.8 GC/100 ml water. A single factor (ANOVA) analysis shows the average concentration of N. fowleri in summer (119.8 GC/100 ml) was significantly higher than in winter (58.6 GC/100 ml) (p < 0.01). Statistically significant positive correlations were found between N. fowleri and qPCR E. coli results and N. fowleri and colilert E. coli (culture method), respectively. A weak positive correlation between E. coli and Enterococcus was observed from both qPCR (r = 0.27, p < 0.05) and culture based method (r = 0.52, p < 0.05). Meanwhile, significant positive correlation between qPCR and culture based methods for E. coli (r = 0.30, p < 0.05) and Enterococcus concentration was observed (r = 0.26, p < 0.05), respectively. Future research is needed to determine whether sediment is a source of N. fowleri found in the water column.

Keywords: brackish water, Escherichia coli, Enterococcus, Naegleria fowleri, primary amoebic meningoencephalitis (PAM), qPCR

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Authors: Huda Ahmed Al Taisan

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This paper investigates a phonological phenomenon, which exhibits variation ‘alternation’ in terms of the uvular consonants [q] and [ʁ] in Hasawi Arabic. This dialect is spoken in Alahsa city, which is located in the Eastern province of Saudi Arabia. To the best of our knowledge, no such research has systematically studied this phenomenon in Hasawi Arabic dialect. This paper is significant because it fills the gap in the literature about this alternation phenomenon in this understudied dialect. A large amount of the data is extracted from several interviews the author has conducted with 10 participants, native speakers of the dialect, and complemented by additional forms from social media. The latter method of collecting the data adds to the significance of the research. The analysis of the data is carried out in Harmonic Serialism Optimality Theory (HS-OT), a version of the Optimality Theoretic (OT) framework, which holds that linguistic forms are the outcome of the interaction among violable universal constraints, and in the recent development of OT into a model that accounts for linguistic variation in harmonic derivational steps. This alternation process is assumed to be phonologically unconditioned and in free variation in other varieties of Arabic dialects in the area. The goal of this paper is to investigate whether this phenomenon is in free variation or governed, what governs this alternation between [q] and [ʁ] and whether the alternation is phonological or other linguistic constraints are in action. The results show that the [q] and [ʁ] alternation is not free and it occurs due to different assimilation processes. Positional, segmental sequence and vowel adjacency factors are in action in Hasawi Arabic.

Keywords: harmonic serialism, Hasawi, uvular, variation

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Authors: Mostafa Mohammadpour, Christoph Kapeller, Christy Li, Josef Scharinger, Christoph Guger

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Interictal spikes provide valuable information on electrocorticography (ECoG), which aids in surgical planning for patients who suffer from refractory epilepsy. However, the shape and temporal dynamics of these spikes remain unclear. The purpose of this work was to analyze the shape of interictal spikes and measure their distance to the seizure onset zone (SOZ) to use in epilepsy surgery. Thirteen patients' data from the iEEG portal were retrospectively studied. For analysis, half an hour of ECoG data was used from each patient, with the data being truncated before the onset of a seizure. Spikes were first detected and grouped in a sequence, then clustered into interictal epileptiform discharges (IEDs) and non-IED groups using two-step clustering. The distance of the spikes from IED and non-IED groups to SOZ was quantified and compared using the Wilcoxon rank-sum test. Spikes in the IED group tended to be in SOZ or close to it, while spikes in the non-IED group were in distance of SOZ or non-SOZ area. At the group level, the distribution for sharp wave, positive baseline shift, slow wave, and slow wave to sharp wave ratio was significantly different for IED and non-IED groups. The distance of the IED cluster was 10.00mm and significantly closer to the SOZ than the 17.65mm for non-IEDs. These findings provide insights into the shape and spatiotemporal dynamics of spikes that could influence the network mechanisms underlying refractory epilepsy.

Keywords: spike propagation, spike pattern, clustering, SOZ

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Authors: Liu Yao, B. T. Wan Maseri, Wan Mohd, B. T. Nurul Izzah, Mohd Shah, Wei Wei

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Effectively managing knowledge has become a vital weapon for businesses to survive or to succeed in the increasingly competitive market. But do they perform environmental analysis when managing knowledge? If yes, how is the level and significance? This paper established a conceptual framework covering the basic knowledge management activities (KMA) to examine their contribution towards organizational performance (OP). Environmental analysis (EA) was then investigated from both internal and external aspects, to identify its effects on that contribution. Data was collected from 400 Chinese SMEs by questionnaires. Cronbach's α and factor analysis were conducted. Regression results show that the external analysis presents higher level than internal analysis. However, the internal analysis mediates the effects of external analysis on the KMA-OP relation and plays more significant role in the relation comparing with the external analysis. Thus, firms shall improve environmental analysis especially the internal analysis to enhance their KM practices.

Keywords: knowledge management, environmental analysis, performance, mediating, small sized enterprises, medium sized enterprises

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Authors: Ian Campbell, Gillian Mitchell, Paul James, Na Li, Ella Thompson

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The genetic cause of the majority of multiple-case breast cancer families remains unresolved. Next generation sequencing has emerged as an efficient strategy for identifying predisposing mutations in individuals with inherited cancer. We are conducting whole exome sequence analysis of germ line DNA from multiple affected relatives from breast cancer families, with the aim of identifying rare protein truncating and non-synonymous variants that are likely to include novel cancer predisposing mutations. Data from more than 200 exomes show that on average each individual carries 30-50 protein truncating mutations and 300-400 rare non-synonymous variants. Heterogeneity among our exome data strongly suggest that numerous moderate penetrance genes remain to be discovered, with each gene individually accounting for only a small fraction of families (~0.5%). This scenario marks validation of candidate breast cancer predisposing genes in large case-control studies as the rate-limiting step in resolving the missing heritability of breast cancer. The aim of this study is to screen genes that are recurrently mutated among our exome data in a larger cohort of cases and controls to assess the prevalence of inactivating mutations that may be associated with breast cancer risk. We are using the Agilent HaloPlex Target Enrichment System to screen the coding regions of 168 genes in 1,000 BRCA1/2 mutation-negative familial breast cancer cases and 1,000 cancer-naive controls. To date, our interim analysis has identified 21 genes which carry an excess of truncating mutations in multiple breast cancer families versus controls. Established breast cancer susceptibility gene PALB2 is the most frequently mutated gene (13/998 cases versus 0/1009 controls), but other interesting candidates include NPSR1, GSN, POLD2, and TOX3. These and other genes are being validated in a second cohort of 1,000 cases and controls. Our experience demonstrates that beyond PALB2, the prevalence of mutations in the remaining breast cancer predisposition genes is likely to be very low making definitive validation exceptionally challenging.

Keywords: predisposition, familial, exome sequencing, breast cancer

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Authors: Yasaman Sanayei, Alireza Bahiraie

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This paper presents a systematic methodology based on the application of artificial neural networks for sequencing batch reactor (SBR). The SBR is a fill-and-draw biological wastewater technology, which is specially suited for nutrient removal. Employing reactive dye by Sphingomonas paucimobilis bacteria at sequence batch reactor is a novel approach of dye removal. The influent COD, MLVSS, and reaction time were selected as the process inputs and the effluent COD and BOD as the process outputs. The best possible result for the discrete pole parameter was a= 0.44. In orderto adjust the parameters of ANN, the Levenberg-Marquardt (LM) algorithm was employed. The results predicted by the model were compared to the experimental data and showed a high correlation with R2> 0.99 and a low mean absolute error (MAE). The results from this study reveal that the developed model is accurate and efficacious in predicting COD and BOD parameters of the dye-containing wastewater treated by SBR. The proposed modeling approach can be applied to other industrial wastewater treatment systems to predict effluent characteristics. Note that SBR are normally operated with constant predefined duration of the stages, thus, resulting in low efficient operation. Data obtained from the on-line electronic sensors installed in the SBR and from the control quality laboratory analysis have been used to develop the optimal architecture of two different ANN. The results have shown that the developed models can be used as efficient and cost-effective predictive tools for the system analysed.

Keywords: artificial neural network, COD removal, SBR, Sphingomonas paucimobilis

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Authors: Jingjie Li, Wenjie Hu

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Phraseological units in academic English texts have been a central focus in recent corpus linguistic research. A wide variety of phraseological units have been explored, including collocations, chunks, lexical bundles, patterns, semantic sequences, etc. This paper describes a special category of clause-level phraseological units, namely, Characteristic Sentence Stems (CSSs), with a view to describing their defining criteria and extraction method. CSSs are contiguous lexico-grammatical sequences which contain a subject-predicate structure and which are frame expressions characteristic of academic writing. The extraction of CSSs consists of six steps: Part-of-speech tagging, n-gram segmentation, structure identification, significance of occurrence calculation, text range calculation, and overlapping sequence reduction. Significance of occurrence calculation is the crux of this study. It includes the computing of both the internal association and the boundary independence of a CSS and tests the occurring significance of the CSS from both inside and outside perspectives. A new normalization algorithm is also introduced into the calculation of LocalMaxs for reducing overlapping sequences. It is argued that many sentence stems are so recurrent in academic texts that the most typical of them have become the habitual ways of making meaning in academic writing. Therefore, studies of CSSs could have potential implications and reference value for academic discourse analysis, English for Academic Purposes (EAP) teaching and writing.

Keywords: characteristic sentence stem, extraction method, phraseological unit, the statistical measure

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Authors: Nazira Kakulia

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The analysis of transformation of institutional changes outlines two important characteristics. These are: the speed of the changes and their sequence. Successful transformation must be carried out in three different stages; On the first stage, macroeconomic stabilization must be achieved with the help of fiscal and monetary tools. Two-tier banking system should be established and the active functions of central bank should be replaced by the passive ones (reserve requirements and refinancing rate), together with the involvement growth of private sector. Fiscal policy by itself here means the creation of tax system which must replace previously existing direct state revenues; the share of subsidies in the state expenses must be reduced also. The second stage begins after reaching the macroeconomic stabilization at a time of change of formal institutes which must stimulate the private business. Corporate legislation creates a competitive environment at the market and the privatization of state companies takes place. Bankruptcy and contract law is created. he third stage is the most extended one, which means the formation of all state structures that is necessary for the further proper functioning of a market economy. These three stages about the cycle period of political and social transformation and the hierarchy of changes can also be grouped by the different methodology: on the first and the most short-term stage the transfer of power takes place. On the second stage institutions corresponding to new goal are created. The last phase of transformation is extended in time and it includes the infrastructural, socio-cultural and socio-structural changes. The main goal of this research is to explore and identify the features of such kind of models.

Keywords: competitive environment, fiscal policy, macroeconomic stabilization, tax system

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Authors: Ali Ben Abbes, ImedRiadh Farah, Vincent Barra

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Remotely sensed data are a significant source for monitoring and updating databases for land use/cover. Nowadays, changes detection of urban area has been a subject of intensive researches. Timely and accurate data on spatio-temporal changes of urban areas are therefore required. The data extracted from multi-temporal satellite images are usually non-stationary. In fact, the changes evolve in time and space. This paper is an attempt to propose a methodology for changes detection in urban area by combining a non-stationary decomposition method and stochastic modeling. We consider as input of our methodology a sequence of satellite images I₁, I₂, … I_n at different periods (t = 1, 2, ..., n). Firstly, a preprocessing of multi-temporal satellite images is applied. (e.g. radiometric, atmospheric and geometric). The systematic study of global urban expansion in our methodology can be approached in two ways: The first considers the urban area as one same object as opposed to non-urban areas (e.g. vegetation, bare soil and water). The objective is to extract the urban mask. The second one aims to obtain a more knowledge of urban area, distinguishing different types of tissue within the urban area. In order to validate our approach, we used a database of Tres Cantos-Madrid in Spain, which is derived from Landsat for a period (from January 2004 to July 2013) by collecting two frames per year at a spatial resolution of 25 meters. The obtained results show the effectiveness of our method.

Keywords: multi-temporal satellite image, urban growth, non-stationary, stochastic model

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Authors: Jovian Cheung, Thomas Kwok, Victor Wong

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Buildings are entwined with smart city developments. Building performance relies heavily on electrical and mechanical (E&M) systems and services accounting for about 40 percent of global energy use. By cohering the advancement of technology as well as energy and operation-efficient initiatives into the buildings, people are enabled to raise building performance and enhance the sustainability of the built environment in their daily lives. Digital transformation in the buildings is the profound development of the city to leverage the changes and opportunities of digital technologies To optimize the building performance, intelligent power quality and energy management system is developed for transforming data into actions. The system is formed by interfacing and integrating legacy metering and internet of things technologies in the building and applying big data techniques. It provides operation and energy profile and actionable insights of a building, which enables to optimize the building performance through raising people awareness on E&M services and energy consumption, predicting the operation of E&M systems, benchmarking the building performance, and prioritizing assets and energy management opportunities. The intelligent power quality and energy management system comprises four elements, namely the Integrated Building Performance Map, Building Performance Dashboard, Power Quality Analysis, and Energy Performance Analysis. It provides predictive operation sequence of E&M systems response to the built environment and building activities. The system collects the live operating conditions of E&M systems over time to identify abnormal system performance, predict failure trends and alert users before anticipating system failure. The actionable insights collected can also be used for system design enhancement in future. This paper will illustrate how intelligent power quality and energy management system provides operation and energy profile to optimize the building performance and actionable insights to revitalize an existing building into a smart building. The system is driving building performance optimization and supporting in developing Hong Kong into a suitable smart city to be admired.

Keywords: intelligent buildings, internet of things technologies, big data analytics, predictive operation and maintenance, building performance

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Authors: Yildiray Keskin, Omer Acan, Murat Akkus

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In this paper, the solution of fractional diffusion equations is presented by means of the reduced differential transform method. Fractional partial differential equations have special importance in engineering and sciences. Application of reduced differential transform method to this problem shows the rapid convergence of the sequence constructed by this method to the exact solution. The numerical results show that the approach is easy to implement and accurate when applied to fractional diffusion equations. The method introduces a promising tool for solving many fractional partial differential equations.

Keywords: fractional diffusion equations, Caputo fractional derivative, reduced differential transform method, partial

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Authors: Mouad Zouina, Benaceur Outtaj

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The proposed work falls within the context of improving data security for m-commerce systems. In this context we have placed under the light some flaws encountered in HTTPS the most used m-commerce protocol, particularly the man in the middle attack, shortly MITM. The man in the middle attack is an active listening attack. The idea of this attack is to target the handshake phase of the HTTPS protocol which is the transition from a non-secure connection to a secure connection in our case HTTP to HTTPS. This paper proposes a solution to fix those flaws based on the upgrade of HSTS standard handshake sequence using the DNSSEC standard.

Keywords: m-commerce, HTTPS, HSTS, DNSSEC, MITM bootstrap vulnerability

Procedia PDF Downloads 384

Authors: Madhuka G. P. D. Udantha, Gihan V. Dias, Surangika Ranathunga

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Today Websites contain very interesting applications. But there are only few methodologies to analyze User navigations through the Websites and formulating if the Website is put to correct use. The web logs are only used if some major attack or malfunctioning occurs. Web Logs contain lot interesting dealings on users in the system. Analyzing web logs has become a challenge due to the huge log volume. Finding interesting patterns is not as easy as it is due to size, distribution and importance of minor details of each log. Web logs contain very important data of user and site which are not been put to good use. Retrieving interesting information from logs gives an idea of what the users need, group users according to their various needs and improve site to build an effective and efficient site. The model we built is able to detect attacks or malfunctioning of the system and anomaly detection. Logs will be more complex as volume of traffic and the size and complexity of web site grows. Unsupervised techniques are used in this solution which is fully automated. Expert knowledge is only used in validation. In our approach first clean and purify the logs to bring them to a common platform with a standard format and structure. After cleaning module web session builder is executed. It outputs two files, Web Sessions file and Indexed URLs file. The Indexed URLs file contains the list of URLs accessed and their indices. Web Sessions file lists down the indices of each web session. Then DBSCAN and EM Algorithms are used iteratively and recursively to get the best clustering results of the web sessions. Using homogeneity, completeness, V-measure, intra and inter cluster distance and silhouette coefficient as parameters these algorithms self-evaluate themselves to input better parametric values to run the algorithms. If a cluster is found to be too large then micro-clustering is used. Using Cluster Signature Module the clusters are annotated with a unique signature called finger-print. In this module each cluster is fed to Associative Rule Learning Module. If it outputs confidence and support as value 1 for an access sequence it would be a potential signature for the cluster. Then the access sequence occurrences are checked in other clusters. If it is found to be unique for the cluster considered then the cluster is annotated with the signature. These signatures are used in anomaly detection, prevent cyber attacks, real-time dashboards that visualize users, accessing web pages, predict actions of users and various other applications in Finance, University Websites, News and Media Websites etc.

Keywords: anomaly detection, clustering, pattern recognition, web sessions

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Authors: Falana Yetunde Olaitan, Ijah U. J. J, Solebo Shakirat O.

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Genetically modified crops are already phenomenally successful and are grown worldwide in more than eighteen countries on more than 67 million hectares. Nigeria, in October 2018, approved Bacillus thuringiensis (Bt) cotton and maize; therefore, the need to carry out environmental risk assessment studies. A total of 15 4L octagonal ceramic pots were filled with 4kg of soil and placed on the bench in 2 rows of 10 pots each and the 3rd row of 5 pots, 1st-row pots were used to plant GM cotton seeds, while the 2nd-row pots were used for non-GM cotton seeds and the 3rd row of 5 pots served as control, all in the screen house. Soil samples for metagenomic DNA extraction were collected at random and at the monthly interval after planting at a distance of 2mm from the plant’s root and at a depth of 10cm using a sterile spatula. Soil samples for physicochemical analysis were collected before planting and after harvesting the GM and non-GM crops as well as from the control soil. The DNA was extracted, quantified and sequenced; Sample 1A (DNA from GM cotton Soil at 1st interval) gave the lowest sequence read with 0.853M while sample 2B (DNA from GM cotton Soil at 2nd interval) gave the highest with 5.785M, others gave between 1.8M and 4.7M. The samples treatment were grouped into four, Group 1 (GM cotton soil from 1 to 3 intervals) had between 800,000 and 5,700,000 strains of microbes (SOM), Group 2 (non GM cotton soil from 1 to 3 intervals) had between 1,400,600 and 4,200,000 SOM, Group 3 (control soil) had between 900,000 and 3,600,000 SOM and Group 4 (initial soil) had between 3,700,000 and 4,000,000 SOM. The microbes observed were predominantly bacteria (including archaea), fungi, dark matter alongside protists and phages. The predominant bacterial groups were the Terrabacteria (Bacillus funiculus, Bacillus sp.), the Proteobacteria (Microvirga massiliensis, sphingomonas sp.) and the Archaea (Nitrososphaera sp.), while the fungi were Aspergillus fischeri and Fusarium falciforme. The comparative analysis between groups was done using JACCARD PERMANOVA beta diversity analysis at P-value not more than 0.76 and there was no significant pair found. The pH for initial, GM cotton, non-GM cotton and control soil were 6.28, 6.26, 7.25, 8.26 and the percentage moisture was 0.63, 0.78, 0.89 and 0.82, respectively, while the percentage Nitrogen was observed to be 17.79, 1.14, 1.10 and 0.56 respectively. Other parameters include, varying concentrations of Potassium (0.46, 1,284.47, 1,785.48, 1,252.83 mg/kg) and Phosphorus (18.76, 17.76, 16.87, 15.23 mg/kg) were recorded for the four treatments respectively. The soil consisted mainly of silt (32.09 to 34.66%) and clay (58.89 to 60.23%), reflecting the soil texture as silty – clay. The results were then tested with ANOVA at less than 0.05 P-value and no pair was found to be significant as well. The results suggest that the GM crops have no significant effect on microbial ecology and physicochemical properties of the soil and, in turn, no direct or indirect effects on human health.

Keywords: genetically modified crop, microbial ecology, physicochemical properties, metagenomics, DNA, soil

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Authors: Lachin Mikjtarnejad, Mohsen Farzaneh

Abstract:

Various microbes, such as fungi and bacteria species, are naturally found in the fruit microbiota, and some of them act as a pathogen and result in fruit rot. Among non-pathogenic microbes, yeasts (single-celled microorganisms belonging to the fungi kingdom) can colonize fruit tissues and interact with them without causing any damage to them. Although yeasts are part of the plant microbiota, there is little information about their interactions with plants in comparison with bacteria and filamentous fungi. According to several existing studies, some yeasts can colonize different plant species and have the biological control ability to suppress some of the plant pathogens. It means those specific yeast-colonized plants are more resistant to some plant pathogens. The major objective of the present investigation is to isolate yeast strains from apple fruit and screen their ability to control Penicillium expansum, the causal agent of blue mold of fruits. In the present study, psychrotrophic and epiphytic yeasts were isolated from apple fruits that were stored at low temperatures (0–1°C). Totally, 42 yeast isolates were obtained and identified by molecular analysis based on genomic sequences of the D1/D2 and ITS1/ITS4 regions of their rDNA. All isolated yeasts were primarily screened by' in vitro dual culture assay against P. expansum by measuring the fungus' relative growth inhibition after 10 days of incubation. The results showed that the mycelial growth of P. expansum was reduced between 41–53% when challenged by promising yeast strains. The isolates with the strongest antagonistic activity belonged to Metschnikowia pulcherrima A13, Rhodotorula mucilaginosa A41, Leucosporidium Scottii A26, Aureobasidium pullulans A19, Pichia guilliermondii A32, Cryptococcus flavescents A25, and Pichia kluyveri A40. The results of seven superior isolates to inhibit blue mold decay on fruit showed that isolates A. pullulans A19, L. scottii A26, and Pi. guilliermondii A32 could significantly reduce the fruit rot and decay with 26 mm, 22 mm and 20 mm zone diameter, respectively, compared to the control sample with 43 mm. Our results show Pi. guilliermondii strain A13 was the most effective yeast isolates in inhibiting P. expansum on apple fruits. In addition, various biological control mechanisms of promising biological isolates against blue mold have been evaluated to date, including competition for nutrients and space, production of volatile metabolites, reduction of spore germination, production of siderophores and production of extracellular lytic enzymes such as chitinase and β-1,3-glucanase. However, the competition for nutrients and the ability to inhibit P. expansum spore growth have been introduced as the prevailing mechanisms among them. Accordingly, in our study, isolates A13, A41, A40, A25, A32, A19 and A26 inhibited the germination of P. expansum, whereas isolates A13 and A19 were the strongest inhibitors of P. expansum mycelia growth, causing 89.13% and 81.75 % reduction in the mycelial surface, respectively. All the promising isolates produced chitinase and β-1,3-glucanase after 3, 5 and 7 days of cultivation. Finally, based on our findings, we are proposing that, Pi. guilliermondiias as an effective biocontrol agent and alternative to chemical fungicides to control the blue mold of apple fruit.

Keywords: yeast, yeast enzymes, biocontrol, post harvest diseases

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Authors: Assad Maalouf, Lunjin Lu, James Lynott

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We present a taint analysis that can automatically detect when string operations result in a string that is free of taints, where all the tainted patterns have been removed. This is an improvement on the conservative behavior of previous taint analyzers, where a string operation on a tainted string always leads to a tainted string unless the operation is manually marked as a sanitizer. The taint analysis is built on top of a string analysis that uses finite state automata to approximate the sets of values that string variables can take during the execution of a program. The proposed approach has been implemented as an extension of FlowDroid and experimental results show that the resulting taint analyzer is much more precise than the original FlowDroid.

Keywords: android, static analysis, string analysis, taint analysis

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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: Zeeshan Khan, Faisal Nouroz, Shumaila Noureen

Abstract:

European or common rabbit (Oryctolagus cuniculus) belongs to class Mammalia, order Lagomorpha of family Leporidae. They are distributed worldwide and are native to Europe (France, Spain and Portugal) and Africa (Morocco and Algeria). LTR retrotransposons are major Class I mobile genetic elements of eukaryotic genomes and play a crucial role in genome expansion, evolution and diversification. They were mostly annotated in various genomes by conventional approaches of homology searches, which restricted the annotation of novel elements. Present work involved de novo identification of LTR retrotransposons by LTR_FINDER in haploid genome of rabbit (2247.74 Mb) distributed in 22 chromosomes, of which 7,933 putative full-length or partial copies were identified containing 69.38 Mb of elements, accounting 3.08% of the genome. Highest copy numbers (731) were found on chromosome 7, followed by chromosome 12 (705), while the lowest copy numbers (27) were detected in chromosome 19 with no elements identified from chromosome 21 due to partially sequenced chromosome, unidentified nucleotides (N) and repeated simple sequence repeats (SSRs). The identified elements ranged in sizes from 1.2 - 25.8 Kb with average sizes between 2-10 Kb. Highest percentage (4.77%) of elements was found in chromosome 15, while lowest (0.55%) in chromosome 19. The most frequent tRNA type was Arginine present in majority of the elements. Based on gained results, it was estimated that rabbit exhibits 15,866 copies having 137.73 Mb of elements accounting 6.16% of diploid genome (44 chromosomes). Further molecular analyses will be helpful in chromosomal localization and distribution of these elements on chromosomes.

Keywords: rabbit, LTR retrotransposons, genome, chromosome

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Authors: Olomon Wu, Hung Lu, Nick Wilkins, Daniel Kerr, Zekeriya Aliyazicioglu, H. K. Hwang

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Multiple Input Multiple Output (MIMO) radar has received increasing attention in recent years. MIMO radar has many advantages over conventional phased array radar such as target detection, resolution enhancement, and interference suppression. In this paper, the results are presented from a simulation study of MIMO Uniformly-Spaced Linear Array (ULA) antennas. The performance is investigated under varied parameters, including varied array size, Pseudo Random (PN) sequence length, number of snapshots, and Signal to Noise Ratio (SNR). The results of MIMO are compared to a traditional array antenna.

Keywords: MIMO radar, phased array antenna, target detection, radar signal processing

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Authors: Proud Arunrangsiwed

Abstract:

The part of “future direction” in the findings of meta-analysis could provide the great direction to conduct the future studies. This study, “The Documentary Analysis of Meta-Analysis Research in Violence of Media” would conclude “future directions” out of 10 meta-analysis papers. The purposes of this research are to find an appropriate research design or an appropriate methodology for the future research related to the topic, “violence of media”. Further research needs to explore by longitudinal and experimental design, and also needs to have a careful consideration about age effects, time spent effects, enjoyment effects, and ordinary lifestyle of each media consumer.

Keywords: aggressive, future direction, meta-analysis, media, violence

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Authors: Nazri Kama, Sufyan Basri, Roslina Ibrahim

Abstract:

It is important to manage the changes in the software to meet the evolving needs of the customer. Accepting too many changes causes delay in the completion and it incurs additional cost. One type of information that helps to make the decision is through change impact analysis. Current impact analysis approaches assume that all classes in the class artifact are completely developed and the class artifact is used as a source of analysis. However, these assumptions are impractical for impact analysis in the software development phase as some classes in the class artifact are still under development or partially developed that leads to inaccuracy. This paper presents a novel impact analysis approach to be used in the software development phase. The significant achievements of the approach are demonstrated through an extensive experimental validation using three case studies.

Keywords: software development, impact analysis, traceability, static analysis.

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Authors: Muhammad SAFDAR, Mehmet Ozaslan, Musarrat Abbas Khan

Abstract:

Babesiosis is a haemoparasitic disease due to the multiplication of protozoan’s parasite, Babesia ovis in the red blood cells of the host, and contributes numerous economical losses, including sheep and goat ruminants. The early identification and successful treatment of Babesia Ovis spp. belong to the key steps of control and health management of livestock resources. The objective of this study was to construct a polymerase chain reaction (PCR) based method for the detection of Babesia spp. in small ruminants and to determine the risk factors involved in the spreading of babesiosis infections. A total of 100 blood samples were collected from 50 sheep and 50 goats along with different areas of Muzaffargarh, Pakistan, from randomly selected herds. Data on the characteristics of sheep and goats were collected through questionnaires. Of 100 blood samples examined, 18 were positive for Babesia ovis upon microscopic studies, whereas 11 were positive for the presence of Babesia spp. by PCR assay. For the recognition of parasitic DNA, a set of 500bp oligonucleotide was designed by PCR amplification with sequence 18S rRNA gene for B. ovis. The prevalence of babesiosis in small ruminant’s sheep and goat detected by PCR was significantly higher in female animals (28%) than male herds (08%). PCR analysis of the reference samples showed that the detection limit of the PCR assay was 0.01%. Taken together, all data indicated that this PCR assay was a simple, fast, specific detection method for Babesia ovis species in small ruminants compared to other available methods.

Keywords: Babesia ovis, PCR amplification, 18S rRNA, sheep and goat

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Authors: Hamed Alipour-Banaei, Farhad Mehdizadeh

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We report the design and characterization of ultra high quality factor filter based on one-dimensional photonic-crystal Thue-Morse sequence structure. The behavior of aperiodic array of photonic crystal structure is numerically investigated and we show that by changing the angle of incident wave, desired wavelengths could be tuned and a tunable filter is realized. Also it is shown that high quality factor filter be achieved in the telecommunication window around 1550 nm, with a device based on Thue-Morse structure. Simulation results show that the proposed structure has a quality factor more than 100000 and it is suitable for DWDM communication applications.

Keywords: Thue-Morse, filter, quality factor, photonic

Procedia PDF Downloads 562