Search results for: Protein sequence annotation

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

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Authors: Amlan Kumar Das, Avinash Marwal, Vikram Pareek

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Liposome plays an important role in medical and pharmaceutical science as e.g. nano scale drug carriers. Liposomes are vesicles of varying size consisting of a spherical lipid bilayer and an aqueous inner compartment. Magnet-driven liposome used for the targeted delivery of drugs to organs and tissues. These liposome preparations contain encapsulated drug components and finely dispersed magnetic particles. Liposomes are vesicles of varying size consisting of a spherical lipid bilayer and an aqueous inner compartment that are generated in vitro. These are useful in terms of biocompatibility, biodegradability, and low toxicity, and can control biodistribution by changing the size, lipid composition, and physical characteristics. Furthermore, liposomes can entrap both hydrophobic and hydrophilic drugs and are able to continuously release the entrapped substrate, thus being useful drug carriers. Magnetic liposomes (MLs) are phospholipid vesicles that encapsulate magneticor paramagnetic nanoparticles. They are applied as contrast agents for magnetic resonance imaging (MRI). The biological synthesis of nanoparticles using plant extracts plays an important role in the field of nanotechnology. Green-synthesized magnetite nanoparticles-protein hybrid has been produced by treating Iron (III) / Iron (II) chloride with the leaf extract of Datura inoxia. The phytochemicals present in the leaf extracts act as a reducing as well stabilizing agents preventing agglomeration, which include flavonoids, phenolic compounds, cardiac glycosides, proteins and sugars. The magnetite nanoparticles-protein hybrid has been trapped inside the aqueous core of the liposome prepared by reversed phase evaporation (REV) method using oleic and linoleic acid which has been shown to be driven under magnetic field confirming the formation magnetic liposome (ML). Chemical characterization of stealth magnetic liposome has been performed by breaking the liposome and release of magnetic nanoparticles. The presence iron has been confirmed by colour complex formation with KSCN and UV-Vis study using spectrophotometer Cary 60, Agilent. This magnet driven liposome using nanoparticles-protein hybrid can be a smart vesicles for the targeted drug delivery.

Keywords: Nanoparticles-Protein Hybrid, Magnetic Liposome.

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Authors: V. Maciuc, Şt. Creangă, I. Gîlcă, V. Ujică

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The paper makes part from a complex research project on Romanian Grey Steppe, a unique breed in terms of biological and cultural-historical importance, on the verge of extinction and which has been included in a preservation programme of genetic resources from Romania. The study of genetic polymorphism of protean fractions, especially kappa-casein, and the genotype relations of these lactoproteins with some quantitative and qualitative features of milk yield represents a current theme and a novelty for this breed. In the estimation of the genetic parameters we used R.E.M.L. (Restricted Maximum Likelihood) method. The main lactoprotein from milk, kappa - casein (K-cz), characterized in the specialized literature as a feature having a high degree of hereditary transmission, behaves as such in the nucleus under study, a value also confirmed by the heritability coefficient (h2 = 0.57 %). We must mention the medium values for milk and fat quantity (h2=0.26, 0.29 %) and the fat and protein percentage from milk having a high hereditary influence h2 = 0.71 - 0.63 %. Correlations between kappa-casein and the milk quantity are negative and strong. Between kappa-casein and other qualitative features of milk (fat content 0.58-0.67 % and protein content 0.77- 0.87%), there are positive and very strong correlations. At the same time, between kappa-casein and β casein (β-cz), β lactoglobulin (β- lg) respectively, correlations are positive having high values (0.37 – 0.45 %), indicating the same causes and determining factors for the two groups of features.

Keywords: breed, genetic preservation, lactoproteins, Romanian Grey Steppe

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Authors: P. Valdiviezo, G. Riofrio, R. Reategui

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This article describes the implementation of an intelligent agent that provides recommendations for educational resources in a virtual learning environment (VLE). It aims to support pending (undeveloped) student learning activities. It begins by analyzing the proposed VLE data model entities in the recommender process. The pending student activities are then identified, which constitutes the input information for the agent. By using the attribute-based recommender technique, the information can be processed and resource recommendations can be obtained. These serve as support for pending activity development in the course. To integrate this technique, we used an ontology. This served as support for the semantic annotation of attributes and recommended files recovery.

Keywords: Learning activities, educational resource, recommender agent, recommendation technique, ontology.

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Authors: Petr Vcelak, Jana Kleckova

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Our Medicine-oriented research is based on a medical data set of real patients. It is a security problem to share patient private data with peoples other than clinician or hospital staff. We have to remove person identification information from medical data. The medical data without private data are available after a de-identification process for any research purposes. In this paper, we introduce an universal automatic rule-based de-identification application to do all this stuff on an heterogeneous medical data. A patient private identification is replaced by an unique identification number, even in burnedin annotation in pixel data. The identical identification is used for all patient medical data, so it keeps relationships in a data. Hospital can take an advantage of a research feedback based on results.

Keywords: DASTA, De-identification, DICOM, Health Level Seven, Medical data, OCR, Personal data

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Authors: Mahdi Fakoor, Seyed Mohammad Navid Ghoreishi

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Composite patching is a common way for reinforcing the cracked pipes and cylinders. The effects of composite patch reinforcement on fracture parameters of a cracked pipe depend on a variety of parameters such as number of layers, angle, thickness, and material of each layer. Therefore, stacking sequence optimization of composite patch becomes crucial for the applications of cracked pipes. In this study, in order to obtain the optimal stacking sequence for a composite patch that has minimum weight and maximum resistance in propagation of cracks, a coupled Multi-Objective Genetic Algorithm (MOGA) and Finite Element Method (FEM) process is proposed. This optimization process has done for longitudinal and transverse semi-elliptical cracks and optimal stacking sequences and Pareto’s front for each kind of cracks are presented. The proposed algorithm is validated against collected results from the existing literature.

Keywords: Multi objective optimization, Pareto front, composite patch, cracked pipe.

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Authors: Yongsuk Jang Kim, Sun-Tae Chung, Boogyun Kim, Seongwon Cho

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Realistic 3D face model is more precise in representing pose, illumination, and expression of face than 2D face model so that it can be utilized usefully in various applications such as face recognition, games, avatars, animations, and etc. In this paper, we propose a 3D face modeling method based on 3D dense morphable shape model. The proposed 3D modeling method first constructs a 3D dense morphable shape model from 3D face scan data obtained using a 3D scanner. Next, the proposed method extracts and matches facial landmarks from 2D image sequence containing a face to be modeled, and then reconstructs 3D vertices coordinates of the landmarks using a factorization-based SfM technique. Then, the proposed method obtains a 3D dense shape model of the face to be modeled by fitting the constructed 3D dense morphable shape model into the reconstructed 3D vertices. Also, the proposed method makes a cylindrical texture map using 2D face image sequence. Finally, the proposed method generates a 3D face model by rendering the 3D dense face shape model using the cylindrical texture map. Through building processes of 3D face model by the proposed method, it is shown that the proposed method is relatively easy, fast and precise.

Keywords: 3D Face Modeling, 3D Morphable Shape Model, 3DReconstruction, 3D Correspondence.

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Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy

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Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.

Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.

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Authors: S.G. Srivani, Chandrasekhar Reddy Atla, K.P.Vittal

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This paper presents the development of adaptive distance relay for protection of parallel transmission line with mutual coupling. The proposed adaptive relay, automatically adjusts its operation based on the acquisition of the data from distance relay of adjacent line and status of adjacent line from line circuit breaker IED (Intelligent Electronic Device). The zero sequence current of the adjacent parallel transmission line is used to compute zero sequence current ratio and the mutual coupling effect is fully compensated. The relay adapts to changing circumstances, like failure in communication from other relays and non - availability of adjacent transmission line. The performance of the proposed adaptive relay is tested using steady state and dynamic test procedures. The fault transients are obtained by simulating a realistic parallel transmission line system with mutual coupling effect in PSCAD. The evaluation test results show the efficacy of adaptive distance relay over the conventional distance relay.

Keywords: Adaptive relaying, distance measurement, mutualcoupling, quadrilateral trip characteristic, zones of protection.

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Authors: Ovidiu Domşa, Nicolae Bold

Abstract:

Using Information and Communication Technologies (ICT) notions in education and three basic processes of education (teaching, learning and assessment) can bring benefits to the pupils and the professional development of teachers. In this matter, we refer to these notions as concepts taken from the informatics area and apply them to the domain of education. These notions refer to genetic algorithms and arborescent structures, used in the specific process of assessment or evaluation. This paper uses these kinds of notions to generate subtrees from a main tree of tests related between them by their degree of difficulty. These subtrees must contain the highest number of connections between the nodes and the lowest number of missing edges (which are subtrees of the main tree) and, in the particular case of the non-existence of a subtree with no missing edges, the subtrees which have the lowest (minimal) number of missing edges between the nodes, where a node is a test and an edge is a direct connection between two tests which differs by one degree of difficulty. The subtrees are represented as sequences. The tests are the same (a number coding a test represents that test in every sequence) and they are reused for each sequence of tests.

Keywords: Chromosome, genetic algorithm, subtree, test.

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Authors: Khampheth Bounnady, Boontee Kruatrachue, Somkiat Wangsiripitak

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This paper proposed high level feature for online Lao handwritten recognition. This feature must be high level enough so that the feature is not change when characters are written by different persons at different speed and different proportion (shorter or longer stroke, head, tail, loop, curve). In this high level feature, a character is divided in to sequence of curve segments where a segment start where curve reverse rotation (counter clockwise and clockwise). In each segment, following features are gathered cumulative change in direction of curve (- for clockwise), cumulative curve length, cumulative length of left to right, right to left, top to bottom and bottom to top ( cumulative change in X and Y axis of segment). This feature is simple yet robust for high accuracy recognition. The feature can be gather from parsing the original time sampling sequence X, Y point of the pen location without re-sampling. We also experiment on other segmentation point such as the maximum curvature point which was widely used by other researcher. Experiments results show that the recognition rates are at 94.62% in comparing to using maximum curvature point 75.07%. This is due to a lot of variations of turning points in handwritten.

Keywords: Handwritten feature, chain code, Lao handwritten recognition.

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Authors: İsmail Hakkı Kalyoncu, Nilda Ersoy, Ayşe Yalcın Elidemir, Muhammed Emin Karalı

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Gilaburu (Viburnum opulus L.) grown naturally in Anatolia. In this study, some physico-chemical (sugar, acid, protein, crude fat, crude fiber, ash etc.) characteristics and mineral composition of Gilaburu fruit have been investigated. The length, width, thickness, weight, total soluble solid, protein, crude ash, crude fiber and crude oil of fruit were found to be 1.12 cm, 1.58 cm, 1.87 cm, 0.87 g, 14.73 %, 0.2 %, 0.11 %, 6.56 % and 0.4 %, respectively. The seed of fruit mean weight, length, width and thickness were determinated as 0.08 g, 7.76 cm, 7.67 cm and 1.66, respectively. In addition 27 mineral elements (Al, Mg, Na, Ba, Ca, Ni, Cd, P, Cr, Pb, S, Cu, Se, Fe, K, Sr, Li, Z, V, Ag, Bi, Co, Mn, B, Ga, In, Ti) were analyzed. Gilaburu (Viburnum opulus L.) fruit was richest in potassium (10764.764 ppm), Mg (1289.088 ppm) and P (1304.169 ppm).

Keywords: Gilaburu (Viburnum opulus L.), nutritional properties, physico-chemical properties.

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Authors: WooYoung Jung, HoYoung Son

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This study presented to reduce earthquake damage and emergency rehabilitation of critical structures such as schools, hightech factories, and hospitals due to strong ground motions associated with climate changes. Regarding recent trend, a strong earthquake causes serious damage to critical structures and then the critical structure might be influenced by sequence aftershocks (or tsunami) due to fault plane adjustments. Therefore, in order to improve seismic performance of critical structures, retrofitted or strengthening study of the structures under aftershocks sequence after emergency rehabilitation of the structures subjected to strong earthquakes is widely carried out. Consequently, this study used composite material for emergency rehabilitation of the structure rather than concrete and steel materials because of high strength and stiffness, lightweight, rapid manufacturing, and dynamic performance. Also, this study was to develop or improve the seismic performance or seismic retrofit of critical structures subjected to strong ground motions and earthquake aftershocks, by utilizing GFRP-Corrugated Infill Panels (GCIP).

Keywords: Composite material, GFRP, Infill Panel, Aftershock, Seismic Retrofitting.

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Authors: Homa Torabizadeh, Mohaddeseh Mikani

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Inulinase from Aspergillus niger was covalently immobilized on magnetic nanoparticles (MNPs/Fe₃O₄) covered with soy protein isolate (SPI/Fe₃O₄) functionalized by bovine serum albumin (BSA) nanoparticles. MNPs are promising enzyme carriers because they separate easily under external magnetic fields and have enhanced immobilized enzyme reusability. As MNPs aggregate simply, surface coating strategy was employed. SPI functionalized by BSA was a suitable candidate for nanomagnetite coating due to its superior biocompatibility and hydrophilicity. Fe₃O₄@SPI-BSA nanoparticles were synthesized as a novel carrier with narrow particle size distribution. Step by step fabrication monitoring of Fe₃O₄@SPI-BSA nanoparticles was performed using field emission scanning electron microscopy and dynamic light scattering. The results illustrated that nanomagnetite with the spherical morphology was well monodispersed with the diameter of about 35 nm. The average size of the SPI-BSA nanoparticles was 80 to 90 nm, and their zeta potential was around −34 mV. Finally, the mean diameter of fabricated Fe₃O₄@SPI-BSA NPs was less than 120 nm. Inulinase enzyme from Aspergillus niger was covalently immobilized through gluteraldehyde on Fe₃O₄@SPI-BSA nanoparticles successfully. Fourier transform infrared spectra and field emission scanning electron microscopy images provided sufficient proof for the enzyme immobilization on the nanoparticles with 80% enzyme loading.

Keywords: High fructose syrup, inulinase immobilization, functionalized magnetic nanoparticles, soy protein isolate.

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Authors: W. Abu Rayyan, A. Singh, A. M. Al-Jaafreh, W. Abu Dayyih, M. Bustami, S. Salem, N. Seder, K. Schröppel

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Hyphal growth and the transcriptional regulation to the host environment are key issues during the pathogenesis of C. albicans. Tec1p is the C. albicans homolog of a TEA transcription factor family, which share a conserved DNA-binding TEA domain in their N-terminal. In order to define a structure-function relationship of the C. albicans Tec1p protein, we constructed several mutations on the N terminal, C terminal or in the TEA binding domain itself by homologous recombination technology. The modifications in the open reading frame of TEC1 were tested for reconstitution of the morphogenetic development of the tec1/tec1 mutant strain CaAS12. Mutation in the TEA consensus sequence did not confer transition to hyphae whereas the reconstitution of the full-length Tec1p has reconstituted hyphal development. A deletion in one of glutamine-rich regions either in the Tec1p N-terminal or the C-terminal in regions of 53-212 or 637–744 aa, respectively, did not restore morphological development in mutant CaAS12 strain. Whereas, the reconstitution with Tec1p mutants other than the glutamate-rich region has restored the morphogenetic switch. Additionally, the deletion of the glutamine-rich region has attenuated the invasive growth and the heat shock resistance of C. albicans. In conclusion, we show that a glutamine-rich region of Tec1p is essential for the hyphal development and mediating adaptation to the host environment of C. albicans.

Keywords: Candida albicans, transcription factor, TEA domain, hyphal formation, morphogenetic development, TEC1, Tet-induced.

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Authors: Fatima Zohra Bissaad, Farid Bounaceur, Nassima Behidj, Nadjiba Chebouti, Fatma Halouane, Bahia Doumandji-Mitiche

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Effect of Beauveria bassiana and Metarhizium anisopliae var. acridum on the 5^th instar nymphs of Schistocerca gregaria was studied in the laboratory. Infection by these both entomopathogenic fungi caused reduction in the hemolymph total protein. The average amounts of total proteins were 2.3, 2.07, 2.09 µg/100 ml of haemolymph in the control and M. anisopliae var. acridum, and B. bassiana based-treatments, respectively. Three types of haemocytes were recognized and identified as prohaemocytes, plasmatocytes and granulocytes. The treatment caused significant reduction in the total haemocyte count and in each haemocyte type on the 9^th day after its application.

Keywords: Beauveria bassiana, haemolymph picture, haemolymph protein, Metarhizium anisopliae var. acridum, Schistocerca gregaria.

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Authors: John N. Ellinas

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In this paper, a new reversible watermarking method is presented that reduces the size of a stereoscopic image sequence while keeping its content visible. The proposed technique embeds the residuals of the right frames to the corresponding frames of the left sequence, halving the total capacity. The residual frames may result in after a disparity compensated procedure between the two video streams or by a joint motion and disparity compensation. The residuals are usually lossy compressed before embedding because of the limited embedding capacity of the left frames. The watermarked frames are visible at a high quality and at any instant the stereoscopic video may be recovered by an inverse process. In fact, the left frames may be exactly recovered whereas the right ones are slightly distorted as the residuals are not embedded intact. The employed embedding method reorders the left frame into an array of consecutive pixel pairs and embeds a number of bits according to their intensity difference. In this way, it hides a number of bits in intensity smooth areas and most of the data in textured areas where resulting distortions are less visible. The experimental evaluation demonstrates that the proposed scheme is quite effective.

Keywords: Stereoscopic video, Reversible watermarking, Disparity compensation, Joint compensation

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Authors: Yin Jie, Qin Qiming, Yin Yong

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As a tool for human spatial cognition and thinking, the map has been playing an important role. Maps are perhaps as fundamental to society as language and the written word. Economic and social development requires extensive and in-depth understanding of their own living environment, from the scope of the overall global to urban housing. This has brought unprecedented opportunities and challenges for traditional cartography . This paper first proposed the concept of scaleless-map and its basic characteristics, through the analysis of the existing multi-scale representation techniques. Then some strategies are presented for automated mapping compilation. Taking into account the demand of automated map compilation, detailed proposed the software - WJ workstation must have four technical features, which are generalization operators, symbol primitives, dynamically annotation and mapping process template. This paper provides a more systematic new idea and solution to improve the intelligence and automation of the scaleless cartography.

Keywords: scaleless-map, strategy, map generalization, automated compilation, WJ workstation.

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Authors: Ziad Abdallah, Mohamad Oueidat, Ali El-Zaart

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Image Multi-label Classification (IMC) assigns a label or a set of labels to an image. The big demand for image annotation and archiving in the web attracts the researchers to develop many algorithms for this application domain. The existing techniques for IMC have two drawbacks: The description of the elementary characteristics from the image and the correlation between labels are not taken into account. In this paper, we present an algorithm (MIML-HOGLPP), which simultaneously handles these limitations. The algorithm uses the histogram of gradients as feature descriptor. It applies the Label Priority Power-set as multi-label transformation to solve the problem of label correlation. The experiment shows that the results of MIML-HOGLPP are better in terms of some of the evaluation metrics comparing with the two existing techniques.

Keywords: Data mining, information retrieval system, multi-label, problem transformation, histogram of gradients.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: Tzong Yuan Wu, Sheng Kuo Hsieh, Tzyy Rong Jinn

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Fip-gts, an immunomodulatory protein purified from Ganoderma tsugae, has been reported to possess therapeutic effects in the treatment of cancer and autoimmune disease. For medicinal application, a recombinant Fip-gts was successfully expressed and purified in Sf21 insect cells by our previously work. It is important to evaluate the immunomodulatory activity of the rFip-gts. To assess the immunomodulatory potential of rFip-gts, the T lymphocytes of murine splenocytes were used in the present study. Results revealed that rFip-gts induced cellular aggregation formation. Additionally, the expression of IL-2 and IFN-r were up-regulated after the treatment of rFip-gts, and a corresponding increased production of IL-2 and IFN-r in a dose-dependent manner. The results showed that rFip-gts has an immunomodulatory activity in inducing Th1 lymphocytes from murine splenocytes released IL-2 and IFN-γ, thus suggest that rFip-gts may have therapeutic potential in vivo as an immune modulator.

Keywords: Fungal immunomodulatory protein, Ganodermatsugae, Interleukin 2, Interferon γ, Lingzhi.

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Authors: Yuanqing Li, Changyi Lei, Zhaopeng Xue, Zhuo Zheng, Yanbo Long

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In agricultural production and breeding, implementing automatic picking robot in orchard farming to reduce human labour and error is challenging. The core function of it is automatic identification based on machine vision. This paper focuses on apple detection and counting in orchards and implements several deep learning methods. Extensive datasets are used and a semi-automatic annotation method is proposed. The proposed deep learning models are in state-of-the-art YOLO family. In view of the essence of the models with various backbones, a multi-dimensional comparison in details is made in terms of counting accuracy, mAP and model memory, laying the foundation for realising automatic precision agriculture.

Keywords: Agricultural object detection, Deep learning, machine vision, YOLO family.

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Authors: Almas Tayebi, Tayeb Saki Nejad, Alireza Shoukofar

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The trial in the city, located 170 kilometers from the Iranian city of Ahvaz was Omidiyeh. The main factor in this project includes 4 levels in control (without hormones), use of hormones in the seed, vegetative and flowering stage respectively. And sub-plots included 3 varieties of vetch in three levels, with local names, was the jewel in the study of light and Auxin in the vegetative and reproductive different times in different varieties of vetch was investigated. This test has been taken in the plots in a randomized complete block with four replications. In order to study the effects of the hormone Auxin in the growth stages (seed, vegetative and flowering) to control (no hormone Auxin) on three local varieties of vetch, the essence of light and plant height, number of pods per plant, seed number The pods, seeds per plant, grain weight, grain yield, plant dry weight and protein content were measured. Among the vetch varieties for plant height, number of pods per plant, a seed per plant, grain weight, grain yield, and plant dry weight and protein levels of 1 percent of plant and seed number per pod per plant at 5% level of There was no significant difference. Interactions for grain yield per plant, grain yield and protein levels of 1 percent and the number of seeds per pod and seed weight are significant differences in levels 5 and plant height and plant dry weight of the interaction were INFLUENCE There was no significant difference in them.

Keywords: Auxin hormones, various periods of growth, production components, vetch

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Authors: P. Grasgruber, J. Cacek, S. Hřebíčková

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The purpose of this study was to test the reliability of various standards that assess the quality of proteins via the “amino-acid score” and serve as a nutritional guideline for both children and adults. The height of young men in 42 European countries, Australia, New Zealand and USA was compared with the average consumption of food (after FAOSTAT, 2009) and a subsequent statistical analysis identified types of food with the most pronounced effect on physical growth. The results show that milk products and pork meat are by far the most significant nutritional factors in this regard. Cereals, vegetables and especially wheat played a strongly negative role. The results generally agreed best with the amino-acid score of proteins according to the standard of FAO 1985. In our opinion, the new standard of FAO 2007 underestimates the importance of tryptophan, which should provoke a debate about new modifications of the FAO guidelines.

Keywords: Protein quality, amino-acid score, physical growth, male height.

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Authors: C. Yaiprasert, K. Jaroensutasinee, M. Jaroensutasinee

Abstract:

To develop a process of extracting pixel values over the using of satellite remote sensing image data in Thailand. It is a very important and effective method of forecasting rainfall. This paper presents an approach for forecasting a possible rainfall area based on pixel values from remote sensing satellite images. First, a method uses an automatic extraction process of the pixel value data from the satellite image sequence. Then, a data process is designed to enable the inference of correlations between pixel value and possible rainfall occurrences. The result, when we have a high averaged pixel value of daily water vapor data, we will also have a high amount of daily rainfall. This suggests that the amount of averaged pixel values can be used as an indicator of raining events. There are some positive associations between pixel values of daily water vapor images and the amount of daily rainfall at each rain-gauge station throughout Thailand. The proposed approach was proven to be a helpful manual for rainfall forecasting from meteorologists by which using automated analyzing and interpreting process of meteorological remote sensing data.

Keywords: Pixel values, satellite image, water vapor, rainfall, image processing.

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Authors: N.Subramanian, U.K.Misra

Abstract:

The aim of this paper is to introduce and study a new concept of strong double χ2 (M,A, Δ) of fuzzy numbers and also some properties of the resulting sequence spaces of fuzzy numbers were examined.

Keywords: Modulus function, fuzzy number, metric space.

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Authors: Abdesselem Dakhli, Wajdi Bellil, Chokri Ben Amar

Abstract:

DNA Barcode provides good sources of needed information to classify living species. The classification problem has to be supported with reliable methods and algorithms. To analyze species regions or entire genomes, it becomes necessary to use the similarity sequence methods. A large set of sequences can be simultaneously compared using Multiple Sequence Alignment which is known to be NP-complete. However, all the used methods are still computationally very expensive and require significant computational infrastructure. Our goal is to build predictive models that are highly accurate and interpretable. In fact, our method permits to avoid the complex problem of form and structure in different classes of organisms. The empirical data and their classification performances are compared with other methods. Evenly, in this study, we present our system which is consisted of three phases. The first one, is called transformation, is composed of three sub steps; Electron-Ion Interaction Pseudopotential (EIIP) for the codification of DNA Barcodes, Fourier Transform and Power Spectrum Signal Processing. Moreover, the second phase step is an approximation; it is empowered by the use of Multi Library Wavelet Neural Networks (MLWNN). Finally, the third one, is called the classification of DNA Barcodes, is realized by applying the algorithm of hierarchical classification.

Keywords: DNA Barcode, Electron-Ion Interaction Pseudopotential, Multi Library Wavelet Neural Networks.

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Authors: A.C. Duarte, C.I.L. Justino, K. Duarte, A.C. Freitas, R. Pereira, P. Chaves, P. Bettencourt, S. Cardoso, T.A.P. Rocha-Santos

Abstract:

This paper aims at overviewing the topics of a research project (CARDIOSENSOR) on the field of health sciences (biomaterials and biomedical engineering). The project has focused on the development of a nanosensor for the assessment of the risk of cardiovascular diseases by the monitoring of C-reactive protein (CRP), which has been currently considered as the best validated inflammatory biomarker associated to cardiovascular diseases. The project involves tasks such as: 1) the development of sensor devices based on field effect transistors (FET): assembly, optimization and validation; 2) application of sensors to the detection of CRP in standard solutions and comparison with enzyme-linked immunosorbent assay (ELISA); and 3) application of sensors to real samples such as blood and saliva and evaluation of their ability to predict the risk of cardiovascular disease.

Keywords: Carbon nanotubes field effect transistors, cardiovascular diseases, C-reactive protein, sensor.

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Authors: Achraf El Allali, John R. Rose

Abstract:

A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

Abstract:

Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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