Search results for: phylogenetic tree

Authors: C. I. Boshoff, S. Steenkamp-Jonker

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Cystic echinococcosis (CE), caused by Echinococcus granulosus is an important parasitic infection in livestock worldwide, with severe zoonotic potential. It is important to understand the variability of Echinococcus granulosus, as genotype variations may influence lifecycle patterns, development rate, and transmission. Cystic Echinococcus samples were collected from domestic animals in Eastern Cape Province, South Africa. A molecular study was performed on 14 hydatid cysts obtained from caprine, ovine and bovine livers in order to determine the Echinococcus granulosus strain present in these hosts. The sequencing of the mitochondrial cytochrome C oxidase subunit I (coxI) gene of the hydatid cysts produced sequences of 400 bp for each sample analysed. These sequences were aligned with those present in GenBank and a phylogenetic tree was constructed. Based on coxI genotype the isolates could be grouped into E. granulosus sensu stricto. The findings of the study represent a pilot molecular study on Echinococcus from domestic animals undertaken in South Africa.

Keywords: Echinococcus granulosus, genotypes, livestock, South Africa

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Authors: K. Umbleja, M. Ichino, H. Yaguchi

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In this paper, we propose a coloring method for multivariate data visualization by using parallel coordinates based on dissimilarity and tree structure information gathered during hierarchical clustering. The proposed method is an extension for proximity-based coloring that suffers from a few undesired side effects if hierarchical tree structure is not balanced tree. We describe the algorithm by assigning colors based on dissimilarity information, show the application of proposed method on three commonly used datasets, and compare the results with proximity-based coloring. We found our proposed method to be especially beneficial for symbolic data visualization where many individual objects have already been aggregated into a single symbolic object.

Keywords: data visualization, dissimilarity-based coloring, proximity-based coloring, symbolic data

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Authors: Houman Tamaddon, Mehrdad Behnia, Masud Behnia

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An accurate study of blood flow is associated with an accurate vascular pattern and geometrical properties of the organ of interest. Due to the complexity of vascular networks and poor accessibility in vivo, it is challenging to reconstruct the entire vasculature of any organ experimentally. The objective of this study is to introduce an innovative approach for the reconstruction of a full vascular tree from available morphometric data. Our method consists of implementing morphometric data on those parts of the vascular tree that are smaller than the resolution of medical imaging methods. This technique reconstructs the entire arterial tree down to the capillaries. Vessels greater than 2 mm are obtained from direct volume and surface analysis using contrast enhanced computed tomography (CT). Vessels smaller than 2mm are reconstructed from available morphometric and distensibility data and rearranged by applying Murray’s Laws. Implementation of morphometric data to reconstruct the branching pattern and applying Murray’s Laws to every vessel bifurcation simultaneously, lead to an accurate vascular tree reconstruction. The reconstruction algorithm generates full arterial tree topography down to the first capillary bifurcation. Geometry of each order of the vascular tree is generated separately to minimize the construction and simulation time. The node-to-node connectivity along with the diameter and length of every vessel segment is established and order numbers, according to the diameter-defined Strahler system, are assigned. During the simulation, we used the averaged flow rate for each order to predict the pressure drop and once the pressure drop is predicted, the flow rate is corrected to match the computed pressure drop for each vessel. The final results for 3 cardiac cycles is presented and compared to the clinical data.

Keywords: blood flow, morphometric data, vascular tree, Strahler ordering system

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Authors: J. K. Alhassan, B. Attah, S. Misra

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Human beings have the ability to make logical decisions. Although human decision - making is often optimal, it is insufficient when huge amount of data is to be classified. medical dataset is a vital ingredient used in predicting patients health condition. In other to have the best prediction, there calls for most suitable machine learning algorithms. This work compared the performance of Artificial Neural Network (ANN) and Decision Tree Algorithms (DTA) as regards to some performance metrics using diabetes data. The evaluations was done using weka software and found out that DTA performed better than ANN. Multilayer Perceptron (MLP) and Radial Basis Function (RBF) were the two algorithms used for ANN, while RegTree and LADTree algorithms were the DTA models used. The Root Mean Squared Error (RMSE) of MLP is 0.3913,that of RBF is 0.3625, that of RepTree is 0.3174 and that of LADTree is 0.3206 respectively.

Keywords: artificial neural network, classification, decision tree algorithms, diabetes mellitus

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Authors: Rajagopal Kavitha, Van Lun Low, Mohd Sofian-Azirun, Chee Dhang Chen, Mohd Yusof Farida Zuraina, Mohd Salleh Ahmad Firdaus, Navaratnam Shanti, Abdul Haiyee Zaibunnisa

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This study investigated the hidden genetic lineages in the oriental latrine fly Chrysomya megacephala (Fabricius) across four states (i.e., Johore, Pahang, Perak and Selangor) and a federal territory (i.e., Kuala Lumpur) in Malaysia using Cytochrome b (Cyt b) genetic marker. The Cyt b phylogenetic tree and haplotype network revealed three distinct genetic lineages of Ch. megacephala. Lineage A, the basal clade was restricted to flies that originated from Kuala Lumpur and Selangor, while Lineages B and C, comprised of flies from all studied populations. An overlap of the three genetically divergent groups of Ch. megacephala was observed. However, the flies from both Kuala Lumpur and Selangor populations consisted of three different lineages, indicating that they are genetically diverse compared to those from Pahang, Perak and Johore.

Keywords: forensic entomology, calliphoridae, mitochondrial DNA, cryptic lineage

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Authors: Lemar Blake, Chris Oura, Ayanna C. N. Phillips Savage

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Improved DNA sequencing technology has greatly enhanced bacterial identification, especially for organisms that are difficult to culture. Mycobacteriosis with consistent hyphema, bilateral exophthalmia, open mouth gape and ocular lesions, were observed in various fish populations at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Objective: To identify the species of Mycobacterium that is affecting aquarium fish at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Method: A total of 13 fish samples were collected and analyzed via: Ziehl-Neelsen, conventional polymerase chain reaction (PCR) and real-time PCR. These tests were carried out simultaneously for confirmation. The following combination of conventional primers: 16s rRNA (564 bp), rpoB (396 bp), sod (408 bp) were used. Concatenation of the gene fragments was carried out to phylogenetically classify the organism. Results: Acid fast non-branching bacilli were detected in all samples from homogenized internal organs. All 13 acid fast samples were positive for Mycobacterium via real-time PCR. Partial gene sequences using all three primer sets were obtained from two samples and demonstrated a novel strain. A strain 99% related to Mycobacterium marinum was also confirmed in one sample, using 16srRNA and rpoB genes. The two novel strains were clustered with the rapid growers and strains that are known to affect humans. Conclusions: Phylogenetic analysis demonstrated two novel Mycobacterium strains with the potential of being zoonotic and one strain 99% related to Mycobacterium marinum.

Keywords: polymerase chain reaction, phylogenetic, DNA sequencing, zoonotic

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Authors: Khin Thanda Win, Chunying Zhang, Sanghyeob Lee

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Mildew resistance locus o (Mlo), a plant-specific gene family with seven-transmembrane (TM), plays an important role in plant resistance to powdery mildew (PM). PM caused by Podosphaera xanthii is a widespread plant disease and probably represents the major fungal threat for many Cucurbits. The recent Cucurbita maxima genome sequence data provides an opportunity to identify and characterize the MLO gene family in this species. Total twenty genes (designated CmaMLO1 through CmaMLO20) have been identified by using an in silico cloning method with the MLO gene sequences of Cucumis sativus, Cucumis melo, Citrullus lanatus and Cucurbita pepo as probes. These CmaMLOs were evenly distributed on 15 chromosomes of 20 C. maxima chromosomes without any obvious clustering. Multiple sequence alignment showed that the common structural features of MLO gene family, such as TM domains, a calmodulin-binding domain and 30 important amino acid residues for MLO function, were well conserved. Phylogenetic analysis of the CmaMLO genes and other plant species reveals seven different clades (I through VII) and only clade IV is specific to monocots (rice, barley, and wheat). Phylogenetic and structural analyses provided preliminary evidence that five genes belonged to clade V could be the susceptibility genes which may play the importance role in PM resistance. This study is the first comprehensive report on MLO genes in C. maxima to our knowledge. These findings will facilitate the functional analysis of the MLOs related to PM susceptibility and are valuable resources for the development of disease resistance in pumpkin.

Keywords: Mildew resistance locus o (Mlo), powdery mildew, phylogenetic relationship, susceptibility genes

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Authors: Ayesha Imtiaz, Darlina Md. Naim

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Family Nemipteridae is among the most abundantly distributed family in Malaysian fish markets due to its high contribution to landing sites of Malaysia. Using an advanced molecular approach that used two mitochondrial (Cytochrome oxidase c I and Cytochrome oxidase b) and one nuclear gene (Recombination activating gene, RAGI) to expose cryptic diversity and phylogenetic relationships among commercially important species of family Nemipteridae. Our research covered all genera (including 31 species out total 45 species) of family Nemipteridae, distributed in Malaysia. We also found certain type of geographical barriers in the South China sea that reduces dispersal and stops a few species to intermix. Northside of the South China Sea (near Vietnam) does not allow genetic diversity to mix with the Southern side of the South China sea (Sarawak) and reduces dispersal. Straits of Malacca reduce the intermixing genetic diversity of South China Sea and the Indian Ocean.

Keywords: Nemipteridae, RAG I, south east Asia, Malaysia

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Authors: Aswandi Anas Husin, Cut Rizlani Kholibrina

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Harvesting camphor resin has been carried out since the beginning of civilization on the west coast of Sumatra. Oil or crystals that containing borneol are harvested from the camphor tree (Dryobalanops aromatica). Non-timber forest products are utilized for the manufacture of fragrances, antiseptics, anti-inflammatory, analgesic as well as effective for the treatment of blocked arteries. Based on exploration on the west coast of Sumatra, these endemic tree species were found remaining growing in groups on small spots in the lowlands to the hills. Some populations are found at an altitude of 700 meters above sea level in Kadabuhan, Jongkong and Sultan Daulat in Subulussalam district, Singkohor and Lake Paris in Aceh Singkil district, and Sirandorung and Manduamas in the north of Barus, Central Tapanuli district. These multi-purpose tree species was also identified as being able to adapt to the Singkil Peat Swamp. The decline in tree population has a direct impact on reducing their productivity. Conventionally, the crystals are harvested by cutting and splitting the stem into wooden blocks. In this way about 1.5-2.5 kg of crystals are obtained with various qualities. Camphor retrieval can also be done by making a notch on a standing tree trunk and collecting liquid resin (ombil) that is removed from the injured resin channel. Twigs and leaves also contain borneol. The aromatic content in this section opens opportunities for the supply of borneol through the distillation process. Vegetative propagation technology is needed to overcome the limitations of available seeds. This breeding strategy for vulnerable species starts with gathering genetic material from various provenances which are then used to support the provision of basic populations, breeding populations, multiplication populations and production populations for extensive development of camphor tree plantations

Keywords: camphor, conservation, natural borneol, productivity, vulnerable species

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Authors: Dharell B. Siano, Wendy C. Mateo, Victorino T. Taylan, Francisco D. Cuaresma

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Biofuel is one of the renewable energy sources adapted by the Philippine government in order to lessen the dependency on foreign fuel and to reduce carbon dioxide emissions. Rain tree pods were seen to be a promising source of bioethanol since it contains significant amount of fermentable sugars. The study was conducted to establish the complete procedure in processing rain tree pods for village level hydrous bioethanol production. Production processes were done for village level hydrous bioethanol production from collection, drying, storage, shredding, dilution, extraction, fermentation, and distillation. The feedstock was sundried, and moisture content was determined at a range of 20% to 26% prior to storage. Dilution ratio was 1:1.25 (1 kg of pods = 1.25 L of water) and after extraction process yielded a sugar concentration of 22 ⁰Bx to 24 ⁰Bx. The dilution period was three hours. After three hours of diluting the samples, the juice was extracted using extractor with a capacity of 64.10 L/hour. 150 L of rain tree pods juice was extracted and subjected to fermentation process using a village level anaerobic bioreactor. Fermentation with yeast (Saccharomyces cerevisiae) can fasten up the process, thus producing more ethanol at a shorter period of time; however, without yeast fermentation, it also produces ethanol at lower volume with slower fermentation process. Distillation of 150 L of fermented broth was done for six hours at 85 °C to 95 °C temperature (feedstock) and 74 °C to 95 °C temperature of the column head (vapor state of ethanol). The highest volume of ethanol recovered was established at with yeast fermentation at five-day duration with a value of 14.89 L and lowest actual ethanol content was found at without yeast fermentation at three-day duration having a value of 11.63 L. In general, the results suggested that rain tree pods had a very good potential as feedstock for bioethanol production. Fermentation of rain tree pods juice can be done with yeast and without yeast.

Keywords: fermentation, hydrous bioethanol, fermentation, rain tree pods, village level

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Authors: Shreya Pare, Parvin Akhter

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Remotely sensing image classification becomes a very challenging task owing to the high dimensionality of hyperspectral images. The pixel-wise classification methods fail to take the spatial structure information of an image. Therefore, to improve the performance of classification, spatial information can be integrated into the classification process. In this paper, the multilevel thresholding algorithm based on a modified fuzzy entropy function is used to perform the segmentation of hyperspectral images. The fuzzy parameters of the MFE function have been optimized by using a new meta-heuristic algorithm based on the Tree-Search algorithm. The segmented image is classified by a large distribution machine (LDM) classifier. Experimental results are shown on a hyperspectral image dataset. The experimental outputs indicate that the proposed technique (MFE-TSA-LDM) achieves much higher classification accuracy for hyperspectral images when compared to state-of-art classification techniques. The proposed algorithm provides accurate segmentation and classification maps, thus becoming more suitable for image classification with large spatial structures.

Keywords: classification, hyperspectral images, large distribution margin, modified fuzzy entropy function, multilevel thresholding, tree search algorithm, hyperspectral image classification using tree search algorithm

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Authors: Yaojun Wang, Yaoqing Wang

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Stock selection is an important decision-making problem. Many machine learning and data mining technologies are employed to build automatic stock-selection system. A profitable stock-selection system should consider the stock’s investment value and the market timing. In this paper, we present a hybrid system including both engage for stock selection. This system uses a case-based reasoning (CBR) model to execute the stock classification, uses a decision-tree model to help with market timing and stock selection. The experiments show that the performance of this hybrid system is better than that of other techniques regarding to the classification accuracy, the average return and the Sharpe ratio.

Keywords: case-based reasoning, decision tree, stock selection, machine learning

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Authors: Wiwin Tyas Istikowati, Futoshi Ishiguri, Haruna Aisho, Budi Sutiya, Imam Wahyudi, Kazuya Iizuka, Shinso Yokota

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The objective of this study was to investigate the anatomical characteristics of three native fast-growing species, terap (Artocarpus elasticus Reinw. ex Blume), medang (Neolitsea latifolia (Blume) S. Moore), and balik angin (Alphitonia excelsa (Fenzel) Reissek ex Benth) growing in the secondary forest in South Kalimantan, Indonesia for evaluating the possibility of tree breeding for wood quality. Cell lengths were investigated for 5 trees in each species at several different height positions (1.0, 3.0, 5.0, 7.0, 9.0, and 11.0 m above the ground). The mean values of fiber and vessel element lengths in terap, medang, and balik angin were 1.52 and 0.44, 1.16 and 0.53, and 1.02 and 0.49 mm, respectively. Fiber length in terap and balik angin gradually increased from pith to bark, whereas it increased up to 2 cm and then became nearly constant to the bark in medang. Vessel element length was almost constant from pith to bark in terap and balik angin, while slightly increased from pith to bark in medang. Fiber length in terap has a fluctuation pattern from ground level to top of the tree. It decreased up to 3 m above the ground, increased up to 5 m, and then decreased to the top of the tree. On the other hand, vessel element length slightly increased up to 5 m above the ground, and then decreased to the top of the tree. Both fiber and vessel element lengths in medang were almost constant from ground level to top of the tree, whereas decreased from ground level to top of the tree in balik angin. Significant difference at 1% level among trees was found in both fiber and vessel element length in both radial and longitudinal directions for terap and medang. Based on obtained results, it is concluded that the wood quality in fiber and vessel element lengths of terap and medang can be improved by tree breeding programs.

Keywords: anatomical properties, fiber length, vessel elements length, fast-growing species

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Authors: M. Khordadmehr, V. R. Ranjbar, R. Norouzi, M. Zeinoddin

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Coccidiosis is recognized as a serious parasitic disease problem limiting quail industry recently. But the data on incidence, clinical signs, species of coccidia and pathological changes in Japanese quail are rare, especially in Iran in spite of the significant improvement of commercial quail breeding in this country in recent decades. Therefore, in the present paper was studied natural infection of quail coccidiosis in three commercial rearing farms with 80% morbidity and 3% mortality rate. For this purpose, fecal sample, oocyst examination, and morphological study were performed beside necropsy, histopathology, and PCR to confirm the diagnosis. In the affected birds, clinical signs included brown diarrhea, weakness, and pale face. In the fecal examination, three species of the genus Eimeria were identified including E. uzura, E. bateri, and E. tsunodai. At necropsy, the main gross lesions were edema, congestion and small blood spots in the small intestine. In histopathologic examination, endogenous stages of the parasites associated with hyperplasia of the intestinal glands, mild congestion, infiltration of mononuclear cells, and edema were observed in the intestine. The molecular study using BSEF and BSER specific primers confirmed the presence of the genus Eimeria in the affected birds. Interestingly, phylogenetic analysis showed relatively high bootstrap values in Japanese quail Eimeria with E. acervuline and E. maxima strains in the chicken. The present study is the first phylogenetic findings on Eimeria of quail which could be valuable for further research on Japanese quail coccidiosis.

Keywords: coccidiosis, Japanese Quail, pathomorphology, phylogenetic analysis

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Authors: Federico Hahn Schlam, Fermín Martínez Solís

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Leaf-cutting ants (Atta cephalotes) forage from mango tree leaves and flowers to feed their colony. Farmers find it difficult to control ants due to the great quantity of trees grown in commercial orchards. In this article, IoT can support farmers for ant detection in real time, as production losses can be considered of 324 US per tree.A wireless sensor network, WSN, was developed to warn the farmer from ant presence in trees during a night. Mango trees were gathered into groups of 9 trees, where the central tree holds the master microcontroller, and the other eight trees presented slave microcontrollers (nodes). At each node, anemitter diode-photodiode unitdetects ants climbing up. A capacitor is chargedand discharged after being sampled every ten minutes. The system usesBLE (Bluetooth Low Energy) to communicate between the master microcontroller by BLE.When ants were detected the number of the tree was transmitted via LoRa from the masterto the producer smartphone to warn him. In this paper, BLE, LoRa, and energy consumption were studied under variable vegetation in the orchard. During 2018, 19 trees were attacked by ants, and ants fed 26.3% of flowers and 73.7% of leaves.

Keywords: BLE, atta cephalotes, LoRa, WSN-smartphone, energy consumption

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Authors: Shokoufeh Abrisham, Seyed Mahmoud Hossieni, Elham Pishbin

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In this paper, a hybrid method based on the fault tree analysis (FTA) and Bayesian networks (BNs) are employed to evaluate the team performance quality of advanced cardiac life support (ACLS) procedures in emergency department. According to American Heart Association (AHA) guidelines, a category relying on staff action leading to clinical incidents and also some discussions with emergency medicine experts, a fault tree model for ACLS procedure is obtained based on the human performance. The obtained FTA model is converted into BNs, and some different scenarios are defined to demonstrate the efficiency and flexibility of the presented model of BNs. Also, a sensitivity analysis is conducted to indicate the effects of team leader presence and uncertainty knowledge of experts on the quality of ACLS. The proposed model based on BNs shows that how the results of risk analysis can be closed to reality comparing to the obtained results based on only FTA in medical procedures.

Keywords: advanced cardiac life support, fault tree analysis, Bayesian belief networks, numan performance, healthcare systems

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Authors: Mini P. Singh, Jagat Ram, Archit Kumar, Tripti Rungta, Jasmine Khurana, Amit Gupta, R. K. Ratho

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Introduction: Human adenovirus is the most common agent involved in viral conjunctivitis. The clinical manifestations vary with different serotypes. The identification of the circulating strains followed by phylogenetic analysis can be helpful in understanding the origin and transmission of the disease. The present study aimed to carry out molecular epidemiology of the adenovirus types in the patients with conjunctivitis presenting to the eye centre of a tertiary care hospital in North India. Materials and Methods: The conjunctival swabs were collected from 23 suspected adenoviral conjunctivitis patients between April-August, 2014 and transported in viral transport media. The samples were subjected to nested PCR targeting hexon gene of human adenovirus. The band size of 956bp was eluted and 8 representative positive samples were subjected to sequencing. The sequences were analyzed by using CLUSTALX2.1 and MEGA 5.1 software. Results: The male: female ratio was found to be 3.6:1. The mean age of presenting patients was 43.95 years (+17.2). Approximately 52.1% (12/23) of patients presented with bilateral involvement while 47.8% (11/23) with unilateral involvement of the eye. Human adenovirus DNA could be detected in 65.2% (15/23) of the patients. The phylogenetic analysis revealed presence of serotype 8 in 7 patients and serotype 4 in one patient. The serotype 8 sequences showed 99-100% identity with Tunisian, Indian and Japanese strains. The adenovirus serotype 4 strains had 100% identity with strains from Tunisia, China and USA. Conclusion: Human adenovirus was found be an important etiological agent for conjunctivitis in our set up. The phylogenetic analysis showed that the predominant circulating strains in our epidemic keratoconjunctivitis were serotypes 8 and 4.

Keywords: conjunctivitis, human adenovirus, molecular epidemiology, phylogenetics

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Authors: Wided Khiari, Adel Karaa

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This study aims to establish a typology of Tunisian listed firms according to their corporate governance characteristics and disclosure quality. The paper uses disclosed scores to examine corporate governance practices of Tunisian listed firms. A content analysis of 46 Tunisian listed firms from 2001 to 2010 has been carried out and a disclosure index developed to determine the level of disclosure of the companies. The disclosure quality is appreciated through the quantity and also through the nature (type) of information disclosed. Applying the decision tree method, the obtained tree diagrams provide ways to know the characteristics of a particular firm regardless of its level of disclosure. Obtained results show that the characteristics of corporate governance to achieve good quality of disclosure are not unique for all firms. These structures are not necessarily all of the recommendations of best practices, but converge towards the best combination. Indeed, in practice, there are companies which have a good quality of disclosure, but are not well-governed. However, we hope that by improving their governance system their level of disclosure may be better. These findings show, in a general way, a convergence towards the standards of corporate governance with a few exceptions related to the specificity of Tunisian listed firms and show the need for the adoption of a code for each context. These findings shed the light on corporate governance features that enhance incentives for good disclosure. It allows identifying, for each firm and in any date, corporate governance determinants of disclosure quality. More specifically, and all being equal, obtained tree makes a rule of decision for the company to know the level of disclosure based on certain characteristics of the governance strategy adopted by the latter.

Keywords: corporate governance, disclosure, decision tree, economics

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Authors: S. Ghorbani, N. I. Polushin

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Vibration during machining process is crucial since it affects cutting tool, machine, and workpiece leading to a tool wear, tool breakage, and an unacceptable surface roughness. This paper applies a nonparametric statistical method, single decision tree (SDT), to identify factors affecting on vibration in machining process. Workpiece material (AISI 1045 Steel, AA2024 Aluminum alloy, A48-class30 Gray Cast Iron), cutting tool (conventional, cutting tool with holes in toolholder, cutting tool filled up with epoxy-granite), tool overhang (41-65 mm), spindle speed (630-1000 rpm), feed rate (0.05-0.075 mm/rev) and depth of cut (0.05-0.15 mm) were used as input variables, while vibration was the output parameter. It is concluded that workpiece material is the most important parameters for natural frequency followed by cutting tool and overhang.

Keywords: cutting condition, vibration, natural frequency, decision tree, CART algorithm

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Authors: Vikas Kumar, Kailash Chandra, Kaomud Tyagi

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The insect order Thysanoptera includes small insects commonly called thrips. As insect vectors, only thrips are capable of Tospoviruses transmission (genus Tospovirus, family Bunyaviridae) affecting various crops. Currently, fifteen species of subfamily Thripinae (Thripidae) have been reported as vectors for tospoviruses. Frankliniella schultzei, which is reported as act as a vector for at least five tospovirses, have been suspected to be a species complex with more than one species. It is one of the historical unresolved issues where, two species namely, F. schultzei Trybom and F. sulphurea Schmutz were erected from South Africa and Srilanaka respectively. These two species were considered to be valid until 1968 when sulphurea was treated as colour morph (pale form) and synonymised under schultzei (dark form) However, these two have been considered as valid species by some of the thrips workers. Parallel studies have indicated that brown form of schultzei is a vector for tospoviruses while yellow form is a non-vector. However, recent studies have shown that yellow populations have also been documented as vectors. In view of all these facts, it is highly important to have a clear understanding whether these colour forms represent true species or merely different populations with different vector carrying capacities and whether there is some hidden diversity in 'Frankliniella schultzei species complex'. In this study, we aim to study the 'Frankliniella schultzei species complex' with molecular spectacles with DNA data from India and Australia and Africa. A total of fifty-five specimens was collected from diverse locations in India and Australia. We generated molecular data using partial fragments of mitochondrial cytochrome c oxidase I gene (mtCOI) and 28S rRNA gene. For COI dataset, there were seventy-four sequences, out of which data on fifty-five was generated in the current study and others were retrieved from NCBI. All the four different tree construction methods: neighbor-joining, maximum parsimony, maximum likelihood and Bayesian analysis, yielded the same tree topology and produced five cryptic species with high genetic divergence. For, rDNA, there were forty-five sequences, out of which data on thirty-nine was generated in the current study and others were retrieved from NCBI. The four tree building methods yielded four cryptic species with high bootstrap support value/posterior probability. Here we could not retrieve one cryptic species from South Africa as we could not generate data on rDNA from South Africa and sequence for rDNA from African region were not available in the database. The results of multiple species delimitation methods (barcode index numbers, automatic barcode gap discovery, general mixed Yule-coalescent, and Poisson-tree-processes) also supported the phylogenetic data and produced 5 and 4 Molecular Operational Taxonomic Units (MOTUs) for mtCOI and 28S dataset respectively. These results of our study indicate the likelihood that F. sulphurea may be a valid species, however, more morphological and molecular data is required on specimens from type localities of these two species and comparison with type specimens.

Keywords: DNA barcoding, species complex, thrips, species delimitation

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Authors: Jae-Hyun Ro, Jong-Kwang Kim, Chang-Hee Kang, Hyoung-Kyu Song

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In multiple input multiple output-orthogonal frequency division multiplexing (MIMO-OFDM) systems, QR decomposition-M algorithm (QRD-M) has suboptimal error performance. However, the QRD-M has still high complexity due to many calculations at each layer in tree structure. To reduce the complexity of the QRD-M, proposed QRD-M modifies existing tree structure by eliminating unnecessary candidates at almost whole layers. The method of the elimination is discarding the candidates which have accumulated squared Euclidean distances larger than calculated threshold. The simulation results show that the proposed QRD-M has same bit error rate (BER) performance with lower complexity than the conventional QRD-M.

Keywords: complexity, MIMO-OFDM, QRD-M, squared Euclidean distance

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Authors: Ehsan Mehryaar

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The rate of penetration is (RoP) one of the vital factors in the cost and time of tunnel boring projects; therefore, predicting it can lead to a substantial increase in the efficiency of the project. RoP is heavily dependent geological properties of the project site and TBM properties. In this study, 151-point data from Queen’s water tunnel is collected, which includes unconfined compression strength, peak slope index, angle with weak planes, and distance between planes of weaknesses. Since the size of the data is small, it was observed that it is imbalanced. To solve that problem synthetic minority oversampling technique is utilized. The model based on the model tree is proposed, where each leaf consists of a support vector machine model. Proposed model performance is then compared to existing empirical equations in the literature.

Keywords: Model tree, SMOTE, rate of penetration, TBM(tunnel boring machine), SVM

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Authors: Olatunde Sunday Eludoyin, Charles Obiechina Olisa

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The study examined the spatial interactions between earthworm abundance (EA) and tree growth characteristics in ecological belts of Western Niger Delta, Nigeria. Eight 20m x 20m quadrat were delimited in the natural vegetation in each of the rainforest (RF), mangrove (M), fresh water swamp (FWS), and guinea savanna (GS) ecological belts to gather data about the tree species (TS) characteristics which included individual number of tree species (IN), diversity (Di), density (De) and richness (Ri). Three quadrats of 1m x 1m were delineated in each of the 20m x 20m quadrats to collect earthworm species the topsoil (0-15cm), and subsoil (15-30cm) and were taken to laboratory for further analysis. Descriptive statistics and inferential statistics were used for data analysis. Findings showed that a total of 19 earthworm species was found, with 58.5% individual species recorded in the topsoil and 41.5% recorded in the subsoil. The total population ofEudriliuseugeniae was predominantly highest in both topsoil (38.4%) and subsoil (27.1%). The total population of individual species of earthworm was least in GS in the topsoil (11.9%) and subsoil (8.4%). A total of 40 different species of TS was recorded, of which 55.5% were recorded in FWS, while RF was significantly highest in the species diversity(0.5971). Regression analysis revealed that Ri, IN, DBH, Di, and De of trees explained 65.9% of the variability of EA in the topsoil, while 46.9 % of the variability of earthworm abundance was explained by the floristic parameters in the subsoil.Similarly, correlation statistics revealed that in the topsoil, EA is positively and significantly correlated with Ri (r=0.35; p<0.05), IN (r=0.523; p<0.05) and De (r=0.469; p<0.05) while DBH was negatively and significantly correlated with earthworm abundance (r=-0.437; p<0.05). In the subsoil, only Ri and DBH correlated significantly with EA. The study concluded that EA in the study locations was highly influenced by tree growth species especially Ri, IN, DBH, Di, and De. The study recommended that the TSabundance should be improved in the study locations to ensure the survival of earthworms for ecosystem functions.

Keywords: interactions, earthworm abundance, tree growth, ecological zones, western niger delta

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Authors: Marinos Xagoraris, Elisavet Lazarou, Eleftherios Alissandrakis, Christos S. Pappas, Petros A. Tarantilis

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Strawberry tree (Arbutus unedo L.) and autumn heather (Erica manipuliflora Salisb.) are important beekeeping plants of Greece. Six monofloral honeys (four strawberry tree, two autumn heather) were analyzed by means of Solid Phase Micro-Extraction (SPME, 60 min, 60 oC) followed by Gas Chromatography coupled to Mass Spectrometry (GC-MS) for the purpose of assessing the botanical origin. A Divinylbenzene/Carboxen/Polydimethylsiloxane (DVB/CAR/PDMS) fiber was employed, and benzophenone was used as internal standard. The volatile compounds with higher concentration (μg/ g of honey expressed as benzophenone) from strawberry tree honey samples, were α-isophorone (2.50-8.12); 3,4,5-trimethyl-phenol (0.20-4.62); 2-hydroxy-isophorone (0.06-0.53); 4-oxoisophorone (0.38-0.46); and β-isophorone (0.02-0.43). Regarding heather honey samples, the most abundant compounds were 1-methoxy-4-propyl-benzene (1.22-1.40); p-anisaldehyde (0.97-1.28); p-anisic acid (0.35-0.58); 2-furaldehyde (0.52-0.57); and benzaldehyde (0.41-0.56). Norisoprenoids are potent floral markers for strawberry-tree honey. β-isophorone is found exclusively in the volatile fraction of this type of honey, while also α-isophorone, 4-oxoisophorone and 2-hydroxy-isophorone could be considered as additional marker compounds. The analysis of autumn heather honey revealed that phenolic compounds are the most abundant and p-anisaldehyde; 1-methoxy-4-propyl-benzene; and p-anisic acid could serve as potent marker compounds. In conclusion, marker compounds for the determination of the botanical origin for these honeys could be identified as several norisoprenoids and phenolic components were found exclusively or in higher concentrations compared to common Greek honey varieties.

Keywords: SPME/GC-MS, volatile compounds, heather honey, strawberry tree honey

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Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major concern to fruit and vegetable production in the USA. Timely detection and identification of these agricultural pests facilitate the possibility of eradication from newly invaded areas. They spread primarily as larvae in infested fruits carried in commerce or personal baggage. Identification of larval stages to species level is difficult but necessary to determine pest loads and their pathways into the USA. The main focus of this study is the New World genus, Anastrepha. Many of its constituent taxa are pests of major economic importance. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed. Elongation factor 1 alpha sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level.

Keywords: anastrepha, diptera, elongation factor, fruit fly

Procedia PDF Downloads 183

Authors: L. Salomon, P. Sklenar

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The Andes hold the highest plant species diversity in the world. How this occurred is one of the most intriguing questions in studies addressing the origin and patterning of plant diversity worldwide. Recently, the explosive adaptive radiations found in high Andean groups have been pointed as triggers to this spectacular diversity. The Andes is the species-richest area for the biggest genus from the Asteraceae family: Senecio. There, the genus presents an incredible diversity of species, striking growth form variation, and large niche span. Even when some studies tried to disentangle the evolutionary story for some Andean species in Senecio, they obtained partially resolved and low supported phylogenies, as expected for recently radiated groups. The high-throughput sequencing (HTS) approaches have proved to be a powerful tool answering phylogenetic questions in those groups whose evolutionary stories are recent and traditional techniques like Sanger sequencing are not informative enough. Although these tools have been used to understand the evolution of an increasing number of Andean groups, nowadays, their scope has not been applied for Senecio. This project aims to contribute to a better knowledge of the mechanisms shaping the hyper diversity of Senecio in the Andean region, using HTS focusing on Senecio ser. Culcitium (Asteraceae), recently recircumscribed. Firstly, reconstructing a highly resolved and supported phylogeny, and after assessing the role of allopatric differentiation, hybridization, and genome duplication in the diversification of the group. Using the Hyb-Seq approach, combining target enrichment using Asteraceae COS loci baits and genome skimming, more than 100 new accessions were generated. HybPhyloMaker and HybPiper pipelines were used for the phylogenetic analyses, and another pipeline in development (Paralogue Wizard) was used to deal with paralogues. RAxML was used to generate gene trees and Astral for species tree reconstruction. Phyparts were used to explore as first step of gene tree discordance along the clades. Fully resolved with moderated supported trees were obtained, showing Senecio ser. Culcitium as monophyletic. Within the group, some species formed well-supported clades with morphologically related species, while some species would not have exclusive ancestry, in concordance with previous studies using amplified fragment length polymorphism (AFLP) showing geographical differentiation. Discordance between gene trees was detected. Paralogues were detected for many loci, indicating possible genome duplications; ploidy level estimation using flow cytometry will be carried out during the next months in order to identify the role of this process in the diversification of the group. Likewise, TreeSetViz package for Mesquite, hierarchical likelihood ratio congruence test using Concaterpillar, and Procrustean Approach to Cophylogeny (PACo), will be used to evaluate the congruence among different inheritance patterns. In order to evaluate the influence of hybridization and Incomplete Lineage Sorting (ILS) in each resultant clade from the phylogeny, Joly et al.'s 2009 method in a coalescent scenario and Paterson’s D-statistic will be performed. Even when the main discordance sources between gene trees were not explored in detail yet, the data show that at least to some degree, processes such as genome duplication, hybridization, and/or ILS could be involved in the evolution of the group.

Keywords: adaptive radiations, Andes, genome duplication, hybridization, Senecio

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Authors: Ilknur Tuncer, Nihayet Bizsel

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The studies in bacterial diversity and antimicrobial resistance in coastal areas are important to understand the variability in the community structures and metabolic activities. In the present study, antimicrobial susceptibility and phylogenetic analysis of bacteria isolated from stations with different depths and influenced by terrestrial and marine fluxes in eastern Aegean Sea were illustrated. 51% of the isolates were found as resistant and 14% showed high MAR index indicating the high-risk sources of contamination in the environment. The resistance and the intermediate levels and high MAR index of the study area were 38–60%, 11–38% and 0–40%, respectively. According to 16S rRNA gene analysis, it was found that the isolates belonged to two phyla Firmicutes and Gammaproteobacteria with the genera Bacillus, Halomonas, Oceanobacillus, Photobacterium, Pseudoalteromonas, Psychrobacter, and Vibrio. 47% of Bacillus strains which were dominant among all isolates were resistant. In addition to phylogenetically diverse bacteria, the variability in resistance, intermediate and high MAR index levels of the study area indicated the effect of geographical differences.

Keywords: bacterial diversity, multiple antibiotic resistance, 16S rRNA genes, Aegean Sea

Procedia PDF Downloads 382

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

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

Keywords: new species, trematoda, phylogeny, cyclocoelidae

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Authors: Sahari Japar, Rodney Jammy, M. A. Maleque

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The fabrication of melaleuca alternifolia fibre reinforced thermoplastic starch composites was successfully done. This paper aims to show the effect of melaleuca alternifolia fibres on mechanical and physical properties of composites by using starch as a matrix. The fibres were extracted from three different part i.e. tea tree trunk (TTT), tea tree bunch (TTB) and tea tree leaf (TTL) and combined with tapioca starch by casting method. All composites showed superior mechanical properties in comparison to TS. The addition of 5% (v/v) fibres as a filler to TS led to the improvement in young’s modulus by 350% for TTB/TS, 282% for TTT/TS and 220% for TTL/TS. The tensile strength also increased to 34.39% for TTL/TS, 82.80% for TTB/TS and 203.18% for TTT/TS respectively. The trend can be correlated to the amount of cellulose in the fibres. For physical properties, it can be seen that, with the addition of fibres, the water absorption and swelling of composites decreased. The addition of melaleuca alternifolia fibre improved mechanical and physical properties of thermoplastic starch composites.

Keywords: melaleuca alternifolia, fibre, starch, mechanical, physical

Procedia PDF Downloads 364

Authors: Saba Arif, Anam Nadeem, Roman Kalvin, Muzaffar Ali, Burhan Ali, Juntakan Taweekun

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Globally transportation sector accounts for around 25% of energy demand and nearly 62% of oil consumed. Therefore, new energy sources are required to introduce for this huge demand replenishment of depleting conventional energy sources. Currently, biofuels such as Jatropha trees as an energy carrier for transportation sector are being utilized effectively round the globe. However, climate conditions at low altitudes with an average annual temperature above 20 degrees Celsius and rainfall of 300-1000mm are considered the most suitable environment for the efficient growth of Jatropha trees. The current study is providing a theoretical survey-based analysis to investigate the effect of rate of cultivation of jatropha trees on the reduction of fuel prices and its environmental benefits. The resulted study shows that jatropha tree’s 100 kg seeds give 80kg oil and the conversion process cost is very small as 890 PKR. Moreover, the extraction of oil from Jatropha tree is tax-free compared to other fuels. The analysis proved very essential for potential assessment of Jatropha regarding future energy fuel for transportation sector at global level. Additionally, it can be very beneficial for increment in the total amount of transportation fuel in Pakistan.

Keywords: jatropha tree, environmental impact, energy contents, theoretical survey

Procedia PDF Downloads 177