Search results for: tree species selection

Authors: Libo Jiang, Huan Li, Rongling Wu

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Ordinary differentiation equations (ODE) have proven to be powerful for reconstructing precise and informative gene regulatory networks (GRNs) from dynamic gene expression data. However, joint modeling and analysis of all genes, essential for the systematical characterization of genetic interactions, are challenging due to high dimensionality and a complex pattern of genetic regulation including activation, repression, and antitermination. Here, we address these challenges by unifying variable selection and game theory through ODE. Each gene within a GRN is co-expressed with its partner genes in a way like a game of multiple players, each of which tends to choose an optimal strategy to maximize its “fitness” across the whole network. Based on this unifying theory, we designed and conducted a real experiment to infer salt tolerance-related GRNs for Euphrates poplar, a hero tree that can grow in the saline desert. The pattern and magnitude of interactions between several hub genes within these GRNs were found to determine the capacity of Euphrates poplar to resist to saline stress.

Keywords: gene regulatory network, ordinary differential equation, game theory, LASSO, saline resistance

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Authors: K. S. Parlak, E. Turan

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The separation of marbles according to the pattern quality is a process made according to expert decision. The classification phase is the most critical part in terms of economic value. In this study, a self-learning system is proposed which performs the classification of marbles quickly and with high success. This system performs ten feature extraction by taking ten marble images from the camera. The marbles are classified by decision tree method using the obtained properties. The user forms the training set by training the system at the marble classification stage. The system evolves itself in every marble image that is classified. The aim of the proposed system is to minimize the error caused by the person performing the classification and achieve it quickly.

Keywords: decision tree, feature extraction, k-means clustering, marble classification

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Authors: Bhojan Dhakal, Naba Raj Devkota, Chet Raj Upreti, Maheshwar Sapkota

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A study was conducted to find out the production potential, nutrient composition, and the variability of the most commonly available fodder trees along with the varying altitude to help optimize the dry matter requirement during winter lean period. The study was carried out from March to June, 2012 in Lho and Prok Village Development Committee of Manaslu Conservation Area (MCA), located in Gorkha district of Nepal. The other objective of the research was to learn the impact of climate change on livestock production linking it with feed availability. The study was conducted in two parts: social and biological. Accordingly, a households (HHs) survey was conducted to collect primary data from 70 HHs, focusing on the perception of respondents on impacts of climatic variability on the feeding management. The next part consisted of understanding yield potential and nutrient composition of the four most commonly available fodder trees (M. azedirach, M. alba, F. roxburghii, F. nemoralis), within two altitudes range: (1500-2000 masl and 2000-2500 masl) by using a RCB design in 2*4 factorial combination of treatments, each replicated four times. Results revealed that majority of the farmers perceived the change in climatic phenomenon more severely within the past five years. Farmers were using different adaptation technologies such as collection of forage from jungle, reducing unproductive animals, fodder trees utilization, and crop by product feeding at feed scarcity period. Ranking of the different fodder trees on the basis of indigenous knowledge and experiences revealed that F. roxburghii was the best-preferred fodder tree species (index value 0.72) in terms overall preferability whereas M. azedirach had highest growth and productivity (index value 0.77), F. roxburghii had highest adoptability (index value 0.69) and palatability (index value 0.69) as well. Similarly, fresh yield and dry matter yield of the each fodder trees was significant (P < 0.01) between the altitude and within species. Fodder trees yield analysis revealed that the highest dry matter (DM) yield (28 kg/tree) was obtained for F. roxburghii but that remained statistically similar (P > 0.05) to the other treatment. On the other hand, most of the parameters: ether extract (EE), acid detergent lignin (ADL), acid detergent fibre (ADF), cell wall digestibility (CWD), relative digestibility (RD), digestible nutrient (TDN), and Calcium (Ca) among the treatments were highly significant (P < 0.01). This indicates the scope of introducing productive and nutritive fodder trees species even at the high altitude to help reduce fodder scarcity problem during winter. The finding also revealed the scope of promoting all available local fodder trees species as crude protein content of these species were similar.

Keywords: fodder trees, yield potential, climate change, nutrient composition

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Authors: M. Pramila Devi, J. Praveena

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In today’s industrial scenario, the expectations and demand of customers are reaching great heights. In order to satisfy the customer requirements the users are increasingly turning towards fourth party logistics (4PL) service providers to manage their total supply chain operations. In this present research, initially, the criteria for the selection of integrated service providers have been identified and an integrated modal based on their inter-relationship has been developed with help of shippers, with this idea of what factors to be considered and their inter-relationships while selecting integrated service provider. Later, various methods deriving the priority weights viz. Analytical Hierarchy Process (AHP) have been employed for 4PL service provider selection. The derived priorities of 4PL alternatives using methods have been critically analyzed and compared for effective selection. The use of the modal indicates that the computed quantitative evaluation can be applied to improve the precision of the selection.

Keywords: analytical hierarchy process, fourth party logistics, priority weight, criteria selection

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Authors: Dhanuj M. Gandikota

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Sensor-derived three-dimensional (3D) point clouds of trees are invaluable in remote sensing analysis for the accurate measurement of key structural metrics, bio-inventory values, spatial planning/visualization, and ecological modeling. Machine learning (ML) holds the potential in addressing the restrictive tradeoffs in cost, spatial coverage, resolution, and information gain that exist in current point cloud sensing methods. Terrestrial laser scanning (TLS) remains the highest fidelity source of both canopy and below-canopy structural features, but usage is limited in both coverage and cost, requiring manual deployment to map out large, forested areas. While aerial laser scanning (ALS) remains a reliable avenue of LIDAR active remote sensing, ALS is also cost-restrictive in deployment methods. Space-borne photogrammetry from high-resolution satellite constellations is an avenue of passive remote sensing with promising viability in research for the accurate construction of vegetation 3-D point clouds. It provides both the lowest comparative cost and the largest spatial coverage across remote sensing methods. However, both space-borne photogrammetry and ALS demonstrate technical limitations in the capture of valuable below-canopy point cloud data. Looking to minimize these tradeoffs, we explored a class of powerful ML algorithms called Deep Learning (DL) that show promise in recent research on 3-D point cloud reconstruction and interpolation. Our research details the efficacy of applying these DL techniques to reconstruct accurate below-canopy point clouds from space-borne and aerial remote sensing through learned patterns of tree species fractal symmetry properties and the supplementation of locally sourced bio-inventory metrics. From our dataset, consisting of tree point clouds obtained from TLS, we deconstructed the point clouds of each tree into those that would be obtained through ALS and satellite photogrammetry of varying resolutions. We fed this ALS/satellite point cloud dataset, along with the simulated local bio-inventory metrics, into the DL point cloud reconstruction architectures to generate the full 3-D tree point clouds (the truth values are denoted by the full TLS tree point clouds containing the below-canopy information). Point cloud reconstruction accuracy was validated both through the measurement of error from the original TLS point clouds as well as the error of extraction of key structural metrics, such as crown base height, diameter above root crown, and leaf/wood volume. The results of this research additionally demonstrate the supplemental performance gain of using minimum locally sourced bio-inventory metric information as an input in ML systems to reach specified accuracy thresholds of tree point cloud reconstruction. This research provides insight into methods for the rapid, cost-effective, and accurate construction of below-canopy tree 3-D point clouds, as well as the supported potential of ML and DL to learn complex, unmodeled patterns of fractal tree growth symmetry.

Keywords: deep learning, machine learning, satellite, photogrammetry, aerial laser scanning, terrestrial laser scanning, point cloud, fractal symmetry

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Authors: I. Diamant, R. Srouji

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Applicant perceptions are attitudes, feelings, and cognitions which individuals have about selection procedures and have been mostly studied in the context of personnel selection. The main aim of the present study is to expand the understanding of applicant perceptions, using the framework of Organizational Justice Theory, in the domain of selection for higher education. The secondary aim is to explore the relationships between individual differences in social anxiety and applicants’ perceptions. The selection process is an accept/reject situation; it was hypothesized that applicants with higher social anxiety would experience negative perceptions and a lower success estimation, especially when subjected to social interaction elements in the process (interview and group simulation). Also, the effects of prior preparation and post-process explanations offered at the end of the selection process were explored. One hundred sixty psychology M.A. program applicants participated in this research, and following the selection process completed questionnaires measuring social anxiety, social exclusion, ratings on several justice dimensions for each of the methods in the selection process, feelings of success, and self-estimation of compatibility. About half of the applicants also received explanations regarding the significance and the aims of the selection process. Results provided support for most of our hypotheses: applicants with higher social anxiety experienced an increased level of social exclusion in the selection process, perceived the selection as less fair and ended with a lower feeling of success relative to those applicants without social anxiety. These relationships were especially salient in the selection procedures which included social interaction. Additionally, preparation for the selection process was positively related to the favorable perception of fairness in the selection process. Finally, contrary to our hypothesis, it was found that explanations did not affect the applicant’s perceptions. The results enhance our understanding of which factors affect applicant perceptions in applicants to higher education studies and contribute uniquely to the understanding of the effect of social anxiety on different aspects of selection experienced by applicants. The findings clearly show that some individuals may be predisposed to react unfavorably to certain selection situations. In an age of increasing awareness towards fairness in evaluation and selection and hiring procedures, these findings may be of relevance and may contribute to the design of future personnel selection methods in general and of higher education selection in particular.

Keywords: applicant perceptions, selection and assessment, organizational justice theory, social anxiety

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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Authors: Anupama Sekhar, Preeti Saryan, Vinita Gowda

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Plants, due to their sedentary lifestyle, have evolved mechanisms to synthesize a huge diversity of complex, specialized chemical metabolites, a majority of them being volatile organic compounds (VOCs). These VOCs are heavily involved in their biotic and abiotic interactions. Since chemical composition could be under the same selection processes as other morphological characters, we test if VOCs can be used to taxonomically distinguish species in the well-studied, fragrant ginger genus -Hedychium (Zingiberaceae). We propose that variations in the volatile profiles are suggestive of adaptation to divergent environments, and their presence could be explained by either phylogenetic conservatism or ecological factors. In this study, we investigate the volatile chemistry within Hedychium, which is endemic to Asian palaeotropics. We used an unsupervised clustering approach which clearly distinguished most taxa, and we used ancestral state reconstruction to estimate phylogenetic signals and chemical trait evolution in the genus. We propose that taxonomically, the chemical composition could aid in species identification, especially in species complexes where taxa are not morphologically distinguishable, and extensive, targeted chemical libraries will help in this effort.

Keywords: chemotaxonomy, dynamic headspace sampling, floral fragrance, floral volatile evolution, gingers, Hedychium

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Authors: Nur Amira nor Arifin, Tashia Marie Anthony, Mohd Ruzlin Mokhtar, Huzainie Shafi Abd Halim

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Cross-linked polyethylene (XLPE) material is being used as the cable insulation for the past decades due to its higher working temperature of 90 ˚C and some other advantages. However, the use of XLPE as an insulating material for underground distribution cables may have subjected to the unforeseeable weather and uncontrollable environmental condition. These unfavorable condition when combine with high electric field may lead to the initiation and growth of water tree in XLPE insulation. There are several studies on numerous nanofillers incorporate into polymer matrix to hinder the growth of tree propagation. Hence, in this study aims to investigate the effect of MgO and rubber nanofillers at different concentration on the electrical tree of XLPE. The nanofillers and XLPE were mixed and later extruded. After extrusion, the material were then fabricated into the desired shape for experimental purposes. The result shows that the electrical tree propagation of XLPE filled with optimize concentration of nanofillers were much slower compared to pure XLPE. In this paper, the effect of nanofillers towards electrical treeing characteristic will be discussed.

Keywords: electrical trees, nanofillers, polymer nanocomposites, XLPE

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Authors: Nubwimana Rachel, Mugabowindekwe Maurice

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Trees play a crucial role in maintaining biodiversity and providing various ecological services. Traditional methods of counting trees are time-consuming, and there is a need for more efficient techniques. However, deep learning makes it feasible to identify the multi-scale elements hidden in aerial imagery. This research focuses on the application of deep learning techniques for tree detection and counting in both forest and non-forest areas through the exploration of the deep learning application for automated tree detection and counting using satellite imagery. The objective is to identify the most effective model for automated tree counting. We used different deep learning models such as YOLOV7, SSD, and UNET, along with Generative Adversarial Networks to generate synthetic samples for training and other augmentation techniques, including Random Resized Crop, AutoAugment, and Linear Contrast Enhancement. These models were trained and fine-tuned using satellite imagery to identify and count trees. The performance of the models was assessed through multiple trials; after training and fine-tuning the models, UNET demonstrated the best performance with a validation loss of 0.1211, validation accuracy of 0.9509, and validation precision of 0.9799. This research showcases the success of deep learning in accurate tree counting through remote sensing, particularly with the UNET model. It represents a significant contribution to the field by offering an efficient and precise alternative to conventional tree-counting methods.

Keywords: remote sensing, deep learning, tree counting, image segmentation, object detection, visualization

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Authors: Sevde D. Karayel, Ediz Atmaca

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Supplier selection subject is vital because of development competitiveness and performance of firms which have right, rapid and with low cost procurement. Considering the fact that competition between firms is no longer on their supply chains, hence it is very clear that performance of the firms’ not only depend on their own success but also success of all departments in supply chain. For this purpose, firms want to work with suppliers which are cost effective, flexible in terms of demand and high quality level for customer satisfaction. However, diversification and redundancy of their expectations from suppliers, supplier selection problems need to be solved as a hard problem. In this study, supplier selection problem is discussed for critical piece, which is using almost all production of products in and has troubles with lead time from supplier, in a firm that produces medical devices. Analyzing policy in the current situation of the firm in the supplier selection indicates that supplier selection is made based on the purchasing department experience and other authorized persons’ general judgments. Because selection do not make based on the analytical methods, it is caused disruptions in production, lateness and extra cost. To solve the problem, AHP and TOPSIS which are multi-criteria decision making techniques, which are effective, easy to implement and can analyze many criteria simultaneously, are used to make a selection among alternative suppliers.

Keywords: AHP-TOPSIS methods, multi-criteria decision making, supplier selection problem, supply chain management

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Authors: Mayuri Roy Choudhury

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In recent times the concept of agrivoltaics has gained popularity due to the dual use of land and the added value provided by photovoltaics in terms of renewable energy and crop production on farms. However, the transition towards agrivoltaics has been slow, and our research tries to investigate the obstacles leading towards the slow progress of agrivoltaics. We applied data science decision tree algorithms to quantify qualitative perceptions of farmers in the United States for agrivoltaics. To date, there has not been much research that mentions farmers' perceptions, as most of the research focuses on the benefits of agrivoltaics. Our study adds value by putting forward the voices of farmers, which play a crucial towards the transition to agrivoltaics in the future. Our results show a mixture of responses in favor of agrivoltaics. Furthermore, it also portrays significant concerns of farmers, which is useful for decision-makers when it comes to formulating policies for agrivoltaics.

Keywords: agrivoltaics, decision-tree algorithms, farmers perception, transition

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Sami Michael Ayodele

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Cordyceps are members of the fungi family Cordycepitaceae which are formally in Clavicipitaceae. They parasitize the larvae and adults of different susceptible arthropods. They are highly priced and have been reported to be highly medicinal. Cordyceps have been used for centuries in traditional medicine in China and other Asian countries. Survey studies were carried out to determine the presence of Cordyceps and another entomopathogenic fungal floral in North Central Nigeria for two consecutive years. Thirty samples were collected, twenty-eight were identified, and two were unidentified. Most identified species belong to Ophiocordyceps species (20samples), Cordyceps species (4samples) and Isaria species (4samples). The species identified were: Cordyceps pseudomilitaris, Cordyceps tuberculata, Cordyceps cylindrical, Ophiocordyceps nutans, O. criminals, O. oxycephala, O. kniphofioides and Isaria sinclairii. The morphological and microscopic features of the collected and identified species were similar to those reported in other countries. This is the first official report on the presence of Cordyceps species in Nigeria. Further collections from different ecological regions of Nigeria will show the richness of the floral diversity of these entomopathogenic and medicinal mushrooms in Nigeria.

Keywords: cordyceps, entomopathogenic, medicinal, North Central, Nigeria

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Authors: Michaela Chovancova, Pavel Niedoba

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For the treatment of acute and chronic lung diseases it is preferred to deliver medicaments by inhalation. The drug is delivered directly to tracheobronchial tree. This way allows the given medicament to get directly into the place of action and it makes rapid onset of action and maximum efficiency. The transport of aerosol particles in the particular part of the lung is influenced by their size, anatomy of the lungs, breathing pattern and airway resistance. This article deals with calculation of airway resistance in the lung model of Horsfield. It solves the problem of determination of the pressure losses in bifurcation and thus defines the pressure drop at a given location in the bronchial tree. The obtained data will be used as boundary conditions for transport of aerosol particles in a central part of bronchial tree realized by Computational Fluid Dynamics (CFD) approach. The results obtained from CFD simulation will allow us to provide information on the required particle size and optimal inhalation technique for particle transport into particular part of the lung.

Keywords: human lungs, bronchial tree, pressure losses, airways resistance, flow, breathing

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Authors: Nasreen Jeelani, Huining Shi , Di An, Lu Xia, Shuqing An

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Heavy metals contamination in aquatic ecosystem is a major environmental problem since its accumulation along the food chain pose public health risk. The concentration of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) in soil and plants species collected from different streams of Suoxu River, China was investigated. This aim was to define the level of pollutants in Suoxu River, find which plant species exhibits the greatest accumulation and to evaluate whether these species could be useful for phytoremediation. While total soil Cd, Cr, Cu, Ni, Pb, and Zn concentrations varied, respectively, from 0.09 to 0.23 , 58.6 to 98, 9.72 to 80.5, 15.3 to 41, 15.2 to 27.3 and 35 to 156 (mg-kg-1), those in plants ranged from 0.035 to 0.49, 2.91 to 75.6, 4.79 to 32.4, 1.27 to 16.1, 0.62 to10.2, 18.9 to 84.6 (mg-kg-1), respectively. Based on BCFs and TFs values, most of the studied species have potential for phytostabilization. The plants with most effective in the accumulation of metals in shoots are Phragmatis australis (TF=2.29) and Iris tectorum (TF =2.07) for Pb. While Chenopodium album, (BCF =3.55), Ranunculus sceleratus, (BCF= 3.0), Polygonum hydropiper (BCF =2.46) for Cd and Iris tectorum (BCF=2.0) for Cu was suitable for phytostabilization. Among the plant species screened for Cd, Cr, Cu, Ni, Pb and Zn, most of the species were efficient to take up more than one heavy metal in roots. Our study showed that the native plant species growing on contaminated sites may have the potential uses for phytoremediation.

Keywords: heavy metals, huaihe river catchments, sediment, plants

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Authors: Elizabeth Starzycka-Korbas, Michal Starzycki, Wojciech Rybinski, Mirosława Dabert

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For a few years, the populations of pathogenic fungi occurring in winter oilseed rape in Malyszyn were analyzed. Brassica napus L. in Poland and in the world is a source of energy for both the men (oil), and animals, as post-extraction middling, as well as a motor fuel (oil, biofuel) therefore studies of this type are very important. The species composition of pathogenic fungi can be an indicator of seed yield. The occurrence of oilseed rape pathogens during several years were analyzed using the sequencing method DNA ITS. The results were compared in the gene bank using the program NCBI / BLAST. In field conditions before harvest of oilseed rape presence of pathogens infesting B. napus has been assessed. For example, in 2015, 150 samples have been isolated and applied to PDA medium for the identification of belonging species. From all population has been selected mycelium of 83 isolates which were sequenced. Others (67 isolates) were pathogenic fungi of the genus Alternaria which are easily to recognize. The population of pathogenic species on oilseed rape have been identified after analyzing the DNA ITS and include: Leptosphaeria sp. 38 (L. maculans 25, L. biglobosa 13), Alternaria sp. 29, Fusarium sp. 3, Sclerotinia sclerotiorum 7, heterogeneous 6, total of 83 isolates. The genus Alternaria sp. fungi wear the largest share of B. napus pathogens in particular years. Another dangerous species for oilseed rape was Leptosphaeria sp. Populations of pathogens in each year were different. The number of pathogens occurring in the field and their composition is very important for breeders and farmers because of the possible selection of the most resistant genotypes for sowing in the next growing season.

Keywords: B. napus, DNA ITS Sequencing, pathogenic fungi, population

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Authors: Miguel Mellado, Cecilia Zapata

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Goats can be exploited in harsh environments due to their capacity to adjust to limited quantity and quality forage sources. In these environments, leguminous trees can be used as supplementary feeds as foliage and fruits of these trees can contribute to maintain or improve production efficiency in ruminants. The objective of this study was to determine the nutritional value of three leguminous trees heavily selected by goats in a xerophyllous shrubland. Chemical composition and in vitro dry matter disappearance (IVDMD) of leaves and pods from leucaena (Leucaena leucocephala), mesquite (Prosopis laevigata) and huisache (Acacia farnesiana) is presented. Crude protein (CP) ranged from 17.3% for leaves of huisache to 21.9% for leucaena. The neutral detergent fiber (NDF) content ranged from 39.0 to 40.3 with no difference among fodder threes. Across tree species, mean IVDMD was 61.6% for pods and 52.2% for leaves. IVDMD for leaves was highest (P < 0.01) for leucaena (54.9%) and lowest for huisache (47.3%). Condensed tannins in an acetonic extract were highest for leaves of huisache (45.3 mg CE/g DM) and lowest for mesquite (25.9 mg CE/g DM). Pods and leaves of huisache presented the highest number of secondary metabolites, mainly related to hydrobenzoic acid and flavonols; leucaena and mesquite presented mainly flavonols and anthocyanins. It was concluded that leaves and pods of leucaena, mesquite and huisache constitute valuable forages for ruminant livestock due to its low fiber, high CP levels, moderate in vitro fermentation characteristics and high mineral content. Keywords: Fodder tree; ruminants; secondary metabolites; minerals; tannins

Keywords: fodder tree, ruminants, secondary metabolites, minerals, tannins

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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: Hala Alshamlan, Ghada Badr, Yousef Alohali

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Cancer is one of the dreadful diseases, which causes considerable death rate in humans. DNA microarray-based gene expression profiling has been emerged as an efficient technique for cancer classification, as well as for diagnosis, prognosis, and treatment purposes. In recent years, a DNA microarray technique has gained more attraction in both scientific and in industrial fields. It is important to determine the informative genes that cause cancer to improve early cancer diagnosis and to give effective chemotherapy treatment. In order to gain deep insight into the cancer classification problem, it is necessary to take a closer look at the proposed gene selection methods. We believe that they should be an integral preprocessing step for cancer classification. Furthermore, finding an accurate gene selection method is a very significant issue in a cancer classification area because it reduces the dimensionality of microarray dataset and selects informative genes. In this paper, we classify and review the state-of-art gene selection methods. We proceed by evaluating the performance of each gene selection approach based on their classification accuracy and number of informative genes. In our evaluation, we will use four benchmark microarray datasets for the cancer diagnosis (leukemia, colon, lung, and prostate). In addition, we compare the performance of gene selection method to investigate the effective gene selection method that has the ability to identify a small set of marker genes, and ensure high cancer classification accuracy. To the best of our knowledge, this is the first attempt to compare gene selection approaches for cancer classification using microarray gene expression profile.

Keywords: gene selection, feature selection, cancer classification, microarray, gene expression profile

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Authors: Yong-Kian Lim, Khan Cheung, Xin Dang, Steven Roberts, Xiaotong Wang, Vengatesen Thiyagarajan

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Unprecedented rate of increased CO₂ level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g., some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors, including OA, can influence the addition and removal of methyl groups through epigenetic modification (e.g., DNA methylation) process to turn gene expression “on or off” as part of a rapid adaptive mechanism to cope with OA. In this study, the above hypothesis was tested through testing the effect of OA, using decreased pH 7.4 as a proxy, on the DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis, at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1; however, over one-third of the larvae raised at pH 7.4 failed to attach to an optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.

Keywords: adaptive plasticity, DNA methylation, larval metamorphosis, ocean acidification

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Authors: Younies Saeed Hassan Mahmoud, Mai Mabrouk, Elsayed Sallam

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Analysing DNA microarray data sets is a great challenge, which faces the bioinformaticians due to the complication of using statistical and machine learning techniques. The challenge will be doubled if the microarray data sets contain missing data, which happens regularly because these techniques cannot deal with missing data. One of the most important data analysis process on the microarray data set is feature selection. This process finds the most important genes that affect certain disease. In this paper, we introduce a technique for imputing the missing data in microarray data sets while performing feature selection.

Keywords: DNA microarray, feature selection, missing data, bioinformatics

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Authors: Je-Seok Shin, Wook-Won Kim, Jin-O Kim

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The offshore wind farm needs to be designed carefully considering economics and reliability aspects. There are many decision-making problems for designing entire offshore wind farm, this paper focuses on an inner grid layout which means the connection between wind turbines as well as between wind turbines and an offshore substation. A methodology proposed in this paper determines the connections and the cable type for each connection section using K-clustering, minimum spanning tree and cable selection algorithms. And then, a cost evaluation is performed in terms of investment, power loss and reliability. Through the cost evaluation, an optimal layout of inner grid is determined so as to have the lowest total cost. In order to demonstrate the validity of the methodology, the case study is conducted on 240MW offshore wind farm, and the results show that it is helpful to design optimally offshore wind farm.

Keywords: offshore wind farm, optimal layout, k-clustering algorithm, minimum spanning algorithm, cable type selection, power loss cost, reliability cost

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Authors: Fahd Sabry Esmail, M. Badr Senousy, Mohamed Ragaie

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In recent years, there has been an explosion in the rate of using technology that help discovering the diseases. For example, DNA microarrays allow us for the first time to obtain a "global" view of the cell. It has great potential to provide accurate medical diagnosis, to help in finding the right treatment and cure for many diseases. Various classification algorithms can be applied on such micro-array datasets to devise methods that can predict the occurrence of Leukemia disease. In this study, we compared the classification accuracy and response time among eleven decision tree methods and six rule classifier methods using five performance criteria. The experiment results show that the performance of Random Tree is producing better result. Also it takes lowest time to build model in tree classifier. The classification rules algorithms such as nearest- neighbor-like algorithm (NNge) is the best algorithm due to the high accuracy and it takes lowest time to build model in classification.

Keywords: data mining, classification techniques, decision tree, classification rule, leukemia diseases, microarray data

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Authors: Hilal Bulut, Serap Saler

Abstract:

Protozoan ciliate epibionts infestation on zooplankton in Cip Dam Lake were studied seasonally, between spring 2014-winter 2015 The ciliates peritrich Epibiont Epistylis sp. (Protozoa, Ciliophora) was found as colony form on some individuals of different zooplanktonic groups, especially rotifers and copepods. Totally 23 zooplankton species (19 species from Rotifera, 3 species from Cladocera and 1 species from Copepoda in Cip Dam Lake were investigated. Rotifers were the most important zooplanktonic group (82.7 % of total) and the taxa observed with epibionts were Keratella, Polyarthra, and Brachionus. The highest densities of infected zooplankton was observed in winter (14265 ind.m-3), the lowest densities of infected zooplankton was found in summer (3056 ind.m-). Rotifers were most infected groups with 75% in this study. Epistylis sp. was found on three species of rotifers and one copepod species. Infestation of Epistylis sp. has been registered for the first time in Cip Dam Lake.

Keywords: copepoda, epibiosis, peritrich, rotifera

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Authors: Oluwafemi Samuel Oyamakin

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The forest in Nigeria is currently estimated to extend to around 9.6 million hectares, but used to expand over central and southern Nigeria decades ago. The forest estate is shrinking due to long-term human exploitation for agricultural development, fuel wood demand, uncontrolled forest harvesting and urbanization, amongst other factors, compounded by population growth in rural areas. Nigeria has lost more than 50% of its forest cover since 1990 and currently less than 10% of the country is forested. The current deforestation rate is estimated at 3.7%, which is one of the highest in the world. Reducing Emissions from Deforestation and forest Degradation plus conservation, sustainable management of forests and enhancement of forest carbon stocks constituted what is referred to as REDD+. This study evaluated some of the existing way of computing carbon stocks using eight indigenous tree species like Mansonia, Shorea, Bombax, Terminalia superba, Khaya grandifolia, Khaya senegalenses, Pines and Gmelina arborea. While these components are the essential elements of REDD+ programme, they can be brought under a broader framework of systems analysis designed to arrive at optimal solutions for future predictions through statistical distribution pattern of carbon sequestrated by various species of tree. Available data on height and diameter of trees in Ibadan were studied and their respective potentials of carbon sequestration level were assessed and subjected to tests so as to determine the best statistical distribution that would describe the carbon sequestration pattern of trees. The result of this study suggests a reasonable statistical distribution for carbons sequestered in simulation studies and hence, allow planners and government in determining resources forecast for sustainable development especially where experiments with real-life systems are infeasible. Sustainable management of forest can then be achieved by projecting future condition of forests under different management regimes thereby supporting conservation and REDD+ programmes in Nigeria.

Keywords: REDD+, carbon, climate change, height and diameter

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Authors: F. O. Oboite, P. G. Comeau

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Advance regeneration is present in many lodgepole pine stands in Alberta. When the overstory pine canopy is killed by Mountain Pine Beetle (MPB) the growth of this advance is likely to increase. Understanding the growth response of these understory tree species is needed to improve mid-term timber supply projections and management decisions. To quantify the growth (diameter, height, height/diameter ratio) responses of black spruce and white spruce to lodgepole pine mortality, sample trees of black and white spruce advance regeneration were selected from 7 lodgepole pine dominated stands (5 attacked; 2 control) in the Foothills Region of western Alberta. Measurements were collected 7-8 years after MPB attack across a wide range of spruce height and stand densities. Analysis was done using mixed model linear regression. Result indicates that there was an increase in both diameter and height growth after MPB attack; however, this increase in growth was delayed for about four years. Both spruce species had similar height response and their height/diameter ratio decreased after release, partly as a result of increased understory light associated with loss of needles in the pine canopy. In addition, the diameter and height growth responses of both spruce species were strongly related to density, prerelease growth and initial size.

Keywords: mountain pine beetle, forest regeneration, lodgepole pine, growth response

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Authors: Rosario Rivera Rubite, Ching-I Peng, Che-Wei Lin, Mark Hughes, Yoshiko Kono, Kuo-Fang Chung

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The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia and compared them with potentially allied species. The three species are clearly assignable to Begonia section Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, Begonia merrilliana, and Begonia sykakiengii. Somatic chromosomes at metaphase were determined to be 2n=30 for B. culasiensis and 2n=28 for both B. merrilliana and B. sykakiengii, which are congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene, and with B. merrilliana and B. sykakiengii being younger species of Pleistocene origin. The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex-situ conservation collections and raising awareness with community groups.

Keywords: conservation, endemic , herbarium , limestone, phylogenetics, taxonomy

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Authors: Soon-Mi Park, Ihn Sook Jeong

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This retrospective study was aimed to identify risk factors of intravenous (IV) infiltration for hospitalized children. The participants were 1,174 children for test and 424 children for validation, who admitted to a general hospital, received peripheral intravenous injection therapy at least once and had complete records. Data were analyzed with frequency and percentage or mean and standard deviation were calculated, and decision tree analysis was used to screen for the most important risk factors for IV infiltration for hospitalized children. The decision tree analysis showed that the most important traditional risk factors for IV infiltration were the use of ampicillin/sulbactam, IV insertion site (lower extremities), and medical department (internal medicine) both in the test sample and validation sample. The correct classification was 92.2% in the test sample and 90.1% in the validation sample. More careful attention should be made to patients who are administered ampicillin/sulbactam, have IV site in lower extremities and have internal medical problems to prevent or detect infiltration occurrence.

Keywords: decision tree analysis, intravenous infiltration, child, validation

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Authors: Kristýna Weissová

Abstract:

This study is focused on two selected model taxa of invertebrates - Hymenoptera: Aculeata and Lepidopterawithnocturnalactivity, recordedatthesitesof lignite dumps and their surroundings in the North Bohemian Lignite Basin, Czech Republic. There search was conducted on 10 landfills, 3 study areas were determined on each landfill - primary and secondary succession and recultivation. A total of 3,202 individuals belonging to 232 species and 17 families of sagebrushinsects were collected. died, 74%of the species occurred on the primary succes sionare as, that is 2x more species than on the reclaimed areas. Of the total number of species and on all areas, 60 rare species were recorded - 29 vulnerable, 21 endangered, 8 critically endangered, and 2 extinct The areas of primary succession were again confirmed to be the richest in terms of rare species, hosting 39 rare species of Hymenoptera: Aculeata. In addition, bothextinct species were represented only on plots of primary succession. The family Crabronidae had the largestre presentation of species on theareasofleft primary succession, the family Halictidae was the most represented on the reclaimed areas and areas of secondary succession. A total of 3,634 moths were collected, assigned to 262 species and 10 families. A similar number of species occurred on the primary succession and reclaimed areas, but the reclaimed area had a greater abundance. Secondary successionsiteshostedha lf as many species and alsocontainedlow abundance compared to other management types. The results show that there claimed areas host a numerically larger group and more species of moths than the successionalareas. Rare species did not occur at any site. A higher number of days in locations without water bodies, wetland vegetation, and locations with a highre presentation of woody species. It is advisable to combine individual types of landscape management in such a way as to create a colorfulmosaic that supports biodiversity. In particular, we recommend incorporating natural successionintoreclamation plans, which is a refuge for many rare species of invertebrates, which has not yetbeenroutinely and purposefully practiced.

Keywords: hymenoptera: aculeata, lepidoptera, reclamation, succession, post-mining ara

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