Search results for: Biological soil conservation planning

Authors: F. L. Motta, M. H. A. Santana

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Humic acids (HA) were produced by a Trichoderma viride strain under submerged fermentation in a medium based on the oil palm empty fruit bunch (EFB) and the main variables of the process were optimized by using response surface methodology. A temperature of 40°C and concentrations of 50g/L EFB, 5.7g/L potato peptone and 0.11g/L (NH4)2SO4 were the optimum levels of the variables that maximize the HA production, within the physicochemical and biological limits of the process. The optimized conditions led to an experimental HA concentration of 428.4±17.5 mg/L, which validated the prediction from the statistical model of 412.0mg/L. This optimization increased about 7–fold the HA production previously reported in the literature. Additionally, the time profiles of HA production and fungal growth confirmed our previous findings that HA production preferably occurs during fungal sporulation. The present study demonstrated that T. viride successfully produced HA via the submerged fermentation of EFB and the process parameters were successfully optimized using a statistics-based response surface model. To the best of our knowledge, the present work is the first report on the optimization of HA production from EFB by a biotechnological process, whose feasibility was only pointed out in previous works.

Keywords: Empty fruit bunch, humic acids, submerged fermentation, Trichoderma viride.

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Authors: Hanife Genç

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The olive fruit fly, Bactrocera oleae (Rossi), is an economically important and endemic pest in olive (Oleae europae) orchards in Turkey. The aim of this study was to determine olive fruit fly infestation in different olive cultivars in the laboratory. Olive fly infested fruits were collected in Çanakkale province to establish wild fly population. After having reproductive olive fly colonies, 14 olive cultivars were tested in the controlled laboratory conditions, at 23±2 °C, 65% RH and 16:8 h (light: dark) photoperiod. The olive samples from 14 different olive cultivars were collected in October 2015, in Campus of Dardanos, Çanakkale Onsekiz Mart University. Observations were carried out detecting some biological parameters such as the number of oviposition stings, active infestation, total infestation, the number of pupae and the adult emergence. The results indicated that oviposition stings were not associated with pupal yield. A few pupae were found within olive fruits which were not able to exit. Screening of the varieties suggested that less susceptible cultivar to olive fruit fly attacks was Arbequin while Gemlik-2M 2/3 showed significant susceptibility. Ovipositional preference of olive fly females and the success of larval development in different olive varieties are crucial for establishing new olive orchards to prevent high olive fruit fly infestation.

Keywords: Infestation, olive fruit fly, olive cultivars, oviposition sting.

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Authors: P. Martínez-Nieto, M. Vanegas-Hoyos, M. Zapata-Pineda, J. Robles-Camargo

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The aquatic plants are a promising renewable energy resource. Lake Fúquene polluting macrophytes, water hyacinth (Eichhornia crassipes C. Mart.) and Brazilian elodea (Egeria densa Planch.), were saccharifiedby different treatments and fermented to ethanol by native yeasts. Among the tested chemical and biological methods for the saccharification, Pleurotus ostreatus at 10% (m/v) was chosen as the best pre-treatment in both macrophytes (P<0.01). Subsequently 49 yeasts were isolated from Lake Fúquene and nine strains were selected, which presented the highest precipitates characteristic of ethanol in the iodoform test. The fermentations from water hyacinth and Brazilian elodea hydrolysates using these yeasts produced ethanol at a rate between 0.38 to 0.80gL-1h-1 and 0.15 to 0.27gL-1h-1 respectively. The ethanol presence was confirmed by gas chromatography–mass spectrometry. The nine yeasts chosen were preliminarily identified as belonging to the genera Candida spp., Brettanomyces sp. and Hansenula spp.

Keywords: Bio-ethanol, Chemical hydrolysis, Invasive aquatic macrophytes, Native yeasts fermenting, P. ostreatus

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Authors: Mohsin T. Mohammed, Zahid A. Khan, Arshad N. Siddiquee

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The field of biomedical materials plays an imperative requisite and a critical role in manufacturing a variety of biological artificial replacements in a modern world. Recently, titanium (Ti) materials are being used as biomaterials because of their superior corrosion resistance and tremendous specific strength, free- allergic problems and the greatest biocompatibility compared to other competing biomaterials such as stainless steel, Co-Cr alloys, ceramics, polymers, and composite materials. However, regardless of these excellent performance properties, Implantable Ti materials have poor shear strength and wear resistance which limited their applications as biomaterials. Even though the wear properties of Ti alloys has revealed some improvements, the crucial effectiveness of biomedical Ti alloys as wear components requires a comprehensive deep understanding of the wear reasons, mechanisms, and techniques that can be used to improve wear behavior. This review examines current information on the effect of thermal and thermomechanical processing of implantable Ti materials on the long-term prosthetic requirement which related with wear behavior. This paper focuses mainly on the evolution, evaluation and development of effective microstructural features that can improve wear properties of bio grade Ti materials using thermal and thermomechanical treatments.

Keywords: Wear Resistance, Heat Treatment, Thermomechanical Processing, Biomedical Titanium Materials.

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Authors: F. Ruiz-Fuster

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Arnold’s redefinition of human motives can sustain a psychology of education which emphasizes the beauty of knowledge and the exercise of intellectual functions. Thus, education instead of focusing on skills and learning by doing would be centered on ‘the widest reaches of the human spirit’. One way to attain it is by developing children’s inherent interest. Arnold takes into account the fact that the desire to know is the inherent interest which leads students to explore and learn. She also emphasizes the need of exercising human functions as thinking, judging and reasoning. According to Arnold, the influence of psychological theories of motivation in education has derived in considering that all learning and school tasks should derive from children’s needs and impulses. The desire to know and the curiosity have not been considered as basic and active as any instinctive drive or basic need, so there has been an attempt to justify and understand how biological drives guide student’s learning. However, understanding motives and motivation not as a drive, an instinct or an impulse guided by our basic needs, but as a want that leads to action can help to understand, from a psychological perspective, how teachers can motivate students to learn, strengthening their desire and interest to reason and discover the whole new world of knowledge.

Keywords: Academic motivation, interests, desire to know, educational psychology, intellectual functions.

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Authors: Eva Tvrdá, Hana Greifová, Peter Ivanič, Norbert Lukáč

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The aim of this study was to evaluate the dose- and time-dependent in vitro effects of berberine (BER), a natural alkaloid with numerous biological properties on bovine spermatozoa during three time periods (0 h, 2 h, 24 h). Bovine semen samples were diluted and cultivated in physiological saline solution containing 0.5% DMSO together with 200, 100, 50, 10, 5, and 1 μmol/L BER. Spermatozoa motility was assessed using the computer assisted semen analyzer. The viability of spermatozoa was assessed by the metabolic (MTT) assay, production of superoxide radicals was quantified using the nitroblue tetrazolium (NBT) test, and chemiluminescence was used to evaluate the generation of reactive oxygen species (ROS). Cell lysates were prepared and the extent of lipid peroxidation (LPO) was evaluated using the TBARS assay. The results of the movement activity showed a significant increase in the motility during long term cultivation in case of concentrations ranging between 1 and 10 μmol/L BER (P < 0.01; P < 0.001; 24 h). At the same time, supplementation of 1, 5 and 10 μmol/L BER led to a significant preservation of the cell viability (P < 0.001; 24 h). BER addition at a range of 1-50 μmol/L also provided a significantly higher protection against superoxide (P < 0.05) and ROS (P < 0.001; P < 0.01) overgeneration as well as LPO (P < 0.01; P<0.05) after a 24 h cultivation. We may suggest that supplementation of BER to bovine spermatozoa, particularly at concentrations ranging between 1 and 50 μmol/L, may offer protection to the motility, viability and oxidative status of the spermatozoa, particularly notable at 24 h.

Keywords: Berberine, bulls, motility, oxidative profile, spermatozoa, viability.

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Authors: Aspasia Koutsokosta, Stefanos Katsavounis

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This paper reviews the model-based qualitative and quantitative Operations Management research in the context of Construction Supply Chain Management (CSCM). Construction industry has been traditionally blamed for low productivity, cost and time overruns, waste, high fragmentation and adversarial relationships. The construction industry has been slower than other industries to employ the Supply Chain Management (SCM) concept and develop models that support the decision-making and planning. However the last decade there is a distinct shift from a project-based to a supply-based approach of construction management. CSCM comes up as a new promising management tool of construction operations and improves the performance of construction projects in terms of cost, time and quality. Modeling the Construction Supply Chain (CSC) offers the means to reap the benefits of SCM, make informed decisions and gain competitive advantage. Different modeling approaches and methodologies have been applied in the multi-disciplinary and heterogeneous research field of CSCM. The literature review reveals that a considerable percentage of the CSC modeling research accommodates conceptual or process models which present general management frameworks and do not relate to acknowledged soft Operations Research methods. We particularly focus on the model-based quantitative research and categorize the CSCM models depending on their scope, objectives, modeling approach, solution methods and software used. Although over the last few years there has been clearly an increase of research papers on quantitative CSC models, we identify that the relevant literature is very fragmented with limited applications of simulation, mathematical programming and simulation-based optimization. Most applications are project-specific or study only parts of the supply system. Thus, some complex interdependencies within construction are neglected and the implementation of the integrated supply chain management is hindered. We conclude this paper by giving future research directions and emphasizing the need to develop optimization models for integrated CSCM. We stress that CSC modeling needs a multi-dimensional, system-wide and long-term perspective. Finally, prior applications of SCM to other industries have to be taken into account in order to model CSCs, but not without translating the generic concepts to the context of construction industry.

Keywords: Construction supply chain management, modeling, operations research, optimization and simulation.

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Authors: S. M. Amin Hosseini, Oriol Pons, Carmen Mendoza Arroyo, Albert de la Fuente

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In the aftermath of a natural disaster, the major challenge most cities and societies face, regardless of their diverse level of prosperity, is to provide temporary housing (TH) for the displaced population (DP). However, the features of TH, which have been applied in previous recovery programs, greatly varied from case to case. This situation demonstrates that providing temporary accommodation for DP in a short period time and usually in great numbers is complicated in terms of satisfying all the beneficiaries’ needs, regardless of the societies’ welfare levels. Furthermore, when previously used strategies are applied to different areas, the chosen strategies are most likely destined to fail, unless the strategies are context and culturally based. Therefore, as the population of disaster-prone cities are increasing, decision-makers need a platform to help to determine all the factors, which caused the outcomes of the prior programs. To this end, this paper aims to assess the problems, requirements, limitations, potential responses, chosen strategies, and their outcomes, in order to determine the main elements that have influenced the TH process. In this regard, and in order to determine a customizable strategy, this study analyses the TH programs of five different cases as: Marmara earthquake, 1999; Bam earthquake, 2003; Aceh earthquake and tsunami, 2004; Hurricane Katrina, 2005; and, L’Aquila earthquake, 2009. The research results demonstrate that the main vertexes of TH are: (1) local characteristics, including local potential and affected population features, (2) TH properties, which needs to be considered in four phases: planning, provision/construction, operation, and second life, and (3) natural hazards impacts, which embraces intensity and type. Accordingly, this study offers decision-makers the opportunity to discover the main vertexes, their subsets, interactions, and the relation between strategies and outcomes based on the local conditions of each case. Consequently, authorities may acquire the capability to design a customizable method in the face of complicated post-disaster housing in the wake of future natural disasters.

Keywords: Post-disaster temporary accommodation, urban resilience, natural disaster, local characteristic.

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Authors: Tommaso Adamo, Gianpaolo Ghiani, Antonio D. Grieco, Emanuela Guerriero

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Batch production plants provide a wide range of scheduling problems. In pharmaceutical industries a batch process is usually described by a recipe, consisting of an ordering of tasks to produce the desired product. In this research work we focused on pharmaceutical production processes requiring the culture of a microorganism population (i.e. bacteria, yeasts or antibiotics). Several sources of uncertainty may influence the yield of the culture processes, including (i) low performance and quality of the cultured microorganism population or (ii) microbial contamination. For these reasons, robustness is a valuable property for the considered application context. In particular, a robust schedule will not collapse immediately when a cell of microorganisms has to be thrown away due to a microbial contamination. Indeed, a robust schedule should change locally in small proportions and the overall performance measure (i.e. makespan, lateness) should change a little if at all. In this research work we formulated a constraint programming optimization (COP) model for the robust planning of antibiotics production. We developed a discrete-time model with a multi-criteria objective, ordering the different criteria and performing a lexicographic optimization. A feasible solution of the proposed COP model is a schedule of a given set of tasks onto available resources. The schedule has to satisfy tasks precedence constraints, resource capacity constraints and time constraints. In particular time constraints model tasks duedates and resource availability time windows constraints. To improve the schedule robustness, we modeled the concept of (a, b) super-solutions, where (a, b) are input parameters of the COP model. An (a, b) super-solution is one in which if a variables (i.e. the completion times of a culture tasks) lose their values (i.e. cultures are contaminated), the solution can be repaired by assigning these variables values with a new values (i.e. the completion times of a backup culture tasks) and at most b other variables (i.e. delaying the completion of at most b other tasks). The efficiency and applicability of the proposed model is demonstrated by solving instances taken from a real-life pharmaceutical company. Computational results showed that the determined super-solutions are near-optimal.

Keywords: Constraint programming, super-solutions, robust scheduling, batch process, pharmaceutical industries.

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Authors: Yi-Chun Kuo, Jo-Chieh Lin

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The objective of a supply chain strategy is to reduce waste and increase efficiency to attain cost benefits, and to guarantee supply chain flexibility when facing the ever-changing market environment in order to meet customer requirements. Strategy implementation aims to fulfill common goals and attain benefits by integrating upstream and downstream enterprises, sharing information, conducting common planning, and taking part in decision making, so as to enhance the overall performance of the supply chain. With the rise of outsourcing and globalization, the increasing dependence on suppliers and customers and the rapid development of information technology, the complexity and uncertainty of the supply chain have intensified, and supply chain vulnerability has surged, resulting in adverse effects on supply chain performance. Thus, this study aims to use supply chain vulnerability as a moderating variable and apply structural equation modeling (SEM) to determine the relationships among supply chain strategy, supply chain integration, and supply chain performance, as well as the moderating effect of supply chain vulnerability on supply chain performance. The data investigation of this study was questionnaires which were collected from the management level of enterprises in Taiwan and China, 149 questionnaires were received. The result of confirmatory factor analysis shows that the path coefficients of supply chain strategy on supply chain integration and supply chain performance are positive (0.497, t= 4.914; 0.748, t= 5.919), having a significantly positive effect. Supply chain integration is also significantly positively correlated to supply chain performance (0.192, t = 2.273). The moderating effects of supply chain vulnerability on supply chain strategy and supply chain integration to supply chain performance are significant (7.407; 4.687). In Taiwan, 97.73% of enterprises are small- and medium-sized enterprises (SMEs) focusing on receiving original equipment manufacturer (OEM) and original design manufacturer (ODM) orders. In order to meet the needs of customers and to respond to market changes, these enterprises especially focus on supply chain flexibility and their integration with the upstream and downstream enterprises. According to the observation of this research, the effect of supply chain vulnerability on supply chain performance is significant, and so enterprises need to attach great importance to the management of supply chain risk and conduct risk analysis on their suppliers in order to formulate response strategies when facing emergency situations. At the same time, risk management is incorporated into the supply chain so as to reduce the effect of supply chain vulnerability on the overall supply chain performance.

Keywords: Supply chain integration, supply chain performance, supply chain vulnerability, structural equation modeling.

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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Authors: Mekhaldi Abdelkader, Bouznad Ahcen, Djibaoui Rachid, Hamoum Hakim

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This study presents an attempt to evaluate the antioxidant potential and antimicrobial activity of methanolic extract, and essential oils prepared from the leaves of sage (Salvia officinalis L.). The content of polyphenol in the methanolic extracts from the leaves of Salvia officinalis was determined spectrophotometrically, calculated as gallic acid and catechin equivalent. The essential oils and methanol extract were also subjected to screenings for the evaluation of their antioxidant activities using 2, 2-diphenyl-1- picrylhydrazyl (DPPH) test. While the plant essential oils showed only weak antioxidant activities, its methanol extract was considerably active in DPPH (IC50 = 37.29 μg/ml) test. Appreciable total polyphenol content (31.25 mg/g) was also detected for the plant methanol extract as gallic acid equivalent in the Folin–Ciocalteu test. The plant was also screened for its antimicrobial activity and good to moderate inhibitions were recorded for its essential oils, and methanol extracts against most of the tested microorganisms. The present investigation revealed that this plant had rich source of antioxidant properties. It is for this reason that sage has found increasing application in food formulations.

Keywords: Antibacterial, Antioxidant, Flavonoid, Polyphenol, Salvia officinalis.

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Authors: Ghada Badr, Arwa Alturki

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The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Alignment, RNA secondary structure, pairwise, component-based, data mining.

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Authors: Juliana A. Fracarolli, Adilson M. Enes, Inácio M. Dal Fabbro, Silvestre Rodrigues

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The dynamic speckle or biospeckle is an interference phenomenon generated at the reflection of a coherent light by an active surface or even by a particulate or living body surface. The above mentioned phenomenon gave scientific support to a method named biospeckle which has been employed to study seed viability, biological activity, tissue senescence, tissue water content, fruit bruising, etc. Since the above mentioned method is not invasive and yields numerical values, it can be considered for possible automation associated to several processes, including selection and sorting. Based on these preliminary considerations, this research work proposed to study the interaction of a laser beam with vegetative samples by measuring the incident light intensity and the transmitted light beam intensity at several vegetative slabs of varying thickness. Tests were carried on fifteen slices of apple tissue divided into three thickness groups, i.e., 4 mm, 5 mm, 18 mm and 22 mm. A diode laser beam of 10mW and 632 nm wavelength and a Samsung digital camera were employed to carry the tests. Outgoing images were analyzed by comparing the gray gradient of a fixed image column of each image to obtain a laser penetration scale into the tissue, according to the slice thickness.

Keywords: Fruit, laser, laser transmission, vegetative tissue.

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Authors: Seyed Mohammad Hosseini, Amirhossein Moghanian

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The main purpose of this research was to design a biomimetic system by freeze-drying method for evaluating the effect of adding 5 and 10 mol. % of zinc (Zn) in 58S bioactive glass and gelatin (5ZnBG/G and 10ZnBG/G) in terms of structural and biological changes. The structural analyses of samples were performed by X-Ray Diffraction (XRD), scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy. Also, 3-(4,5dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and alkaline phosphatase (ALP) activity tests were carried out for investigation of MC3T3-E1 cell behaviors. The SEM results demonstrated the spherical shape of the formed hydroxyapatite (HA) phases and also HA characteristic peaks were detected by XRD spectroscopy after 3 days of immersion in the simulated body fluid (SBF) solution. Meanwhile, FTIR spectra proved that the intensity of P–O peaks for 5ZnBG/G was more than 10ZnBG/G and control samples. Moreover, the results of ALP activity test illustrated that the optimal amount of Zn (5ZnBG/G) caused a considerable enhancement in bone cell growth. Taken together, the scaffold with 5 mol.% Zn was introduced as an optimal sample because of its higher biocompatibility, in vitro bioactivity and growth of MC3T3-E1 cells in comparison with other samples in bone tissue engineering.

Keywords: Scaffold, gelatin, modified bioactive glass, ALP, bone tissue engineering.

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Authors: K.Kadirgama, M.M.Noor, K.A. Abou-El-Hossein, H.H.Habeeb, M.M. Rahman, B.Mohamad, R.A. Bakar

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Cutting fluids, usually in the form of a liquid, are applied to the chip formation zone in order to improve the cutting conditions. Cutting fluid can be expensive and represents a biological and environmental hazard that requires proper recycling and disposal, thus adding to the cost of the machining operation. For these reasons dry cutting or dry machining has become an increasingly important approach; in dry machining no coolant or lubricant is used. This paper discussed the effect of the dry cutting on cutting force and tool life when machining aerospace materials (Haynes 242) with using two different coated carbide cutting tools (TiAlN and TiN/MT-TiCN/TiN). Response surface method (RSM) was used to minimize the number of experiments. ParTiAlN Swarm Optimisation (PSO) models were developed to optimize the machining parameters (cutting speed, federate and axial depth) and obtain the optimum cutting force and tool life. It observed that carbide cutting tool coated with TiAlN performed better in dry cutting compared with TiN/MT-TiCN/TiN. On other hand, TiAlN performed more superior with using of 100 % water soluble coolant. Due to the high temperature produced by aerospace materials, the cutting tool still required lubricant to sustain the heat transfer from the workpiece.

Keywords: Dry cutting, partial swarm optimisation, response surface method, tool life

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Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: A. Gruzdz, A. Ihnatowicz, J. Siddiqi, B. Akhgar

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MATCH project [1] entitle the development of an automatic diagnosis system that aims to support treatment of colon cancer diseases by discovering mutations that occurs to tumour suppressor genes (TSGs) and contributes to the development of cancerous tumours. The constitution of the system is based on a) colon cancer clinical data and b) biological information that will be derived by data mining techniques from genomic and proteomic sources The core mining module will consist of the popular, well tested hybrid feature extraction methods, and new combined algorithms, designed especially for the project. Elements of rough sets, evolutionary computing, cluster analysis, self-organization maps and association rules will be used to discover the annotations between genes, and their influence on tumours [2]-[11]. The methods used to process the data have to address their high complexity, potential inconsistency and problems of dealing with the missing values. They must integrate all the useful information necessary to solve the expert's question. For this purpose, the system has to learn from data, or be able to interactively specify by a domain specialist, the part of the knowledge structure it needs to answer a given query. The program should also take into account the importance/rank of the particular parts of data it analyses, and adjusts the used algorithms accordingly.

Keywords: Bioinformatics, gene expression, ontology, selforganizingmaps.

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Authors: Theodore N.S. Karfakis, Anna Andrade, Carolina Volkmer-Castilho, Dennis R. Valle, Eric Arets, Paul van Gardingen

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The aim of the work presented here was to either use existing forest dynamic simulation models or calibrate a new one both within the SYMFOR framework with the purpose of examining changes in stand level basal area and functional composition in response to selective logging considering trees > 10 cm d.b.h for two areas of undisturbed Amazonian non flooded tropical forest in Brazil and one in Peru. Model biological realism was evaluated for forest in the undisturbed and selectively logged state and it was concluded that forest dynamics were realistically represented. Results of the logging simulation experiments showed that in relation to undisturbed forest simulation subject to no form of harvesting intervention there was a significant amount of change over a 90 year simulation period that was positively proportional to the intensity of logging. Areas which had in the dynamic equilibrium of undisturbed forest a greater proportion of a specific ecological guild of trees known as the light hardwoods (LHW’s) seemed to respond more favorably in terms of less deviation but only within a specific range of baseline forest composition beyond which compositional diversity became more important. These finds are in line partially with practical management experience and partiality basic systematics theory respectively.

Keywords: Amazonbasin, ecological species guild, selective logging, simulation modeling.

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Authors: Mughal Yar M, Israr Ul Haq, Bushra Noman

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The stem cells have ability to differentiated themselves through mitotic cell division and various range of specialized cell types. Cellular differentiation is a way by which few specialized cell develops into more specialized.This paper studies the fundamental problem of computational schema for an artificial neural network based on chemical, physical and biological variables of state. By doing this type of study system could be model for a viable propagation of various economically important stem cells differentiation. This paper proposes various differentiation outcomes of artificial neural network into variety of potential specialized cells on implementing MATLAB version 2009. A feed-forward back propagation kind of network was created to input vector (five input elements) with single hidden layer and one output unit in output layer. The efficiency of neural network was done by the assessment of results achieved from this study with that of experimental data input and chosen target data. The propose solution for the efficiency of artificial neural network assessed by the comparatative analysis of “Mean Square Error" at zero epochs. There are different variables of data in order to test the targeted results.

Keywords: Computational shcmin, meiosis, mitosis, neuralnetwork, Stem cell SOM;

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Authors: M. Pandi, K. Premalatha

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The DNA microarray technology concurrently monitors the expression levels of thousands of genes during significant biological processes and across the related samples. The better understanding of functional genomics is obtained by extracting the patterns hidden in gene expression data. It is handled by clustering which reveals natural structures and identify interesting patterns in the underlying data. In the proposed work clustering gene expression data is done through an Advanced Nelder Mead (ANM) algorithm. Nelder Mead (NM) method is a method designed for optimization process. In Nelder Mead method, the vertices of a triangle are considered as the solutions. Many operations are performed on this triangle to obtain a better result. In the proposed work, the operations like reflection and expansion is eliminated and a new operation called spread-out is introduced. The spread-out operation will increase the global search area and thus provides a better result on optimization. The spread-out operation will give three points and the best among these three points will be used to replace the worst point. The experiment results are analyzed with optimization benchmark test functions and gene expression benchmark datasets. The results show that ANM outperforms NM in both benchmarks.

Keywords: Spread out, simplex, multi-minima, fitness function, optimization, search area, monocyte, solution, genomes.

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Authors: Tausif A. Ishtiaque, Zarrin T. Tasin, Kazi S. Akter

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Current trend of urban expansion, especially in the developing countries has caused significant changes in land cover, which is generating great concern due to its widespread environmental degradation. Energy consumption of the cities is also increasing with the aggravated heat island effect. Distribution of land surface temperature (LST) is one of the most significant climatic parameters affected by urban land cover change. Recent increasing trend of LST is causing elevated temperature profile of the built up area with less vegetative cover. Gradual change in land cover, especially decrease in vegetative cover is enhancing the Urban Heat Island (UHI) effect in the developing cities around the world. Increase in the amount of urban vegetation cover can be a useful solution for the reduction of UHI intensity. LST and Normalized Difference Vegetation Index (NDVI) have widely been accepted as reliable indicators of UHI and vegetation abundance respectively. Chittagong, the second largest city of Bangladesh, has been a growth center due to rapid urbanization over the last several decades. This study assesses the intensity of UHI in Chittagong city by analyzing the relationship between LST and NDVI based on the type of land use/land cover (LULC) in the study area applying an integrated approach of Geographic Information System (GIS), remote sensing (RS), and regression analysis. Land cover map is prepared through an interactive supervised classification using remotely sensed data from Landsat ETM+ image along with NDVI differencing using ArcGIS. LST and NDVI values are extracted from the same image. The regression analysis between LST and NDVI indicates that within the study area, UHI is directly correlated with LST while negatively correlated with NDVI. It interprets that surface temperature reduces with increase in vegetation cover along with reduction in UHI intensity. Moreover, there are noticeable differences in the relationship between LST and NDVI based on the type of LULC. In other words, depending on the type of land usage, increase in vegetation cover has a varying impact on the UHI intensity. This analysis will contribute to the formulation of sustainable urban land use planning decisions as well as suggesting suitable actions for mitigation of UHI intensity within the study area.

Keywords: Land cover change, land surface temperature, normalized difference vegetation index, urban heat island.

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Authors: Hekmatpanah, M.

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Since the beginning of human history, human activities have caused many changes in the environment. Today, a particular attention should be paid to gaining knowledge about water quality of wetlands which are pristine natural environments rich in genetic reserves. If qualitative conditions of industrial areas (in terms of both physicochemical and biological conditions) are not addressed properly, they could cause disruption in natural ecosystems, especially in rivers. With regards to the quality of water resources, determination of pollutant sources plays a pivotal role in engineering projects as well as designing water quality control systems. Thus, using different methods such as flow duration curves, dischargepollution load model and frequency analysis by HYFA software package, risk of various industrial pollutants in international and ecologically important Gavkhoni wetland is analyzed. In this study, a station located at Varzaneh City is used as the last station on Zayanderud River, from where the river water is discharged into the wetland. Results showed that elements- concentrations often exceeded the allowed level and river water can endanger regional ecosystem. In addition, if the river discharge is managed on Q25 basis, this basis can lower concentrations of elements, keeping them within the normal level.

Keywords: Pollutants Risk, Industry, Flow Discharge, Management, Gavkhoni Wetland

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Authors: M.S. Mazăre, A. M. Pană, L. M. Ştefan, M. Silion, M. Bălan, G. Bandur, L. M. Rusnac

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In the last decade, carbohydrates have attracted great attention as renewable resources for the chemical industry. Carbohydrates are abundantly found in nature in the form of monomers, oligomers and polymers, or as components of biopolymers and other naturally occurring substances. As natural products, they play important roles in conferring certain physical, chemical, and biological properties to their carrier molecules.The synthesis of this particular carbohydrate glycomonomer is part of our work to obtain biodegradable polymers. Our current paper describes the synthesis and characterization of a novel carbohydrate glycomonomer starting from D-glucose, in several synthesis steps, that involve the protection/deprotection of the D-glucose ring via acetylation, tritylation, then selective deprotection of the aromaticaliphatic protective group, in order to obtain 1,2,3,4-tetra-O-acetyl- 6-O-allyl-β-D-glucopyranose. The glycomonomer was then obtained by the allylation in drastic conditions of 1,2,3,4-tetra-O-acetyl-6-Oallyl- β-D-glucopyranose with allylic alcohol in the presence of stannic chloride, in methylene chloride, at room temperature. The proposed structure of the glycomonomer, 2,3,4-tri-O-acetyl-1,6-di- O-allyl-β-D-glucopyranose, was confirmed by FTIR, NMR and HPLC-MS spectrometry. This glycomonomer will be further submitted to copolymerization with certain acrylic or methacrylic monomers in order to obtain competitive plastic materials for applications in the biomedical field.

Keywords: allylation, D-glucose, glycomonomer, trityl chloride

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Authors: C. Ardil

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This paper presents an original application of multiple criteria decision making analysis theory to the evaluation of aircraft selection problem. The selection of an optimal, efficient and reliable fleet, network and operations planning policy is one of the most important factors in aircraft selection problem. Given that decision making in aircraft selection involves the consideration of a number of opposite criteria and possible solutions, such a selection can be considered as a multiple criteria decision making analysis problem. This study presents a new integrated approach to decision making by considering the multiple criteria utility theory and the maximal regret minimization theory methods as well as aircraft technical, economical, and environmental aspects. Multiple criteria decision making analysis method uses different normalization techniques to allow criteria to be aggregated with qualitative and quantitative data of the decision problem. Therefore, selecting a suitable normalization technique for the model is also a challenge to provide data aggregation for the aircraft selection problem. To compare the impact of different normalization techniques on the decision problem, the vector, linear (sum), linear (max), and linear (max-min) data normalization techniques were identified to evaluate aircraft selection problem. As a logical implication of the proposed approach, it enhances the decision making process through enabling the decision maker to: (i) use higher level knowledge regarding the selection of criteria weights and the proposed technique, (ii) estimate the ranking of an alternative, under different data normalization techniques and integrated criteria weights after a posteriori analysis of the final rankings of alternatives. A set of commercial passenger aircraft were considered in order to illustrate the proposed approach. The obtained results of the proposed approach were compared using Spearman's rho tests. An analysis of the final rank stability with respect to the changes in criteria weights was also performed so as to assess the sensitivity of the alternative rankings obtained by the application of different data normalization techniques and the proposed approach.

Keywords: Normalization Techniques, Aircraft Selection, Multiple Criteria Decision Making, Multiple Criteria Decision Making Analysis, MCDMA

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Authors: Dyah Iswantini, Trivadila, Novik Nurhidayat, Waras Nurcholis

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The antioxidant compounds are needed for the food, beverages, and pharmaceuticals industry. For this purpose, an appropriate method is required to measure the antioxidant properties in various types of samples. Spectrophotometric method usually used has some weaknesses, including the high price, long sample preparation time, and less sensitivity. Among the alternative methods developed to overcome these weaknesses is antioxidant biosensor based on superoxide dismutase (SOD) enzyme. Therefore, this study was carried out to measure the SOD activity originating from Deinococcus radiodurans and to determine its kinetics properties. Carbon paste electrode modified with ferrocene and immobilized SOD exhibited anode and cathode current peak at potential of +400 and +300mv respectively, in both pure SOD and SOD of D. radiodurans. This indicated that the current generated was from superoxide catalytic dismutation reaction by SOD. Optimum conditions for SOD activity was at pH 9 and temperature of 27.50C for D. radiodurans SOD, and pH 11 and temperature of 200C for pure SOD. Dismutation reaction kinetics of superoxide catalyzed by SOD followed the Lineweaver-Burk kinetics with D. radiodurans SOD KMapp value was smaller than pure SOD. The result showed that D. radiodurans SOD had higher enzyme-substrate affinity and specificity than pure SOD. It concluded that D. radiodurans SOD had a great potential as biological recognition component for antioxidant biosensor.

Keywords: Antioxidant biosensor, Deinococcus radiodurans, enzyme kinetic, superoxide dismutase (SOD).

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Authors: Hachem Ben Naceur, Amel Ben Rejeb Jenhani, Mohamed Salah Romdhane

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Endemic Artemia franciscana populations can be found throughout the American continent and also as an introduced specie in several country all over the world, such as in the Mediterranean region where Artemia franciscana was identified as an invasive specie replacing native Artemia parthenogenetica and Artemia salina. In the present study, the characterization of the new invasive Artemia franciscana reported from Sabkhet Halk El-Menzel (Tunisia) was done based on the cysts biometry, nauplii instar-I length, Adult sexual dimorphism and fatty acid profile. The mean value of the diameter of non-decapsulated and decapsulated cysts, chorion thickness and naupliar length is 235.8, 226.3, 4.75 and 426.8 μm, respectively. Sexual dimorphism for adults specimen showed that maximal distance between compound eyes, diameter for compound eyes, length of first antenna and the abdomen length compared to the total body length ratio, are the most important variables for males and females discrimination with a total contribution of 62.39 %. The analysis of fatty acid methyl esters profile of decapsulated cysts resulted in low levels of linolenic acid (LLA, C18:3n-3) and high levels of eicosapentaenoic acid (EPA, C20:5n-3) with 3.11 and 11.10 %, respectively. Low quantity of docosahexaenoic acid (DHA, 22:6n-3) was also observed with 0.17 mg.g-1 dry weight.

Keywords: Invasive Artemia franciscana, biometry, sexualdimorphism, fatty acid, Tunisia.

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Authors: Cathal Merz, Gareth O’Donnell

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Coil reinforced thin-walled (CRTW) tubes are used in medicine to treat problems affecting blood vessels within the body through minimally invasive procedures. The CRTW tube considered in this research makes up part of such a device and is inserted into the patient via their femoral or brachial arteries and manually navigated to the site in need of treatment. This procedure replaces the requirement to perform open surgery but is limited by reduction of blood vessel lumen diameter and increase in tortuosity of blood vessels deep in the brain. In order to maximize the capability of these procedures, CRTW tube devices are being manufactured with decreasing wall thicknesses in order to deliver treatment deeper into the body and to allow passage of other devices through its inner diameter. This introduces significant stresses to the device materials which have resulted in an observed increase in the breaking of the proximal segment of the device into two separate pieces after it has failed by buckling. As there is currently no international standard for measuring the mechanical properties of these CRTW tube devices, it is difficult to accurately analyze this problem. The aim of the current work is to address this discrepancy in the biomedical device industry by developing a measurement system that can be used to quantify the effect of process and design changes on CRTW tube performance, aiding in the development of better performing, next generation devices. Using materials testing frames, micro-computed tomography (micro-CT) imaging, experiment planning, analysis of variance (ANOVA), T-tests and regression analysis, test methods have been developed for assessing the impact of process and design changes on the device. The major findings of this study have been an insight into the suitability of buckle and three-point bend tests for the measurement of the effect of varying processing factors on the device’s performance, and guidelines for interpreting the output data from the test methods. The findings of this study are of significant interest with respect to verifying and validating key process and design changes associated with the device structure and material condition. Test method integrity evaluation is explored throughout.

Keywords: Buckling, coil reinforced thin-walled tubes, fracture, test method.

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

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Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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Authors: A. Taqaddas

Abstract:

Purpose: Planning and dosimetry of different VMAT algorithms (SmartArc, Ergo++, Autobeam) is compared with IMRT for Head and Neck Cancer patients. Modelling was performed to rule out the causes of discrepancies between planned and delivered dose. Methods: Five HNC patients previously treated with IMRT were re-planned with SmartArc (SA), Ergo++ and Autobeam. Plans were compared with each other and against IMRT and evaluated using DVHs for PTVs and OARs, delivery time, monitor units (MU) and dosimetric accuracy. Modelling of control point (CP) spacing, Leaf-end Separation and MLC/Aperture shape was performed to rule out causes of discrepancies between planned and delivered doses. Additionally estimated arc delivery times, overall plan generation times and effect of CP spacing and number of arcs on plan generation times were recorded. Results: Single arc SmartArc plans (SA4d) were generally better than IMRT and double arc plans (SA2Arcs) in terms of homogeneity and target coverage. Double arc plans seemed to have a positive role in achieving improved Conformity Index (CI) and better sparing of some Organs at Risk (OARs) compared to Step and Shoot IMRT (ss-IMRT) and SA4d. Overall Ergo++ plans achieved best CI for both PTVs. Dosimetric validation of all VMAT plans without modelling was found to be lower than ss-IMRT. Total MUs required for delivery were on average 19%, 30%, 10.6% and 6.5% lower than ss-IMRT for SA4d, SA2d (Single arc with 2⁰ Gantry Spacing), SA2Arcs and Autobeam plans respectively. Autobeam was most efficient in terms of actual treatment delivery times whereas Ergo++ plans took longest to deliver. Conclusion: Overall SA single arc plans on average achieved best target coverage and homogeneity for both PTVs. SA2Arc plans showed improved CI and some OARs sparing. Very good dosimetric results were achieved with modelling. Ergo++ plans achieved best CI. Autobeam resulted in fastest treatment delivery times.

Keywords: Dosimetry, Intensity Modulated Radiotherapy, Optimization Algorithms, Volumetric Modulated Arc Therapy.

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