Search results for: marine biology

Authors: Georgi Yordanov Georgiev, Michael Daly, Erin Gombos, Amrit Vinod, Gajinder Hoonjan

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Measures of complexity and entropy have not converged to a single quantitative description of levels of organization of complex systems. The need for such a measure is increasingly necessary in all disciplines studying complex systems. To address this problem, starting from the most fundamental principle in Physics, here a new measure for quantity of organization and rate of self-organization in complex systems based on the principle of least (stationary) action is applied to a model system - the central processing unit (CPU) of computers. The quantity of organization for several generations of CPUs shows a double exponential rate of change of organization with time. The exact functional dependence has a fine, S-shaped structure, revealing some of the mechanisms of self-organization. The principle of least action helps to explain the mechanism of increase of organization through quantity accumulation and constraint and curvature minimization with an attractor, the least average sum of actions of all elements and for all motions. This approach can help describe, quantify, measure, manage, design and predict future behavior of complex systems to achieve the highest rates of self organization to improve their quality. It can be applied to other complex systems from Physics, Chemistry, Biology, Ecology, Economics, Cities, network theory and others where complex systems are present.

Keywords: Organization, self-organization, complex system, complexification, quantitative measure, principle of least action, principle of stationary action, attractor, progressive development, acceleration, stochastic.

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Authors: A. Guellati, F-M Lounis, N. Guemras, K. Daoud

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Micro droplet formation is considered as a growing emerging area of research due to its wide-range application in chemistry as well as biology. The mechanism of micro droplet formation using two immiscible liquids running through a T-junction has been widely studied. We believe that the flow of these two immiscible phases can be of greater important factor that could have an impact on out-flow hydrodynamic behavior, the droplets generated and the size of the droplets. In this study, the type of the capillary tubes used also represents another important factor that can have an impact on the generation of micro droplets. The tygon capillary tubing with hydrophilic inner surface doesn't allow regular out-flows due to the fact that the continuous phase doesn't adhere to the wall of the capillary inner surface. Teflon capillary tubing, presents better wettability than tygon tubing, and allows to obtain steady and regular regimes of out-flow, and the micro droplets are homogeneoussize. The size of the droplets is directly dependent on the flows of the continuous and dispersed phases. Thus, as increasing the flow of the continuous phase, to flow of the dispersed phase stationary, the size of the drops decreases. Inversely, while increasing the flow of the dispersed phase, to flow of the continuous phase stationary, the size of the droplet increases.

Keywords: Microfluidic system, micro droplets generation, T-junction.

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Authors: Alaa Al Hawari, Mohammad Khader, Wael El Hasan, Mahmoud Alijla, Ammar Manawi, Abdelbaki Benamour

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The production of aluminum alloys and ingots – starting from the processing of alumina to aluminum, and the final cast product – was studied using a Life Cycle Assessment (LCA) approach. The studied aluminum supply chain consisted of a carbon plant, a reduction plant, a casting plant, and a power plant. In the LCA model, the environmental loads of the different plants for the production of 1 ton of aluminum metal were investigated. The impact of the aluminum production was assessed in eight impact categories. The results showed that for all of the impact categories the power plant had the highest impact only in the cases of Human Toxicity Potential (HTP) the reduction plant had the highest impact and in the Marine Aquatic Eco-Toxicity Potential (MAETP) the carbon plant had the highest impact. Furthermore, the impact of the carbon plant and the reduction plant combined was almost the same as the impact of the power plant in the case of the Acidification Potential (AP). The carbon plant had a positive impact on the environment when it come to the Eutrophication Potential (EP) due to the production of clean water in the process. The natural gas based power plant used in the case study had 8.4 times less negative impact on the environment when compared to the heavy fuel based power plant and 10.7 times less negative impact when compared to the hard coal based power plant.

Keywords: Life cycle assessment, aluminum production, Supply chain.

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Authors: Francisco Javier Reyes Salazar, Héctor Mauricio Ramírez

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The coastal zones are home to mangrove swamps, coral reefs, and seagrass ecosystems, which are the most biodiverse and fragile on the planet. These areas support a great diversity of marine life; they are also extraordinarily important for humans in the provision of food, water, wood, and other associated goods and services; they also contribute to climate regulation. The lack of an automated model that generates information on the dynamics of changes in coastlines and coastal erosion is identified as a central problem. In this paper, coastlines were determined from 1984 to 2020 on the Google Earth Engine platform from Landsat and Sentinel images. Then, we determined the Modified Normalized Difference Water Index (MNDWI) and used Digital Shoreline Analysis System (DSAS) v5.0. Starting from the 2020 coastline; the 10-year prediction (Year 2031) was determined with the erosion of 238.32 hectares and an accretion of 181.96 hectares. For the 20-year prediction (Year 2041) will be presented an erosion of 544.04 hectares and an accretion of 133.94 hectares. The erosion and accretion of Playa Muelle in the municipality of Puerto Colombia were established, which will register the highest value of erosion. The coverage that presented the greatest change was that of artificialized territories.

Keywords: Coastline, coastal erosion, MNDWI, Google Earth Engine, Colombia.

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Authors: Md. Ashikur Rahman Khan, M. M. Rahman, K. Kadirgama

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Artificial neural networks (ANN) are used in distinct researching fields and professions, and are prepared by cooperation of scientists in different fields such as computer engineering, electronic, structure, biology and so many different branches of science. Many models are built correlating the parameters and the outputs in electrical discharge machining (EDM) concern for different types of materials. Up till now model for Ti-5Al-2.5Sn alloy in the case of electrical discharge machining performance characteristics has not been developed. Therefore, in the present work, it is attempted to generate a model of material removal rate (MRR) for Ti-5Al-2.5Sn material by means of Artificial Neural Network. The experimentation is performed according to the design of experiment (DOE) of response surface methodology (RSM). To generate the DOE four parameters such as peak current, pulse on time, pulse off time and servo voltage and one output as MRR are considered. Ti-5Al-2.5Sn alloy is machined with positive polarity of copper electrode. Finally the developed model is tested with confirmation test. The confirmation test yields an error as within the agreeable limit. To investigate the effect of the parameters on performance sensitivity analysis is also carried out which reveals that the peak current having more effect on EDM performance.

Keywords: Ti-5Al-2.5Sn, material removal rate, copper tungsten, positive polarity, artificial neural network, multi-layer perceptron.

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Authors: P. Kowalska, P. Gabka, K. Kamieniarz, M. Kamieniarz, W. Stryla, P. Guzik, T. Krauze

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We have developed a computer program consisting of 6 subtests assessing the children hand dexterity applicable in the rehabilitation medicine. We have carried out a normative study on a representative sample of 285 children aged from 7 to 15 (mean age 11.3) and we have proposed clinical standards for three age groups (7-9, 9-11, 12-15 years). We have shown statistical significance of differences among the corresponding mean values of the task time completion. We have also found a strong correlation between the task time completion and the age of the subjects, as well as we have performed the test-retest reliability checks in the sample of 84 children, giving the high values of the Pearson coefficients for the dominant and non-dominant hand in the range 0.740.97 and 0.620.93, respectively. A new MATLAB-based programming tool aiming at analysis of cardiologic RR intervals and blood pressure descriptors, is worked out, too. For each set of data, ten different parameters are extracted: 2 in time domain, 4 in frequency domain and 4 in Poincaré plot analysis. In addition twelve different parameters of baroreflex sensitivity are calculated. All these data sets can be visualized in time domain together with their power spectra and Poincaré plots. If available, the respiratory oscillation curves can be also plotted for comparison. Another application processes biological data obtained from BLAST analysis.

Keywords: Biomedical data base processing, Computer software, Hand dexterity, Heart rate and blood pressure variability.

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Authors: Jameela Ali Alkrimi, Loay E. George, Azizah Suliman, Abdul Rahim Ahmad, Karim Al-Jashamy

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Red blood cells (RBCs) are among the most commonly and intensively studied type of blood cells in cell biology. Anemia is a lack of RBCs is characterized by its level compared to the normal hemoglobin level. In this study, a system based image processing methodology was developed to localize and extract RBCs from microscopic images. Also, the machine learning approach is adopted to classify the localized anemic RBCs images. Several textural and geometrical features are calculated for each extracted RBCs. The training set of features was analyzed using principal component analysis (PCA). With the proposed method, RBCs were isolated in 4.3secondsfrom an image containing 18 to 27 cells. The reasons behind using PCA are its low computation complexity and suitability to find the most discriminating features which can lead to accurate classification decisions. Our classifier algorithm yielded accuracy rates of 100%, 99.99%, and 96.50% for K-nearest neighbor (K-NN) algorithm, support vector machine (SVM), and neural network RBFNN, respectively. Classification was evaluated in highly sensitivity, specificity, and kappa statistical parameters. In conclusion, the classification results were obtained within short time period, and the results became better when PCA was used.

Keywords: Red blood cells, pre-processing image algorithms, classification algorithms, principal component analysis PCA, confusion matrix, kappa statistical parameters, ROC.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

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The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Lakshman Singh, Rajeshwar Singh, Naveen Kumar Singh, Davinder Singh, Pargat Singh

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Tungsten Inert Gas (TIG) welding is a high quality welding process used to weld the thin metals and their alloy. 5083 Aluminium alloys play an important role in engineering and metallurgy field because of excellent corrosion properties, ease of fabrication and high specific strength coupled with best combination of toughness and formability.

TIG welding technique is one of the precise and fastest processes used in aerospace, ship and marine industries. TIG welding process is used to analyze the data and evaluate the influence of input parameters on tensile strength of 5083 Al-alloy specimens with dimensions of 100mm long x 15mm wide x 5mm thick. Welding current (I), gas flow rate (G) and welding speed (S) are the input parameters which effect tensile strength of 5083 Al-alloy welded joints. As welding speed increased, tensile strength increases first till optimum value and after that both decreases by increasing welding speed further. Results of the study show that maximum tensile strength of 129 MPa of weld joint are obtained at welding current of 240 Amps, gas flow rate of 7 Lt/min and welding speed of 98 mm/min. These values are the optimum values of input parameters which help to produce efficient weld joint that have good mechanical properties as a tensile strength.

Keywords: 5083 Aluminium alloy, Gas flow rate, TIG welding, Welding current, Welding speed and Tensile strength.

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Authors: F. Kashanian, M. M. Masoudi, A. Akbari, A. Shamloo, M. R. Zand, S. S. Salehi

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Nano-sized materials present new opportunities in biology and medicine and they are used as biomedical tools for investigation, separation of molecules and cells. To achieve more effective cancer therapy, it is essential to select cancer cells exactly. This research suggests that using the antibody-functionalized nontoxic Arginine-doped magnetic nanoparticles (A-MNPs), has been prosperous in detection, capture, and magnetic separation of circulating tumor cells (CTCs) in tumor tissue. In this study, A-MNPs were synthesized via a simple precipitation reaction and directly immobilized Ep-CAM EBA-1 antibodies over superparamagnetic A-MNPs for Mucin BCA-225 in breast cancer cell. The samples were characterized by vibrating sample magnetometer (VSM), FT-IR spectroscopy, Tunneling Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM). These antibody-functionalized nontoxic A-MNPs were used to capture breast cancer cell. Through employing a strong permanent magnet, the magnetic separation was achieved within a few seconds. Antibody-Conjugated nontoxic Arginine-doped Fe₃O₄ nanoparticles have the potential for the future study to capture CTCs which are released from tumor tissue and for drug delivery, and these results demonstrate that the antibody-conjugated A-MNPs can be used in magnetic hyperthermia techniques for cancer treatment.

Keywords: Tumor tissue, antibody, magnetic nanoparticle, CTCs capturing.

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Authors: Indrijuli Magsari Putri, Dicky R. Munaf

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The purpose of this paper is to guide the effort in improving the economic added value of Indonesian fisheries product through post fishing program, which is cold storage program. Indonesia's fisheries potential has been acknowledged by the world. FAO (2009) stated that Indonesia is one of the tenth highest producers of fishery products in the world. Based on BPS (Statistics Indonesia data), the national fisheries production in 2011 reached 5.714 million tons, which 93.55% came from marine fisheries and 6.45% from open waters. Indonesian territory consist of 2/3 of Indonesian waters, has given enormous benefits for Indonesia, especially fishermen. To improve the economic level of fishermen requires efforts to develop fisheries business unit. On of the efforts is by improving the quality of products which are marketed in the regional and international levels. It is certainly need the support of the existence of various fishery facilities (infrastructure to superstructure), one of which is cold storage. Given the many benefits of cold storage as a means of processing of fishery resources, Indonesia Maritime Security Coordinating Board (IMSCB) as one of the maritime institutions for maritime security and safety, has a program to empower the coastal community through encourages the development of cold storage in the middle and lower fishery business unit. The development of cold storage facilities which able to run its maximum role requires synergistic efforts of various parties.

Keywords: Cold Storage, Fish, Regulation.

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Authors: L. Vujičić, Ž. Ivković, Ž. Boneta

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There is a widespread belief in everyday discourse that science subjects (physics, chemistry and biology) are, along with math, the most difficult school subjects in the education of an individual. This assumption is usually justified by the following facts: low GPA in these subjects, the number of pupils who fail these subjects is high in comparison to other subjects, and the number of pupils interested in continuing their studies in the fields with a focus on science subjects is lower compared to non-science-oriented fields. From that perspective, the project: “Could it be different? How do children explore it?” becomes extremely interesting because it is focused on young children and on the introduction of new methods, with aim of arousing interest in scientific literacy development in 10 kindergartens by applying the methodology of an action research, with an ethnographic approach. We define scientific literacy as a process of encouraging and nurturing the research and explorative spirit in children, as well as their natural potential and abilities that represent an object of scientific research: to learn about exploration by conducting exploration. Upon project completion, an evaluation questionnaire was created for the parents of the children who had participated in the project, as well as for those whose children had not been involved in the project. The purpose of the first questionnaire was to examine the level of satisfaction with the project implementation and its outcomes among those parents whose children had been involved in the project (N=142), while the aim of the second questionnaire was to find out how much the parents of the children not involved (N=154) in this activity were interested in this topic.

Keywords: Documenting, early childhood education, evaluation questionnaire for parents, scientific literacy development.

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Authors: Azam Fazelpour, Saeed R. Dehghani, Vlastimil Masek, Yuri S. Muzychka

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This study employs a method based on image analyses and structure information to detect accumulated ice on known structures. The icing of marine vessels and offshore structures causes significant reductions in their efficiency and creates unsafe working conditions. Image processing methods are used to measure ice loads automatically. Most image processing methods are developed based on captured image analyses. In this method, ice loads on structures are calculated by defining structure coordinates and processing captured images. A pyramidal structure is designed with nine cylindrical bars as the known structure of experimental setup. Unsymmetrical ice accumulated on the structure in a cold room represents the actual case of experiments. Camera intrinsic and extrinsic parameters are used to define structure coordinates in the image coordinate system according to the camera location and angle. The thresholding method is applied to capture images and detect iced structures in a binary image. The ice thickness of each element is calculated by combining the information from the binary image and the structure coordinate. Averaging ice diameters from different camera views obtains ice thicknesses of structure elements. Comparison between ice load measurements using this method and the actual ice loads shows positive correlations with an acceptable range of error. The method can be applied to complex structures defining structure and camera coordinates.

Keywords: Camera calibration, Ice detection, ice load measurements, image processing.

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Authors: Sarkar M. A. Kawsar, Sarkar M. A. Mamun, Md S. Rahman, Hidetaro Yasumitsu, Yasuhiro Ozeki

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The present study has been taken to explore the screening of in vitro antimicrobial activities of D-galactose-binding sponge lectin (HOL-30). HOL-30 was purified from the marine demosponge Halichondria okadai by affinity chromatography. The molecular mass of the lectin was determined to be 30 kDa with a single polypeptide by SDS-PAGE under non-reducing and reducing conditions. HOL-30 agglutinated trypsinized and glutaraldehydefixed rabbit and human erythrocytes with preference for type O erythrocytes. The lectin was subjected to evaluation for inhibition of microbial growth by the disc diffusion method against eleven human pathogenic gram-positive and gram-negative bacteria. The lectin exhibited strong antibacterial activity against gram-positive bacteria, such as Bacillus megaterium and Bacillus subtilis. However, it did not affect against gram-negative bacteria such as Salmonella typhi and Escherichia coli. The largest zone of inhibition was recorded of Bacillus megaterium (12 in diameter) and Bacillus subtilis (10 mm in diameter) at a concentration of the lectin (250 μg/disc). On the other hand, the antifungal activity of the lectin was investigated against six phytopathogenic fungi based on food poisoning technique. The lectin has shown maximum inhibition (22.83%) of mycelial growth of Botrydiplodia theobromae at a concentration of 100 μg/mL media. These findings indicate that the lectin may be of importance to clinical microbiology and have therapeutic applications.

Keywords: Antibacterial, Halichondria okadai, Inhibition zone, Lectin.

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Authors: Anis S. Shuib, Peter R. Hoskins, William J. Easson

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Cardiovascular diseases, principally atherosclerosis, are responsible for 30% of world deaths. Atherosclerosis is due to the formation of plaque. The fatty plaque may be at risk of rupture, leading typically to stroke and heart attack. The plaque is usually associated with a high degree of lumen reduction, called a stenosis.It is increasingly recognized that the initiation and progression of disease and the occurrence of clinical events is a complex interplay between the local biomechanical environment and the local vascular biology. The aim of this study is to investigate the flow behavior through a stenosed artery. A physical experiment was performed using an artery model and blood analogue fluid. An axisymmetric model constructed consists of contraction and expansion region that follow a mathematical form of cosine function. A 30% diameter reduction was used in this study. The flow field was measured using particle image velocimetry (PIV). Spherical particles with 20μm diameter were seeded in a water-glycerol-NaCl mixture. Steady flow Reynolds numbers are 250. The area of interest is the region after the stenosis where the flow separation occurs. The velocity field was measured and the velocity gradient was investigated. There was high particle concentration in the recirculation zone. High velocity gradient formed immediately after the stenosis throat created a lift force that enhanced particle migration to the flow separation area.

Keywords: Stenosis artery, Biofluid mechanics, PIV

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Authors: Joel S. Mtebe, Aron Kondoro, Mussa M. Kissaka, Elia Kibga

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Sub-Saharan Africa is described as the second fastest growing in mobile phone penetration in the world more than in the United States or the European Union. Mobile phones have been used to provide a lot of opportunities to improve people’s lives in the region such as in banking, marketing, entertainment, and paying for various bills such as water, TV, and electricity. However, the potential of mobile phones to enhance teaching and learning has not been explored. This study presents an experience of developing and delivering SMS based quiz questions used to assess mastery of subject content knowledge of science and mathematics secondary school teachers in Tanzania. The SMS quizzes were used as a follow up support mechanism to 500 teachers who participated in a project to upgrade subject content knowledge of teachers in science and mathematics subjects in Tanzania. Quizzes of 10-15 questions were sent to teachers each week for 8 weeks and the results were analyzed using SPSS. Results show that teachers who participated in chemistry and biology subjects have better performance compared to those who participated in mathematics and physics subjects. Teachers reported some challenges that led to poor performance, This research has several practical implications for those who are implementing or planning to use mobile phones in teaching and learning especially in rural secondary schools in sub-Saharan Africa.

Keywords: Mobile learning, e-learning, educational technologies, SMS, secondary education, assessment.

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Authors: Eusebio A. Jiménez-Arévalo, Deifilia Ahuatzi-Chacón, Juvencio Galíndez-Mayer, Cleotilde Juárez-Ramírez, Nora Ruiz-Ordaz

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Bendiocarb is a known toxic xenobiotic that presents acute and chronic risks for freshwater invertebrates and estuarine and marine biota; thus, the treatment of water contaminated with the insecticide is of concern. In this paper, a bacterial community with the capacity to grow in bendiocarb as its sole carbon and nitrogen source was isolated by enrichment techniques in batch culture, from samples of a composting plant located in the northeast of Mexico City. Eight cultivable bacteria were isolated from the microbial community, by PCR amplification of 16 rDNA; Pseudoxanthomonas spadix (NC_016147.2, 98%), Ochrobacterium anthropi (NC_009668.1, 97%), Staphylococcus capitis (NZ_CP007601.1, 99%), Bosea thiooxidans. (NZ_LMAR01000067.1, 99%), Pseudomonas denitrificans. (NC_020829.1, 99%), Agromyces sp. (NZ_LMKQ01000001.1, 98%), Bacillus thuringiensis. (NC_022873.1, 97%), Pseudomonas alkylphenolia (NZ_CP009048.1, 98%). NCBI accession numbers and percentage of similarity are indicated in parentheses. These bacteria were regarded as the isolated species for having the best similarity matches. The ability to degrade bendiocarb by the immobilized bacterial community in a packed bed biofilm reactor, using as support volcanic stone fragments (tezontle), was evaluated. The reactor system was operated in batch using mineral salts medium and 30 mg/L of bendiocarb as carbon and nitrogen source. With this system, an overall removal efficiency (η_bend) rounding 90%, was reached.

Keywords: Bendiocarb, biodegradation, biofilm reactor, carbamate insecticide.

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Authors: Kent Salomonsson, Xuefang Zhao, Sara Kallin

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Human soft tissue is loaded and deformed by any activity, an effect known as a stress-strain relationship, and is often described by a load and tissue elongation curve. Several advances have been made in the fields of biology and mechanics of soft human tissue. However, there is limited information available on in vivo tissue mechanical characteristics and behavior. Confident mechanical properties of human soft tissue cannot be extrapolated from e.g. animal testing. Thus, there is need for non invasive methods to analyze mechanical characteristics of soft human tissue. In the present study, the internal mechanical conditions of the lower limb, which is subject to an external load, is studied by use of the finite element method. A detailed finite element model of the lower limb is made possible by use of MRI scans. Skin, fat, bones, fascia and muscles are represented separately and the material properties for them are obtained from literature. Previous studies have been shown to address macroscopic deformation features, e.g. indentation depth, to a large extent. However, the detail in which the internal anatomical features have been modeled does not reveal the critical internal strains that may induce hypoxia and/or eventual tissue damage. The results of the present study reveals that lumped material models, i.e. averaging of the material properties for the different constituents, does not capture regions of critical strains in contrast to more detailed models.

Keywords: FEM, human soft tissue, indentation, properties.

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Authors: F. Noto, M. Castro, R. Garraffo, An. Mirabella, A. Rizzo, G. Cuttone

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The door fan test is a verification procedure on the tightness of a room, necessary following the installation of saturation extinguishing systems and made mandatory according to the UNI 15004-1: 2019 standard whenever a gas extinguishing system is designed and installed. The door fan test was carried out at the Portopalo di Capo Passero headquarters of the Southern National Laboratories and highlighted how the Data Processing Center (CED) is perfectly up to standard, passing the door fan test in an excellent way. The Southern National Laboratories constitute a solid research reality, well established in the international scientific panorama. The CED in the Portopalo site has been expanded, so the extinguishing system has been expanded according to a detailed design. After checking the correctness of the design to verify the absence of air leaks, we carried out the door fan test. The activities of the Laboratori Nazionali del Sud (LNS) are mainly aimed at basic research in the field of Nuclear Physics, Nuclear and Particle Astrophysics. The Portopalo site will host some of the largest submarine wired scientific research infrastructures built in Europe and in the world, such as KM3NeT and EMSO ERIC; in particular, the site research laboratory in Portopalo will host the power supply and data acquisition systems of the underwater infrastructures, and a technological backbone will be created, unique in the Mediterranean, capable of allowing the connection, at abyssal depths, of dozens of real-time surveying and research structures of the marine environment deep.

Keywords: KM3Net, fire protection, door fan test, CED.

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Authors: Sayyed R Mousavi

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The Far From Most Strings Problem (FFMSP) is to obtain a string which is far from as many as possible of a given set of strings. All the input and the output strings are of the same length, and two strings are said to be far if their hamming distance is greater than or equal to a given positive integer. FFMSP belongs to the class of sequences consensus problems which have applications in molecular biology. The problem is NP-hard; it does not admit a constant-ratio approximation either, unless P = NP. Therefore, in addition to exact and approximate algorithms, (meta)heuristic algorithms have been proposed for the problem in recent years. On the other hand, in the recent years, hybrid algorithms have been proposed and successfully used for many hard problems in a variety of domains. In this paper, a new metaheuristic algorithm, called Constructive Beam and Local Search (CBLS), is investigated for the problem, which is a hybridization of constructive beam search and local search algorithms. More specifically, the proposed algorithm consists of two phases, the first phase is to obtain several candidate solutions via the constructive beam search and the second phase is to apply local search to the candidate solutions obtained by the first phase. The best solution found is returned as the final solution to the problem. The proposed algorithm is also similar to memetic algorithms in the sense that both use local search to further improve individual solutions. The CBLS algorithm is compared with the most recent published algorithm for the problem, GRASP, with significantly positive results; the improvement is by order of magnitudes in most cases.

Keywords: Bioinformatics, Far From Most Strings Problem, Hybrid metaheuristics, Matheuristics, Sequences consensus problems.

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Authors: Sitansu Kumar Verma, Soni Yadav, Jitendra Singh, Shraddha, Ajay Kumar

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MicroRNAs (miRNAs), a class of approximately 22 nucleotide long non coding RNAs which play critical role in different biological processes. The mature microRNA is usually 19–27 nucleotides long and is derived from a bigger precursor that folds into a flawed stem-loop structure. Mature micro RNAs are involved in many cellular processes that encompass development, proliferation, stress response, apoptosis, and fat metabolism by gene regulation. Resent finding reveals that certain viruses encode their own miRNA that processed by cellular RNAi machinery. In recent research indicate that cellular microRNA can target the genetic material of invading viruses. Cellular microRNA can be used in the virus life cycle; either to up regulate or down regulate viral gene expression Computational tools use in miRNA target prediction has been changing drastically in recent years. Many of the methods have been made available on the web and can be used by experimental researcher and scientist without expert knowledge of bioinformatics. With the development and ease of use of genomic technologies and computational tools in the field of microRNA biology has superior tremendously over the previous decade. This review attempts to give an overview over the genome wide approaches that have allow for the discovery of new miRNAs and development of new miRNA target prediction tools and databases.

Keywords: MicroRNAs, computational tools, gene regulation, databases, RNAi.

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Authors: Kuncoro Harto Widodo, Joewono Soemardjito, Dwi Ardianta Kurniawan

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Currently, the demand for marine and fisheries commodity in Yogyakarta, Indonesia continues to increase. The existing condition shows that the aquaculture supply cannot be supplied by Yogyakarta region itself, but still need to be supported by regions outside Yogyakarta. The effort to optimize the market is initiated by reviewing and designing the supply chain of production and trade of aquaculture commodity in order to create the implementation of aquaculture production and trade commodity optimally. This formulated supply chain model indicates 4 performance indicators of measurable success in terms of: (1) efficiency; (2) flexibility; (3) responsiveness; and (4) quality. These indicators had been exercised as the success benchmarks for priority marketing management in local level as well as national level. The result of this research indicates that if the catfish fishery system is managed as business as usual then the catfish demand in Yogyakarta region will experience to increase in the future. The increase of demand is inline with the increase of number of people in Yogyakarta and also the fluctuation of catfish consumption per capita. The highest production of catfish will experience in the third year approximately 30,118 tons. Other result of the research indicates that the catfish demand in Yogyakarta region cannot be supplied yet from the local region. Therefore, to fulfill the supply from outside Yogyakarta region, the local farmers should improve the supply through land extension. The fluctuation of commodity price will experience in the future annually and the catfish supply from outside Yogyakarta region will be lowering the price in the market.

Keywords: Supply chain model, catfish, efficiency, flexibility

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Authors: Werner Sandmann, Verena Wolf

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Stochastic models of biological networks are well established in systems biology, where the computational treatment of such models is often focused on the solution of the so-called chemical master equation via stochastic simulation algorithms. In contrast to this, the development of storage-efficient model representations that are directly suitable for computer implementation has received significantly less attention. Instead, a model is usually described in terms of a stochastic process or a "higher-level paradigm" with graphical representation such as e.g. a stochastic Petri net. A serious problem then arises due to the exponential growth of the model-s state space which is in fact a main reason for the popularity of stochastic simulation since simulation suffers less from the state space explosion than non-simulative numerical solution techniques. In this paper we present transition class models for the representation of biological network models, a compact mathematical formalism that circumvents state space explosion. Transition class models can also serve as an interface between different higher level modeling paradigms, stochastic processes and the implementation coded in a programming language. Besides, the compact model representation provides the opportunity to apply non-simulative solution techniques thereby preserving the possible use of stochastic simulation. Illustrative examples of transition class representations are given for an enzyme-catalyzed substrate conversion and a part of the bacteriophage λ lysis/lysogeny pathway.

Keywords: Computational Modeling, Biological Networks, Stochastic Models, Markov Chains, Transition Class Models.

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Authors: Wilson Handoko, Farshid Pahlevani, Isha Singla, Himanish Kumar, Veena Sahajwalla

Abstract:

Aluminium bronze alloys are well known for their superior abrasion, tensile strength and non-magnetic properties, due to the co-presence of iron (Fe) and aluminium (Al) as alloying elements and have been commonly used in many industrial applications. However, continuous exposure to the marine environment will accelerate the risk of a tendency to Al bronze alloys parts failures. Although a higher level of corrosion resistance properties can be achieved by modifying its elemental composition, it will come at a price through the complex manufacturing process and increases the risk of reducing the ductility of Al bronze alloy. In this research, the use of ironmaking slag and waste plastic as the input source for surface modification of Al bronze alloy was implemented. Microstructural analysis conducted using polarised light microscopy and scanning electron microscopy (SEM) that is equipped with energy dispersive spectroscopy (EDS). An electrochemical corrosion test was carried out through Tafel polarisation method and calculation of protection efficiency against the base-material was determined. Results have indicated that uniform modified surface which is as the result of selective diffusion process, has enhanced corrosion resistance properties up to 12.67%. This approach has opened a new opportunity to access various industrial utilisations in commercial scale through minimising the dependency on natural resources by transforming waste sources into the protective coating in environmentally friendly and cost-effective ways.

Keywords: Aluminium bronze, waste-based surface modification, Tafel polarisation, corrosion resistance.

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Authors: Inci Develioglu, Hasan Firat Pulat

Abstract:

Sustainable development is one of the most important topics in today's world, and it is also an important research topic for geoenvironmental engineering. Dredging process is performed to expand the river and port channel, flood control and accessing harbors. Every year large amount of sediment are dredged for these purposes. Dredged marine soils can be reused as filling materials, road and foundation embankments, construction materials and wildlife habitat developments. In this study, geotechnical engineering properties and compressibility behavior of dredged soil obtained from the Izmir Bay were investigated. The samples with four different organic matter contents were obtained and particle size distributions, consistency limits, pH and specific gravity tests were performed. The consolidation tests were conducted to examine organic matter content (OMC) effects on compressibility behavior of dredged soil. This study has shown that the OMC has an important effect on the engineering properties of dredged soils. The liquid and plastic limits increased with increasing OMC. The lowest specific gravity belonged to sample which has the maximum OMC. The specific gravity values ranged between 2.76 and 2.52. The maximum void ratio difference belongs to sample with the highest OMC (De_11% = 0.38)_. As the organic matter content of the samples increases, the change in the void ratio has also increased. The compression index increases with increasing OMC.

Keywords: Compressibility, consolidation, geotechnical properties, organic matter content, organic soils.

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Authors: J. P. Panda, K. Sasmal, H. V. Warrior

Abstract:

Eddy viscosity models in turbulence modeling can be mainly classified as linear and nonlinear models. Linear formulations are simple and require less computational resources but have the disadvantage that they cannot predict actual flow pattern in complex geophysical flows where streamline curvature and swirling motion are predominant. A constitutive equation of Reynolds stress anisotropy is adopted for the formulation of eddy viscosity including all the possible higher order terms quadratic in the mean velocity gradients, and a simplified model is developed for actual oceanic flows where only the vertical velocity gradients are important. The new model is incorporated into the one dimensional General Ocean Turbulence Model (GOTM). Two realistic oceanic test cases (OWS Papa and FLEX' 76) have been investigated. The new model predictions match well with the observational data and are better in comparison to the predictions of the two equation k-epsilon model. The proposed model can be easily incorporated in the three dimensional Princeton Ocean Model (POM) to simulate a wide range of oceanic processes. Practically, this model can be implemented in the coastal regions where trasverse shear induces higher vorticity, and for prediction of flow in estuaries and lakes, where depth is comparatively less. The model predictions of marine turbulence and other related data (e.g. Sea surface temperature, Surface heat flux and vertical temperature profile) can be utilized in short term ocean and climate forecasting and warning systems.

Keywords: Eddy viscosity, turbulence modeling, GOTM, CFD.

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Authors: Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo Eduardo Sánchez Gutiérrez, Pedro Pablo González Pérez

Abstract:

A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented here is devoted to the study of protein folding, initially with a bead-like description of the chain and with the widely used model of hydrophobic and polar residues (HP model). Some details of the platform design are presented along with its capabilities and also are revised some explorations of the protein folding problems with different types of discrete space. It is also shown the capability of the platform to incorporate specific tools for the structural analysis of the runs in order to understand and improve the optimization process. Accordingly, the results obtained demonstrate that the ensemble of computational tools into a single platform is worthwhile by itself, since experiments developed on it can be designed to fulfill different levels of information in a self-consistent fashion. By now, it is being explored how an experiment design can be useful to create a computational agent to be included within the platform. These inclusions of designed agents –or software pieces– are useful for the better accomplishment of the tasks to be developed by the platform. Clearly, while the number of agents increases the new version of the virtual laboratory thus enhances in robustness and functionality.

Keywords: genetic algorithms, multi-agent systems, bioinformatics, optimization, protein folding, structural biology.

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Authors: Sarisa Pechpoothong

Abstract:

The research is to minimize environmental damage pertinent to maritime activities about the operation of lighter boat anchorage and its tugboat. The guidance on upgrading current harbor service and infrastructure has been provided to Kho Sichang Municpality. This will involve a study of the maritime logistics of the water area under jurisdiction of the Sichang island Municipality and possible recommendations may involve charging taxes, regulations and fees. With implementing these recommendations will help in protection of the marine environment and in increasing operator functionality. Additionally, our recommendation is to generate a consistent revenue stream to the municipality. The action items contained in this research are feasible and effective, the success of these initiatives are heavily dependent upon successful promotion and enforcement. Promoting new rules and regulations effectively and peacefully can be done through theories and techniques used in the psychology of persuasion. In order to assure compliance with the regulations, the municipality must maintain stringent patrols and fines for violators. In order to become success, the Municipality must preserve a consistent, transparent and significant enforcement system. Considering potential opportunities outside of the current state of the municipality, the authors recommend that Koh Sichang be given additional jurisdiction to capture value from the master vessels, as well as to confront the more significant environmental challenges these vessels pose. Finally, the authors recommend that the Port of Koh Sichang Island obtain a free port status in order to increase economic viability and overall sustainability.

Keywords: Harbor, Garbage Collection Service, Environment, Off-shore port.

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Authors: Rosmini Yanti, Safira Aviolita, Marsetio

Abstract:

Indonesia has several straits that are very important as a shipping lane, including the Sunda Strait and the Lombok Strait, which are the part of the Indonesian Archipelagic Sea Lane (IASL). An increase in traffic on the Marine Archipelago makes the task of monitoring sea routes increasingly difficult. Indonesia has proposed the establishment of a Traffic Separation Scheme (TSS) in the Sunda Strait and the Lombok Strait and the country now has the right to be able to conceptualize the TSS as well as the obligation to regulate it. Indonesia has the right to maintain national safety and sovereignty. In setting the TSS, Indonesia needs to issue national regulations that are in accordance with international law and the general provisions of the IMO (International Maritime Organization) can then be used as guidelines for maritime safety and security in the Sunda Strait and the Lombok Strait. The research method used is a qualitative method with the concept of linguistic and visual data collection. The source of the data is the analysis of documents and regulations. The results show that the determination of TSS was justified by International Law, in accordance with article 22, article 41, and article 53 of the United Nations Convention on the Law of the Sea (UNCLOS) 1982. The determination of TSS by the Indonesian government would be in accordance with COLREG (International Convention on Preventing Collisions at Sea) 10, which has been designed to follow IASL. Thus, TSS can provide a function as a safety and monitoring medium to minimize ship accidents or collisions, including the warship and aircraft of other countries that cross the IASL.

Keywords: Archipelago State, maritime law, maritime security, traffic separation scheme.

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Authors: K. F. Khan, Samsuddin Khan

Abstract:

The Paleoproterozoic phosphorite deposit of Sallopat block of Banswara district of Rajasthan belongs to kalinjara formation of lunavada group of Aravalli Super Group. The phosphorites are found to occur as massive, brecciated, laminated and stromatolitic associated with calcareous quartzite, interbedded dolomite and multi coloured chert. The phosphorites are showing alternate brown and grey coloured concentric rims which are composed of phosphate, calcite and quartz minerals. Petro-mineralogical studies of phosphorite samples using petrological microscope, XRD, FEG- SEM and EDX reveal that apatite-(CaF) and apatite-(CaOH) are phosphate minerals which are intermixed with minor amount of carbonate materials. Sporadic findings of the uniform tiny granules of partially anisotropic apatite-(CaF) along with dolomite, calcite, quartz, muscovite, zeolite and other gangue minerals have been observed with the replacement of phosphate material by quartz and carbonate. The presence of microbial filaments of organic matter and alternate concentric rims of stromatolitic structure may suggest that the deposition of the phosphate took place in shallow marine oxidizing environmental conditions leading to the formation of phosphorite layers as primary biogenic precipitates by bacterial or algal activities. Different forms and texture of phosphate minerals may be due to environmental vicissitudes at the time of deposition followed by some replacement processes and biogenic activities.

Keywords: Petro-mineralogy, phosphorites, sallopat, apatite.

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