Search results for: rice bran protein.

Authors: Shohei Nakai, Yasuhiro Yamada

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Weed suppression and weeding are necessary measures for rice cultivation. Weed suppression precedes the process of weeding. It means suppressing the growth of young weeds and creating a weed-less environment. If we suppress the growth of weeds, we can reduce the number of weeds in a paddy field. This would result in a reduction of the weeding work load. In this paper, we will show how we developed a weed suppression robot for the purpose of reducing the weeding work load. The robot has a laser range finder for autonomous mobility and a robot arm for weed suppression. It travels along the rice rows without stepping on and injuring the rice plants in a paddy field. The robot arm applies force to the weed seedlings and thereby suppresses the growth of weeds. This paper will explain the methodology of the autonomous mobile, the experiment in weed suppression, and the method of controlling the robot’s posture on uneven ground.

Keywords: Mobile robot, Paddy field, Robot arm, Weed.

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Authors: Burçin Saltık, Levent Genç

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In this study, it was aimed to determine a route for identification of rice cultivation areas within Thrace and Marmara regions of Turkey using remote sensing and GIS. Landsat 8 (OLI-TIRS) imageries acquired in production season of 2013 with 181/32 Path/Row number were used. Four different seasonal images were generated utilizing original bands and different transformation techniques. All images were classified individually using supervised classification techniques and Land Use Land Cover Maps (LULC) were generated with 8 classes. Areas (ha, %) of each classes were calculated. In addition, district-based rice distribution maps were developed and results of these maps were compared with Turkish Statistical Institute (TurkSTAT; TSI)’s actual rice cultivation area records. Accuracy assessments were conducted, and most accurate map was selected depending on accuracy assessment and coherency with TSI results. Additionally, rice areas on over 4° slope values were considered as mis-classified pixels and they eliminated using slope map and GIS tools. Finally, randomized rice zones were selected to obtain maximum-minimum value ranges of each date (May, June, July, August, September images separately) NDVI, LSWI, and LST images to test whether they may be used for rice area determination via raster calculator tool of ArcGIS. The most accurate classification for rice determination was obtained from seasonal LSWI LULC map, and considering TSI data and accuracy assessment results and mis-classified pixels were eliminated from this map. According to results, 83151.5 ha of rice areas exist within study area. However, this result is higher than TSI records with an area of 12702.3 ha. Use of maximum-minimum range of rice area NDVI, LSWI, and LST was tested in Meric district. It was seen that using the value ranges obtained from July imagery, gave the closest results to TSI records, and the difference was only 206.4 ha. This difference is normal due to relatively low resolution of images. Thus, employment of images with higher spectral, spatial, temporal and radiometric resolutions may provide more reliable results.

Keywords: Landsat 8 (OLI-TIRS), LULC, spectral indices, rice.

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Authors: Prajna Metta, Yanti Rusyanti, Nunung Rusminah, Bremmy Laksono

Abstract:

The decrease of neutrophil chemotaxis function may cause increased susceptibility to aggressive periodontitis (AP). Neutrophil chemotaxis is affected by formyl peptide receptor 1 (FPR1), which when activated will respond to bacterial chemotactic peptide formyl methionyl leusyl phenylalanine (FMLP). FPR1 protein value is decreased in response to a wide number of inflammatory stimuli in AP patients. This study was aimed to assess the alteration of FPR1 protein value in AP patients and if FPR1 protein value could be used as an indicator of neutrophil chemotaxis dysfunction in AP. This is a case control study with 20 AP patients and 20 control subjects. Three milliliters of peripheral blood were drawn and analyzed for FPR1 protein value with ELISA. The data were statistically analyzed with Mann-Whitney test (p>0,05). Results showed that the mean value of FPR1 protein value in AP group is 0,353 pg/mL (0,11 to 1,18 pg/mL) and the mean value of FPR1 protein value in control group is 0,296 pg/mL (0,05 to 0,88 pg/mL). P value 0,787 > 0,05 suggested that there is no significant difference of FPR1 protein value in both groups. The present study suggests that FPR1 protein value has no significance alteration in AP patients and could not be used as an indicator of neutrophil chemotaxis dysfunction.

Keywords: Aggressive periodontitis, chemotaxis dysfunction, FPR1 protein value, neutrophil.

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Authors: Phakamas Rachamontree, Theerawut Phusantisampan, Natthakorn Woravutthikul, Peerapong Pornwongthong, Malinee Sriariyanun

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A total of 115 yeast strains isolated from local cassava processing wastes were measured for crude protein content. Among these strains, the strain MSY-2 possessed the highest protein concentration (>3.5 mg protein/mL). By using molecular identification tools, it was identified to be a strain of Pichia kudriavzevii based on similarity of D1/D2 domain of 26S rDNA region. In this study, to optimize the protein production by MSY-2 strain, Response Surface Methodology (RSM) was applied. The tested parameters were the carbon content, nitrogen content, and incubation time. Here, the value of regression coefficient (R2) = 0.7194 could be explained by the model which is high to support the significance of the model. Under the optimal condition, the protein content was produced up to 3.77 g per L of the culture and MSY-2 strain contains 66.8 g protein per 100 g of cell dry weight. These results revealed the plausibility of applying the novel strain of yeast in single-cell protein production.

Keywords: Single cell protein, response surface methodology, yeast, cassava processing waste.

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Authors: Franklin Nantui Mabe, Samuel A. Donkoh, Seidu Al-Hassan

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Rice yields among agro-ecological zones are heterogeneous. Farmers, researchers and policy makers are making frantic efforts to bridge rice yield gaps between agro-ecological zones through the promotion of improved agricultural technologies (IATs). Farmers are also modifying these IATs and blending them with indigenous farming practices (IFPs) to form farmer innovation systems (FISs). Also, different metafrontier models have been used in estimating productivity performances and their drivers. This study used the two-step stochastic metafrontier model to estimate the productivity performances of rice farmers and their determining factors in GSZ, FSTZ and CSZ. The study used both primary and secondary data. Farmers in CSZ are the most technically efficient. Technical inefficiencies of farmers are negatively influenced by age, sex, household size, education years, extension visits, contract farming, access to improved seeds, access to irrigation, high rainfall amount, less lodging of rice, and well-coordinated and synergized adoption of technologies. Albeit farmers in CSZ are doing well in terms of rice yield, they still have the highest potential of increasing rice yield since they had the lowest TGR. It is recommended that government through the ministry of food and agriculture, development partners and individual private companies promote the adoption of IATs as well as educate farmers on how to coordinate and synergize the adoption of the whole package. Contract farming concept and agricultural extension intensification should be vigorously pursued to the latter.

Keywords: Efficiency, farmer innovation systems, improved agricultural technologies, two-step stochastic metafrontier approach.

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Authors: Sansanee Sansiribhan, Orrawan Rewthong, Anusorn Rattanathanaophat, Sarun Saensiriphan

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The objective of this work was to study potential of rice straw for power plant in the Central region of Thailand. Provincial power plant capacity was studied. The results showed that provinces central region had potential for small power plants with a capacity of over 10 MW in 13 provinces, 1-10 MW in 6 provinces and less than 1 MW in 3 provinces.

Keywords: Rice straw, Power plant, Central region, Thailand.

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Authors: Jie Sun, Guoyou Yin, Xianqing Zhang, Qiusheng She, Zhaohui Xie, Lanying Chen, Anfang Zhao

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To assess the effects of functional protein on osteoblast, Large quantity of high-purity osteoblasts had been cultivated successfully by adopting sequential enzyme digestion. The growth curve of osteoblasts was protracted by cell counting. Proliferation of osteoblasts was assessed by MTT colorimetry. The experimental results show the functional protein can enhance proliferation, the properties of adhesion and discuss the effect of osteopontin on osteoblast.

Keywords: functional protein, osteoblast, MTT

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Authors: Essam Al-Daoud

Abstract:

A New features are extracted and compared to improve the prediction of protein-protein interactions. The basic idea is to select and use the best set of features from the Tensor matrices that are produced by the frequency vectors of the protein sequences. Three set of features are compared, the first set is based on the indices that are the most common in the interacting proteins, the second set is based on the indices that tend to be common in the interacting and non-interacting proteins, and the third set is constructed by using random indices. Moreover, three encoding strategies are compared; that are based on the amino asides polarity, structure, and chemical properties. The experimental results indicate that the highest accuracy can be obtained by using random indices with chemical properties encoding strategy and support vector machine.

Keywords: protein-protein interactions, random indices, encoding strategies, support vector machine.

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Authors: P. C. Tewari, Parveen Kumar

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The paper describes the availability analysis of milling system of a rice milling plant using probabilistic approach. The subsystems under study are special purpose machines. The availability analysis of the system is carried out to determine the effect of failure and repair rates of each subsystem on overall performance (i.e. steady state availability) of system concerned. Further, on the basis of effect of repair rates on the system availability, maintenance repair priorities have been suggested. The problem is formulated using Markov Birth-Death process taking exponential distribution for probable failures and repair rates. The first order differential equations associated with transition diagram are developed by using mnemonic rule. These equations are solved using normalizing conditions and recursive method to drive out the steady state availability expression of the system. The findings of the paper are presented and discussed with the plant personnel to adopt a suitable maintenance policy to increase the productivity of the rice milling plant.

Keywords: Markov process, milling system, availability modeling, rice milling plant.

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Authors: S. Bangphan, P. Bangphan, T. Boonkang

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Quality control helps industries in improvements of its product quality and productivity. Statistical Process Control (SPC) is one of the tools to control the quality of products that turning practice in bringing a department of industrial engineering process under control. In this research, the process control of a turning manufactured at workshops machines. The varying measurements have been recorded for a number of samples of a rice polished cylinder obtained from a number of trials with the turning practice. SPC technique has been adopted by the process is finally brought under control and process capability is improved.

Keywords: Rice polished cylinder, statistical process control, control charts, process capability.

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Authors: N. Mongkontanawat

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This research aimed to demonstrate probiotic germinated native black rice juice fermentation by lactic acid bacteria (Lactobacillus casei TISTR 390). Germinated native black rice juice was inoculated with a 24-h old lactic culture and incubated at 30 °C for 72 hours. Changes in pH, acidity, total soluble solid, and viable cell counts during fermentation under controlled conditions at 0-h, 24-h, 48-h, and 72-h fermentations were evaluated. The study found out that the change in pH and total soluble solid of probiotic germinated black rice juice significantly (p ≤ 0.05) decreased at 72-h fermentation (5.67±0.12 to 2.86±0.04 and 7.00±0.00 to 6.40±0.00 ºbrix at 0-h and 72-h fermentations, respectively). On the other hand, the amount of titratable acidity expressed as lactic acid and the viable cell count significantly (p≤0.05) increased at 72-h fermentation (0.11±0.06 to 0.43±0.06 (% lactic acid) and 3.60 x 10⁶ to 2.75 x 10⁸ CFU/ml at 0-h and 72-h fermentations, respectively). Interestingly, the amount of γ-Amino Butyric Acid (GABA) had a significant difference (p≤0.05) twice as high as that of the control group (0.25±0.01 and 0.13±0.01 mg/100g, respectively). In addition, the free radical scavenging capacity assayed by DPPH method also showed that the IC₅₀ values were significantly (p≤0.05) higher than the control (147.71±0.96 and 202.55±1.24 mg/ml, respectively). After 4 weeks of cold storage at 4 °C, the viable cell counts of lactic acid bacteria reduced to 1.37 x 10⁶ CFU/ml. In conclusion, fermented germinated native black rice juice could be served as a healthy beverage for vegans and people who are allergic to cow milk products.

Keywords: Germinated native black rice, probiotic, lactic acid bacteria, Lactobacillus casei.

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Authors: Nahid A. Ali, Salma H. Ahmed, ElShazali A. Mohamed, Isam A. Mohamed Ahmed, Elfadil E.Babiker

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The effect of cross linking of the protein isolates of three legumes with the microbial enzyme transglutaminase (EC 2.3.2.13) on the functional properties at different NaCl concentration was studied. The reduction in the total free amino groups (OD340) of the polymerized protein showed that TGase treatment cross-linking the protein subunit of each legume. The solubility of the protein polymer of each legume was greatly improved at high concentration of NaCl. At 1.2 M NaCl the solubility of the native legumes protein was significantly decreased but after polymerization slightly improved. Cross linked proteins were less turbid on heating to higher temperature as compared to native proteins and the temperature at which the protein turns turbid also increased in the polymerized proteins. The emulsifying and foaming properties of the protein polymer were greatly improved at all concentrations of NaCl for all legumes.

Keywords: Functional properties, Legumes, Protein isolate, NaCl, Transglutaminase.

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Authors: Jin Choi, Zahra Aminikhoei, Yi-Oh Kim, Sang-Min Lee

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A feeding experiment was conducted to determine the optimum dietary protein and lipid levels for juvenile fancy carp. Eight experimental diets were formulated to contain four protein levels (200, 300, 400 and 500 g kg-1) with two lipid levels (70 and 140 g kg-1). Triplicate groups of fish (initial weight, 12.1±0.2 g fish-1) were hand-fed the diets to apparent satiation for 8 weeks. Fish growth performance, feed utilization and feed intake were significantly (P<0.0001) affected by dietary protein level, but not by dietary lipid level (P>0.05). Weight gain and feed efficiency ratio tended to increase as dietary protein level increased up to 400 and 500 g kg-1, respectively. Daily feed intake of fish decreased with increasing dietary protein level and that of fish fed diet contained 500 g kg-1 protein was significantly lower than other fish groups. The protein efficiency ratio of fish fed 400 and 500 g kg-1 protein was lower than that of fish fed 200 and 300 g kg-1 protein. Moisture, crude protein and crude lipid contents of muscle and liver were significantly affected by dietary protein, but not by dietary lipid level (P>0.05). The increase in dietary lipid level resulted in an increase in linoleic acid in liver and muscle paralleled with a decrease in n-3 highly unsaturated fatty acids content in muscle of fish. In considering these results, it was concluded that the diet containing 400 g kg-1 protein with 70 g kg-1 lipid level is optimal for growth and efficient feed utilization of juvenile fancy carp.

Keywords: Fancy carp, Dietary protein, Dietary lipid, Fatty acid.

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Authors: T. A. Abegunde, O. B. Oyewole, T. A. Sanni

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A process of conversion of flour from three varieties of cassava, namely Odongbo, ofege and TMS30752 to ethanol using α-amylase locally sourced from germinated unhusked paddy rice and yeast isolated from palm wine was developed. It involves the germination of paddy rice for a period of 15days to produce α-amylase for starch hydrolysis and isolation of yeast from palm wine for fermentation. The results showed that optimum amylase yield of “ofada” rice paddy was at 6^th day germination which was 576.9ml/g. Ethanol yield for TMS30572 (440.3%) was significantly higher than “Odongbo” (160.2%) and “Ofege’’ (115.1%), Sugar conversion efficiency were 311.0%v/v, 268.2%v/v and 186.84%v/v for TMS30572, “Odongbo” and “Ofege” respectively. The ethanol boiling points were 78^oC, 76^oC and 80^oC for TMS30572, “Odongbo” and “Ofege” respectively. This study showed that cassava varieties affects quality of ethanol produced and germination of “ofada” rice for 6 days ensures optimum production of crude amylase enzyme.

Keywords: Cassava, ethanol, fermentation, hydrolysis, α-amylase.

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Authors: Novi Khila Firani, Elisa Nesdyaningtyas

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Kwashiorkor is one of nutritional problem in Indonesia, which lead to decrease immune system. This condition causes susceptibility to infectious disease, especially tuberculosis. Development of new tuberculosis vaccine will be an important strategy to eliminate tuberculosis in kwashiorkor. Previous research showed that 38-kDa Mycobacterium tuberculosis protein is one of the potent immunogen. However, the role of oral immunization with 38- kDa Mycobacterium tuberculosis protein to the number of lymphocytes in the rat model of kwashiorkor is still unknown. We used kwashiorkor rat model groups with 4% and 2% low protein diet. Oral immunization with 38-kDa Mycobacterium tuberculosis protein given with 2 booster every week. The lymphocytes number were measured by flowcytometry. There was no significant difference between the number of lymphocytes in the normal rat group and the kwashiorkor rat groups. It may reveal the role of 38-kDa Mycobacterium tuberculosis protein as a potent immunogen that can increase the lymphocytes number from kwashiorkor rat model same as normal rat.

Keywords: kwashiorkor rat, lymphocytes, 38-kDa Mycobacterium tuberculosis protein

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Authors: S. Safi, M. Frikel, M. M'Saad, A. Zeroual

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This paper describes a blind algorithm for estimating a time varying and frequency selective fading channel. In order to identify blindly the impulse response of these channels, we have used Higher Order Statistics (HOS) to build our algorithm. In this paper, we have selected two theoretical frequency selective channels as the Proakis-s 'B' channel and the Macchi-s channel, and one practical frequency selective fading channel called Broadband Radio Access Network (BRAN A). The simulation results in noisy environment and for different data input channel, demonstrate that the proposed method could estimate the phase and magnitude of these channels blindly and without any information about the input, except that the input excitation is i.i.d (Identically and Independent Distributed) and non-Gaussian.

Keywords: Frequency response, system identification, higher order statistics, communication channels, phase estimation.

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Authors: M. Michael Gromiha, Kiyonobu Yokota, Kazuhiko Fukui

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We have developed an energy based approach for identifying the binding sites and important residues for binding in protein-protein complexes. We found that the residues and residuepairs with charged and aromatic side chains are important for binding. These residues influence to form cation-¤Ç, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein-protein complexes and found good agreement with experiments. The analysis on surrounding hydrophobicity reveals that the binding residues are less hydrophobic than non-binding sites, which suggests that the hydrophobic core are important for folding and stability whereas the surface seeking residues play a critical role in binding. Further, the propensity of residues in the binding sites of receptors and ligands, number of medium and long-range contacts, and influence of neighboring residues will be discussed.

Keywords: Protein-protein interactions, energy based approach;binding sites, propensity, long-range contacts, hydrophobicity

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Authors: Chun-Wei Tung, Chyn Liaw, Shinn-Jang Ho, Shinn-Ying Ho

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Protein subchloroplast locations are correlated with its functions. In contrast to the large amount of available protein sequences, the information of their locations and functions is less known. The experiment works for identification of protein locations and functions are costly and time consuming. The accurate prediction of protein subchloroplast locations can accelerate the study of functions of proteins in chloroplast. This study proposes a Random Forest based method, ChloroRF, to predict protein subchloroplast locations using interpretable physicochemical properties. In addition to high prediction accuracy, the ChloroRF is able to select important physicochemical properties. The important physicochemical properties are also analyzed to provide insights into the underlying mechanism.

Keywords: Chloroplast, Physicochemical properties, Proteinlocations, Random Forests.

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Authors: Eliza. E. Camaso, Guiller. B. Damian, Miguelito. F. Isip, Ronaldo T. Alberto

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Land-cover maps were important for many scientific, ecological and land management purposes and during the last decades, rapid decrease of soil fertility was observed to be due to land use practices such as rice cultivation. High-precision land-cover maps are not yet available in the area which is important in an economy management. To assure   accurate mapping of land cover to provide information, remote sensing is a very suitable tool to carry out this task and automatic land use and cover detection. The study did not only provide high precision land cover maps but it also provides estimates of rice production area that had undergone chemical degradation due to fertility decline. Land-cover were delineated and classified into pre-defined classes to achieve proper detection features. After generation of Land-cover map, of high intensity of rice cultivation, soil fertility degradation assessment in rice production area due to fertility decline was created to assess the impact of soils used in agricultural production. Using Simple spatial analysis functions and ArcGIS, the Land-cover map of Municipality of Quezon in Nueva Ecija, Philippines was overlaid to the fertility decline maps from Land Degradation Assessment Philippines- Bureau of Soils and Water Management (LADA-Philippines-BSWM) to determine the area of rice crops that were most likely where nitrogen, phosphorus, zinc and sulfur deficiencies were induced by high dosage of urea and imbalance N:P fertilization. The result found out that 80.00 % of fallow and 99.81% of rice production area has high soil fertility decline.

Keywords: Aerial image, land-cover, LiDAR, soil fertility degradation.

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Authors: Alhaji M. H. Conteh, Xiangbin Yan, Alfred V. Gborie

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The goal of this study was to increase the awareness of the description and assessments of rice acreage response and to offer mechanisms for agricultural policy scrutiny. The ordinary least square (OLS) technique was utilized to determine the coefficients of acreage response models for the rice varieties. The magnitudes of the coefficients (λ) of both the ROK lagged and NERICA lagged acreages were found positive and highly significant, which indicates that farmers’ adjustment rate was very low. Regarding lagged actual price for both the ROK and NERICE rice varieties, the short-run price elasticitieswere lower than long-run, which is suggesting a long term adjustment of the acreage under the crop.

However, the apparent recommendations for policy transformation are to open farm gate prices and to decrease government’s involvement in agricultural sector especially in the acquisition of agricultural inputs. Impending research have to be centered on how this might be better realized. Necessary conditions should be made available to the private sector by means of minimizing price volatility. In accordance with structural reforms, it is necessary to convey output prices to farmers with minimum distortion. There is need to eradicate price subsidies and control, which generate distortion in the market in addition to huge financial costs.

Keywords: Acreage response, rate of adjustment, rice varieties, Sierra Leone.

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Authors: Shaibu Baanni Azumah, William Adzawla

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Rice is an important staple crop, with current demand higher than the domestic supply in Ghana. This has led to a high and unfavourable import bill. Therefore, recent policies and interventions in the agricultural sub-sector aim at promoting various improved agricultural technologies in order to improve domestic production and reduce the importation of rice. In this study, we examined the effect of the adoption of Urea Deep Placement (UDP) technology by rice farmers on the position of the production frontier. This involved 200 farmers selected through a multi stage sampling technique in the Northern region of Ghana. A Cobb-Douglas stochastic frontier model was fitted. The result showed that the adoption of UDP technology shifts the output frontier outward and also move the farmers closer to the frontier. Farmers were also operating under diminishing returns to scale which calls for redress. Other factors that significantly influenced rice production were farm size, labour, use of certified seeds and NPK fertilizer. Although there was an opportunity for improvement, the farmers were highly efficient (92%), compared to previous studies. Farmers’ efficiency was improved through increased education, household size, experience, access to credit, and lack of extension service provision by MoFA. The study recommends the revision of Ghana’s agricultural policy to include the UDP technology. Agricultural Extension officers of the Ministry of Food and Agriculture (MoFA) should be trained on the UDP technology to support IFDC’s drive to improve adoption by rice farmers. Rice farmers are also encouraged to expand their farm lands, improve plant population, and also increase the usage of fertilizer to improve yields. Mechanisms through which credit can be made easily accessible and effectively utilised should be identified and promoted.

Keywords: Efficiency, rice farmers, stochastic frontier, UDP technology.

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Authors: Natarajan. E, Ganapathy Sundaram. E

Abstract:

Fixed-bed slow pyrolysis experiments of rice husk have been conducted to determine the effect of pyrolysis temperature, heating rate, particle size and reactor length on the pyrolysis product yields. Pyrolysis experiments were performed at pyrolysis temperature between 400 and 600°C with a constant heating rate of 60°C/min and particle sizes of 0.60-1.18 mm. The optimum process conditions for maximum liquid yield from the rice husk pyrolysis in a fixed bed reactor were also identified. The highest liquid yield was obtained at a pyrolysis temperature of 500°C, particle size of 1.18-1.80 mm, with a heating rate of 60°C/min in a 300 mm length reactor. The obtained yield of, liquid, gas and solid were found be in the range of 22.57-31.78 %, 27.75-42.26 % and 34.17-42.52 % (all weight basics) respectively at different pyrolysis conditions. The results indicate that the effects of pyrolysis temperature and particle size on the pyrolysis yield are more significant than that of heating rate and reactor length. The functional groups and chemical compositions present in the liquid obtained at optimum conditions were identified by Fourier Transform-Infrared (FT-IR) spectroscopy and Gas Chromatography/ Mass Spectroscopy (GC/MS) analysis respectively.

Keywords: Slow pyrolysis, Rice husk, Recycling, Biomass.

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Authors: Do Phuc, Nguyen Thi Kim Phung

Abstract:

In this paper, we represent protein structure by using graph. A protein structure database will become a graph database. Each graph is represented by a spectral vector. We use Jacobi rotation algorithm to calculate the eigenvalues of the normalized Laplacian representation of adjacency matrix of graph. To measure the similarity between two graphs, we calculate the Euclidean distance between two graph spectral vectors. To cluster the graphs, we use M-tree with the Euclidean distance to cluster spectral vectors. Besides, M-tree can be used for graph searching in graph database. Our proposal method was tested with graph database of 100 graphs representing 100 protein structures downloaded from Protein Data Bank (PDB) and we compare the result with the SCOP hierarchical structure.

Keywords: Eigenvalues, m-tree, graph database, protein structure, spectra graph theory.

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Authors: Omar GACI, Stefan BALEV, Antoine DUTOT

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In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.

Keywords: interaction network, protein structure, community structure detection.

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Authors: Chan Weng Howe, Mohd Saberi Mohamad

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Protein residue contact map is a compact representation of secondary structure of protein. Due to the information hold in the contact map, attentions from researchers in related field were drawn and plenty of works have been done throughout the past decade. Artificial intelligence approaches have been widely adapted in related works such as neural networks, genetic programming, and Hidden Markov model as well as support vector machine. However, the performance of the prediction was not generalized which probably depends on the data used to train and generate the prediction model. This situation shown the importance of the features or information used in affecting the prediction performance. In this research, support vector machine was used to predict protein residue contact map on different combination of features in order to show and analyze the effectiveness of the features.

Keywords: contact map, protein residue contact, support vector machine, protein structure prediction

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Reet Kamal Kaur

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Protein structure determination and prediction has been a focal research subject in the field of bioinformatics due to the importance of protein structure in understanding the biological and chemical activities of organisms. The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 70%.

Keywords: Protein, Secondary Structure, Prediction, DNA, RNA.

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Authors: S. Bangphan, P. Bangphan, T.Boonkang

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Implementation of response surface methodology (RSM) was employed to study the effects of two factor (rubber clearance and round per minute) in brown rice peeling machine of The optimal BROKENS yield (19.02, average of three repeats),.The optimized composition derived from RSM regression was analyzed using Regression analysis and Analysis of Variance (ANOVA). At a significant level α = 0.05, the values of Regression coefficient, R 2 (adj)were 97.35 % and standard deviation were 1.09513. The independent variables are initial rubber clearance, and round per minute parameters namely. The investigating responses are final rubber clearance, and round per minute (RPM). The restriction of the optimization is the designated.

Keywords: Brown rice, Response surface methodology(RSM), Rubber clearance, Round per minute (RPM), Peeling machine.

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Authors: Omer Nebil Yaveroglu, Tolga Can

Abstract:

In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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Authors: Norzita Ngadi, John Abrahamson, Conan Fee, Ken Morison

Abstract:

Nonspecific protein adsorption generally occurs on any solid surfaces and usually has adverse consequences. Adsorption of proteins onto a solid surface is believed to be the initial and controlling step in biofouling. Surfaces modified with end-tethered poly(ethylene glycol) (PEG) have been shown to be protein-resistant to some degree. In this study, the adsorption of β-casein and lysozyme was performed on 6 different types of surfaces where PEG was tethered onto stainless steel by polyethylene imine (PEI) through either OH or NHS end groups. Protein adsorption was also performed on the bare stainless steel surface as a control. The adsorption was conducted at 23 °C and pH 7.2. In situ QCM-D was used to determine PEG adsorption kinetics, plateau PEG chain densities, protein adsorption kinetics and plateau protein adsorbed quantities. PEG grafting density was the highest for a NHS coupled chain, around 0.5 chains / nm2. Interestingly, lysozyme which has smaller size than β-casein, appeared to adsorb much less mass than that of β- casein. Overall, the surface with high PEG grafting density exhibited a good protein rejection.

Keywords: QCM-D, PEG, stainless steel, β-casein, lysozyme.

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Authors: Rania A. Abul Seoud, Nahed H. Solouma, Abou-Baker M. Youssef, Yasser M. Kadah

Abstract:

Due to the ever growing amount of publications about protein-protein interactions, information extraction from text is increasingly recognized as one of crucial technologies in bioinformatics. This paper presents a Protein Interaction Extraction System using a Link Grammar Parser from biomedical abstracts (PIELG). PIELG uses linkage given by the Link Grammar Parser to start a case based analysis of contents of various syntactic roles as well as their linguistically significant and meaningful combinations. The system uses phrasal-prepositional verbs patterns to overcome preposition combinations problems. The recall and precision are 74.4% and 62.65%, respectively. Experimental evaluations with two other state-of-the-art extraction systems indicate that PIELG system achieves better performance. For further evaluation, the system is augmented with a graphical package (Cytoscape) for extracting protein interaction information from sequence databases. The result shows that the performance is remarkably promising.

Keywords: Link Grammar Parser, Interaction extraction, protein-protein interaction, Natural language processing.

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