Search results for: rice bran protein.

Authors: Hasan Basri Jumin, Abdur Rahman, M. Nur, Ernita, Tati Maharani

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The swamp land contains high levels of iron and aluminum, as well as a low pH. Calcium and magnesium present in the rice husk ash can mitigate plant poisoning, thereby enhancing plant growth and fertility. Two main factors were considered in the study: The dosage of rice husk, and the rhizobium inoculant dosage, which was varied at 0.0 g/kg seed, 4.0 g/kg seed, 8.0 g/kg seed, and 12.0 g/kg seed. The plants were cultivated under controlled lighting conditions with a photoperiod of 11.45 to 12.15 hours. The combination of rhizobium inoculant and rice husk ash has demonstrated an interacting effect on the production of fresh weight in long bean pods. The mean relative growth rate, net assimilation rate, and pod fresh weight are increased by a combination of husk rice ash and rhizobium inoculant. Rice husk ash enhances nitrogen availability in the soil, even in cases of poor nutritional conditions. Rhizobium plays an active role in nitrogen fixation from the atmosphere, as it enhances both intercellular and symbiotic nitrogen capabilities in long beans. The combination of rice husk ash and rhizobium can effectively contribute to thriving soil conditions.

Keywords: Aluminum, calcium, fixation, iron, nitrogen.

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Authors: Mohd F. Taha, Chong F. Kiat, Maizatul S. Shaharun, Anita Ramli

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The abundance and availability of rice husk, an agricultural waste, make them as a good source for precursor of activated carbon. In this work, rice husk-based activated carbons were prepared via base treated chemical activation process prior the carbonization process. The effect of carbonization temperatures (400, 600 and 800oC) on their pore structure was evaluated through morphology analysis using scanning electron microscope (SEM). Sample carbonized at 800oC showed better evolution and development of pores as compared to those carbonized at 400 and 600oC. The potential of rice husk-based activated carbon as an alternative adsorbent was investigated for the removal of Ni(II), Zn(II) and Pb(II) from single metal aqueous solution. The adsorption studies using rice husk-based activated carbon as an adsorbent were carried out as a function of contact time at room temperature and the metal ions were analyzed using atomic absorption spectrophotometer (AAS). The ability to remove metal ion from single metal aqueous solution was found to be improved with the increasing of carbonization temperature. Among the three metal ions tested, Pb(II) ion gave the highest adsorption on rice husk-based activated carbon. The results obtained indicate the potential to utilize rice husk as a promising precursor for the preparation of activated carbon for removal of heavy metals.

Keywords: Activated carbon, metal ion adsorption, rice husk, wastewater treatment.

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Authors: Kalyan Kumar Moulick

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In this paper, the author studied the possibilities of using Rice Husk Ash (RHA) available in India; to produce concrete. Experiments conducted with RHA obtained from West Bengal, India; to replace cement partially to produce concrete of grade M10, M15, M20, M25 and M30. The concrete produced in the laboratory by replacing cement by 5%, 10%, 15%, 20%, 25% and 30% RHA. Compressive strength tests carried out to determine the strength of concrete. Cost analysis and comparison done to show the cost effectiveness of RHA Concrete. Traditional uses of Rice Husk in India pointed out and the advantages of using RHA in making concrete highlighted. Suggestion provided regarding prospective application of RHA concrete in India; which in turn will definitely reduce the cost of concrete and environmental friendly due to utilization of waste and replacement of Cement.

Keywords: Cement replacement, Concrete, Environmental friendly, Rice Husk Ash.

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Authors: Rujijan Vichivanives, Kittiya Poonsilp, Canasanan Wanavijit

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This research aims to create mobile tools to analyze rice disease quickly and easily. The principle of object-oriented software engineering and objective-C language were used for software development methodology and the principle of decision tree technique was used for analysis method. Application users can select the features of rice disease or the color appears on the rice leaves for recognition analysis results on iOS mobile screen. After completing the software development, unit testing and integrating testing method were used to check for program validity. In addition, three plant experts and forty farmers have been assessed for usability and benefit of this system. The overall of users’ satisfaction was found in a good level, 57%. The plant experts give a comment on the addition of various disease symptoms in the database for more precise results of the analysis. For further research, it is suggested that image processing system should be developed as a tool that allows users search and analyze for rice diseases more convenient with great accuracy.

Keywords: Rice disease, analysis system, mobile application, iOS operating system.

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Authors: T. N. M. El Sebai, A. A.Khattab, Wafaa M. Abd-El Rahim, H. Moawad

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Fungal mutant strains have produced cellulase and xylanase enzymes, and have induced high hydrolysis with enhanced of rice straw. The mutants were obtained by exposing Penicillium strain to UV-light treatments. Screening and selection after treatment with UV-light were carried out using cellulolytic and xylanolytic clear zones method to select the hypercellulolytic and hyperxylanolytic mutants. These mutants were evaluated for their cellulase and xylanase enzyme production as well as their abilities for biodegradation of rice straw. The mutant 12 UV/1 produced 306.21% and 209.91% cellulase and xylanase, respectively, as compared with the original wild type strain. This mutant showed high capacity of rice straw degradation. The effectiveness of tested mutant strain and that of wild strain was compared in relation to enhancing the composting process of rice straw and animal manures mixture. The results obtained showed that the compost product of inoculated mixture with mutant strain (12 UV/1) was the best compared to the wild strain and un-inoculated mixture. Analysis of the composted materials showed that the characteristics of the produced compost were close to those of the high quality standard compost. The results obtained in the present work suggest that the combination between rice straw and animal manure could be used for enhancing the composting process of rice straw and particularly when applied with fungal decomposer accelerating the composting process.

Keywords: Rice straw, composting, UV mutants, Penicillium.

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Authors: N.A.Johan, S.R.M.Kutty, M. H. Isa, N.S.Muhamad, H.Hashim

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Many non-conventional adsorbent have been studied as economic alternative to commercial activated carbon and mostly agricultural waste have been introduced such as rubber leaf powder and hazelnut shell. Microwave Incinerated Rice Husk Ash (MIRHA), produced from the rice husk is one of the low-cost materials that were used as adsorbent of heavy metal. The aim of this research was to study the feasibility of using MIRHA500 and MIRHA800 as adsorbent for the removal of Cu(II) metal ions from aqueous solutions by the batch studies. The adsorption of Cu(II) into MIRHA500 and MIRH800 favors Fruendlich isotherm and imply pseudo – kinetic second order which applied chemisorptions

Keywords: Copper (II) aqueous solution, batch study, MIRHA500, MIRHA800, Microwave Incinerated Rice Husk Ash(MIRHA)

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

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Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

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The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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Authors: Manpreet Singh, Parminder Kaur Wadhwa, Surinder Kaur

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The drug discovery process starts with protein identification because proteins are responsible for many functions required for maintenance of life. Protein identification further needs determination of protein function. Proposed method develops a classifier for human protein function prediction. The model uses decision tree for classification process. The protein function is predicted on the basis of matched sequence derived features per each protein function. The research work includes the development of a tool which determines sequence derived features by analyzing different parameters. The other sequence derived features are determined using various web based tools.

Keywords: Sequence Derived Features, decision tree.

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Authors: Waraporn Apiwatanapiwat, Pilanee Vaithanomsat, Phanu Somkliang, Taweesiri Malapant

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This was the first document revealing the investigation of protein hydrolysate production optimization from J. curcas cake. Proximate analysis of raw material showed 18.98% protein, 5.31% ash, 8.52% moisture and 12.18% lipid. The appropriate protein hydrolysate production process began with grinding the J. curcas cake into small pieces. Then it was suspended in 2.5% sodium hydroxide solution with ratio between solution/ J. curcas cake at 80:1 (v/w). The hydrolysis reaction was controlled at temperature 50 °C in water bath for 45 minutes. After that, the supernatant (protein hydrolysate) was separated using centrifuge at 8000g for 30 minutes. The maximum yield of resulting protein hydrolysate was 73.27 % with 7.34% moisture, 71.69% total protein, 7.12% lipid, 2.49% ash. The product was also capable of well dissolving in water.

Keywords: Production, protein hydrolysate, Jatropha curcas cake, optimization.

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Authors: Megawati, Wahyudi B. Sediawan, Hary Sulistyo, Muslikhin Hidayat

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Rice husk is a lignocellulosic source that can be converted to ethanol. Three hundreds grams of rice husk was mixed with 1 L of 0.18 N sulfuric acid solutions then was heated in an autoclave. The reaction was expected to be at constant temperature (isothermal), but before that temperature was achieved, reaction has occurred. The first liquid sample was taken at temperature of 140 0C and repeated every 5 minute interval. So the data obtained are in the regions of non-isothermal and isothermal. It was observed that the degradation has significant effects on the ethanol production. The kinetic constants can be expressed by Arrhenius equation with the frequency factors for hydrolysis and sugar degradation of 1.58 x 105 1/min and 2.29 x 108 L/mole/min, respectively, while the activation energies are 64,350 J/mole and 76,571 J/mole. The highest ethanol concentration from fermentation is 1.13% v/v, attained at 220 0C.

Keywords: degradation, ethanol, hydrolysis, rice husk

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Authors: Megawati, Wahyudi B. Sediawan, Hary Sulistyo, Muslikhin Hidayat

Abstract:

Rice husk is a lignocellulosic source that can be converted to ethanol. Three hundreds grams of rice husk was mixed with 1 L of 0.18 N sulfuric acid solutions then was heated in an autoclave. The reaction was expected to be at constant temperature (isothermal), but before that temperature was achieved, reaction has occurred. The first liquid sample was taken at temperature of 140 0C and repeated every 5 minute interval. So the data obtained are in the regions of non-isothermal and isothermal. It was observed that the degradation has significant effects on the ethanol production. The kinetic constants can be expressed by Arrhenius equation with the frequency factors for hydrolysis and sugar degradation of 1.58 x 105 min-1 and 2.29 x 108 L/mole-min, respectively, while the activation energies are 64,350 J/mole and 76,571 J/mole. The highest ethanol concentration from fermentation is 1.13% v/v, attained at 220 0C.

Keywords: degradation, ethanol, hydrolysis, rice husk.

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Authors: Shaibu Baanni Azumah, Ignatius Tindjina, Stella Obanyi, Tara N. Wood

Abstract:

This study examined the effect of Urea Deep Placement (UDP) technology on the output of irrigated rice farmers in the northern region of Ghana. Multi-stage sampling technique was used to select 142 rice farmers from the Golinga and Bontanga irrigation schemes, around Tamale. A treatment effect model was estimated at two stages; firstly, to determine the factors that influenced farmers’ decision to adopt the UDP technology and secondly, to determine the effect of the adoption of the UDP technology on the output of rice farmers. The significant variables that influenced rice farmers’ adoption of the UPD technology were sex of the farmer, land ownership, off-farm activity, extension service, farmer group participation and training. The results also revealed that farm size and the adoption of UDP technology significantly influenced the output of rice farmers in the northern region of Ghana. In addition to the potential of the technology to improve yields, it also presents an employment opportunity for women and youth, who are engaged in the deep placement of Urea Super Granules (USG), as well as in the transplantation of rice. It is recommended that the government of Ghana work closely with the IFDC to embed the UDP technology in the national agricultural programmes and policies. The study also recommends an effective collaboration between the government, through the Ministry of Food and Agriculture (MoFA) and the International Fertilizer Development Center (IFDC) to train agricultural extension agents on UDP technology in the rice producing areas of the country.

Keywords: Northern Ghana, output, irrigation rice farmers, treatment effect model, urea deep placement.

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Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: Baby Joseph, Sankarganesh Palaniyandi

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The enzyme alkaline protease production was determined under solid state fermentation using the soil bacteria Serratia marcescens sp7. The maximum production was obtained from wheat bran medium than ground nut shell and chemically defined medium. The physiological fermentation factors such as pH of the medium (pH 8), Temperature (40oC) and incubation time (48 hrs) played a vital role in alkaline protease production in all the above. 100Mm NaCl has given better resolution during elution of the enzymes. The enzyme production was found to be associated with growth of the bacterial culture.

Keywords: Alkaline protease, Wheat bran, Ground nut shell, Serratia marcescens

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Authors: Noor Zuhaira Abd Aziz, Rahmah Mohamed, Mohd Muizz Fahimi M.

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Rice husk and kenaf filled with calcium carbonate (CaCO3) and high density polyethylene (HDPE) composite were prepared separately using twin-screw extruder at 50rpm. Different filler loading up to 30 parts of rice husk particulate and kenaf fiber were mixed with the fixed 30% amount of CaCO3 mineral filler to produce rice husk/CaCO3/HDPE and kenaf/CaCO3/HDPE hybrid composites. In this study, the effects of natural fiber for both rice husk and kenaf in CaCO3/HDPE composite on physical, mechanical and morphology properties were investigated. Field Emission Scanning Microscope (FeSEM) was used to investigate the impact fracture surfaces of the hybrid composite. The property analyses showed that water absorption increased with the presence of kenaf and rice husk fillers. Natural fibers in composite significantly influence water absorption properties due to natural characters of fibers which contain cellulose, hemicellulose and lignin structures. The result showed that 10% of additional natural fibers into hybrid composite had caused decreased flexural strength, however additional of high natural fiber (>10%) filler loading has proved to increase its flexural strength.

Keywords: Hybrid composites, Water absorption, Mechanical properties.

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Authors: I. Bagheri, M.B. Dehpour

Abstract:

The effect of moisture content and loading rate on mechanical strength of 12 brown rice grain varieties was determined. The results showed that the rupture force of brown rice grain decreased by increasing the moisture content and loading rate. The highest rupture force values was obtained at the moisture content of 8% (w.b.) and loading rate of 10 mm/min; while the lowest rupture force corresponded to the moisture content of 14% (w.b.) and loading rate of 15 mm/min. The 12 varieties were divided into three groups, namely local short grain varieties, local long grain varieties and improved long grain varieties. It was observed that the rupture strength of the three groups were statistically different from each other (P<0.01). It was revealed that the brown rice rupture at lower levels of moisture content was in the form of sudden failure with less deformation; while at higher levels of moisture content the grain rupture was in the form of gradually crushing with more deformation.

Keywords: Brown rice, loading rate, moisture content, ruptureforce

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Authors: Wisnu Adi Yulianto, Agus Slamet, Sri Luwihana, Septian Albar Dwi Suprayogi

Abstract:

Parboiled rice was developed to produce rice, which has a low glycemic index for diabetics. However, diabetics also have a chromium (Cr) deficiency. Thus, it is important to fortify rice with Cr to increase the Cr content. Moreover, parboiled rice becomes rancid easily and has a musty odor, rendering the rice unfavorable. Natural herbs such as pandan leaves (Pandanus amaryllifolius Roxb.), bay leaves (Syzygium polyanthum [Wigh] Walp) and cinnamon bark powder (Cinnamomon cassia) are commonly added to food as aroma enhancers. Previous research has shown that these herbs could improve insulin sensitivity. The purpose of this study was to evaluate the effect of herbal extract coatings on the cooking quality and the preference level of chromium fortified - parboiled rice (CFPR). The rice grain variety used for this experiment was Ciherang and the fortificant was CrCl3. The three herbal extracts used for coating the CFPR were cinnamon, pandan and bay leaf, with concentration variations of 3%, 6%, and 9% (w/w) for each of the extracts. The samples were analyzed for their alkali spreading value, cooking time, elongation, water uptake ratio, solid loss, colour and lightness; and their sensory properties were determined by means of an organoleptic test. The research showed that coating the CFPR with pandan and cinnamon extracts at a concentration of 3% each produced a preferred CFPR. When coated with those herbal extracts the CFPR had the following cooking quality properties: alkali spreading value 5 (intermediate gelatinization temperature), cooking time, 26-27 min, color value, 14.95-15.00, lightness, 42.30 – 44.06, elongation, 1.53 – 1.54, water uptake ratio , 4.05-4.06, and solid loss, 0.09/100 g – 0.13 g/100 g.

Keywords: Bay leaves, chromium, cinnamon, pandan leaves, parboiled rice.

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Authors: Long Van Hoang, Mitsuyasu Yabe

Abstract:

Environmental factors affect agriculture production productivity and efficiency resulted in changing of profit efficiency. This paper attempts to estimate the impacts of environmental factors to profitability of rice farmers in the Red River Delta of Vietnam. The dataset was extracted from 349 rice farmers using personal interviews. Both OLS and MLE trans-log profit functions were used in this study. Five production inputs and four environmental factors were included in these functions. The estimation of the stochastic profit frontier with a two-stage approach was used to measure profitability. The results showed that the profit efficiency was about 75% on the average and environmental factors change profit efficiency significantly beside farm specific characteristics. Plant disease, soil fertility, irrigation apply and water pollution were the four environmental factors cause profit loss in rice production. The result indicated that farmers should reduce household size, farm plots, apply row seeding technique and improve environmental factors to obtain high profit efficiency with special consideration is given for irrigation water quality improvement.

Keywords: Profit efficiency; Profit function; Environmental factors; OLS and MLE estimations; Rice Production; Vietnam

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.

Keywords: Anonymous protein sequence, Gene Ontology, Protein sequence annotation, Protein sequence alignment

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

Abstract:

Understanding proteins functions is a major goal in the post-genomic era. Proteins usually work in context of other proteins and rarely function alone. Therefore, it is highly relevant to study the interaction partners of a protein in order to understand its function. Machine learning techniques have been widely applied to predict protein-protein interactions. Kernel functions play an important role for a successful machine learning technique. Choosing the appropriate kernel function can lead to a better accuracy in a binary classifier such as the support vector machines. In this paper, we describe a Bayesian kernel for the support vector machine to predict protein-protein interactions. The use of Bayesian kernel can improve the classifier performance by incorporating the probability characteristic of the available experimental protein-protein interactions data that were compiled from different sources. In addition, the probabilistic output from the Bayesian kernel can assist biologists to conduct more research on the highly predicted interactions. The results show that the accuracy of the classifier has been improved using the Bayesian kernel compared to the standard SVM kernels. These results imply that protein-protein interaction can be predicted using Bayesian kernel with better accuracy compared to the standard SVM kernels.

Keywords: Bioinformatics, Protein-protein interactions, Bayesian Kernel, Support Vector Machines.

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Authors: G. Spada, E. Gavini, P. Giunchedi

Abstract:

Aim of this work was to compare the efficacy of two loading methods of proteins onto polymeric nanocarriers: adsorption and encapsulation methods. Preliminary studies of protein loading were done using Bovine Serum Albumin (BSA) as model protein. Nanocarriers were prepared starting from polylactic co-glycolic acid (PLGA) polymer; production methods used are two different variants of emulsion evaporation method. Nanoparticles obtained were analyzed in terms of dimensions by Dynamic Light Scattering and Loading Efficiency of BSA by Bradford Assay. Loaded nanoparticles were then submitted to in-vitro protein dissolution test in order to study the effect of the delivery system on the release rate of the protein.

Keywords: Drug delivery, nanoparticles, PLGA, proteinadsorption, protein encapsulation.

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Authors: Md. Harunur Rashid, Md. Keramat Ali Molla, Tarif Uddin Ahmed

Abstract:

The purpose of this paper is to investigate the durability of cement mortar in presence of Rice Husk Ash (RHA). The strength and durability of mortar with different replacement level (0%, 10%, 15%, 20%, 25% and 30%) of Ordinary Portland Cement (OPC) by RHA is investigated here. RHA was manufactured from an uncontrolled burning process. Test samples were prepared with river sand of FM 2.73. Samples were kept in controlled environment up to test time. The results show that addition of RHA was shown better results for 20% replacement level than OPC at 90 days. In durability test all samples passed for 20 cycles except 25% and 30% replacement level.

Keywords: Rice Husk Ash; durability; mortar, graded sand.

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Authors: Waranya Pongpaiboon, Warangkana Srichamnong, Supat Chaiyakul

Abstract:

Enzymatic modification of rice flour can produce highly functional derivatives use in food industries. This study aimed to evaluate the physical properties and resistant starch content of rice flour residues hydrolyzed by α-amylase. Rice flour hydrolyzed by α-amylase (60 and 300 u/g) for 1, 24 and 48 hours were investigated. Increasing enzyme concentration and hydrolysis time resulted in decreased rice flour residue’s lightness (L*) but increased redness (a*) and yellowness (b*) of rice flour residues. The resistant starch content and peak viscosity increased when hydrolysis time increased. Pasting temperature, trough viscosity, breakdown, final viscosity, setback and peak time of the hydrolyzed flours were not significantly different (p>0.05). The morphology of native flour was smooth without observable pores and polygonal with sharp angles and edges. However, after hydrolysis, granules with a slightly rough and porous surface were observed and a rough and porous surface was increased with increasing hydrolyzed time. The X-ray diffraction patterns of native flour showed A-type configuration, which hydrolyzed flour showed almost 0% crystallinity indicated that both amorphous and crystalline structures of starch were simultaneously hydrolyzed by α-amylase.

Keywords: α-Amylase, Enzymatic hydrolysis, Pasting properties, Resistant starch

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Authors: Frank Emmert Streib

Abstract:

The classification of the protein structure is commonly not performed for the whole protein but for structural domains, i.e., compact functional units preserved during evolution. Hence, a first step to a protein structure classification is the separation of the protein into its domains. We approach the problem of protein domain identification by proposing a novel graph theoretical algorithm. We represent the protein structure as an undirected, unweighted and unlabeled graph which nodes correspond the secondary structure elements of the protein. This graph is call the protein graph. The domains are then identified as partitions of the graph corresponding to vertices sets obtained by the maximization of an objective function, which mutually maximizes the cycle distributions found in the partitions of the graph. Our algorithm does not utilize any other kind of information besides the cycle-distribution to find the partitions. If a partition is found, the algorithm is iteratively applied to each of the resulting subgraphs. As stop criterion, we calculate numerically a significance level which indicates the stability of the predicted partition against a random rewiring of the protein graph. Hence, our algorithm terminates automatically its iterative application. We present results for one and two domain proteins and compare our results with the manually assigned domains by the SCOP database and differences are discussed.

Keywords: Graph partitioning, unweighted graph, protein domains.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: Y. S. Lee, F. Malek, E. M. Cheng, W. W. Liu, F. H. Wee, M. N. Iqbal, Z. Liyana, B. S. Yew, F. S. Abdullah

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This paper presents the electromagnetic interference (EMI) shielding effectiveness of rice husk and carbon nanotubes (RHCNTs) composites in the X-band region (8.2-12.4 GHz). The difference weight ratio of carbon nanotubes (CNTs) were mix with the rice husk. The rectangular waveguide technique was used to measure the complex permittivity of the RHCNTs composites materials. The complex permittivity is represented in terms of both the real and imaginary parts of permittivity in X-band frequency. The conductivity of RHCNTs shows increasing when the ratio of CNTs mixture increases. The composites materials were simulated using Computer Simulation Technology (CST) Microwave Studio simulation software. The shielding effectiveness of RHCNTs and pure rice husk was compared. The highest EMI SE of 30 dB is obtained for RHCNTs composites of 10 wt % CNTs with 10mm thickness.

Keywords: EMI Shielding effectiveness, Carbon nanotube, Composite materials, Waveguide, X-band.

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Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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Authors: T. Boonkang, C. Santhaweesuk, N. Pianthong, P. Neeramon, A. Phimhlo, S. Bangphan

Abstract:

The objective of this research was to apply metakaolin from northeast of Thailand as a binder in the casting process of rice polishing cylinder in replacement of the imported calcined magnesite cement and to reduce the production cost of the cylinder. Metakaolin was obtained from three different regions (Udon Thani, Nakhon Phanom, and Ubon Ratchathani). The design of experiment analysis using the MINITAB Release 14 based on the compressive strength and tensile strength testing was conducted. According to the analysis results, it was found that the optimal proportions were calcined magnesite cement: metakaolin from Udon Thani, Nakhon Phanom and Ubon Ratchathani equal to 63:37, 71:29, and 100:0, respectively. When used this formula to cast the cylinder and test the rice milling, it was found that the average broken rice percent was 32.52 and 38.29 for the cylinder contained the metakaolin from Udon Thani and Nakhon Phanom, respectively, which implied that the cylinder which contained the metakaolin from Udon Thani has higher efficiency than the cylinder which contained the metakaolin from Nakhon Phanom at 0.05 level of statistical significance. Whereas, the average wear rate of cylinder from both resources were 7.27 and 6.53 g/h, respectively.

Keywords: Binder, casting, metakaolin, rice polishing cylinder.

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Authors: Alhaji M. H. Conteh, Xiangbin Yan, Issa Fofana, Brima Gegbe, Tamba I. Isaac

Abstract:

Rice grain is Sierra Leone’s staple food and the nation imports over 120,000 metric tons annually due to a shortfall in its cultivation. Thus, the insufficient level of the crop's cultivation in Sierra Leone is caused by many problems and this led to the endlessly widening supply and demand for the crop within the country. Consequently, this has instigated the government to spend huge money on the importation of this grain that would have been otherwise cultivated domestically at a cheaper cost. Hence, this research attempts to explore the response of rice supply with respect to its demand in Sierra Leone within the period 1980-2010. The Nerlovian adjustment model to the Sierra Leone rice data set within the period 1980-2010 was used. The estimated trend equations revealed that time had significant effect on output, productivity (yield) and area (acreage) of rice grain within the period 1980-2010 and this occurred generally at the 1% level of significance. The results showed that, almost the entire growth in output had the tendency to increase in the area cultivated to the crop. The time trend variable that was included for government policy intervention showed an insignificant effect on all the variables considered in this research. Therefore, both the short-run and long-run price response was inelastic since all their values were less than one. From the findings above, immediate actions that will lead to productivity growth in rice cultivation are required. To achieve the above, the responsible agencies should provide extension service schemes to farmers as well as motivating them on the adoption of modern rice varieties and technology in their rice cultivation ventures.

Keywords: Nerlovian adjustment model, price elasticities, Sierra Leone, Trend equations.

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