Search results for: Protein Length

Authors: M. Khairulmazidah, A. B. Nurul Nadiah, A. R. Rumiza

Abstract:

Formulation of biological profile is one of the modern roles of forensic anthropologist. The present study was conducted to estimate height using foot and shoeprint length of Malaysian population. The present work can be very useful information in the process of identification of individual in forensic cases based on shoeprint evidence. It can help to narrow down suspects and ease the police investigation. Besides, stature is important parameters in determining the partial identify of unidentified and mutilated bodies. Thus, this study can help the problem encountered in cases of mass disaster, massacre, explosions and assault cases. This is because it is very hard to identify parts of bodies in these cases where people are dismembered and become unrecognizable. Samples in this research were collected from 200 Malaysian adults (100 males and 100 females) with age ranging from 20 to 45 years old. In this research, shoeprint length were measured based on the print of the shoes made from the flat shoes. Other information like gender, foot length and height of subject were also recorded. The data was analyzed using IBM® SPSS Statistics 19 software. Results indicated that, foot length has a strong correlation with stature than shoeprint length for both sides of the feet. However, in the unknown, where the gender was undetermined have shown a better correlation in foot length and shoeprint length parameter compared to males and females analyzed separately. In addition, prediction equations are developed to estimate the stature using linear regression analysis of foot length and shoeprint length. However, foot lengths give better prediction than shoeprint length. 

Keywords: Forensic anthropology, foot length, shoeprints, stature estimation.

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Authors: İsmail Hakkı Kalyoncu, Nilda Ersoy, Ayşe Yalcın Elidemir, Cansu Dolek

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Some physico-chemical characteristics and mineral composition of 'Karayemis' (Prunus laurocerasus L.) fruits which grown naturally in Norteast Turkey was studied. 28 minerals ( Al, Mg, B, Mn, Co, Na, Ca, Ni, Cd, P, Cr, Pb, Cu, S, Fe, Zn, K, Sr, Li, As, V, Ag, Ba, Br, Ga, In, Se, Ti) were analyzed and 19 minerals were present at ascertainable levels. Karayemis fruit was richest in potassium (7938.711 ppm), magnesium (1242.186 ppm) and calcium (1158.853 ppm). And some physico-chemical characteristics of Karayemis fruit was investigated. Fruit length, fruit width, fruit thickness, fruit weight, total soluble solids, colour, protein, crude ash, crude fiber, crude oil values were determined as 2.334 cm, 1.884 cm, 2.112 cm, 5.35 g, 20.1 %, S99M99Y99, 0.29 %, 0.22 %, 6.63 % and 0.001 %, respectively. The seed of fruit mean weight, length, width and thickness were found to be 0.41 g, 1.303 cm, 0.921 cm and 0.803, respectively.

Keywords: Prunus laurocerasus L., physico-chemical properties, nutritional properties.

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Authors: Omar Gaci, Stefan Balev

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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 identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: interaction network, protein structure, small-world network.

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Authors: Amin Eslami, Jafar Bolouri Bazaz

Abstract:

Excavation and retaining walls are of challenging issues in civil engineering. In this study, the behavior of one important type of supporting systems called Contiguous Bored Pile (CBP) retaining wall is investigated using a physical model. Besides, a comparison is made between two modes of free end piles (soft bed) and fixed end piles (stiff bed). Also a back calculation of effective length (the real free length of pile) is done by measuring lateral deflection of piles in different stages of excavation in both aforementioned cases. Based on observed results, for the fixed end mode, the effective length to free length ratio (Leff/L0) is equal to unity in initial stages of excavation and less than 1 in its final stages in a decreasing manner. While this ratio for free end mode, remains constant during all stages of excavation and is always less than unity.

Keywords: Contiguous Bored Pile Wall, Effective Length, Fixed End, Free End, Free Length.

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Authors: Omima E. Fadlallah, Abdullahi H. El Tinay, Elfadil E. Babiker

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Sorghum flour was supplemented with 15 and 30% chickpea flour. Sorghum flour and the supplement were fermented at 35 oC for 0, 8, 16, and 24 h. Changes in pH, titrable acidity, total soluble solids, protein content, in vitro protein digestibility and amino acid composition were investigated during fermentation and/or after supplementation of sorghum flour with chickpea. The pH of the fermenting material decreased sharply with a concomitant increase in the titrable acidity. The total soluble solids remained unchanged with progressive fermentation time. The protein content of sorghum cultivar was found to be 9.27 and that of chickpea was 22.47%. The protein content of sorghum cultivar after supplementation with15 and 30% chickpea was significantly (P ≤ 0.05) increased to 11.78 and 14.55%, respectively. The protein digestibility also increased after fermentation from 13.35 to 30.59 and 40.56% for the supplements, respectively. Further increment in protein content and digestibility was observed when supplemented and unsupplemented samples were fermented for different periods of time. Cooking of fermented samples was found to increase the protein content slightly and decreased digestibility for both supplements. Amino acid content of fermented and fermented and cooked supplements was determined. Supplementation was found to increase the lysine and therionine content. Cooking following fermentation decreased lysine, isoleucine, valine and sulfur containg amino acids.

Keywords: Amino acid, Chickpea, Cooking, Fermentation, protein, Sorghum.

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Authors: Dilip Nath

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A study has been conducted on the available aquatic invertebrates in the river Dhansiri at Dimapur site. The study confirmed that the river body composed of aquatic macroinvertebrate community in two phyla viz., Arthropods and Molluscs. Total ten species have been identified from there as the source of alternative protein food for the common people. Not only the protein source they are also the component of aquatic food chain and indicators of aquatic ecosystem. Proper management and strategies to promote the edible invertebrates can be considered as the alternative protein and alternative income source for the common people for sustainable livelihood improvement.

Keywords: Dhansiri, Dimapur, invertebrates, livelihood improvement, protein

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Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang

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Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.

Keywords: Protein structure, binding site, functional prediction

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

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The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: Jaruwan Chutrtong

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This research aims to study consumer acceptance of Tempeh from various raw materials (type of bean) and determine protein contents for comparison. Tempeh made from soybean, peanut, white kidney bean and sesame in the ratio: - soybean:sesame =1:0.1, soybean:white kidney:sesame =1:1:0.1, soybean:peanut:sesame =1:1:0.1 and peanut:white kidney bean: sesame =1:1:0.1. The study found that consumer is most satisfied with appearances on soybean mixed with white kidney and black sesame tempeh (3.98). The most satisfied tempeh with textures is soybean mixed with peanut and black sesame tempeh (4.00). The most satisfied tempeh with odor is peanut mixed with white kidney bean and black sesame tempeh (4.04). And the most satisfied tempeh with flavor is peanut mixed with white kidney bean and black sesame tempeh (4.2). The amount of protein in production, soybean tempeh has the highest protein. When we add sesame seeds, it made the protein content slightly decreased (1.86 and 0.6 %). When we use peanut as raw material, the protein content decreased 15.3%. And when we use white kidney bean as raw material, the protein content decreased (22.77- 26.11%). 

Keywords: Acceptance, bean, protein content, tempeh.

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Authors: Abdelatief S. H. El-Jasser

Abstract:

The aim of the present study was to investigate the chemical and biological properties of local cowpea seed protein cultivated in Gizan region. The results showed that the cowpea and its products contain high level of protein (22.9-77.6%), high carbohydrates (9.4-64.3%) and low fats (0.1-0.3%). The trypsin and chymotrypsin activities were found to be 32.2 and 15.2 units, respectively. These activities were not affected in both defatted and protein concentrate whereas they were significantly reduced in isolated protein and cooked samples. The phytate content of cooked and concentrated cowpea samples varied from 0.25% -0.32%, respectively. Tannin content was found to be 0.4% and 0.23% for cooked and raw samples, respectively. The in vitro protein digestibility was very high in cowpea seeds (75.04-78.76%). The biological evaluation using rats showed that the group fed with animal feed containing casein gain more weight than those fed with that containing cowpea. However, the group fed with cooked cowpea gain more weight than those fed with uncooked cowpea. On the other hand, in vivo digestion showed high value (98.33%) among the group consumed casein compared to other groups those consumed cowpea contains feed. This could be attributed to low antinutritional factors in casein contains feed compared to those of cowpea contains feed because cooking significantly increased the digestion rate (80.8% to 83.5%) of cowpea contains feed. Furthermore, the biological evaluation was high (91.67%) of casein containing feed compared to that of cowpea containing feed (80.83%-87.5%). The net protein utilization (NPU) was higher (89.67%) in the group fed with casein containing feed than that of cowpea containing feed (56.33%-69.67%).

Keywords: Biological properties, Cowpea seed protein, Antinutritional factors, In vitro digestibility

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Authors: Ali Nouri Emamzadeh, Akbar Yaghobfar

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The experiment was conducted to evaluate digestibility quantities of protein in Canola Meals (CMs) between caecectomised and intact adult Rhode Island Red (RIR) cockerels with using conventional addition method (CAM) for 7 d: a 4-d adaptation and a 3-d experiment period on the basis of a completely randomized design with 4 replicates. Results indicated that caecectomy decreased (P<0.05) apparent and true digestibility quantities of protein for CMs, except for CMs 2 and 3. The mean apparent and true digestibility quantities for all CMs in caecectomised (80.5 and 81.4%, respectively) were (3.1 and 3.3%, respectively) less (P<0.05) than intact cockerels (83.6 and 84.7%, respectively). Therefore, the caecectomy method increases accuracy of the digestibility measurements of protein for this meal in bioassays based on excreta collection in adult cockerels.

Keywords: Adult cockerels, caecectomy, canola meals, proteindigestibility.

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Authors: J. Suwanprateeb, F. Thammarakcharoen

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Calcium phosphate coating (CaP) has been employed for protein delivery, but the typical direct protein adsorption on the coating led to low incorporation content and fast release of the protein from the coating. By using bovine serum albumin (BSA) as a model protein, rapid biomimetic co-precipitation between calcium phosphate and BSA was employed to control the distribution of BSA within calcium phosphate coating during biomimetic formation on titanium surface for only 6 h at 50oC in an accelerated calcium phosphate solution. As a result, the amount of BSA incorporation and release duration could be increased by using a rapid biomimetic coprecipitation technique. Up to 43 fold increases in the BSA incorporation content and the increase from 6 h to more than 360 h in release duration compared to typical direct adsorption technique were observed depending on the initial BSA concentration used during coprecipitation (1, 10 and 100 μg.ml-1). From x-ray diffraction and Fourier transform infrared spectroscopy studies, the coating composition was not altered with the incorporation of BSA by this rapid biomimetic co-precipitation and mainly comprised octacalcium phosphate and hydroxyapatite. However, the microstructure of calcium phosphate crystals changed from straight, plate-like units to curved, plate-like units with increasing BSA content.

Keywords: Biomimetic, Calcium Phosphate Coating, Protein, Titanium.

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

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Poly (ethylene glycol) (PEG) molecules attached to surfaces have shown high potential as a protein repellent due to their flexibility and highly water solubility. A quartz crystal microbalance recording frequency and dissipation changes (QCM-D) has been used to study the adsorption from aqueous solutions, of lysozyme and α-lactalbumin proteins (the last with and without calcium) onto modified stainless steel surfaces. Surfaces were coated with poly(ethylene imine) (PEI) and silicate before grafting on PEG molecules. Protein adsorption was also performed on the bare stainless steel surface as a control. All adsorptions were conducted at 23°C and pH 7.2. The results showed that the presence of PEG molecules significantly reduced the adsorption of lysozyme and α- lactalbumin (with calcium) onto the stainless steel surface. By contrast, and unexpected, PEG molecules enhanced the adsorption of α-lactalbumin (without calcium). It is suggested that the PEG -α- lactalbumin hydrophobic interaction plays a dominant role which leads to protein aggregation at the surface for this latter observation. The findings also lead to the general conclusion that PEG molecules are not a universal protein repellent. PEG-on-PEI surfaces were better at inhibiting the adsorption of lysozyme and α-lactalbumin (with calcium) than with PEG-on-silicate surfaces.

Keywords: Stainless steel, PEG, QCM-D, protein, PEI layer, silicate layer.

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Authors: Ferial M. Abu-Salem, Marwa H. Mahmoud, M. H. El-Kalyoub, A. Y. Gibriel, Azza Abou-Arab

Abstract:

In order to characterize the soy protein hydrolysate obtained in this study, gel chromatography on Sephadex G-25 was used to perform the separation of the peptide mixture and electrophoresis in SDS-polyacrylamide gel has been employed. Protein hydrolysate gave high antioxidant activities, but didn't give any antimicrobial activities. The antioxidant activities of protein hydrolysate was in the same trend of peptide content which gave high antioxidant activities and high peptide content between fractions 15 to 50. With increasing peptide concentrations, the scavenging effect on DPPH radical increased until about 70%, thereafter reaching a plateau. In compare to different concentrations of BHA, which exhibited higher activity (90%), soybean protein hydrolysate exhibited high antioxidant activities (70%) at a concentration of 1.45 mg/ml at fraction 25. Electrophoresis analysis indicated that, low- MW hydrolysate fractions (F1) appeared, on average, to have higher DPPH scavenging activities than high-MW fractions. These results revealed that soybean peptides probably contain substances that were proton donors and could react with free radicals to convert them to stable diamagnetic molecules. 

Keywords: Antioxidant peptides, hydrolysis, protein hydrolysate, peptide fractions.

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Authors: Sudarat Jiamyangyuen, Tipawan Thongsook, Riantong Singanusong, Chanida Saengtubtim

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Rice bran is normally used as a raw material for rice bran oil production or sold as feed with a low price. Conventionally, the protein in defatted rice bran was extracted using alkaline extraction and acid precipitation, which involves in chemical usage and lowering some nutritious component. This study was conducted in order to extract of rice bran protein concentrate (RBPC) from defatted rice bran using enzymes and employing polysaccharides in a precipitating step. The properties of RBPC obtained will be compared to those of a control sample extracted using a conventional method. The results showed that extraction of protein from rice bran using enzymes exhibited the higher protein recovery compared to that extraction with alkaline. The extraction conditions using alcalase 2% (v/w) at 50 C, pH 9.5 gave the highest protein (2.44%) and yield (32.09%) in extracted solution compared to other enzymes. Rice bran protein concentrate powder prepared by a precipitation step using alginate (protein in solution: alginate 1:0.016) exhibited the highest protein (27.55%) and yield (6.84%). Precipitation using alginate was better than that of acid. RBPC extracted with alkaline (ALK) or enzyme alcalase (ALC), then precipitated with alginate (AL) (samples RBP-ALK-AL and RBP-ALC-AL) yielded the precipitation rate of 75% and 91.30%, respectively. Therefore, protein precipitation using alginate was then selected. Amino acid profile of control sample, and sample precipitated with alginate, as compared to casein and soy protein isolated, showed that control sample showed the highest content among all sample. Functional property study of RBP showed that the highest nitrogen solubility occurred in pH 8-10. There was no statically significant between emulsion capacity and emulsion stability of control and sample precipitated by alginate. However, control sample showed a higher of foaming capacity and foaming stability compared to those of sample precipitated with alginate. The finding was successful in terms of minimizing chemicals used in extraction and precipitation steps in preparation of rice bran protein concentrate. This research involves in a production of value-added product in which the double amount of protein (28%) compared to original amount (14%) contained in rice bran could be beneficial in terms of adding to food products e.g. healthy drink with high protein and fiber. In addition, the basic knowledge of functional property of rice bran protein concentrate was obtained, which can be used to appropriately select the application of this value-added product from rice bran.

Keywords: Alginate, carrageenan, rice bran, rice bran protein.

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Authors: Ji-Hyon Kil, Kew-Cheol Shim, Kyoung-Ae Park, Kyoungho Kim

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Ambrosia trifida L. is designated as invasive alien species by the Act on the Conservation and Use of Biodiversity by the Ministry of Environment, Korea. The purpose of present paper was to investigate the inhibitory effects of aqueous extracts of A.trifida on the development of root hairs of Triticum aestivum L., and Allium tuberosum Rottler ex Spreng and the electrophoretic protein patterns of their radicles. The development of root hairs was inhibited by increasing of aqueous extract concentrations. Through SDS-PAGE, the electrophoretic protein bands of extracted proteins from their radicles were appeared in controls, but protein bands of specific molecular weight disappeared or weakened in treatments. In conclusion, inhibitory effects of A. trifida made two receptor species changed morphologically, and at the molecular level in early growth stage.

Keywords: Ambrosia trifida L., invasive alien species, inhibitory effect, root hair, electrophoretic protein, radicle.

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

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Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Zelmina Lubovac, Björn Olsson, Jonas Gamalielsson

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This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

Keywords: Modules, systems biology, protein interactionnetworks, yeast.

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Authors: Namal A. Senanayake, A. Beg, Withana C. Prasad

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This paper analyzes the patterns of the Monte Carlo data for a large number of variables and minterms, in order to characterize the circuit path length behavior. We propose models that are determined by training process of shortest path length derived from a wide range of binary decision diagram (BDD) simulations. The creation of the model was done use of feed forward neural network (NN) modeling methodology. Experimental results for ISCAS benchmark circuits show an RMS error of 0.102 for the shortest path length complexity estimation predicted by the NN model (NNM). Use of such a model can help reduce the time complexity of very large scale integrated (VLSI) circuitries and related computer-aided design (CAD) tools that use BDDs.

Keywords: Monte Carlo data, Binary decision diagrams, Neural network modeling, Shortest path length estimation.

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: N. AboulAtta, G. Ezizah, N. Yousif , S. Fathy

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The stilling basins are commonly used to dissipate the energy and protect the downstream floor from erosion. The aim of the present experimental work is to improve the roughened stilling basin using T-shape roughness instead of the regular cubic one and design this new shape. As a result of the present work the best intensity and the best roughness length are identified. Also, it is found that the T-shape roughness save materials and reduce the jump length compared to the cubic one. Sensitivity analysis was performed and it was noticed that the change in the length of jump is more sensitive to the change in roughness length than the change in intensity.

Keywords: hydraulic jump, energy dissipater, roughened bed, stilling basin.

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Authors: Akbar Soleimani, Alireza Heravi Moussavi, Mohsen Danesh Mesgaran, Abolqasem Golian

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Twenty - nine Holstein cows were used to evaluate the effects of different dry period (DP) lengths on milk yield and composition, some blood metabolites, and complete blood count (CBC). Cows were assigned to one of 2 treatments: 1) 60-d dry period, 2) 35-d DP. Milk yield, from calving to 60 days, was not different for cows on the treatments (p =0.130). Cows in the 35-d DP produced more milk protein and SNF compare with cows in treatment 1 (p ≤ 0.05). Serum glucose, non-esterified fatty acids (NEFA), beta hydroxyl butyrate acid (BHBA), blood urea nitrogen (BUN), urea, and glutamic oxaloacetic transaminase (GOT) were all similar among the treatments. Body condition score (BCS), body weight (BW), complete blood count (CBC) and health problems were similar between the treatments. The results of this study demonstrated we can reduce the dry period length to 35 days with no problems.

Keywords: complete blood count, dairy cows, dry period, milk yield

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: Ivan Pavic, Fran Galetic, Tomislava Pavic Kramaric

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The purpose of this article is to analyze the degree of concentration in the banking market in EU member states as well as to determine the impact of the length of EU membership on the degree of concentration. In that sense several analysis were conducted, specifically, panel analysis, calculation of correlation coefficient and regression analysis of the impact of the length of EU membership on the degree of concentration. Panel analysis was conducted to determine whether there is a similar trend of concentration in three groups of countries - countries with a low, moderate and high level of concentration. The conducted panel analysis showed that in EU countries with a moderate level of concentration, the level of concentration decreases. The calculation of correlation showed that, to some extent, with other influential factors, the length of EU membership negatively affects the market concentration of the banking market. Using the regression analysis for investigation of the influence of the length of EU membership on the level of concentration in the banking sector in a particular country, the results reveal that there is a negative effect of the length in EU membership on market concentration, although it is not significantly influential variable.

Keywords: Banking sector, concentration, EU

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Authors: Dariush Semnani, Mohammad Sheikhzadeh

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Circular knitting machine makes the fabric with more than two knitting tools. Variation of yarn tension between different knitting tools causes different loop length of stitches duration knitting process. In this research, a new intelligent method is applied to control loop length of stitches in various tools based on ideal shape of stitches and real angle of stitches direction while different loop length of stitches causes stitches deformation and deviation those of angle. To measure deviation of stitch direction against variation of tensions, image processing technique was applied to pictures of different fabrics with constant front light. After that, the rate of deformation is translated to needed compensation of loop length cam degree to cure stitches deformation. A fuzzy control algorithm was applied to loop length modification in knitting tools. The presented method was experienced for different knitted fabrics of various structures and yarns. The results show that presented method is useable for control of loop length variation between different knitting tools based on stitch deformation for various knitted fabrics with different fabric structures, densities and yarn types.

Keywords: Circular knitting, Radon transformation, Knittedfabric, Regularity, Fuzzy control

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

Abstract:

In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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Authors: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

Abstract:

Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: Whey powder, temperature, denaturation, reverse phase – HPLC.

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Authors: Marios Poulos, Eirini Maliagani, Minas Paschopoulos, George Bokos

Abstract:

The purpose of my research proposal is to demonstrate that there is a relationship between EEG and endometrial cancer. The above relationship is based on an Aristotelian Syllogism; since it is known that the 14-3-3 protein is related to the electrical activity of the brain via control of the flow of Na+ and K+ ions and since it is also known that many types of cancer are associated with 14-3-3 protein, it is possible that there is a relationship between EEG and cancer. This research will be carried out by well-defined diagnostic indicators, obtained via the EEG, using signal processing procedures and pattern recognition tools such as neural networks in order to recognize the endometrial cancer type. The current research shall compare the findings from EEG and hysteroscopy performed on women of a wide age range. Moreover, this practice could be expanded to other types of cancer. The implementation of this methodology will be completed with the creation of an ontology. This ontology shall define the concepts existing in this research-s domain and the relationships between them. It will represent the types of relationships between hysteroscopy and EEG findings.

Keywords: Bioinformatics, Protein 14-3-3, EEG, Endometrial cancer, Ontology.

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Authors: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar

Abstract:

Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.

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