Search results for: microsomal triglyceride transfer protein

Authors: Jamaludin Sallim, Rozlina Mohamed, Roslina Abdul Hamid

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In this paper, we proposed an Ant Colony Optimization (ACO) algorithm together with Traveling Salesman Problem (TSP) approach to investigate the clustering problem in Protein Interaction Networks (PIN). We named this combination as ACOPIN. The purpose of this work is two-fold. First, to test the efficacy of ACO in clustering PIN and second, to propose the simple generalization of the ACO algorithm that might allow its application in clustering proteins in PIN. We split this paper to three main sections. First, we describe the PIN and clustering proteins in PIN. Second, we discuss the steps involved in each phase of ACO algorithm. Finally, we present some results of the investigation with the clustering patterns.

Keywords: ant colony optimization algorithm, searching algorithm, protein functional module, protein interaction network

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Authors: Myunggon Yoon, Jung-Ho Moon

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In this paper, we present a transfer function representation of a general one-dimensional combustor. The input of the transfer function is a heat rate perturbation of a burner and the output is a flow velocity perturbation at the burner. This paper considers a general combustor model composed of multiple cans with different cross sectional areas, along with a non-zero flow rate.

Keywords: combustor, dynamics, thermoacoustics, transfer function

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Authors: Islam Tarek, Moataz Soliman

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With the amazing development of nanoscience’s and the discovery of the unique properties of nanometric materials, the ideas of scientists and researchers headed to take advantage of this progress in various fields, and one of the most important of these areas is the field of heat transfer and benefit from it in saving energy used for heat transfer, so nanometric materials were used to improve the properties of heat transfer fluids and increase the efficiency of the liquid. In this paper, we will compare two types of heat transfer fluid, one industrial type (the base fluid is a mix of ethylene glycol and deionized water ) and another natural oils(the base fluid is a mix of jatropha oil and expired olive oil), explaining the method of preparing each of them, starting from the method of preparing CNT, collecting and sorting jatropha seeds, and the most appropriate method for extracting oil from them, and characterization the both of two fluids and when to use both.

Keywords: nanoscience, heat transfer, thermal conductivity, jatropha oil

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Authors: Surabhi Pandey, Pavuluri Srinivasa Rao

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Extrusion processing is a high-temperature short time (HTST) treatment which can improve protein quality and digestibility together with retaining active nutrients. In-vitro protein digestibility of plant protein-based foods is generally enhanced by extrusion. The current study aimed to investigate the effect of extrusion cooking on in-vitro protein digestibility (IVPD) and conformational modification of protein in green banana flour extrudates. Green banana flour was extruded through a co-rotating twin-screw extruder varying the moisture content, barrel temperature, screw speed in the range of 10-20 %, 60-80 °C, 200-300 rpm, respectively, at constant feed rate. Response surface methodology was used to optimise the result for IVPD. Fourier-transform infrared spectroscopy (FTIR) analysis provided a convenient and powerful means to monitor interactions and changes in functional and conformational properties of extrudates. Results showed that protein digestibility was highest in extrudate produced at 80°C, 250 rpm and 15% feed moisture. FTIR analysis was done for the optimised sample having highest IVPD. FTIR analysis showed that there were no changes in primary structure of protein while the secondary protein structure changed. In order to explain this behaviour, infrared spectroscopy analysis was carried out, mainly in the amide I and II regions. Moreover, curve fitting analysis showed the conformational changes produced in the flour due to protein denaturation. The quantitative analysis of the changes in the amide I and II regions provided information about the modifications produced in banana flour extrudates.

Keywords: extrusion, FTIR, protein conformation, raw banana flour, SDS-PAGE method

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Authors: Yufen Qin

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Text sentiment transfer is an important branch of text style transfer. The goal is to generate text with another sentiment attribute based on a text with a specific sentiment attribute while maintaining the content and semantic information unrelated to sentiment unchanged in the process. There are currently two main challenges in this field: no parallel corpus and text attribute entanglement. In response to the above problems, this paper proposed a novel solution: Mask-Prompt-Rerank. Use the method of masking the sentiment words and then using prompt regeneration to transfer the sentence sentiment. Experiments on two sentiment benchmark datasets and one formality transfer benchmark dataset show that this approach makes the performance of small pre-trained language models comparable to that of the most advanced large models, while consuming two orders of magnitude less computing and memory.

Keywords: language model, natural language processing, prompt, text sentiment transfer

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Authors: Gulcin Yildiz, Hao Feng

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Soybean proteins are the most widely used and researched proteins in the food industry. Due to soy allergies among consumers, however, alternative legume proteins having similar functional properties have been studied in recent years. These alternative proteins are also expected to have a price advantage over soy proteins. One such protein that has shown good potential for food applications is pea protein. Besides the favorable functional properties of pea protein, it also contains fewer anti-nutritional substances than soy protein. However, a comparison of the physicochemical properties of pea protein isolate (PPI)-starch nanocomplexes and soy protein isolate (SPI)-starch nanocomplexes treated by ultrasound has not been well documented. This study was undertaken to investigate the effects of ultrasound treatment on the physicochemical properties of PPI-starch and SPI-starch nanocomplexes. Pea protein isolate (85% pea protein) provided by Roquette (Geneva, IL, USA) and soy protein isolate (SPI, Pro-Fam® 955) obtained from the Archer Daniels Midland Company were adjusted to different pH levels (2-12) and treated with 5 minutes of ultrasonication (100% amplitude) to form complexes with starch. The soluble protein content was determined by the Bradford method using BSA as the standard. The turbidity of the samples was measured using a spectrophotometer (Lambda 1050 UV/VIS/NIR Spectrometer, PerkinElmer, Waltham, MA, USA). The volume-weighted mean diameters (D4, 3) of the soluble proteins were determined by dynamic light scattering (DLS). The emulsifying properties of the proteins were evaluated by the emulsion stability index (ESI) and emulsion activity index (EAI). Both the soy and pea protein isolates showed a U-shaped solubility curve as a function of pH, with a high solubility above the isoelectric point and a low one below it. Increasing the pH from 2 to 12 resulted in increased solubility for both the SPI and PPI-starch complexes. The pea nanocomplexes showed greater solubility than the soy ones. The SPI-starch nanocomplexes showed better emulsifying properties determined by the emulsion stability index (ESI) and emulsion activity index (EAI) due to SPI’s high solubility and high protein content. The PPI had similar or better emulsifying properties at certain pH values than the SPI. The ultrasound treatment significantly decreased the particle sizes of both kinds of nanocomplex. For all pH levels with both proteins, the droplet sizes were found to be lower than 300 nm. The present study clearly demonstrated that applying ultrasonication under different pH conditions significantly improved the solubility and emulsify¬ing properties of the SPI and PPI. The PPI exhibited better solubility and emulsifying properties than the SPI at certain pH levels

Keywords: emulsifying properties, pea protein isolate, soy protein isolate, ultrasonication

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Authors: Zahra Yadollahi, Marjan Motiei, Natalia Kazantseva, Petr Saha

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Chitosan (CS)-whey protein isolate (WPI) core-shell nanoparticles were synthesized through self-assembly of whey protein isolated polyanions and chitosan polycations in the presence of tripolyphosphate (TPP) as a crosslinker. The formation of this type of nanostructures with narrow particle size distribution is crucial for developing delivery systems since the functional characteristics highly depend on their sizes. To achieve this goal, the nanostructure was optimized by varying the concentrations of WPI, CS, and TPP in the reaction mixture. The chemical characteristics, surface morphology, and particle size of the nanoparticles were evaluated.

Keywords: whey protein isolated, chitosan, nanoparticles, delivery system

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Authors: Bayram Sahin, Hourieh Bayramian, Emre Mandev, Murat Ceylan

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In industrial applications, the demand for the enhancement of heat transfer is a common engineering problem. The use of additives to heat transfer fluid is a technique applied to enhance the heat transfer performance of base fluids. In this study, the thermal performance of nanofluids consisting of SiO2 particles and deionized water in circular microchannels was investigated experimentally. SiO2 nanoparticles with diameter of 15 nm were added to water to prepare nanofluids with 0.2% and 0.4% volume fractions. Heat transfer characteristics were calculated by using temperature, flow and pressure measurements. The thermal conductivity and viscosity values required for the calculations are measured separately. It is observed that the Nusselt number increases at the all volume fraction of particles, by increasing the Reynolds number and the volumetric ratios of the particles. The highest heat transfer enhancement is obtained at Re = 2160 and 0.4 % vol. by 14% under the condition of a constant pumping power.

Keywords: nanofluid, microchannel, heat transfer, SiO2-water nanofluid

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Authors: Makan Cheraghpour, Seyed Ahmad Hosseini, Damoon Ashtary-Larky, Saeed Shirali, Matin Ghanavati, Meysam Alipour

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Background: In addition to reducing body weight, the low-calorie diets can reduce the lean body mass. It is hypothesized that in addition to reducing the body weight, the low-calorie diets can maintain the lean body mass. So, the current study aimed at evaluating the effects of high-protein diet with calorie restriction on body composition in overweight and obese individuals. Methods: 36 obese and overweight subjects were divided randomly into two groups. The first group received a normal-protein, low-energy diet (RDA), and the second group received a high-protein, low-energy diet (2×RDA). The anthropometric indices including height, weight, body mass index, body fat mass, fat free mass, and body fat percentage were evaluated before and after the study. Results: A significant reduction was observed in anthropometric indices in both groups (high-protein, low-energy diets and normal-protein, low-energy diets). In addition, more reduction in fat free mass was observed in the normal-protein, low-energy diet group compared to the high -protein, low-energy diet group. In other the anthropometric indices, significant differences were not observed between the two groups. Conclusion: Independently of the type of diet, low-calorie diet can improve the anthropometric indices, but during a weight loss, high-protein diet can help the fat free mass to be maintained.

Keywords: diet, high-protein, body mass index, body fat percentage

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Authors: Thanyaporn Senarai, Rapeepun Vanichviriyakit, Shinji Miyata, Chihiro Sato, Prapee Sretarugsa, Wattana Weerachatyanukul, Ken Kitajima

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In this study, we characterized a region-specific 250 kDa protein that was secreted of MSD fluid, which is believed to play dual functions in forming a spermatophoric wall for sperm physical protection, and in sperm membrane modification as part of sperm maturation process. The partial amino acid sequence and N-terminal sequencing revealed that the MSD-specific 250 kDa protein showed a high similarity with a plasma-rich protein, α-2 macroglobulin (α2M), so termed pp-α2M. This protein was a large glycoprotein contained predominantly mannose and GlcNAc. The expression of pp-α2M mRNA was detected in spermatic duct (SD), androgenic gland (AG) and hematopoietic tissue, while the protein expression was rather specific to the apical cytoplasm of MSD epithelium. The secretory pp-α2M in MSD fluid was acquired onto the MSD sperm membrane and was also found within the matrix of the acrosome. Distally, pp-α2M was removed from spermathecal sperm membrane, while its level kept constant in the sperm AC. Together the results indicate that pp-α2M is a 250 kDa region-specific secretory protein which plays roles in sperm physical protection and also acts as maturation factor in the P. pelagicus sperm.

Keywords: alpha-2 macroglobulin, blue swimming crab, sperm maturation, spermatic duct

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Authors: Mardiati Zain, Yetti Marlida, Elihasridas Elihasridas, Erpomen Erpomen, Andri Andri

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Background: Livestock productivity is greatly influenced by the energy and protein balance in diet. This study aimed to determine the energy and protein balance of male Simenthal cattle diet with protein and energy levels. The experimental design used was a randomized block design (RBD) 2x3x3 factorial design. There are two factors namely A level of energy diet that is 65% and 70% TDN. Factor B is a protein level of diet used were 10, 12 and 14% and each treatment is repeated three times. The weight of Simenthal cattle used ranged between 240 - 300 kg. Diet consisted of ammoniated rice straw and concentrated with ratio 40:60. Concentrate consisted of palm kernel cake, rice brain, cassava, mineral, and urea. The variables measured were digestibility of dry matter, organic matter and fiber, dry matter intake, daily gain, feed efficiency and blood characteristic. Results: There was no interaction between protein and energy level of diet on the nutrients intake (DM intake, OM intake, CP intake), weight gain and efficiency (P < 0.01). There was an interaction between protein and energy level of diet on digestibility (DM, OM, CP and allantoin urine (P > 0.01) Nutrients intake decreases with increasing levels of energy and protein diet, while nutrient digestibility, Avarage daily gain and feed efficiency increases with increasing levels of energy and protein diet. Conclusions: The result can be concluded that the best treatment was A2B1 which is energy level 70% TDN and protein 10%, where are dry matter intake 7.66 kg/d, daily gain 1.25 kg/d, feed efficiency 16.12%, and dry matter and organic matter digestibility 64.08 and 69.42% respectively.

Keywords: energy and protein ratio, simenthal cattle, rice straw ammoniated, digestibility

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Farhad Hekmatipour, M. A. Akhavan-Behabadi, Farzad Hekmatipour

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In this paper, experiments were conducted to investigate the heat transfer of Copper Oxide-Heat Transfer Oil (CuO-HTO) nanofluid laminar flow in vertical smooth and microfin tubes as the surface temperature is constant. The effect of adding the nanoparticle to base fluid and Richardson number on the heat transfer enhancement is investigated as Richardson number increases from 0.1 to 0.7. The experimental results demonstrate that the combined forced-natural convection heat transfer rate may be improved significantly with an increment of mass nanoparticle concentration from 0% to 1.5%. In this experiment, a correlation is also proposed to predict the mixed convection heat transfer rate of CuO-HTO nanofluid flow. The maximum deviation of both correlations is less than 14%. Moreover, a correlation is presented to estimate the Nusselt number inside vertical smooth and microfin tubes as Rayleigh number is between 2´105 and 6.8´106 with the maximum deviation of 12%.

Keywords: mixed convection, heat transfer, nanofluid, vertical tube, microfin tube

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Authors: F. A. Hamad, S. He

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In this paper, the average heat transfer characteristics for a cross flow cylinder of 16 mm diameter in a vertical pipe has been studied for single-phase flow (water/oil) and multicomponent (non-boiling) flow (water-air, water-oil, oil-air and water-oil-air). The cylinder is uniformly heated by electrical heater placed at the centre of the element. The results show that the values of average heat transfer coefficients for water are around four times the values for oil flow. Introducing air as a second phase with water has very little effect on heat transfer rate, while the heat transfer increased by 70% in case of oil. For water–oil flow, the heat transfer coefficient values are reflecting the percentage of water up to 50%, but increasing the water more than 50% leads to a sharp increase in the heat transfer coefficients to become close to the values of pure water. The enhancement of heat transfer by mixing two phases may be attributed to the changes in flow structure near to cylinder surface which lead to thinner boundary layer and higher turbulence. For three-phase flow, the heat transfer coefficients for all cases fall within the limit of single-phase flow of water and oil and are very close to pure water values. The net effect of the turbulence augmentation due to the introduction of air and the attenuation due to the introduction of oil leads to a thinner boundary layer of oil over the cylinder surface covered by a mixture of water and air bubbles.

Keywords: circular cylinder, cross flow, hear transfer, multicomponent multiphase flow

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Authors: V. G. Rifert, V. V. Gorin, V. V. Sereda, V. V. Treputnev

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The analysis of heat transfer design methods in condensing inside plain tubes under existing influence of shear stress is presented in this paper. The existing discrepancy in more than 30-50% between rating heat transfer coefficients and experimental data has been noted. The analysis of existing theoretical and semi-empirical methods of heat transfer prediction is given. The influence of a precise definition concerning boundaries of phase flow (it is especially important in condensing inside horizontal tubes), shear stress (friction coefficient) and heat flux on design of heat transfer is shown. The substantiation of boundary conditions of the values of parameters, influencing accuracy of rated relationships, is given. More correct relationships for heat transfer prediction, which showed good convergence with experiments made by different authors, are substantiated in this work.

Keywords: film condensation, heat transfer, plain tube, shear stress

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Authors: Agung Sujatmiko

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One of the purposes of patent licensing was to transfer technology from developed countries to developing countries. For this reason, the role of the patent license agreement was very important and had a function as a tool to achieve technological development. This goal was very good, but in fact, many problems and obstacles arose in its implementation, so the technology transfer that had been implemented had not given good results. For this reason, it was necessary to find a solution so that technology could switch properly. The problem approach used the statutory and conceptual approaches. The analysis used was deductive by analyzing general laws and regulations and then concluding. Several regulations related to technology transfer were the main source to find answers to why technology transfer was difficult to achieve and what caused it. Once the cause was known, a solution would be sought.

Keywords: license, patent, technology, tie in clause

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Authors: Im-Nam Jang, Yong-Sik Ahn

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In this study sintered wick was formed in a heat pipe through the process of sintering a mixture of copper powder with particle sizes of 100μm and 200μm, mixed with a pore-forming agent. The heat pipe's thermal resistance, which affects its heat transfer efficiency, is determined during manufacturing according to powder type, thickness of the sintered wick, and filling rate of the working fluid. Heat transfer efficiency was then tested at various inclination angles (0°, 45°, 90°) to evaluate the performance of heat pipes. Regardless of the filling amount and test angle, the 200μm copper powder type exhibited superior heat transfer efficiency compared to the 100μm type. After analyzing heat transfer performance at various filling rates between 20% and 50%, it was determined that the heat pipe's optimal heat transfer capability occurred at a working fluid filling rate of 30%. The width of the wick was directly related to the heat transfer performance.

Keywords: heat pipe, heat transfer performance, effective pore size, capillary force, sintered wick

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Authors: Seongryong Kang, Woonjin Kim, Sungjoo Lee

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Under the environment of fierce competition and globalized economy, international technology collaboration has gained increasing attention as a way to improve innovation efficiency. While international technology transfer helps a firm to acquire necessary technology in a short period of time, it also has a risk; embedding external technology from overseas partners may cause a transaction cost due to the regional, cultural and language barriers, which tend to offset the benefits of such transfer. Though a number of previous studies have focused on the effects of technology in-transfer on firm performance, few have conducted in the context of international technology transfer. To fill this gap, this study aims to investigate the impact of international technology in-transfer on firm performance – both innovation and financial performance, with a particular emphasis on the diversity and intensity of such transfer. To do this, we adopted technology balance payment (TBP) data of Korean firms from 2010 to 2011, where an intermediate regression analysis was used to identify the intermediate effects of absorptive capacity. The analysis results indicate that i) the diversity and intensity of international technology transfer influence innovation performance by improving R&D capability positively; and ii) the diversity has a positive impact but the intensity has a negative impact on financial performance through the intermediation of R&D intensity. The research findings are expected to provide meaningful implications for establishing global technology strategy and developing policy programs to facilitate technology transfer.

Keywords: diversity, intensity, international technology acquisition, performance, technology transfer

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Authors: Alexander A. Tokmakov

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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

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Authors: Hamid Reza Goshayeshi

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The effect of ɑ(alpha) Fe2O3 and ɤ(gamma)Fe2O3 particles on the heat transfer performance of an oscillating heat pipe was investigated experimentally. Kerosene was used as the base fluid for the OHP. Six size particles with average diameters of 10 nm, 20 nm, and 30 nm ɑFe2O3 and ɤFe2O3 were investigated, respectively. Experimental results show that the ɤFe2O3 particles added in the OHP significantly affect the heat transfer performance. When the OHP was charged with kerosene and 20 nm ɤ Fe2O3 particles, the OHP can achieve the best heat transfer performance among six particles investigated in this research.

Keywords: copper oscillating heat pipe, heat transfer, flow, comparison of ɑ(alpha)Fe2O3 and ɤ(gamma)Fe2O3, increase heat transfer

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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 under two phyla viz., Arthropods and Molluscs. Total 10 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: Sri Rahayu, M. Dwi Susan, Aris Soewondo, W. M. Agung Pramana

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Semen is an organic fluid (seminal plasma) that contain spermatozoa. Proteins are one of the major seminal plasma components that modulate sperm functionality, influence sperm capacitation and maintaining the stability of the membrane. Semen freezing is a procedure to preserve sperm cells. The process causes decrease in sperm viability due to temperature shock and oxidation stress. Oxidation stress is a disturbance on phosphorylation that increases ROS concentration, and it produces lipid peroxide in spermatozoa membrane resulted in high MDA (malondialdehyde) concentration. The objective of this study was to examine the effect of freezing on protein and MDA profile of bovine sperm cell and seminal plasma after freezing. Protein and MDA of sperm cell and seminal plasma were isolated from 10 sample. Protein profiles was analyzed by SDS PAGE with separating gel 12,5 %. The concentration of MDA was measured by spectrophotometer. The results of the research indicated that freezing of semen cause lost of the seminal plasma proteins with molecular with 20, 10, and 9 kDa. In addition, the result research showed that protein of the sperm (26, 10, 9, 7, and 6 kDa) had been lost. There were difference MDA concentration of seminal plasma and sperm cell were increase after freezing. MDA concentration of seminal plasma before and after freezing were 2.2 and 2.4 nmol, respectively. MDA concentration of sperm cell before and after freezing were 1,5 and 1.8 nmol, respectively. In conclusion, there were differences protein profiles of spermatozoa before and after semen freezing and freezing cause increasing of the MDA concentration.

Keywords: MDA, semen freezing, SDS PAGE, protein profile

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Authors: Aakansha Gupta, Neha Vadnere, Tapasvi Soni, M. Anbarsi

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Protein secondary structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Some aspects of protein functions and genome analysis can be predicted by secondary structure prediction. This is used to help annotate sequences, classify proteins, identify domains, and recognize functional motifs. In this paper, we represent protein secondary structure as a mathematical model. To extract and predict the protein secondary structure from the primary structure, we require a set of parameters. Any constants appearing in the model are specified by these parameters, which also provide a mechanism for efficient and accurate use of data. To estimate these model parameters there are many algorithms out of which the most popular one is the EM algorithm or called the Expectation Maximization Algorithm. These model parameters are estimated with the use of protein datasets like RS126 by using the Bayesian Probabilistic method (data set being categorical). This paper can then be extended into comparing the efficiency of EM algorithm to the other algorithms for estimating the model parameters, which will in turn lead to an efficient component for the Protein Secondary Structure Prediction. Further this paper provides a scope to use these parameters for predicting secondary structure of proteins using machine learning techniques like neural networks and fuzzy logic. The ultimate objective will be to obtain greater accuracy better than the previously achieved.

Keywords: model parameters, expectation maximization algorithm, protein secondary structure prediction, bioinformatics

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Authors: Mohammed Hakim Jafferali, Balaje Vijayaraghavan, Ricardo A. Figueroa, Ellinor Crafoord, Veronica J. Larsson, Einar Hallberg, Santhosh Gudise

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The nuclear envelope which surrounds the chromatin of eukaryotic cells contains more than a hundred transmembrane proteins. Mutations in some genes encoding nuclear envelope proteins give rise to human diseases including neurological disorders. The function of many nuclear envelope proteins is not well established. This is partly because nuclear envelope proteins and their interactions are difficult to study due to the inherent resistance to extraction of nuclear envelope proteins. We have developed a novel method called MCLIP, to identify interacting partners of nuclear envelope proteins in live cells. Using MCLIP, we found three new binding partners of the inner nuclear membrane protein Samp1: the intermediate filament protein Lamin B1, the LINC complex protein Sun1 and the G-protein Ran. Furthermore, using in vitro studies, we show that Samp1 binds both Emerin and Ran directly. We have also studied the interaction between Samp1 and Ran in detail. The results show that the Samp1 binds stronger to RanGTP than RanGDP. Samp1 is the first transmembrane protein known to bind Ran and it is tempting to speculate that Samp1 may provide local binding sites for RanGTP at membranes.

Keywords: MCLIP, nuclear envelope, ran, Samp1

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Authors: Minho Bang, Seok Min Choi, Jun Su Park, Hokyu Moon, Hyung Hee Cho

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Present study investigates the effect of unsteady wakes on heat transfer in blade tip. Heat/mass transfer was measured in blade tip region depending on a variety of strouhal number by naphthalene sublimation technique. Naphthalene sublimation technique measures heat transfer using a heat/mass transfer analogy. Experiments are performed in linear cascade which is composed of five turbine blades and rotating rods. Strouhal number of inlet flow are changed ranging from 0 to 0.22. Reynolds number is 100,000 based on 11.4 m/s of outlet flow and axial chord length. Three different squealer tip geometries such as base squealer tip, vertical rib squealer tip, and camber line squealer tip are used to study how unsteady wakes affect heat transfer on a blade tip. Depending on squealer tip geometry, different flow patterns occur on a blade tip. Also, unsteady wakes cause reduced tip leakage flow and turbulent flow. As a result, as strouhal number increases, heat/mass transfer coefficients decrease due to the reduced leakage flow. As strouhal number increases, heat/ mass transfer coefficients on a blade tip increase in vertical rib squealer tip.

Keywords: gas turbine, blade tip, heat transfer, unsteady wakes

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Authors: Srikrishna Pramanik, Sree Chithra, Saurabh Rai, Sameeksha Agrawal, Debanggana Shil, Saptarshi Mukherjee

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The understanding of interactions between organic chromophores and biologically useful luminescent noble metal nanoclusters (NCs) leading to an energy transfer process that has applications in light-harvesting materials is still in its nascent stage. This work describes a photoluminescent supramolecular assembly, made in two stages, employing an energy transfer process between silver (Ag) NCs as the donor and a host-guest system as the acceptor that can find potential applications in diverse fields. Initially, we explored the host-guest chemistry between a cationic guest, Ethidium Bromide and the anionic host Cucurbit[8]uril using spectroscopic and calorimetric techniques to decipher their interaction mechanism in modulating photophysical properties of the chromophore. Next, we synthesized a series of blue-emitting AgNCs using different templates such as protein, peptides, and cyclodextrin. The as-prepared AgNCs were characterized by various spectroscopic techniques. We have established that these AgNCs can be employed as donors in the FRET process with the above acceptor for FRET-based emission color tuning. Our in-depth studies revealed that surface ligands play a key role in modulating FRET efficiency. Overall, by employing a non-covalent strategy, we have tried to develop FRET pairs using blue-emitting NCs and a host-guest complex, which could find potential applications in constructing advanced white light-emitting, anti-counterfeiting materials, and developing biosensors.

Keywords: absorption spectroscopy, cavities, energy transfer, fluorescence, fluorescence resonance energy transfer

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Authors: Yi-Hui Lai, Chih-Hsiang Yang, Li-Chung Hsu

Abstract:

The inflammasome is a protein complex that modulates caspase-1 activity, resulting in proteolytic cleavage of proinflammatory cytokines such as IL-1β and IL-18, into their bioactive forms. It has been shown that the inflammasomes play a crucial role in the clearance of pathogenic infection and tissue repair. However, dysregulated inflammasome activation contributes to a wide range of human diseases such as cancers and auto-inflammatory diseases. Yet, regulation of NLRP3 inflammasome activation remains largely unknown. We discovered a novel DEAD box protein, whose biological function has not been reported, not only negatively regulates NLRP3 inflammasome activation by interfering NLRP3 inflammasome assembly and cellular localization but also mitigate pyroptosis upon pathogen evasion. The DEAD-box protein is the first DEAD-box protein gets involved in modulation of the inflammasome activation. In our study, we found that caspase-1 activation and mature IL-1β production were largely enhanced upon LPS challenge in the DEAD box-containing protein- deleted THP-1 macrophages and bone marrow-derived macrophages (BMDMs). In addition, this DEAD box-containing protein migrates from the nucleus to the cytoplasm upon LPS stimulation, which is required for its inhibitory role in NLRP3 inflammasome activation. The DEAD box-containing protein specifically interacted with the LRR motif of NLRP3 via its DEAD domain. Furthermore, due to the crucial role of the NLRP3 LRR domain in the recruitment of NLRP3 to mitochondria and binding to its adaptor ASC, we found that the interaction of NLRP3 and ASC was downregulated in the presence of the DEAD box-containing protein. In addition to the mechanical study, we also found that this DEAD box protein protects host cells from inflammasome-triggered cell death in response to broad-ranging pathogens such as Candida albicans, Streptococcus pneumoniae, etc., involved in nosocomial infections and severe fever shock. Collectively, our results suggest that this novel DEAD box molecule might be a key therapeutic strategy for various infectious diseases.

Keywords: inflammasome, inflammation, innate immunity, pyroptosis

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Authors: Lee Derk Huan, Nur Irmawati

Abstract:

This paper aims to investigate the heat transfer and fluid flow characteristics of nanofluids used in spray cooling systems. The effect of spray height, type of nanofluids and concentration of nanofluids are numerically investigated. Five different nanofluids such as AgH2O, Al2O3, CuO, SiO2 and TiO2 with volume fraction range of 0.5% to 2.5% are used. The results revealed that the heat transfer performance decreases as spray height increases. It is found that TiO2 has the highest transfer coefficient among other nanofluids. In dilute spray conditions, low concentration of nanofluids is observed to be more effective in heat removal in a spray cooling system.

Keywords: numerical investigation, spray cooling, heat transfer, nanofluids

Procedia PDF Downloads 439

Authors: Han-Taw Chen, Chung-Hou Lai, Tzu-Hsiang Lin, Ge-Jang He

Abstract:

This study applies the inverse method and three-dimensional CFD commercial software in conjunction with the experimental temperature data to investigate the heat transfer and fluid flow characteristics of the plate-fin heat sink in a closed rectangular enclosure for various values of fin height. The inverse method with the finite difference method and the experimental temperature data is applied to determine the heat transfer coefficient. The k-ε turbulence model is used to obtain the heat transfer and fluid flow characteristics within the fins. To validate the accuracy of the results obtained, the comparison of the average heat transfer coefficient is made. The calculated temperature at selected measurement locations on the plate-fin is also compared with experimental data.

Keywords: inverse method, FLUENT, k-ε model, heat transfer characteristics, plate-fin heat sink

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Authors: Jamerson Felipe Pereira Lima, Jeane Cecília Bezerra de Melo

Abstract:

The difficulty and cost related to obtaining of protein tertiary structure information through experimental methods, such as X-ray crystallography or NMR spectroscopy, helped raising the development of computational methods to do so. An approach used in these last is prediction of tridimensional structure based in the residue chain, however, this has been proved an NP-hard problem, due to the complexity of this process, explained by the Levinthal paradox. An alternative solution is the prediction of intermediary structures, such as the secondary structure of the protein. Artificial Intelligence methods, such as Bayesian statistics, artificial neural networks (ANN), support vector machines (SVM), among others, were used to predict protein secondary structure. Due to its good results, artificial neural networks have been used as a standard method to predict protein secondary structure. Recent published methods that use this technique, in general, achieved a Q3 accuracy between 75% and 83%, whereas the theoretical accuracy limit for protein prediction is 88%. Alternatively, to achieve better results, support vector machines prediction methods have been developed. The statistical evaluation of methods that use different AI techniques, such as ANNs and SVMs, for example, is not a trivial problem, since different training sets, validation techniques, as well as other variables can influence the behavior of a prediction method. In this study, we propose a prediction method based on artificial neural networks, which is then compared with a selected SVM method. The chosen SVM protein secondary structure prediction method is the one proposed by Huang in his work Extracting Physico chemical Features to Predict Protein Secondary Structure (2013). The developed ANN method has the same training and testing process that was used by Huang to validate his method, which comprises the use of the CB513 protein data set and three-fold cross-validation, so that the comparative analysis of the results can be made comparing directly the statistical results of each method.

Keywords: artificial neural networks, protein secondary structure, protein structure prediction, support vector machines

Procedia PDF Downloads 583