Search results for: c- reactive protein

Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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Authors: A.C. Duarte, C.I.L. Justino, K. Duarte, A.C. Freitas, R. Pereira, P. Chaves, P. Bettencourt, S. Cardoso, T.A.P. Rocha-Santos

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This paper aims at overviewing the topics of a research project (CARDIOSENSOR) on the field of health sciences (biomaterials and biomedical engineering). The project has focused on the development of a nanosensor for the assessment of the risk of cardiovascular diseases by the monitoring of C-reactive protein (CRP), which has been currently considered as the best validated inflammatory biomarker associated to cardiovascular diseases. The project involves tasks such as: 1) the development of sensor devices based on field effect transistors (FET): assembly, optimization and validation; 2) application of sensors to the detection of CRP in standard solutions and comparison with enzyme-linked immunosorbent assay (ELISA); and 3) application of sensors to real samples such as blood and saliva and evaluation of their ability to predict the risk of cardiovascular disease.

Keywords: Carbon nanotubes field effect transistors, cardiovascular diseases, C-reactive protein, sensor.

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Authors: Kasra Afsahi, Maryam Soheilifar

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Cerebrovascular accident (CVA) is a neurological side effect of COVID-19 disease wit high rate in pandemics. Effect of COVID-19 disease on disorder is unclear. In this cohort, patients with COVID-19 disease were assessed. 60 CVA cases were assessed in a referral hospital in 2020. The major factor was mortality and the cases were those with and without death. The groups were compared for all features about mortality in the patients with COVID-19 and CVA. Totally 23 out of 60 cases (38.3%) were expired. In univariate analysis there was significant association for death by ischemic heart disease (P = 0.015), high-severity stroke (P = 0.012), high C-reactive protein (CRP) (P = 0.001), high ESR (P = 0.009), pleural effusion (P = 0.005), pericardial effusion (P = 0.027), cardiomegaly (P = 0.005), ground glass opacity (P = 0.001), and consolidation (P = 0.001). Among these factors, there was significant association only for CRP (P = 0.001) and consolidation (P = 0.003) in multivariate analysis. Mortality in the cases with COVID-19-related CVA is one-third and it has relationship to elevated CRP and finding the consolidation in the computerized tomography scan of the lungs.

Keywords: COVID-19, stroke, prognosis, C-reactive protein, CRP.

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Authors: Pradeep Bhagawath, K.N. Prabhu, Satyanarayan

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Wetting characteristics of reactive (Sn–0.7Cu solder) and non– reactive (castor oil) wetting of liquids on Cu and Ag plated Al substrates have been investigated. Solder spreading exhibited capillary, gravity and viscous regimes. Oils did not exhibit noticeable spreading regimes. Solder alloy showed better wettability on Ag coated Al substrate compared to Cu plating. In the case of castor oil, Cu coated Al substrate exhibited good wettability as compared to Ag coated Al substrates. The difference in wettability during reactive wetting of solder and non–reactive wetting of oils is attributed to the change in the surface energies of Al substrates brought about by the formation of intermetallic compounds (IMCs).

Keywords: Wettability, contact angle, solder, castor oil, IMCs.

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Authors: Annis Lai Chu Fung

Abstract:

This study is to fill up a research gap on examining the differences in normative beliefs (namely acceptance of weaknesses, acceptance of provoked aggression, and acceptance of unprovoked aggression) among different subtypes of aggressors and non-aggressors (reactive aggressors, proactive aggressors, reactive-proactive aggressors, and non-aggressors). 2,236 students (1,372 males and 864 females), aged from 11 to 18, completed a self-reported questionnaire. Results revealed that (a) schoolchildren with reactive-proactive aggression have the highest acceptance of provoked aggression, the highest acceptance of unprovoked aggression, and the lowest acceptance of weakness; (b) schoolchildren with proactive aggression have higher acceptance of unprovoked aggression and lower acceptance of weakness than reactive aggressors; and (c) schoolchildren without aggression have the lowest acceptance of provoked aggression, the lowest acceptance of unprovoked aggression, and the highest acceptance of weakness.

Keywords: Normative belief, schoolchildren, reactive, proactive, aggression.

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Authors: C. Chompuchan, T. Satapanajaru, P. Suntornchot, P. Pengthamkeerati

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Residual dye contents in textile dyeing wastewater have complex aromatic structures that are resistant to degrade in biological wastewater treatment. The objectives of this study were to determine the effectiveness of nanoscale zerovalent iron (NZVI) to decolorize Reactive Black 5 (RB5) and Reactive Red 198 (RR198) in synthesized wastewater and to investigate the effects of the iron particle size, iron dosage and solution pHs on the destruction of RB5 and RR198. Synthesized NZVI was confirmed by transmission electron microscopy (TEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The removal kinetic rates (kobs) of RB5 (0.0109 min-1) and RR198 (0.0111 min-1) by 0.5% NZVI were many times higher than those of microscale zerovalent iron (ZVI) (0.0007 min-1 and 0.0008 min-1, respectively). The iron dosage increment exponentially increased the removal efficiencies of both RB5 and RR198. Additionally, lowering pH from 9 to 5 increased the decolorization kinetic rates of both RB5 and RR198 by NZVI. The destruction of azo bond (N=N) in the chromophore of both reactive dyes led to decolorization of dye solutions.

Keywords: decolorization, nanoscale zerovalent iron, Reactive Black 5, Reactive Red 198.

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Authors: M. Susithra, R. Gnanadass

Abstract:

Ancillary services are support services which are essential for humanizing and enhancing the reliability and security of the electric power system. Reactive power ancillary service is one of the important ancillary services in a restructured electricity market which determines the cost of supplying ancillary services and finding of how this cost would change with respect to operating decisions. This paper presents a new formation that can be used to minimize the Independent System Operator (ISO)’s total payment for reactive power ancillary service. The modified power flow tracing algorithm estimates the availability of reserve reactive power for ancillary service. In order to find optimum reactive power dispatch, Biogeography based optimization method (BPO) is proposed. Market Reactive Clearing Price (MRCP) is then estimated and it encourages generator companies (GENCOs) to participate in an ancillary service. Finally, optimal weighting factor and real time utilization factor of reactive power give the minimum ISO’s total payment. The effectiveness of proposed design is verified using IEEE 30 bus system.

Keywords: Biogeography based optimization method, Power flow tracing method, Reactive generation capability curve and Reactive power ancillary service.

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Authors: Yanchao Wang, Rajshekhar Sunderraman

Abstract:

This paper presents an algebraic approach to optimize queries in domain-specific database management system for protein structure data. The approach involves the introduction of several protein structure specific algebraic operators to query the complex data stored in an object-oriented database system. The Protein Algebra provides an extensible set of high-level Genomic Data Types and Protein Data Types along with a comprehensive collection of appropriate genomic and protein functions. The paper also presents a query translator that converts high-level query specifications in algebra into low-level query specifications in Protein-QL, a query language designed to query protein structure data. The query transformation process uses a Protein Ontology that serves the purpose of a dictionary.

Keywords: Domain-Specific Data Management, Protein Algebra, Protein Ontology, Protein Structure Data.

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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: P. Nammalvar, P. Meganathan, A. Balamuguran

Abstract:

Among various active filters, shunt active filter is a viable solution for reactive power and harmonics compensation. In this paper, the SRF plan is used to generate current reference for compensation and conventional PI controllers were used as the controller to compensate the reactive power. The design of the closed loop controllers is reserved simple by modeling them as first order systems. Computationally uncomplicated and efficient SVM system is used in the present work for better utilization of dc bus voltage. The rating of shunt active filter has been finalized based on the reactive power demand of the selected reactive load. The proposed control and SVM technique are validated by simulating in MATLAB software.

Keywords: Shunt Active Filter, Space vector pulse width modulation, Voltage Source Converter, Reactive Power, Synchronous Reference Frame, Point of common coupling.

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Authors: Atefeh Pourshafie, Mohsen. Saniei, S. S. Mortazavi, A. Saeedian

Abstract:

In this paper optimal capacitor placement problem has been formulated in a restructured distribution network. In this scenario the distribution network operator can consider reactive energy also as a service that can be sold to transmission system. Thus search for optimal location, size and number of capacitor banks with the objective of loss reduction, maximum income from selling reactive energy to transmission system and return on investment for capacitors, has been performed. Results is influenced with economic value of reactive energy, therefore problem has been solved for various amounts of it. The implemented optimization technique is genetic algorithm. For any value of reactive power economic value, when reverse of investment index increase and change from zero or negative values to positive values, the threshold value of selling reactive power has been obtained. This increasing price of economic parameter is reasonable until the network losses is less than loss before compensation.

Keywords: capacitor placement, deregulated electric market, distribution network optimization.

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

Abstract:

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: 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: P. Góes, J. Manzi

Abstract:

This paper focuses on the development of an energy efficiency index that will be applied to reactive systems, which is based in the First and Second Law of Thermodynamics, by giving particular consideration to the concept of maximum entropy. Among the requirements of such energy efficiency index, the practical feasibility must be essential. To illustrate the performance of the proposed index, such an index was used as decisive factor of evaluation for the optimization process of an industrial reactor. The results allow the conclusion to be drawn that the energy efficiency index applied to the reactive system is consistent because it extracts the information expected of an efficient indicator, and that it is useful as an analytical tool besides being feasible from a practical standpoint. Furthermore, it has proved to be much simpler to use than tools based on traditional methodologies.

Keywords: Energy efficiency, maximum entropy, reactive systems.

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Authors: A. Hamidi, S. Khelladi, L. Illoul, A. Tcharkhtchi

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Reactive rotational molding (RRM) is a process to manufacture hollow plastic parts with reactive material has several advantages compared to conventional roto molding of thermoplastic powders: process cycle time is shorter; raw material is less expensive because polymerization occurs during processing and high-performance polymers may be used such as thermosets, thermoplastics or blends. However, several phenomena occur during this process which makes the optimization of the process quite complex. In this study, we have used a mixture of isocyanate and polyol as a reactive system. The chemical transformation of this system to polyurethane has been studied by thermal analysis and rheology tests. Thanks to these results of the curing process and rheological measurements, the kinetic and rheokinetik of polyurethane was identified. Smoothed Particle Hydrodynamics, a Lagrangian meshless method, was chosen to simulate reactive fluid flow in 2 and 3D configurations of the polyurethane during the process taking into account the chemical, and chemiorehological results obtained experimentally in this study.

Keywords: Reactive rotational molding, free surface flows, simulation, smoothed particle hydrodynamics, surface tension.

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Authors: Aniruddha Bhattacharya, Pranab Kumar Chattopadhyay

Abstract:

Optimal reactive power flow is an optimization problem with one or more objective of minimizing the active power losses for fixed generation schedule. The control variables are generator bus voltages, transformer tap settings and reactive power output of the compensating devices placed on different bus bars. Biogeography- Based Optimization (BBO) technique has been applied to solve different kinds of optimal reactive power flow problems subject to operational constraints like power balance constraint, line flow and bus voltages limits etc. BBO searches for the global optimum mainly through two steps: Migration and Mutation. In the present work, BBO has been applied to solve the optimal reactive power flow problems on IEEE 30-bus and standard IEEE 57-bus power systems for minimization of active power loss. The superiority of the proposed method has been demonstrated. Considering the quality of the solution obtained, the proposed method seems to be a promising one for solving these problems.

Keywords: Active Power Loss, Biogeography-Based Optimization, Migration, Mutation, Optimal Reactive Power Flow.

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Authors: Mohammed Amroune, Hadi Sebaa, Tarek Bouktir

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Reactive power limit of power system is one of the major causes of voltage instability. The only way to save the system from voltage instability is to reduce the reactive power load or add additional reactive power to reaching the point of voltage collapse. In recent times, the application of FACTS devices is a very effective solution to prevent voltage instability due to their fast and very flexible control. In this paper, voltage stability assessment with SVC and TCSC devices is investigated and compared in the modified IEEE 30-bus test system. The fast voltage stability indicator (FVSI) is used to identify weakest bus and to assess the voltage stability of power system.

Keywords: SVC, TCSC, Voltage stability, Fast Voltage Stability Index (FVSI), Reactive power.

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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

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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: Mustafa M. Donma, Orkide Donma

Abstract:

A growing list of cancers might be influenced by obesity. Obesity is associated with an increased risk for the occurrence and development of some cancers. Inflammation can lead to cancer. It is one of the characteristic features of cancer and plays a critical role in cancer development. C-reactive protein (CRP) is under evaluation related to the new and simple prognostic factors in patients with metastatic renal cell cancer. Obesity can predict and promote systemic inflammation in healthy adults. BMI is correlated with hs-CRP. In this study, SII index and CRP values were evaluated in children with normal BMI and those within the range of different obesity grades to detect the tendency towards cancer in pediatric obesity. A total of one hundred and ninety-four children; thirty-five children with normal BMI, twenty overweight (OW), forty-seven obese (OB) and ninety-two morbid obese (MO) participated in the study. Age- and sex-matched groups were constituted using BMI-for age percentiles. Informed consent was obtained. Ethical Committee approval was taken. Weight, height, waist circumference (C), hip C, head C and neck C of the children were measured. The complete blood count test was performed. C-reactive protein analysis was performed. Statistical analyses were performed using SPSS. The degree for statistical significance was p≤0.05. SII index values were progressively increasing starting from normal weight (NW) to MO children. There is a statistically significant difference between NW and OB as well as MO children. No significant difference was observed between NW and OW children, however, a correlation was observed between NW and OW children. MO constitutes the only group, which exhibited a statistically significant correlation between SII index and CRP. Obesity-related bladder, kidney, cervical, liver, colorectal, endometrial cancers are still being investigated. Obesity, characterized as a chronic low-grade inflammation, is a crucial risk factor for colon cancer. Elevated childhood BMI values may be indicative of processes leading to cancer, initiated early in life. Prevention of childhood adiposity may decrease the cancer incidence in adults. To authors’ best knowledge, this study is the first to introduce SII index values during obesity of varying degrees of severity. It is suggested that this index seems to affect all stages of obesity with an increasing tendency and may point out the concomitant status of obesity and cancer starting from very early periods of life.

Keywords: Children, c- reactive protein, systemic immune-inflammation index, obesity.

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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: Mohammad Mirjalili, Hamid Akbarpour

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In this work, a bleached well cotton sample was dyed with reactive yellow105 dye and subsequently, the dyed sample was exposed to the plasma condition containing Nitrogen gas at 1 and 5 minutes of plasma exposure time, respectively. The effect of plasma on surface morphology fabric was studied by Scanning Electronic Microscope (SEM). CIELab, K/S, and %R of samples (treated and untreated samples) were measured by a reflective spectrophotometer, and consequently, the experiments show that the sample dyed with Reactive yellow 105 after being washed, with the increase in the operation time of plasma, its dye fastness decreases. In addition, the increase in plasma operation time at constant pressure would increase the destructing effect on the surface morphology of samples dyed with reactive yellow105.

Keywords: Cotton fabric, cold nitrogen plasma, reflective spectrophotometer, electronic scanning microscope (SEM), reactive yellow105 dye.

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

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

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

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

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

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

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

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

Abstract:

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

Keywords: functional protein, osteoblast, MTT

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