Search results for: microarray gene expression

Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

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Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity.

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Authors: Alan S. Hoback

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Most people see human faces in car front and back ends because of the process of pareidolia. 96 people were surveyed to see how many of them saw a face in the vehicle styling. Participants were aged 18 to 72 years. 94% of the participants saw faces in the front-end design of production models. All participants that recognized faces indicated that most styles showed some degree of an angry expression. It was found that women were more likely to see faces in inanimate objects. However, with respect to whether women were more likely to perceive anger in the vehicle design, the results need further clarification. Survey responses were correlated to the design features of vehicles to determine what cues the respondents were likely looking at when responding. Whether the features looked anthropomorphic was key to anger perception. Features such as the headlights which could represent eyes and the air intake that could represent a mouth had high correlations to trends in scores. Results are compared among models, makers, by groupings of body styles classifications for the top 12 brands sold in the US, and by year for the top 20 models sold in the US in 2016. All of the top models sold increased in perception of an angry expression over the last 20 years or since the model was introduced, but the relative change varied by body style grouping.

Keywords: Aggressive driving, face recognition, road rage, vehicle styling.

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Authors: Suprijanto, Linda Sari, Vebi Nadhira , IGN. Merthayasa. Farida I.M

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Detection of human emotions has many potential applications. One of application is to quantify attentiveness audience in order evaluate acoustic quality in concern hall. The subjective audio preference that based on from audience is used. To obtain fairness evaluation of acoustic quality, the research proposed system for multimodal emotion detection; one modality based on brain signals that measured using electroencephalogram (EEG) and the second modality is sequences of facial images. In the experiment, an audio signal was customized which consist of normal and disorder sounds. Furthermore, an audio signal was played in order to stimulate positive/negative emotion feedback of volunteers. EEG signal from temporal lobes, i.e. T3 and T4 was used to measured brain response and sequence of facial image was used to monitoring facial expression during volunteer hearing audio signal. On EEG signal, feature was extracted from change information in brain wave, particularly in alpha and beta wave. Feature of facial expression was extracted based on analysis of motion images. We implement an advance optical flow method to detect the most active facial muscle form normal to other emotion expression that represented in vector flow maps. The reduce problem on detection of emotion state, vector flow maps are transformed into compass mapping that represents major directions and velocities of facial movement. The results showed that the power of beta wave is increasing when disorder sound stimulation was given, however for each volunteer was giving different emotion feedback. Based on features derived from facial face images, an optical flow compass mapping was promising to use as additional information to make decision about emotion feedback.

Keywords: Multimodal Emotion Detection, EEG, Facial Image, Optical Flow, compass mapping, Brain Wave

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Authors: Aditya Arya, Hairin Taha, Ataul Karim Khan, Nayiar Shahid, Hapipah Mohd Ali, Mustafa Ali Mohd

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This study has investigated the antidiabetic and antioxidant potential of Pseudovaria macrophylla bark extract on streptozotocin–nicotinamide induced type 2 diabetic rats. LCMSQTOF and NMR experiments were done to determine the chemical composition in the methanolic bark extract. For in vivo experiments, the STZ (60 mg/kg/b.w, 15 min after 120 mg/kg/1 nicotinamide, i.p.) induced diabetic rats were treated with methanolic extract of Pseuduvaria macrophylla (200 and 400 mg/kg·bw) and glibenclamide (2.5 mg/kg) as positive control respectively. Biochemical parameters were assayed in the blood samples of all groups of rats. The pro-inflammatory cytokines, antioxidant status and plasma transforming growth factor βeta-1 (TGF-β1) were evaluated. The histological study of the pancreas was examined and its expression level of insulin was observed by immunohistochemistry. In addition, the expression of glucose transporters (GLUT 1, 2 and 4) were assessed in pancreas tissue by western blot analysis. The outcomes of the study displayed that the bark methanol extract of Pseuduvaria macrophylla has potentially normalized the elevated blood glucose levels and improved serum insulin and C-peptide levels with significant increase in the antioxidant enzyme, reduced glutathione (GSH) and decrease in the level of lipid peroxidation (LPO). Additionally, the extract has markedly decreased the levels of serum pro-inflammatory cytokines and transforming growth factor beta-1 (TGF-β1). Histopathology analysis demonstrated that Pseuduvaria macrophylla has the potential to protect the pancreas of diabetic rats against peroxidation damage by downregulating oxidative stress and elevated hyperglycaemia. Furthermore, the expression of insulin protein, GLUT-1, GLUT-2 and GLUT-4 in pancreatic cells was enhanced. The findings of this study support the anti-diabetic claims of Pseudovaria macrophylla bark.

Keywords: Diabetes mellitus, Pseuduvaria macrophylla, alkaloids, caffeic acid.

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Authors: Olatinwo M. O., Oyeleke Olaosebikan, David Henry O.

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Rain attenuation plays a lot of roles in the design of satellite and terrestrial microwave radio links, hence a good knowledge of its effect is of great interest to Engineers and scientists in that it is often required to give a high level of accuracy of the rainrate distribution that expresses rainrate from the lowest value to the highest. This study proposes a model to express rainrate parameters alpha (α) and beta (β) as a function of geographical location at 0.01% of the time. The tropical locations used in the development of the effect were Ilorin, Ile-Ife, Douala, Dar-es-Selam, Nairobi, Lusaka, and Brazilia.

This expression clearly confirms the variability of rainfall from place to place. When consistency test was carried out using the expression to generate rainrate for each location examined, the result obtained was reliable for rain intensities between 5mm/h and 200mm/h. The variability of α and β with latitude also shows that different latitudes have different cumulative rain distribution. The model proposed in this study would be one of the useful tools to Radio Engineers since the precipitation effect in the design of satellite and terrestrial microwave radio links is among the factors to consider when designing communication systems.

Keywords: Rain rate, attenuation, geographical location.

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Authors: Achitphol Chookaew, Paramee Thongsukhsai, Patamarerk Engsontia, Narongwit Nakwan, Pritsana Raugrut

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Lung cancer is one of the most common malignancies and primary cause of death due to cancer worldwide. Non-small cell lung cancer (NSCLC) is the main subtype in which majority of patients present with advanced-stage disease. Herein, we analyzed differentially expressed genes to find potential biomarkers for lung cancer diagnosis as well as prognostic markers. We used transcriptome data from our 2 NSCLC patients and public data (GSE81089) composing of 8 NSCLC and 10 normal lung tissues. Differentially expressed genes (DEGs) between NSCLC and normal tissue and between early-stage and late-stage NSCLC were analyzed by the DESeq2. Pairwise correlation was used to find the DEGs with false discovery rate (FDR) adjusted p-value £ 0.05 and |log2 fold change| ³ 4 for NSCLC versus normal and FDR adjusted p-value £ 0.05 with |log2 fold change| ³ 2 for early versus late-stage NSCLC. Bioinformatic tools were used for functional and pathway analysis. Moreover, the top ten genes in each comparison group were verified the expression and survival analysis via GEPIA. We found 150 up-regulated and 45 down-regulated genes in NSCLC compared to normal tissues. Many immnunoglobulin-related genes e.g., IGHV4-4, IGHV5-10-1, IGHV4-31, IGHV4-61, and IGHV1-69D were significantly up-regulated. 22 genes were up-regulated, and five genes were down-regulated in late-stage compared to early-stage NSCLC. The top five DEGs genes were KRT6B, SPRR1A, KRT13, KRT6A and KRT5. Keratin 6B (KRT6B) was the most significantly increased gene in the late-stage NSCLC. From GEPIA analysis, we concluded that IGHV4-31 and IGKV1-9 might be used as diagnostic biomarkers, while KRT6B and KRT6A might be used as prognostic biomarkers. However, further clinical validation is needed.

Keywords: Bioinformatics, differentially expressed genes, non-small cell lung cancer, transcriptomics.

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Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

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Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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Authors: Hui-Chuan Chu, Min-Ju Liao, Wei-Kai Cheng, William Wei-Jen Tsai, Yuh-Min Chen

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Avoiding learning failures in mathematics e-learning environments caused by emotional problems in students with autism has become an important topic for combining of special education with information and communications technology. This study presents an adaptive emotional adjustment model in mathematics e-learning for students with autism, emphasizing the lack of emotional perception in mathematics e-learning systems. In addition, an emotion classification for students with autism was developed by inducing emotions in mathematical learning environments to record changes in the physiological signals and facial expressions of students. Using these methods, 58 emotional features were obtained. These features were then processed using one-way ANOVA and information gain (IG). After reducing the feature dimension, methods of support vector machines (SVM), k-nearest neighbors (KNN), and classification and regression trees (CART) were used to classify four emotional categories: baseline, happy, angry, and anxious. After testing and comparisons, in a situation without feature selection, the accuracy rate of the SVM classification can reach as high as 79.3-%. After using IG to reduce the feature dimension, with only 28 features remaining, SVM still has a classification accuracy of 78.2-%. The results of this research could enhance the effectiveness of eLearning in special education.

Keywords: Emotion classification, Physiological and facial Expression measures, Students with autism, Mathematics e-learning.

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Authors: Chiung-Tsun Kuoa, Tzu-Hao Liu, Fang-Yi Lin, Tai-Hao Hsu, Hui-Yin Chen

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Hyperglycemia-mediated accumulation of advanced glycation end-products (AGEs) play a pivotal role in the development of diabetic complications by inducing inflammation. In the present study, we evaluated the possible effects of water/ethanol (1/1, v/v) extracts (WEE) and its fractions from Canarium album Raeusch. (Chinese olive) which is a fruit used on AGEs-stimulated oxidative stress and inflammation in monocytes and vascular endothelial cells. Co-incubation of EA.hy926 endothelial cells with WEE and its fractions for 24h resulted in a significant decrease of monocyte–endothelial cell adhesion, the expression of ICAM-1, generation of intracellular ROS and depletion of GSH induced by AGEs. Chinese olive fruit extracts also reduced the expression of pro-inflammatory mediates, such as TNF-α, IL-1β and IL-6 in THP-1 cells. These findings suggested that Chinese olive fruit was able to protect vascular endothelium from dysfunction induced by AGEs. 

Keywords: Advanced glycation end-products (AGEs), Canarium album Raeusch, endothelial dysfunction, inflammation.

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Authors: Eleftheria Tzamali, Panayiota Poirazi, Ioannis G. Tollis, Martin Reczko

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Stable bacterial polymorphism on a single limiting resource may appear if between the evolved strains metabolic interactions take place that allow the exchange of essential nutrients [8]. Towards an attempt to predict the possible outcome of longrunning evolution experiments, a network based on the metabolic capabilities of homogeneous populations of every single gene knockout strain (nodes) of the bacterium E. coli is reconstructed. Potential metabolic interactions (edges) are allowed only between strains of different metabolic capabilities. Bacterial communities are determined by finding cliques in this network. Growth of the emerged hypothetical bacterial communities is simulated by extending the metabolic flux balance analysis model of Varma et al [2] to embody heterogeneous cell population growth in a mutual environment. Results from aerobic growth on 10 different carbon sources are presented. The upper bounds of the diversity that can emerge from single-cloned populations of E. coli such as the number of strains that appears to metabolically differ from most strains (highly connected nodes), the maximum clique size as well as the number of all the possible communities are determined. Certain single gene deletions are identified to consistently participate in our hypothetical bacterial communities under most environmental conditions implying a pattern of growth-condition- invariant strains with similar metabolic effects. Moreover, evaluation of all the hypothetical bacterial communities under growth on pyruvate reveals heterogeneous populations that can exhibit superior growth performance when compared to the performance of the homogeneous wild-type population.

Keywords: Bacterial polymorphism, clique identification, dynamic FBA, evolution, metabolic interactions.

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Authors: Georgi Bebrov, Rozalina Dimova

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In the field of quantum secure communication, there is no evaluation that characterizes quantum secure communication (QSC) protocols in a complete, general manner. The current paper addresses the problem concerning the lack of such an evaluation for QSC protocols by introducing an optimality evaluation, which is expressed as the average over the three main parameters of QSC protocols: efficiency, security, and practicality. For the efficiency evaluation, the common expression of this parameter is used, which incorporates all the classical and quantum resources (bits and qubits) utilized for transferring a certain amount of information (bits) in a secure manner. By using criteria approach whether or not certain criteria are met, an expression for the practicality evaluation is presented, which accounts for the complexity of the QSC practical realization. Based on the error rates that the common quantum attacks (Measurement and resend, Intercept and resend, probe attack, and entanglement swapping attack) induce, the security evaluation for a QSC protocol is proposed as the minimum function taken over the error rates of the mentioned quantum attacks. For the sake of clarity, an example is presented in order to show how the optimality is calculated.

Keywords: Quantum cryptography, quantum secure communcation, quantum secure direct communcation security, quantum secure direct communcation efficiency, quantum secure direct communcation practicality.

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Authors: P. Narrima, C. Y. Looi, M. A. Mohd, H. M. Ali

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Persea declinata (Bl.) Kosterm is a member of the Lauraceae family, widely distributed in Southeast Asia. It is from the same genus with avocado (Persea americana Mill), which is widely consumed as food and for medicinal purposes. In the present study, we examined the anticancer properties of Persea declinata (Bl.) Kosterm bark methanolic crude extract (PDM). PDM exhibited a potent antiproliferative effect in MCF-7 human breast cancer cells, with an IC50 value of 16.68 .g/mL after 48h of treatment. We observed that PDM caused cell cycle arrest and subsequent apoptosis in MCF-7 cells, as exhibited by increased population at G0/G1 phase, higher lactate dehydrogenase (LDH) release, and DNA fragmentation. Mechanistic studies showed that PDM caused significant elevation in ROS production, leading to perturbation of mitochondrial membrane potential, cell permeability, and activation of caspases-3/7. On the other hand, real-time PCR and Western blot analysis showed that PDM treatment increased the expression of the proapoptotic molecule, Bax, but decreased the expression of prosurvival proteins, Bcl-2 and Bcl-xL, in a dose-dependent manner. These findings imply that PDM could inhibit proliferation in MCF-7 cells via cell cycle arrest and apoptosis induction, indicating its potential as a therapeutic agent worthy of further development.

Keywords: Antiproliferative, apoptosis, MCF-7 human breast cancer, Persea declinata.

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Authors: Mouse, cardiac myocytes, computer simulation, action potential.

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Heterogeneous repolarization causes dispersion of the T-wave and has been linked to arrhythmogenesis. Such heterogeneities appear due to differential expression of ionic currents in different regions of the heart, both in healthy and diseased animals and humans. Mice are important animals for the study of heart diseases because of the ability to create transgenic animals. We used our previously reported model of mouse ventricular myocytes to develop 2D mouse ventricular tissue model consisting of 14,000 cells (apical or septal ventricular myocytes) and to study the stability of action potential propagation and Ca2+ dynamics. The 2D tissue model was implemented as a FORTRAN program code for highperformance multiprocessor computers that runs on 36 processors. Our tissue model is able to simulate heterogeneities not only in action potential repolarization, but also heterogeneities in intracellular Ca2+ transients. The multicellular model reproduced experimentally observed velocities of action potential propagation and demonstrated the importance of incorporation of realistic Ca2+ dynamics for action potential propagation. The simulations show that relatively sharp gradients of repolarization are predicted to exist in 2D mouse tissue models, and they are primarily determined by the cellular properties of ventricular myocytes. Abrupt local gradients of channel expression can cause alternans at longer pacing basic cycle lengths than gradual changes, and development of alternans depends on the site of stimulation.

Keywords: Mouse, cardiac myocytes, computer simulation, action potential

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Authors: Badr Alsulami, Ahmed S. Elamary

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This paper summarizes and presents main results of an in-depth numerical analysis dealing with the shear buckling resistance of aluminum plate girders. The studies conducted have permitted the development of a simple design expression to determine the critical shear buckling stress in aluminum web panels. This expression takes into account the effects of reduction of strength in aluminum alloys due to welding process. Ultimate shear resistance (USR) of plate girders can be obtained theoretically using Cardiff theory or Hӧglund’s theory. USR of aluminum alloy plate girders predicted theoretically using BS8118 appear inconsistent when compared with test data. Theoretical predictions based on Hӧglund’s theory, are more realistic. Cardiff theory proposed to predict the USR of steel plate girders only. Welded aluminum alloy plate girders studied experimentally by others; the USR resulted from tests are reviewed. Comparison between the test results with the values obtained from Hӧglund’s theory, BS8118 design method and Cardiff theory performed theoretically. Finally, a new equation based on Cardiff tension-field theory, proposed to predict theoretically the USR of aluminum plate girders.

Keywords: Shear resistance, Aluminum, Cardiff theory, Hӧglund's theory, Plate girder.

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Authors: NattapongTecharattanased

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The purpose of this research was to study the factors that influenced the success of mobile phone entrepreneurs at Central Plaza. The sample group included 187 entrepreneurs at Central Plaza. A questionnaire was utilized as a tool to collect data. Statistics used in this research included frequency, percentage, mean, and standard deviation. Independent- sample t- test, one way ANOVA, and multiple regression analysis. Data were analyzed by using Statistical Package for the Social Sciences.The findings disclosed that the majority of respondents were male between 25-40 years old, and held an undergraduate degree. The average income of respondents was between 15,001-25,000 baht. The majority of respondents had less than 5 years of working experience. In terms of personality, the findings revealed that expression and agreement were ranked at the highest level. Whereas, emotion stability, consciousness, open to new experience were ranked at high. From the hypotheses testing, the findings revealed that different genders had different success in their mobile phone business with different income from the last 6 months. However, difference in age, income, level of education, and experience affected the success in terms of income, number of customers, and overall success of business. Moreover, the factors of personalities included expression, agreement, emotion stability, consciousness, open to new experience, and competitive strategy. From the findings, these factors were able to predict mobile phone business success at 66.9 percent.

Keywords: Entrepreneur, Influencing Factors, Success, Mobile Phone Business.

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Authors: N. Baspinar, A. Basoglu, O. Ozdemir, C. Ozel, F. Terzi, O. Yaman

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Current research is targeting new molecular mechanisms that underlie non-alcoholic fatty liver disease (NAFLD) and associated metabolic disorders like non-alcoholic steatohepatitis (NASH). Forty New Zealand White rabbits have been used and fed a high protein (HP) and energy diet based on grains and containing 11.76 MJ/kg. Boron added to 3 experimental groups’ drinking waters (30 mg boron/L) as boron compounds. Biochemical analysis including boron levels, and nuclear magnetic resonance (NMR) based metabolomics evaluation, and mRNA expression of peroxisome proliferator-activated receptor (PPAR) family was performed. LDLcholesterol concentrations alone were decreased in all the experimental groups. Boron levels in serum and feces were increased. Content of acetate was in about 2x higher for anhydrous borax group, at least 3x higher for boric acid group. PPARα mRNA expression was significantly decreased in boric acid group. Anhydrous borax attenuated mRNA levels of PPARγ, which was further suppressed by boric acid. Boron supplementation decreased the degenerative alterations in hepatocytes. Except borax group other boron groups did not have a pronounced change in tubular epithels of kidney. In conclusion, high protein and energy diet leads hepatocytes’ degenerative changes which can be prevented by boron supplementation. Boric acid seems to be more effective in this situation.

Keywords: High protein and energy diet, boron, metabolomic, transcriptomic.

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Authors: Surajit Debnath, Soma Addya

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Human genome is not only the evolutionary summation of all advantageous events, but also houses lesions of deleterious foot prints. A single gene mutation sometimes may express multiple consequences in numerous tissues and a linear relationship of the genotype and the phenotype may often be obscure. ß Thalassemia minor, a transfusion independent mild anaemia, coupled with environment among other factors may articulate into phenotypic pleotropy with Hypocholesterolemia, Vitamin D deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological alterations. Occurrence of Pancreatic insufficiency, resultant steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2 4.60% and Hb Adult 84.80% and altered Hemogram) with increased Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2 (9.5mg/ml) indicate towards a cascade of phenotypic pleotropy where the ß Thalassemia mutation ,be it in the 5’ cap site of the mRNA , differential splicing etc in heterozygous state is effecting several metabolic pathways. Compensatory extramedulary hematopoiesis may not coped up well with the stressful life style of the young individual and increased erythropoietic stress with high demand for cholesterol for RBC membrane synthesis may have resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia may have caused the pancreatic insufficiency, leading to Vitamin D deficiency. This may in turn have caused the secondary hyperparathyroidism to sustain serum Calcium level. Irritability and stress intolerance of the patient was a cumulative effect of the vicious cycle of metabolic compromises. From these findings we propose that the metabolic deficiencies in the ß Thalassemia mutations may be considered as the phenotypic display of the pleotropy to explain the genetic epidemiology. According to the recommendations from the NIH Workshop on Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model, study design of observations should be informed by gene-environment hypotheses and results of a study (genetic diseases) should be published to inform future hypotheses. Variety of approaches is needed to capture data on all possible aspects, each of which is likely to contribute to the etiology of disease. Speakers also agreed that there is a need for development of new statistical methods and measurement tools to appraise information that may be missed out by conventional method where large sample size is needed to segregate considerable effect. A meta analytic cohort study in future may bring about significant insight on to the title comment.

Keywords: Genetic disease, Genetic epidemiology, Heterozygous, Phenotype, Pleotropy, ß Thalassemia minor, Metabolic compromises.

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Authors: T. Yamaguchi, Y. Fujii, A. Takita, T. Kanai

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To compute dynamic characteristics of nonlinear viscoelastic springs with elastic structures having huge degree-of-freedom, Yamaguchi proposed a new fast numerical method using finite element method [1]-[2]. In this method, restoring forces of the springs are expressed using power series of their elongation. In the expression, nonlinear hysteresis damping is introduced. In this expression, nonlinear complex spring constants are introduced. Finite element for the nonlinear spring having complex coefficients is expressed and is connected to the elastic structures modeled by linear solid finite element. Further, to save computational time, the discrete equations in physical coordinate are transformed into the nonlinear ordinary coupled equations using normal coordinate corresponding to linear natural modes. In this report, the proposed method is applied to simulation for impact responses of a viscoelastic shock absorber with an elastic structure (an S-shaped structure) by colliding with a concentrated mass. The concentrated mass has initial velocities and collides with the shock absorber. Accelerations of the elastic structure and the concentrated mass are measured using Levitation Mass Method proposed by Fujii [3]. The calculated accelerations from the proposed FEM, corresponds to the experimental ones. Moreover, using this method, we also investigate dynamic errors of the S-shaped force transducer due to elastic mode in the S-shaped structure.

Keywords: Transient response, Finite Element analysis, Numerical analysis, Viscoelastic shock absorber, Force transducer.

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Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko

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Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.

Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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Authors: B. Chouhan, A. Denesyuk, J. Heino, M. S. Johnson, K. Denessiouk

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Integrins are a large family of multidomain α/β cell signaling receptors. Some integrins contain an additional inserted I domain, whose earliest expression appears to be with the chordates, since they are observed in the urochordates Ciona intestinalis (vase tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins of earlier diverging species. The domain-s presence is viewed as a hallmark of integrins of higher metazoans, however in vertebrates, there are clearly three structurally-different classes: integrins without I domains, and two groups of integrins with I domains but separable by the presence or absence of an additional αC helix. For example, the αI domains in collagen-binding integrins from Osteichthyes (bony fish) and all higher vertebrates contain the specific αC helix, whereas the αI domains in non-collagen binding integrins from vertebrates and the αI domains from earlier diverging urochordate integrins, i.e. tunicates, do not. Unfortunately, within the early chordates, there is an evolutionary gap due to extinctions between the tunicates and cartilaginous fish. This, coupled with a knowledge gap due to the lack of complete genomic data from surviving species, means that the origin of collagen-binding αC-containing αI domains remains unknown. Here, we analyzed two available genomes from Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes – cartilaginous fish) and Petromyzon marinus (sea lamprey; Agnathostomata), and several available Expression Sequence Tags from two Chondrichthyes species: Raja erinacea (little skate) and Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore hagfish; Agnathostomata), which evolutionary reside between the urochordates and osteichthyes. In P. marinus, we observed several fragments coding for the αC-containing αI domain, allowing us to shed more light on the evolution of the collagen-binding integrins.

Keywords: Integrin αI domain, integrin evolution, collagen binding, structure, αC helix

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Authors: Giani Gradinaru

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Biodiversity crisis is one of the many crises that started at the turn of the millennia. Concrete form of expression is still disputed, but there is a relatively high consensus regarding the high rate of degradation and the urgent need for action. The strategy of action outlines a strong economic component, together with the recognition of market mechanisms as the most effective policies to protect biodiversity. In this context, biodiversity and ecosystem services are natural assets that play a key role in economic strategies and technological development to promote development and prosperity. Developing and strengthening policies for transition to an economy based on efficient use of resources is the way forward. To emphasize the co-viability specific to the connection economyecosystem services, scientific approach aimed on one hand how to implement policies for nature conservation and on the other hand, the concepts underlying the economic expression of ecosystem services- value, in the context of current technology. Following the analysis of business opportunities associated with changes in ecosystem services was concluded that development of market mechanisms for nature conservation is a trend that is increasingly stronger individualized within recent years. Although there are still many controversial issues that have already given rise to an obvious bias, international organizations and national governments have initiated and implemented in cooperation or independently such mechanisms. Consequently, they created the conditions for convergence between private interests and social interests of nature conservation, so there are opportunities for ongoing business development which leads, among other things, the positive effects on biodiversity. Finally, points out that markets fail to quantify the value of most ecosystem services. Existing price signals reflect at best, only a proportion of the total amount corresponding provision of food, water or fuel.

Keywords: ecosystem services, economic evaluation, nature conservation

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Authors: Dwitya Elvira, Eryati Darwin

Abstract:

Background: Graves’ disease (GD) is an autoimmune thyroid disease. Imbalance of Th1/Th2 cells and T-regulatory (Treg)/Th17 cells was thought to play pivotal role in the pathogenesis of GD. Treg FoxP3 produced TGF-β to maintain regulatory function, and Th17 cells produced IL-17 as cytokines that were thought in mediating several autoimmune diseases. The aim of this study is to assess the role of IL-17 and TGF-β in the pathogenesis of GD and to investigate its correlation with Thyroid Stimulating Hormone Receptor Antibody (TRAb) and Treg FoxP3 expression. Method: 30 GD patients and 27 age and sex-matched controls were enrolled in this study. Diagnosis of GD was based on clinical and biochemical of GD. Serum IL-17, TGF-β, TRAb, and FoxP3 were measured by enzyme-linked immunosorbent assay (ELISA). Data were analyzed by using SPSS 21.0 (SPSS Inc.). Spearman rank correlation test was used for assessment of correlation. The statistical significance was accepted as P<0.05. Result: There was no significant correlation between IL-17 and TGF-β serum with expression of FoxP3 level in GD, but there was significant correlation between TGF-β and TRAb serum level (P<0.05). Serum levels of IL-17 and TGF-β were found to be elevated in patient group compared to control, where mean values of IL-17 were 14.43±2.15 pg/mL and TGF-β were 10.44±3.19 pg/mL in patients group; and in control group, level of IL-17 were 7.1±1.45 pg/mL and TGF-β were 4.95±1.35 pg/mL. Conclusion: Serum Il-17 and TGF-β were elevated in GD patients that reflect the role of inflammatory and regulatory cytokines activation in pathogenesis of GD. There was significant correlation between TGF-β and TRAb, revealing that Treg cytokines may play a role in pathogenesis of GD.

Keywords: IL-17, TGF-β, FoxP3, Graves’ disease.

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Authors: Jing Zhang, Lian Wu, Jie-ming Qu, Chun-xue Bai, Mervyn J Merrilees, Peter N Black

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COPD is characterized by loss of elastic fibers from small airways and alveolar walls, with the decrease in elastin increasing with disease severity. It is unclear why there is a lack of repair of elastic fibers. We have examined fibroblasts cultured from lung tissue from normal and COPD subjects to determine if the secretory profile explains lack of tissue repair. In this study, fibroblasts were cultured from lung parenchyma of bronchial carcinoma patients with varying degrees of COPD; controls (non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe COPD (GOLD 2-3, n=12). Measurements were made of proliferation, senescence-associated beta-galactosidase-1, mRNA expression of IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was found that GOLD 2-3 fibroblasts proliferated more slowly (p<0.01) and had higher levels of senescence-associated beta-galactosidase-1 (p<0.001) than controls (non-COPD). GOLD 2-3 fibroblasts showed significant increases in mRNA and/or protein for IL-6, IL-8, MMP-1, PGE2, versican (p<0.01) and tropoelastin (p<0.05). mRNA expression and/or protein levels of tropoelastin (p<0.01), versican (p<0.02), IL-6 (p<0.05) and IL-8 (p<0.05) were negatively correlated with FEV1%. Insoluble elastin was not increased. In summary, fibroblasts from moderate to severe COPD subjects display a secretory phenotype with up-regulation of inflammatory molecules including the matrix proteoglycan versican, and increased soluble, but not insoluble, elastin. Versican inhibits assembly of tropoelastin into insoluble elastin and we conclude that the pro-inflammatory phenotype of COPD fibroblasts it is not compatible with repair elastic fibers.

Keywords: COPD, pulmonary fibroblasts, pro-inflammatory phenotype, versican, elastin

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Authors: Razagh Hafezi, Ahmad Keshavarz, Vida Moshfegh

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This paper presents a novel algorithm of stereo correspondence with rank transform. In this algorithm we used the genetic algorithm to achieve the accurate disparity map. Genetic algorithms are efficient search methods based on principles of population genetic, i.e. mating, chromosome crossover, gene mutation, and natural selection. Finally morphology is employed to remove the errors and discontinuities.

Keywords: genetic algorithm, morphology, rank transform, stereo correspondence

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Authors: Sadaf Moeez, Madiha Khalid, Zoya Khalid, Sania Shaheen, Sumbul Khalid

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Background: Inter-individual variation in response to metformin, which has been considered as a first line therapy for T2DM treatment is considerable. In the current study, it was aimed to investigate the impact of two genetic variants Leu125Phe (rs77474263) and Gly64Asp (rs77630697) in gene SLC47A1 on the clinical efficacy of metformin in T2DM Pakistani patients. Methods: The study included 800 T2DM patients (400 metformin responders and 400 metformin non-responders) along with 400 ethnically matched healthy individuals. The genotypes were determined by allele-specific polymerase chain reaction. In-silico analysis was done to confirm the effect of the two SNPs on the structure of genes. Association was statistically determined using SPSS software. Results: Minor allele frequency for rs77474263 and rs77630697 was 0.13 and 0.12. For SLC47A1 rs77474263 the homozygotes of one mutant allele ‘T’ (CT) of rs77474263 variant were fewer in metformin responders than metformin non-responders (29.2% vs. 35.5 %). Likewise, the efficacy was further reduced (7.2% vs. 4.0 %) in homozygotes of two copies of ‘T’ allele (TT). Remarkably, T2DM cases with two copies of allele ‘C’ (CC) had 2.11 times more probability to respond towards metformin monotherapy. For SLC47A1 rs77630697 the homozygotes of one mutant allele ‘A’ (GA) of rs77630697 variant were fewer in metformin responders than metformin non-responders (33.5% vs. 43.0 %). Likewise, the efficacy was further reduced (8.5% vs. 4.5%) in homozygotes of two copies of ‘A’ allele (AA). Remarkably, T2DM cases with two copies of allele ‘G’ (GG) had 2.41 times more probability to respond towards metformin monotherapy. In-silico analysis revealed that these two variants affect the structure and stability of their corresponding proteins. Conclusion: The present data suggest that SLC47A1 Leu125Phe (rs77474263) and Gly64Asp (rs77630697) polymorphisms were associated with the therapeutic response of metformin in T2DM patients of Pakistan.

Keywords: Diabetes, T2DM, SLC47A1, Pakistan, polymorphism.

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Authors: Samy A. Selim, Nashwa I. Hagag

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Abstract–The objectives of the current study are to determine the prevalence, etiological agents, drug susceptibility pattern and plasmid profile of Acinetobacter baumannii isolates from Hospital-Acquired Infections (HAI) at Community Hospital, Al Jouf Province, Saudi Arabia. A total of 1890 patients had developed infection during hospital admission and were included in the study. Among those who developed nosocomial infections, 15(9.4), 10(2.7) and 118 (12.7) had respiratory tract infection (RTI), blood stream infections (BSI) and urinary tract (UTI) respectively. A total of 268 bacterial isolates were isolated from nosocomial infection. S. aureus was reported in 23.5% for of the total isolates followed by Klebsiella pneumoniae (17.5%), E. coli (17.2%), P. aeruginosa (11.9%), coagulase negative staphylococcus (9%), A. baumannii (7.1%), Enterobacter spp. (3.4%), Citrobacter freundii (3%), Proteus mirabilis (2.6%), and Proteus vulgaris and Enterococcous faecalis (0.7%). Isolated organisms are multi-drug resistant, predominantly Gram-positive pathogens with a high incidence of methicillin-resistant S. aureus, extended spectrum beta lactamase and vancomycin resistant enterococci organisms. The RFLP (Fragment Length Polymorphisms) patterns of plasmid preparations from isolated A. baumannii isolates had altered RFLP patterns, possibly due to the presence of plasmid(s). Five A. baumannii isolates harbored plasmids all of which were not less than 2.71kbp in molecular weight. Hence, it showed that the gene coding for the isolates were located on the plasmid DNA while the remaining isolates which have no plasmid might showed gene coding for antibiotic resistance being located on chromosomal DNA. Nosocomial infections represent a current problem in Community Hospital, Al Jouf Province, Saudi Arabia. Problems associated with SSI include infection with multidrug resistant pathogens which are difficult to treat and are associated with increased mortality.

Keywords: Hospital-Acquired Infections, Acinetobacter baumannii, antibiotic resistance, plasmid profile, RFLP patterns, Al Jouf Province, Saudi Arabia

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Authors: Jörg Linde, Ekaterina Buyko, Robert Altwasser, Udo Hahn, Reinhard Guthke

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Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.

Keywords: Pathogen, network inference, text-mining, Candida albicans, LASSO, mutual information, reverse engineering, linear regression, modelling.

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Authors: Antonella Bandiera

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A new sythetic gene coding for a Human Elastin-Like Polypeptide was constructed and expressed. The recombinant product was tested as coating agent to realize a surface suitable for cell growth. Coatings showed peculiar features and different human cell lines were seeded and cultured. All cell lines tested showed to adhere and proliferate on this substrate that has been shown also to exert a specific effect on cells, depending on cell type.

Keywords: elastin, recombinant protein, coating, cell adhesion.

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Authors: Kejun Zhuang, Hailong Zhu

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The dynamics of a delayed mathematical model for Hes1 oscillatory expression are investigated. The linear stability of positive equilibrium and existence of local Hopf bifurcation are studied. Moreover, the global existence of large periodic solutions has been established due to the global bifurcation theorem.

Keywords: Hes1, Hopf bifurcation, time delay, transcriptional repression loop

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