Search results for: protein structure

Authors: Azadeh Shahbazi

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This study tries to find out the determinants of capital structure in hotel industry in 7 important hotel chains in USA within the period of 12 years of 2000 to 2012. The study is used a panel pooled regression to realize the relation among different variables. Results show that the variables which could make changes in the capital structure of firms are Non-Debt Tax Shield and Tangibility.

Keywords: capital structure, service industry, hospitality, finance

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: biosensor, DNA, biomarker, molecular dynamics simulation

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Authors: G. Vici, L. Cesanelli, L. Belli, R. Ceci, V. Polzonetti

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Several factors contribute to success in sport and diet is one of them. Evidence-based sport nutrition guidelines underline the importance of macro- and micro-nutrients’ balance and timing in order to improve athlete’s physical status and performance. Nevertheless, a high content of proteins is commonly found in resistance training athletes’ diet with carbohydrate intake that is not enough or not well planned. The aim of the study was to evaluate the impact of different protein and carbohydrate diet contents on body composition and sport performance on a group of resistance training athletes. Subjects were divided as study group (n=16) and control group (n=14). For a period of 4 months, both groups were subjected to the same resistance training fitness program with study group following a specific diet and control group following an ab libitum diet. Body compositions were evaluated trough anthropometric measurement (weight, height, body circumferences and skinfolds) and Bioimpedence Analysis. Physical strength and training status of individuals were evaluated through the One Repetition Maximum test (RM1). Protein intake in studied group was found to be lower than in control group. There was a statistically significant increase of body weight, free fat mass and body mass cell of studied group respect to the control group. Fat mass remains almost constant. Statistically significant changes were observed in quadriceps and biceps circumferences, with an increase in studied group. The MR1 test showed improvement in study group’s strength but no changes in control group. Usually people consume hyper-proteic diet to achieve muscle mass development. Through this study, it was possible to show that protein intake fixed at 1,7 g/kg/d can meet the individual's needs. In parallel, the increased intake of carbohydrates, focusing on quality and timing of assumption, has enabled the obtainment of desired results with a training protocol supporting a hypertrophic strategy. Therefore, the key point seems related to the planning of a structured program both from a nutritional and training point of view.

Keywords: body composition, diet, exercise, protein

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Authors: Sukrat Sinha, Abhay Kumar, Shanthy Sundaram

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The Leishmania homologue of activated C kinase (LACK) is known T cell epitope from soluble Leishmania antigens (SLA) that confers protection against Leishmania challenge. This antigen has been found to be highly conserved among Leishmania strains. LACK has been shown to be protective against L. donovani challenge. A comprehensive analysis of several LACK sequences was completed. The analysis shows a high level of conservation, lower variability and higher antigenicity in specific portions of the LACK protein. This information provides insights for the potential consideration of LACK as a putative candidate in the context of visceral Leishmaniasis vaccine target.

Keywords: bioinformatics, genome assembly, leishmania activated protein kinase c (lack), next-generation sequencing

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Authors: Faride Hashemiannejad, Shima Oloomi

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Imagination is one of the important elements of creative thinking which as a skill needs attention by the educational system. Although most students learn reading, writing, and arithmetic skills well, they lack high level thinking skills like creative thinking. Therefore, in the information age and in the beginning of entry to knowledge-based society, the educational system needs to think over its goals and mission, and concentrate on creativity-based curriculum. From among curriculum elements-goals, content, method and evaluation “method” is a major domain whose reform can pave the way for fostering imagination and creativity. The purpose of this study was examining the relationship between creativity development and curriculum. Research questions were: (1) is there a relationship between the cognitive-emotional structure of the classroom and creativity development? (2) Is there a relationship between the environmental-social structure of the classroom and creativity development? (3) Is there a relationship between the thinking structure of the classroom and creativity development? (4) Is there a relationship between the physical structure of the classroom and creativity development? (5) Is there a relationship between the instructional structure of the classroom and creativity development? Method: This research is a applied research and the research method is Correlational research. Participants: The total number of participants in this study included 894 students from High school through 11th grade from seven schools of seven zones in Mashad city. Sampling Plan: Sampling was selected based on Random Multi State. Measurement: The dependent measure in this study was: (a) the Test of Creative Thinking, (b) The researcher-made questionnaire includes five fragments, cognitive, emotional structure, environmental social structure, thinking structure, physical structure, and instructional structure. The Results Show: There was significant relationship between the cognitive-emotional structure of the classroom and student’s creativity development (sig=0.139). There was significant relationship between the environmental-social structure of the classroom and student’s creativity development (sig=0.006). There was significant relationship between the thinking structure of the classroom and student’s creativity development (sig=0.004). There was not significant relationship between the physical structure of the classroom and student’s creativity development (sig=0.215). There was significant relationship between the instructional structure of the classroom and student’s creativity development (sig=0.003). These findings denote if students feel secure, calm and confident, they can experience creative learning. Also the quality of coping with students’ questions, imaginations and risks can influence on their creativity development.

Keywords: imagination, creativity, curriculum, bioinformatics, biomedicine

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Authors: Carol N. Flores-Fernández, Guadalupe Espilco, Cynthia Esquerre, Amparo I. Zavaleta

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Saline environments represent a valuable source of enzymes with novel properties and particular features for application in food, pharmaceutical and chemical industry. This study focuses on the isolation and screening of hydrolase-producing bacteria from Chilca salterns and the evaluation of their biotechnological potential. Soil samples were collected from Chilca salterns in Peru. For the isolation, medium containing 0.2 % of yeast extract, 5 % of NaCl and 10 % of the soil sample was used. After 72 h of incubation at 37 °C, serial dilutions were made up to 10−12 dilutions, spread on agar plates with 0.5 % of yeast extract and 5 % of NaCl, and incubated at 37 °C for 48 h. Screening of hydrolase-producing bacteria was carried out for cellulases, amylases, lipases, DNase, and proteases on specific media. Moreover, protease-producing bacteria were tested using protein extracted from the following legumes as substrate: Glycine max, Lupinus mutabilis, Pisum sativum, Erythrina edulis, Cicer arietinum, Phaseolus vulgaris and Vicia faba. A total of 16 strains were isolated from soil samples. On the screening media; 75, 44, 81 and 50 % were cellulase, amylase, DNase and protease producers, respectively. Also, 19 % of the isolates produced all the hydrolytic enzymes above mentioned. Lipase producers were not found. The 37 % and 12 % of the strains grew at 20 % and 30 % of salt concentration, respectively. In addition, 75 % of the strains grew at pH range between 5 and 10. From the total of protease-producing bacteria, 100 % hydrolyzed Glycine max, Lupinus mutabilis, and Pisum sativum protein, while 87 % hydrolyzed Erythrina edulis and Cicer arietinum protein. Finally, 75 % and 50 % of the strains hydrolyzed Phaseolus vulgaris and Vicia faba protein, respectively. Hydrolase-producing bacteria isolated from Chilca salterns in Peru grew at high salt concentrations and wide range of pH. In addition, protease-producing bacteria hydrolyzed protein from different sources such as leguminous. These enzymes have great biotechnological potential and could be used for different industrial processes and applications.

Keywords: bacteria, extracellular, hydrolases, Peru, salterns

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Authors: Ajibade T., Omotesho O. A., Ayinde O. E, Ajibade E. T., Muhammad-Lawal A.

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This study was carried out to examine the extent and magnitude of food security amongst farming rural households in Nigeria. Data used for this study was collected from a total of two hundred and forty rural farming households using a two-stage random sampling technique. The main tools of analysis for this study include descriptive statistics and a constructed food security index using the identification and aggregation procedure. The headcount ratio in this study reveals that 71% of individuals in the study area were food secure with an average per capita calorie and protein availability of 4,213.92kcal and 99.98g respectively. The aggregated household daily calorie availability and daily protein availability per capita were 3,634.57kcal and 84.08g respectively which happens to be above the food security line of 2,470kcal and 65g used in this study. The food insecure households fell short of the minimum daily per capita calorie and protein requirement by 2.1% and 24.9%. The study revealed that the area is food insecure due to unequal distribution of the available food amongst the sampled population. The study recommends that the households should empower themselves financially in order to enhance their ability to afford the food during both on and off seasons. Also, processing and storage of farm produce should be enhanced in order to improve on availability throughout the year.

Keywords: farming household, food security, identification and aggregation, food security index

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Authors: Jae Bok Heo, Yun Mi Lee, Hee Rang Yun

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Several GTPases are required for ribosome biogenesis and assembly. We recently characterized rice (Oryza sativa) nuclear/nucleolar GTPase 2 (OsNug2), belonging to the YlqF/YawG family of GTPases, as playing a role in pre-60S ribosomal subunit maturation. To investigate the potential factors involved in regulating the function of OsNug2, yeast two-hybrid screens were carried out using OsNug2 as bait. Rice serine/threonine kinase 1 (OsSTK1) was identified as a potential interacting protein candidate. In vitro pull down and bimolecular fluorescence complementation assays confirmed the interaction between OsNug2 and OsSTK1, and like green fluorescent protein-tagged OsNug2, green fluorescent protein-tagged OsSTK1 was targeted to the nucleus of Arabidopsis protoplasts. OsSTK1 was not found to affect the GTP-binding activity of OsNug2; however, when recombinant OsSTK1 was included in OsNug2 assay reaction mixtures, OsSTK1 increased the GTPase activity of OsNug2. To test whether OsSTK1 phosphorylates OsNug2 in vitro, a kinase assay was performed. OsSTK1 was found to have weak autophosphorylation activity and strongly phosphorylated serine 209 of OsNug2. Yeast complementation testing resulted in a GAL::OsNug2(S209N) mutant-harboring yeast strain exhibiting a growth-defective phenotype on galactose medium at 39°C, divergent from that of a yeast strain harboring GAL::OsNug2. The intrinsic GTPase activity of mutant OsNug2(S209N) was found to be similar to that of OsNug2, was not fully enhanced upon weak binding of OsSTK1. Our findings reported here indicate that OsSTK1 functions as a positive regulator protein of OsNug2 by enhancing the GTPase activity of OsNug2, and that the phosphorylation of serine 209 of OsNug2 is essential for the complete function of OsNug2 in ribosome biogenesis.

Keywords: OsSTK1, OsNug2, GTPase activity, GTP binding activity, phosphorylation

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Authors: Ren Zuo Wang

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In this paper, in order to investigate the behavior of the wood structure, the non-linearity of wood material model in LS-DYNA is adopted. It is difficult and less efficient to conduct the experiment of the ancient wood structure, hence LS-DYNA software can be used to simulate nonlinear responses of ancient wood structure. In LS-DYNA software, there is material model called *MAT_WOOD or *MAT_143. This model is to simulate a single-element response of the wood subjected to tension and compression under the parallel and the perpendicular material directions. Comparing with the exact solution and numerical simulations results using LS-DYNA, it demonstrates the accuracy and the efficiency of the proposed simulation method.

Keywords: LS-DYNA, wood structure, single-element simulations, MAT_143

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Authors: Behnaz Moradijamei, Michael Higgins

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Identifying community structure is a critical task in analyzing social media data sets often modeled by networks. Statistical models such as the stochastic block model have proven to explain the structure of communities in real-world network data. In this work, we develop a goodness-of-fit test to examine community structure's existence by using a distinguishing property in networks: cyclic structures are more prevalent within communities than across them. To better understand how communities are shaped by the cyclic structure of the network rather than just the number of edges, we introduce a novel method for deciding on the existence of communities. We utilize these structures by using renewal non-backtracking random walk (RNBRW) to the existing goodness-of-fit test. RNBRW is an important variant of random walk in which the walk is prohibited from returning back to a node in exactly two steps and terminates and restarts once it completes a cycle. We investigate the use of RNBRW to improve the performance of existing goodness-of-fit tests for community detection algorithms based on the spectral properties of the adjacency matrix. Our proposed test on community structure is based on the probability distribution of eigenvalues of the normalized retracing probability matrix derived by RNBRW. We attempt to make the best use of asymptotic results on such a distribution when there is no community structure, i.e., asymptotic distribution under the null hypothesis. Moreover, we provide a theoretical foundation for our statistic by obtaining the true mean and a tight lower bound for RNBRW edge weights variance.

Keywords: hypothesis testing, RNBRW, network inference, community structure

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Authors: Agustyas Tjiptaningrum, Intanri Kurniati, Fadilah Fadilah, Linda Erlina, Tiwuk Susantiningsih

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Coronavirus disease-19 (COVID-19) is still one of the health problems. It can be a severe condition that is caused by a cytokine storm. In a cytokine storm, several proinflammatory cytokines are released massively. It destroys epithelial cells, and subsequently, it can cause death. The anti-inflammatory agent can be used to decrease the number of severe Covid-19 conditions. Melaleuca cajuputi is a plant that has antiviral, antibiotic, antioxidant, and anti-inflammatory activities. This study was carried out to analyze the prediction mechanism of the M. cajuputi extract from Lampung, Indonesia, as an anti-inflammatory agent for COVID-19. This study constructed a database of protein host target that was involved in the inflammation process of COVID-19 using data retrieval from GeneCards with the keyword “SARS-CoV2”, “inflammation,” “cytokine storm,” and “acute respiratory distress syndrome.” Subsequent protein-protein interaction was generated by using Cytoscape version 3.9.1. It can predict the significant target protein. Then the analysis of the Gene Ontology (GO) and KEGG pathways was conducted to generate the genes and components that play a role in COVID-19. The result of this study was 30 nodes representing significant proteins, namely NF-κβ, IL-6, IL-6R, IL-2RA, IL-2, IFN2, C3, TRAF6, IFNAR1, and DOX58. From the KEGG pathway, we obtained the result that NF-κβ has a role in the production of proinflammatory cytokines, which play a role in the COVID-19 cytokine storm. It is an important factor for macrophage transcription; therefore, it will induce inflammatory gene expression that encodes proinflammatory cytokines such as IL-6, TNF-α, and IL-1β. In conclusion, the blocking of NF-κβ is the prediction mechanism of the M. cajuputi extract as an anti-inflammation agent for COVID-19.

Keywords: antiinflammation, COVID-19, cytokine storm, NF-κβ, M. cajuputi

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Authors: Marina Passero, Tianhua Zhai, Zuyi (Jacky) Huang

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Alzheimer’s disease has become a major public health issue, as indicated by the increasing populations of Americans living with Alzheimer’s disease. After decades of extensive research in Alzheimer’s disease, only seven drugs have been approved by Food and Drug Administration (FDA) to treat Alzheimer’s disease. Five of these drugs were designed to treat the dementia symptoms, and only two drugs (i.e., Aducanumab and Lecanemab) target the progression of Alzheimer’s disease, especially the accumulation of amyloid-b plaques. However, controversial comments were raised for the accelerated approvals of either Aducanumab or Lecanemab, especially with concerns on safety and side effects of these two drugs. There is still an urgent need for further drug discovery to target the biological processes involved in the progression of Alzheimer’s disease. Excessive cholesterol has been found to accumulate in the brain of those with Alzheimer’s disease. Cholesterol can be synthesized in both the blood and the brain, but the majority of biosynthesis in the adult brain takes place in astrocytes and is then transported to the neurons via ApoE. The blood brain barrier separates cholesterol metabolism in the brain from the rest of the body. Various proteins contribute to the metabolism of cholesterol in the brain, which offer potential targets for Alzheimer’s treatment. In the astrocytes, SREBP cleavage-activating protein (SCAP) binds to Sterol Regulatory Element-binding Protein 2 (SREBP2) in order to transport the complex from the endoplasmic reticulum to the Golgi apparatus. Cholesterol is secreted out of the astrocytes by ATP-Binding Cassette A1 (ABCA1) transporter. Lipoprotein receptors such as triggering receptor expressed on myeloid cells 2 (TREM2) internalize cholesterol into the microglia, while lipoprotein receptors such as Low-density lipoprotein receptor-related protein 1 (LRP1) internalize cholesterol into the neuron. Cytochrome P450 Family 46 Subfamily A Member 1 (CYP46A1) converts excess cholesterol to 24S-hydroxycholesterol (24S-OHC). Cholesterol has been approved for its direct effect on the production of amyloid-beta and tau proteins. The addition of cholesterol to the brain promotes the activity of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), secretase, and amyloid precursor protein (APP), which all aid in amyloid-beta production. The reduction of cholesterol esters in the brain have been found to reduce phosphorylated tau levels in mice. In this work, a computational pipeline was developed to identify the protein targets involved in cholesterol regulation in brain and further to identify chemical compounds as the inhibitors of a selected protein target. Since extensive evidence shows the strong correlation between brain cholesterol regulation and Alzheimer’s disease, a detailed literature review on genes or pathways related to the brain cholesterol synthesis and regulation was first conducted in this work. An interaction network was then built for those genes so that the top gene targets were identified. The involvement of these genes in Alzheimer’s disease progression was discussed, which was followed by the investigation of existing clinical trials for those targets. A ligand-protein docking program was finally developed to screen 1.5 million chemical compounds for the selected protein target. A machine learning program was developed to evaluate and predict the binding interaction between chemical compounds and the protein target. The results from this work pave the way for further drug discovery to regulate brain cholesterol to combat Alzheimer’s disease.

Keywords: Alzheimer’s disease, drug discovery, ligand-protein docking, gene-network analysis, cholesterol regulation

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Ehsan Khademi, Mahdi Jalili

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Despite the special features of bipartite networks, they are common in many systems. Real-world bipartite networks may show community structure, similar to what one can find in one-mode networks. However, the interpretation of the community structure in bipartite networks is different as compared to one-mode networks. In this manuscript, we compare a number of available methods that are frequently used to discover community structure of bipartite networks. These networks are categorized into two broad classes. One class is the methods that, first, transfer the network into a one-mode network, and then apply community detection algorithms. The other class is the algorithms that have been developed specifically for bipartite networks. These algorithms are applied on a model network with prescribed community structure.

Keywords: community detection, bipartite networks, co-clustering, modularity, network projection, complex networks

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Authors: Youngseok Kim, Chul Park, Jonghwa Yi, Sangsik Choi

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The 2-MHz Side Scan SONAR (SSS) attached to the boat for inspection of underwater structures is affected by shaking. It is difficult to determine the exact scale of damage of structure. In this study, a motion sensor is attached to the inside of the 2-MHz SSS to get roll, pitch, and yaw direction data, and developed the image stabilization tool to correct the sonar image. We checked that reliable data can be obtained with an average error rate of 1.99% between the measured value and the actual distance through experiment. It is possible to get the accurate sonar data to inspect damage in underwater structure.

Keywords: image stabilization, motion sensor, safety inspection, sonar image, underwater structure

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Authors: Li Feng, Cheng Zhang, Chuanzhou Yuang

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Understanding the macromolecular structure of low-rank coal is very important for its gasification and liquefaction. The pyrolysis is one of the methods of analyzing the macromolecular structure of coal. The gaseous products decomposed directly by the raw lignite at 500 °C and indirectly by tar products from raw lignite pyrolysis at 500 °C were investigated and compared by thermogravimetry, gas chromatography and mass spectrum coupled instrument system (TG/GC/MS) in this paper. The results show that 52 kinds of products were found from the raw lignite and 70 kinds of products from the tar. The pyrolysis products directly from the lignite appear more monocyclic aromatic hydrocarbons and less substituent groups or branch chain, compared with the products from the tar. There is less linear chain and double bonds structure in the tar, which can be speculated that linear chain and double bonds structure took part in the generation of condensed rings and other reactions. There are more kinds of phenol and furan in the tar, which indicate that these products may be generated from the secondary reaction. The formation process of phenol, phenol naphthalene, naphthene and furan are discussed.

Keywords: composition and structure, lignite, pyrolysis of coal, tar, TG/GC/MS

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Authors: E. Oke, A. O. Ladokun, J. O. Daramola, O. M. Onagbesan

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There has been a growing interest on the effects of access to pasture on poultry health status. However, there is a paucity of data on the relative benefits of grass and legume pastures. An experiment was conducted to determine the effects of rearing systems {deep litter system (DL), deep litter with access to legumes (LP) or grass (GP) pastures} haematology and serum chemistry of ISA Brown layers. The study involved the use of two hundred and forty 12 weeks old pullets. The birds were reared until 60 weeks of age. Eighty birds were assigned to each treatment; each treatment had four replicates of 20 birds each. Blood samples (2.5 ml) were collected from the wing vein of two birds per replicate and serum chemistry and haematological parameters were determined. The results showed that there were no significant differences between treatments in all the parameters considered at 18 weeks of age. At 24 weeks old, the percentage of heterophyl (HET) in DL and LP were similar but higher than that of GP. The ratio of H:L was higher (P<0.05) in DL than those of LP and GP while LP and GP were comparable. At week 38 of age, the percentage of PCV in the birds in LP and GP were similar but the birds in DL had significantly lower level than that of GP. In the early production phase, serum total protein of the birds in LP was similar to that of GP but higher (P<0.05) than that of DL. At the peak production phase (week 38), the total protein in GP and DL were similar but significantly lower than that of LP. The albumin level in LP was greater (P<0.05) than GP but similar to that of DL. In the late production phase, the total protein in LP was significantly higher than that of DL but similar to that of GP. It was concluded that rearing chickens in either grass or legume pasture did not have deleterious effects on the health of laying chickens but improved some parameters including blood protein and HET/lymphocyte.

Keywords: rearing systems, stylosanthes, cynodon serum chemistry, haematology, hen

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Authors: Yuhua Wang, Mu Li, Jinggen Liu

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Aim: To investigate the different effects of heroin and milk in activating the corticostriatal system that plays a critical role in reward reinforcement learning. Methods: Male SD rats were trained daily for 15 d to self-administer heroin or milk tablets in a classic runway drug self-administration model. Immunohistochemical assay was used to quantify Arc protein expression in the medial prefrontal cortex (mPFC), the nucleus accumbens (NAc), the dorsomedial striatum (DMS) and the ventrolateral striatum (VLS) in response to chronic self-administration of heroin or milk tablets. NMDA receptor antagonist MK801 (0.1 mg/kg) or dopamine D1 receptor antagonist SCH23390 (0.03 mg/kg) were intravenously injected at the same time as heroin was infused intravenously. Results: Runway training with heroin resulted in robust enhancement of Arc expression in the mPFC, the NAc and the DMS on d 1, 7, and 15, and in the VLS on d 1 and d 7. However, runway training with milk led to increased Arc expression in the mPFC, the NAc and the DMS only on d 7 and/or d 15 but not on d 1. Moreover, runway training with milk failed to induce increased Arc protein in the VLS. Both heroin-seeking behavior and Arc protein expression were blocked by MK801 or SCH23390 administration. Conclusion: The VLS is likely to be critically involved in drug-seeking behavior. The NMDA and D1 receptor-dependent Arc expression is important in drug-seeking behavior.

Keywords: arc, mesocorticolimbic system, drug rewarding behavior, NMDA receptor

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić

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The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.

Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR

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Authors: Ovidiu Vlaicu, Leontina Banica, Dan Otelea, Andrei-Jose Petrescu, Costin-Ioan Popescu

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Hepatitis C Virus (HCV) infects 170 million peoples worldwide. Major advances have been made recently in HCV standard of care with interferon-free therapy being already approved. Despite major progress in HCV therapy, the genotype associated treatment efficacy and toxicity still represent issues to address. To identify endogenous factors involved in different stages of HCV life cycle, we have developed a trans-packaging system for HCV subgenomic replicons lacking core protein gene. Huh7 cells were used to generate a packaging cell line expressing the core protein in an inducible manner. The core packaging cell line was able to trans-complemented various subgenomic replicons to secret infectious trans-complemented HCV particles (HCV-TCP). Further, we constructed subgenomic replicons with foreign epitopes suitable for immunoaffinity purification or fluorescence microscopy studies. We have shown that the insertion has not effects on the efficacy of trans-complementation yielding similar titers to the control subgenomic replicon. This system will be a valuable tool in studying pre- and post-assembly events in HCV life cycle and for the fast identification of HCV assembly inhibitors.

Keywords: assembly inhibitors, core protein, HCV, trans-complementation

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Authors: Mizam Doğan

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In service life; structures can be damaged if they are subjected to dead and live loads which are greater than design values. For preventing this case; possible loads must be correctly calculated, structure must be designed according to determined loads, and structure must not be used out of its function. If loading case of the structure changes when its function changes; it must be reinforced for continuing it is new function. Reinforcement is a process that is made by increasing the existing strengths of structural system elements of the structure as reinforced concrete walls, beams, and slabs. Reinforcement can be done by casting reinforced concrete, placing steel and fiber structural elements. In this paper, reinforcing of columns and slabs of a structure of which function is changed is studied step by step. This reinforcement is made for increasing vertical and lateral load carrying capacity of the building. Not for repairing damaged structural system.

Keywords: strengthening, RC slabs, seismic load, steel beam, structural irregularity

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Authors: Nikhil Agrawal, Adam A. Skelton

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Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Mansi Srivastava, Uzma Saqib, Adnan Naim, Anjali Roy, Dongfang Liu, Deepak Bhatnagar, Ravinder Ravinder, Mirza S. Baig

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Macrophages polarize to proinflammatory M1 or anti-inflammatory M2 states with distinct physiological functions. This transition within the M1 to M2 phenotypes decides the nature, duration, and severity of an inflammatory response. However, inspite of a substantial understanding of the fate of these phenotypes, the underlying molecular mechanisms are not well understood. We have investigated the role of Neuronal nitric oxide synthase (NOS1) mediated regulation of Activator protein 1 (AP-1) transcription factor in macrophages as a critical effector of macrophage phenotypic change. Activator protein 1 (AP-1) is a group of dimeric transcription factors composed of jun, Fos, and ATF family proteins. We determined that NOS1-derived nitric oxide (NO) facilitate Fos and jun interaction which induces IL12 & IL23 expression. Pharmacological inhibition of NOS1 inhibits Fos and jun interaction but increases ATF2 and Fos dimerization. Switching of Fos and jun dimer to ATF2 and jun dimerization switches phenotype from IL–12high IL-23high IL-10low to IL–12low IL-23lowIL-10high phenotype, respectively. Together, these findings highlight a key role of the TLR4-NOS1-AP1 signaling axis in regulating macrophage polarization.

Keywords: inflammation, macrophage, lipopolysaccharide (LPS), proinflammatory cytokines, activator protein 1 (AP-1), neuronal nitric oxide synthase (NOS1)

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Authors: Ho Young Son, Bu Seog Ju, Woo Young Jung

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This study presents the seismic safety evaluation of weir structure subjected to strong earthquake ground motions, as a flood defense structure in civil engineering structures. The seismic safety analysis procedure was illustrated through development of Finite Element (FE) and InFinite Element (IFE) method in ABAQUS platform. The IFE model was generated by CINPS4, 4-node linear one-way infinite model as a sold continuum infinite element in foundation areas of the weir structure and then nonlinear FE model using friction model for soil-structure interactions was applied in this study. In order to understand the complex behavior of weir structures, nonlinear time history analysis was carried out. Consequently, it was interesting to note that the compressive stress gave more vulnerability to the weir structure, in comparison to the tensile stress, during an earthquake. The stress concentration of the weir structure was shown at the connection area between the weir body and stilling basin area. The stress both tension and compression was reduced in IFE model rather than FE model of weir structures.

Keywords: seismic, numerical analysis, FEM, weir, boundary condition

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Authors: Jeisson Alejandro Triana, Maria Fernanda Quiceno Vallejo, Patricia del Portillo, Juan Manuel Anzola

Abstract:

Most of the known antimicrobials so far discovered are secondary metabolites. The potential for new natural products of this category increases as new microbial genomes and metagenomes are being sequenced. Despite the advances, there is no systematic way to interrogate metagenomic clones for their potential to contain clusters of genes related to these pathways. Here we analyzed 52 biosynthetic pathways from the AntiSMASH database at the protein domain level in order to identify domains of high specificity and sensitivity with respect to specific biosynthetic pathways. These domains turned out to have various degrees of divergence at the DNA level. We propose PCR assays targetting such domains in-silico and corroborated one by Sanger sequencing.

Keywords: bioinformatic, anti smash, antibiotics, secondary metabolites, natural products, protein domains

Procedia PDF Downloads 161

Authors: Youn Young Shim, Ji Hye Kim, Jae Youl Cho, Martin J. T. Reaney

Abstract:

Flaxseed (Linum usitatissimum L.) is gaining popularity in the food industry as a superfood due to its health-promoting properties. The flax plant synthesizes an array of biologically active cyclic peptides or linusorbs (LOs, a.k.a. cyclolinopeptides) from three or more ribosome-derived precursors. [1–9-NαC]-linusorb B3 and [1–9-NαC]-linusorb B2, suppress immunity, induce apoptosis in human epithelial cancer cell line (Calu-3) cells, and inhibit T-cell proliferation, but the mechanism of LOs action is unknown. Using gene expression analysis in nematode cultures and human cancer cell lines, we have observed that LOs exert their activity, in part, through induction of apoptosis. Specific LOs’ properties include: 1) distribution throughout the body after flaxseed consumption; 2) induce heat shock protein (HSP) 70A production as an indicator of stress and address the issue in Caenorhabditis elegans (exposure of nematode cultures to [1–9-NαC]-linusorb B3 induced a 30% increase in production of the HSP 70A protein); 3) induce apoptosis in Calu-3 cells; and 4) modulate regulatory genes in microarray analysis. These diverse activities indicate that LOs might induce apoptosis in cancer cells or act as versatile platforms to deliver a variety of biologically active molecules for cancer therapy.

Keywords: flaxseed, linusorb, cyclic peptide, orbitides, heat shock protein, apoptosis, anti-cancer

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Authors: Murat Avci, Fatih Kosar, Ismail Yilmaz

Abstract:

In this study, structure-flow interaction for water brake mechanism is studied with Abaqus CEL approach. The water brake mechanism is used for dynamic systems such as sled system on rail. For the achievement of these system tests, structure-flow interaction should be investigated in detail. This study is about a sled test of an aircraft subsystem which rises to supersonic speeds thanks to rocket engines. To decrease or to stop the thrusting rocket sleds, water brake mechanisms are used. Water brake mechanism provides the deceleration of the structures that have supersonic speeds. Therefore, structure-flow interaction may cause damage to the water brake mechanism. To verify all design revisions with system tests are so costly so that some decisions are taken in accordance with numerical methods. In this study, structure-flow interaction that belongs to water brake mechanism is solved with Abaqus CEL approach. Fluid and deformation on the structure behaviors are modeled at the same time thanks to CEL approach. Provided analysis results are corrected with the dynamic tests. Deformation zones seen in numerical analysis are also observed in dynamic tests. Finally, Johnson-Cook material model parameters used for this analysis are proven, and it is understood that these parameters can be used for dynamic analysis like water brake mechanism.

Keywords: aircraft, rocket, structure-flow, supersonic

Procedia PDF Downloads 143

Authors: Reham H. Soliman, Noha Noufal, Howayda AbdelAal

Abstract:

Calcium/calmodulin-dependent serine protein kinase (CASK) belongs to the membrane-associated guanylate kinase (MAGUK) family and has been proposed as a mediator of cell-cell adhesion and proliferation, which can contribute to tumorogenesis. CASK has been linked as a good prognostic factor with some tumor subtypes, while considered as a poor prognostic marker in others. To our knowledge, no sufficient evidence of CASK role in colorectal cancer is available. The aim of this study is to evaluate the expression of Calcium/calmodulin-dependent serine protein kinase (CASK) in non-mucinous colorectal adenocarcinoma and adenomatous polyps as precursor lesions and assess its prognostic significance. The study included 42 cases of conventional colorectal adenocarcinoma and 15 biopsies of adenomatous polyps with variable degrees of dysplasia. They were reviewed for clinicopathological prognostic factors and stained by CASK; mouse, monoclonal antibody using heat-induced antigen retrieval immunohistochemical techniques. The results showed that CASK protein was significantly overexpressed (p <0.05) in CRC compared with adenoma samples. The CASK protein was overexpressed in the majority of CRC samples with 85.7% of cases showing moderate to strong expression, while 46.7% of adenomas were positive. CASK overexpression was significantly correlated with both TNM stage and grade of differentiation (p <0.05). There was a significantly higher expression in tumor samples with early stages (I/II) rather than advanced stage (III/IV) and with low grade (59.5%) rather than high grade (40.5%). Another interesting finding was found among the adenomas group, where the stronger intensity of staining was observed in samples with high grade dysplasia (33.3%) than those of lower grades (13.3%). In conclusion, this study shows that there is significant overexpression of CASK protein in CRC as well as in adenomas with high grade dysplasia. This indicates that CASK is involved in the process of carcinogenesis and functions as a potential trigger of the adenoma-carcinoma cascade. CASK was significantly overexpressed in early stage and low-grade tumors rather than tumors with advanced stage and higher histological grades. This suggests that CASK protein is a good prognostic factor. We suggest that CASK affects CRC in two different ways derived from its physiology. CASK as part of MAGUK family can stimulate proliferation and through its cell membrane localization and as a mediator of cell-cell adhesion might contribute in tumor confinement and localization.

Keywords: CASK, colorectal cancer, overexpression, prognosis

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Authors: J. O. Idoko, C. N. Michael, T. O. Fasuan

Abstract:

This study investigated the effects of cooking time, seed-to-water ratio and soaking time on proximate and functional properties of African walnut seed using Box-Behnken design and Response Surface Methodology (BBD-RSM) with a view to increase its utilization in the food industry. African walnut seeds were sorted washed, soaked, cooked, dehulled, sliced, dried and milled. Proximate analysis and functional properties of the samples were evaluated using standard procedures. Data obtained were analyzed using descriptive and inferential statistics. Quadratic models were obtained to predict the proximate and functional qualities as a function of cooking time, seed-to-water ratio and soaking time. The results showed that the crude protein ranged between 11.80% and 23.50%, moisture content ranged between 1.00% and 4.66%, ash content ranged between 3.35% and 5.25%, crude fibre ranged from 0.10% to 7.25% and carbohydrate ranged from 1.22% to 29.35%. The functional properties showed that soluble protein ranged from 16.26% to 42.96%, viscosity ranged from 23.43 mPas to 57 mPas, emulsifying capacity ranged from 17.14% to 39.43% and water absorption capacity ranged from 232% to 297%. An increase in the volume of water used during cooking resulted in loss of water soluble protein through leaching, the length of soaking time and the moisture content of the dried product are inversely related, ash content is inversely related to the cooking time and amount of water used, extraction of fat is enhanced by increase in soaking time while increase in cooking and soaking times result into decrease in fibre content. The results obtained indicated that African walnut could be used in several food formulations as protein supplement and binder.

Keywords: African walnut, functional properties, proximate analysis, response surface methodology

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Authors: Sun Il Yu, Jung Hyun Joo, Hwa Sung Shin

Abstract:

Astrocytes are known as dominant cells in CNS and play a role as a supporter of CNS activity and regeneration. Recently, three-dimensional culture of astrocytes were actively applied to understand in vivo astrocyte works. Electrospun nanofibers are attractive for 3D cell culture system because they have a high surface to volume ratio and porous structure, and have already been used for 3D astrocyte cultures. In this research, the stiffness of cellulose acetate (CA) nanofiber was controlled by heat treatment. As stiffness increased, astrocyte cell viability and adhesion increased. Reactivity of astrocyte was also upregulated in stiffer CA nanofiber in terms of GFAP, an intermediate filament protein. Finally, we demonstrated that stiffness-controllable CA is attractive for astrocyte tissue engineering.

Keywords: astrocyte, cellulose acetate, nanofiber, tissue scaffold

Procedia PDF Downloads 346