Search results for: target gene database

Authors: Philipp Galkin

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Government policy is a critical factor in the understanding of energy markets. Regardless, it is rarely approached systematically from a research perspective. Gaining a precise understanding of what policies exist, their intended outcomes, geographical extent, duration, evolution, etc. would enable the research community to answer a variety of questions that, for now, are either oversimplified or ignored. Policy, on its surface, also seems a rather unstructured and qualitative undertaking. There may be quantitative components, but incorporating the concept of policy analysis into quantitative analysis remains a challenge. The KAPSARC Energy Policy Database (KEPD) is intended to address these two energy policy research limitations. Our approach is to represent policies within a quantitative library of the specific policy measures contained within a set of legal documents. Each of these measures is recorded into the database as a single entry characterized by a set of qualitative and quantitative attributes. Initially, we have focused on the major laws at the national level that regulate coal in China. However, KAPSARC is engaged in various efforts to apply this methodology to other energy policy domains. To ensure scalability and sustainability of our project, we are exploring semantic processing using automated computer algorithms. Automated coding can provide a more convenient input data for human coders and serve as a quality control option. Our initial findings suggest that the methodology utilized in KEPD could be applied to any set of energy policies. It also provides a convenient tool to facilitate understanding in the energy policy realm enabling the researcher to quickly identify, summarize, and digest policy documents and specific policy measures. The KEPD captures a wide range of information about each individual policy contained within a single policy document. This enables a variety of analyses, such as structural comparison of policy documents, tracing policy evolution, stakeholder analysis, and exploring interdependencies of policies and their attributes with exogenous datasets using statistical tools. The usability and broad range of research implications suggest a need for the continued expansion of the KEPD to encompass a larger scope of policy documents across geographies and energy sectors.

Keywords: China, energy policy, policy analysis, policy database

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Authors: Anna D. Kotrova, Alexandr N. Shishkin, Elena I. Ermolenko

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The aim. To study the quantitative and qualitative colon bacteria ratio from patients with metabolic syndrome. Materials and methods. Fecal samples from patients of 2 groups were identified and analyzed: the first group was formed by patients with metabolic syndrome, the second one - by healthy individuals. The metagenomics method was used with the analysis of 16S rRNA gene sequences. The libraries of the variable sites (V3 and V4) gene 16S RNA were analyzed using the MiSeq device (Illumina). To prepare the libraries was used the standard recommended by Illumina, a method based on two rounds of PCR. Results. At the phylum level in the microbiota of patients with metabolic syndrome compared to healthy individuals, the proportion of Tenericutes was reduced, the proportion of Actinobacteria was increased. At the genus level, in the group with metabolic syndrome, relative to the second group was increased the proportion of Lachnospira. Conclusion. Changes in the colon bacteria ratio in the gut microbiota of patients with metabolic syndrome were found both at the type and the genus level. In the metabolic syndrome group, there is a decrease in the proportion of bacteria that do not have a cell wall. To confirm the revealed microbiota features in patients with metabolic syndrome, further study with a larger number of samples is required.

Keywords: gut microbiota, metabolic syndrome, metagenomics, tenericutes

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Authors: Haruka Ito, Toru Maruyama, Michihiro Ito, Chuya Shinzato, Hiroyuki Fujimura, Yoshikatsu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

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Clarifying symbiotic relationships is one of the most important theme for understanding the marine eco-system. Coral reef has been regarded as an important environmental resource. Coral holobiont composed by coral, symbiotic microalgae zooxanthellae, and bacteria have complexed relationship. Zooxanthellae mainly supply organic matter to the host corals through their photosynthetic activity. The symbiotic relationship is indispensable for corals but may easily collapses due to the rise of seawater temperature. However, the molecular mechanism how seawater temperature influences their relationships still remain unclear. In this study, the transcriptomic analysis has applied to elucidate the coral-zooxanthellae relationships under high seawater temperature stress. To observe reactions of corals and zooxanthellae against the rise of seawater temperature, meta-gene expression in coral have been analyzed. The branches from six different colonies of a stony coral, Acropora tenuis, were sampled at nine times by 2016 at two locations, Ishikawabaru and South of Sesoko Island, Okinawa, Japan. The mRNAs extracted from the branches including zooxanthellae were sequenced by illumina HiSeq. Gene Set Enrichment Analysis (GSEA) based on hyper geometric distribution was performed. The seawater temperature at 2016 summer was unusually high, which was caused by El Niño event, and the number of zooxanthellae in coral was decreased in August. GSEA derived the several specific genes expressed in A. tenuis under heat stress conditions. The upregulated genes under heat stress highly related with infection immunity. The downregulated genes significantly contained cell cycle related genes. Thu, it is considered that heat stress cause disorder in cell metabolism of A. tenuis, resulting in serious influence to coral holobiont.

Keywords: coral, symbiosis, thermal stress response, transcriptome analysis

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Authors: Alvarez M., Chapela M. J., Balboa E., Rubianes D., Sinde E., Fernandez de Ana C., Rodríguez-Blanco A.

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The gut microbiota plays an important role as gut inflammation could contribute to colorectal cancer development; however, this role is still not fully understood, and tools able to prevent this progression are yet to be developed. The main objective of this study was to monitor the effects of a mushroom extracts formulation in gut microbial community composition of an Azoxymethane (AOM)/Dextran sodium sulfate (DSS) mice model of inflammation-linked carcinogenesis. For the in vivo study, 41 adult male mice of the C57BL / 6 strain were obtained. 36 of them have been induced in a state of colon carcinogenesis by a single intraperitoneal administration of AOM at a dose of 12.5 mg/kg; the control group animals received instead of the same volume of 0.9% saline. DSS is an extremely toxic polysaccharide sulfate that causes chronic inflammation of the colon mucosa, favoring the appearance of severe colitis and the production of tumors induced by AOM. Induction by AOM/DSS is an interesting platform for chemopreventive intervention studies. This time the model was used to monitor gut microbiota changes as a result of supplementation with a specific mushroom extracts formulation previously shown to have prebiotic activity. The animals have been divided into three groups: (i) Cancer + mushroom extracts formulation experimental group: to which the MicoDigest2.0 mushroom extracts formulation developed by Hifas da Terra S.L has been administered dissolved in drinking water at an estimated concentration of 100 mg / ml. (ii) Control group of animals with Cancer: to which normal water has been administered without any type of treatment. (iii) Control group of healthy animals: these are the animals that have not been induced cancer or have not received any treatment in drinking water. This treatment has been maintained for a period of 3 months, after which the animals were sacrificed to obtain tissues that were subsequently analyzed to verify the effects of the mushroom extract formulation. A microbiological analysis has been carried out to compare the microbial communities present in the intestines of the mice belonging to each of the study groups. For this, the methodology of massive sequencing by molecular analysis of the 16S gene has been used (Ion Torrent technology). Initially, DNA extraction and metagenomics libraries were prepared using the 16S Metagenomics kit, always following the manufacturer's instructions. This kit amplifies 7 of the 9 hypervariable regions of the 16S gene that will then be sequenced. Finally, the data obtained will be compared with a database that makes it possible to determine the degree of similarity of the sequences obtained with a wide range of bacterial genomes. Results obtained showed that, similarly to certain natural compounds preventing colorectal tumorigenesis, a mushroom formulation enriched the Firmicutes and Proteobacteria phyla and depleted Bacteroidetes. Therefore, it was demonstrated that the consumption of the mushroom extracts’ formulation developed could promote the recovery of the microbial balance that is disrupted in the mice model of carcinogenesis. More preclinical and clinical studies are needed to validate this promising approach.

Keywords: carcinogenesis, microbiota, mushroom extracts, inflammation

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Authors: Tzu-Hao Li, Yen-Ying Kung, Chang-Youh Tsai

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Oral dryness is a common chief complaint among patients with Sjőgren syndrome (SS), which is a disorder currently known as autoantibodies production; however, to author’s best knowledge, there has been no satisfying pharmacy to relieve the associated symptoms. Hence the effectiveness of other non-pharmacological interventions such as acupuncture should be accessed. We conducted a meta-analysis of randomized clinical trials (RCTs) which evaluated the effectiveness of xerostomia in SS. PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), Chongqing Weipu Database (CQVIP), China Academic Journals Full-text Database, AiritiLibrary, Chinese Electronic Periodicals Service (CEPS), China National Knowledge Infrastructure (CNKI) Database were searches through May 12, 2018 to select studies. Data for evaluation of subjective and objective xerostomia was extracted and was assessed with random-effects meta-analysis. After searching, a total of 541 references were yielded and five RCTs were included, covering 340 patients dry mouth resulted from SS, among whom 169 patients received acupuncture and 171 patients were control group. Acupuncture group was associated with higher subjective response rate (odds ratio 3.036, 95% confidence interval [CI] 1.828 – 5.042, P < 0.001) and increased salivary flow rate (weighted mean difference [WMD] 3.066, 95% CI 2.969 – 3.164, P < 0.001), as an objective marker. In addition, two studies examined IgG levels, which were lower in the acupuncture group (WMD -166.857, 95% CI -233.138 - -100.576, P < 0.001). Therefore, in the present meta-analysis, acupuncture improves both subjective and objective markers of dry mouth with autoantibodies reduction in patients with SS and is considered as an option of non-pharmacological treatment for SS.

Keywords: acupuncture, meta-analysis, Sjogren syndrome, xerostomia

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Authors: Daniel Benson, Yundan Gong, Hannah Kirk

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Advancement in national language processing techniques has led to increased data processing speeds, and reduced the need for cumbersome, manual data processing that is often required when processing data from multilateral organizations for specific purposes. As such, using named entity recognition (NER) modeling and the Organisation of Economically Developed Countries (OECD) Creditor Reporting System database, we present the first geotagged dataset of OECD donor Official Development Assistance (ODA) projects on a global, subnational basis. Our resulting data contains 52,086 ODA projects geocoded to subnational locations across 115 countries, worth a combined $87.9bn. This represents the first global, OECD donor ODA project database with geocoded projects. We use this new data to revisit old questions of how ‘well’ donors allocate ODA to the developing world. This understanding is imperative for policymakers seeking to improve ODA effectiveness.

Keywords: international aid, geocoding, subnational data, natural language processing, machine learning

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Authors: Eunsu Jang, Kang Park

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In developing an armored ground combat vehicle (AGCV), it is a very important step to analyze the vulnerability (or the survivability) of the AGCV against enemy’s attack. In the vulnerability analysis, the penetration equations are usually used to get the penetration depth and check whether a bullet can penetrate the armor of the AGCV, which causes the damage of internal components or crews. The penetration equations are derived from penetration experiments which require long time and great efforts. However, they usually hold only for the specific material of the target and the specific type of the bullet used in experiments. Thus, penetration simulation using ANSYS can be another option to calculate penetration depth. However, it is very important to model the targets and select the input parameters in order to get an accurate penetration depth. This paper performed a sensitivity analysis of input parameters of ANSYS on the accuracy of the calculated penetration depth. Two conflicting objectives need to be achieved in adopting ANSYS in penetration analysis: maximizing the accuracy of calculation and minimizing the calculation time. To maximize the calculation accuracy, the sensitivity analysis of the input parameters for ANSYS was performed and calculated the RMS error with the experimental data. The input parameters include mesh size, boundary condition, material properties, target diameter are tested and selected to minimize the error between the calculated result from simulation and the experiment data from the papers on the penetration equation. To minimize the calculation time, the parameter values obtained from accuracy analysis are adjusted to get optimized overall performance. As result of analysis, the followings were found: 1) As the mesh size gradually decreases from 0.9 mm to 0.5 mm, both the penetration depth and calculation time increase. 2) As diameters of the target decrease from 250mm to 60 mm, both the penetration depth and calculation time decrease. 3) As the yield stress which is one of the material property of the target decreases, the penetration depth increases. 4) The boundary condition with the fixed side surface of the target gives more penetration depth than that with the fixed side and rear surfaces. By using above finding, the input parameters can be tuned to minimize the error between simulation and experiments. By using simulation tool, ANSYS, with delicately tuned input parameters, penetration analysis can be done on computer without actual experiments. The data of penetration experiments are usually hard to get because of security reasons and only published papers provide them in the limited target material. The next step of this research is to generalize this approach to anticipate the penetration depth by interpolating the known penetration experiments. This result may not be accurate enough to be used to replace the penetration experiments, but those simulations can be used in the early stage of the design process of AGCV in modelling and simulation stage.

Keywords: ANSYS, input parameters, penetration depth, sensitivity analysis

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Teklehaimanot Hailesslasie Teklu

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Recent developments in targeted genome editing accelerated genetic research and opened new potentials to improve crops for better yields and quality. Given the significance of cereal crops as a primary source of food for the global population, the utilization of contemporary genome editing techniques like CRISPR/Cas9 is timely and crucial. CRISPR/Cas technology has enabled targeted genomic modifications, revolutionizing genetic research and exploration. Application of gene editing through CRISPR/Cas9 in enhancing sorghum is particularly vital given the current ecological, environmental, and agricultural challenges exacerbated by climate change. As sorghum is one of the main staple foods of our region and is known to be a resilient crop with a high potential to overcome the above challenges, the application of genome editing technology will enhance the investigation of gene functionality. CRISPR/Cas9 enables the improvement of desirable sorghum traits, including nutritional value, yield, resistance to pests and diseases, and tolerance to various abiotic stresses. Furthermore, CRISPR/Cas9 has the potential to perform intricate editing and reshape the existing elite sorghum varieties, and introduce new genetic variations. However, current research primarily focuses on improving the efficacy of the CRISPR/Cas9 system in successfully editing endogenous sorghum genes, making it a feasible and successful undertaking in sorghum improvement. Recent advancements and developments in CRISPR/Cas9 techniques have further empowered researchers to modify additional genes in sorghum with greater efficiency. Successful application and advancement of CRISPR techniques in sorghum will aid not only in gene discovery and the creation of novel traits that regulate gene expression and functional genomics but also in facilitating site-specific integration events. The purpose of this review is, therefore, to elucidate the current advances in sorghum genome editing and highlight its potential in addressing food security issues. It also assesses the efficiency of CRISPR-mediated improvement and its long-term effects on crop improvement and host resistance against parasites, including tissue-specific activity and the ability to induce resistance. This review ends by emphasizing the challenges and opportunities of CRISPR technology in combating parasitic plants and proposing directions for future research to safeguard global agricultural productivity.

Keywords: CRISPR/Cas9, genome editing, quality, sorghum, stress, yield

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Authors: Laurent Maurin, Mervi Toivanen

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This paper estimates euro area banks’ internal target capital ratios and investigates whether banks’ adjustment to the targets have an impact on credit supply and holding of securities during the financial crisis in 2005-2011. Using data on listed banks and country-specific macro-variables a partial adjustment model is estimated in a panel context. The results indicate, firstly, that an increase in the riskiness of banks’ balance sheets influences positively on the target capital ratios. Secondly, the adjustment towards higher equilibrium capital ratios has a significant impact on banks’ assets. The impact is found to be more size-able on security holdings than on loans, thereby suggesting a pecking order.

Keywords: Euro area, capital ratios, credit supply, partial adjustment model

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Authors: Shagufta Jabeen, Faez Jesse Firdaus Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung Chie Tan, Wai Yan Yee, Abdul Rahman Omar

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Pasteurella multocida is associated with acute, as well as, chronic infections in avian and bovine such as pasteurellosis and hemorrhagic septicemia (HS) in cattle and buffaloes. Iron is one of the most important nutrients for pathogenic bacteria including Pasteurella and acts as a cofactor or prosthetic group in several essential enzymes and is needed for amino acid, pyrimidine, and DNA biosynthesis. In our recent study, we showed that 2% of Pasteurella multocida serotype A strain PMTB2.1 encode for iron regulating genes (Accession number CP007205.1). Genome sequencing of other Pasteurella multocida serotypes namely PM70 and HB01 also indicated up to 2.5% of the respective genome encode for iron regulating genes, suggesting that Pasteurella multocida genome comprises of multiple systems for iron uptake. Since P. multocida PMTB2.1 has more than 40 CDs out of 2097 CDs (approximately 2%), encode for iron-regulated. The gene expression profiling of four iron-regulating genes namely fbpb, yfea, fece and fur were characterized under iron-restricted environment. The P. multocida strain PMTB2.1 was grown in broth with and without iron chelating agent and samples were collected at different time points. Relative mRNA expression profile of these genes was determined using Taqman probe based real-time PCR assay. The data analysis, normalization with two house-keeping genes and the quantification of fold changes were carried out using Bio-Rad CFX manager software version 3.1. Results of this study reflect that iron reduced environment has significant effect on expression profile of iron regulating genes (p < 0.05) when compared to control (normal broth) and all evaluated genes act differently with response to iron reduction in media. The highest relative fold change of fece gene was observed at early stage of treatment indicating that PMTB2.1 may utilize its periplasmic protein at early stage to acquire iron. Furthermore, down-regulation expression of fece with the elevated expression of other genes at later time points suggests that PMTB2.1 control their iron requirements in response to iron availability by down-regulating the expression of iron proteins. Moreover, significantly high relative fold change (p ≤ 0.05) of fbpb gene is probably associated with the ability of P. multocida to directly use host iron complex such as hem, hemoglobin. In addition, the significant increase (p ≤ 0.05) in fbpb and yfea expressions also reflects the utilization of multiple iron systems in P. multocida strain PMTB2.1. The findings of this study are very much important as relative scarcity of free iron within hosts creates a major barrier to microbial growth inside host and utilization of outer-membrane proteins system in iron acquisition probably occurred at early stage of infection with P. multocida. In conclusion, the presence and utilization of multiple iron system in P. multocida strain PMTB2.1 revealed the importance of iron in the survival of P. multocida.

Keywords: iron-related genes, real-time PCR, gene expression profiling, fold changes

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Authors: Muhammad Saad Shoaib Khan, Rasbin Basnet, Qingyao Shu

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Phospholipids are one of the major classes of lipid comprising 10% of total grain lipid in rice. Phospholipids are the main phosphorus containing lipid in the rice endosperm, contributing to rice palatability and seed storage property. However, in the rice grain, the majority of phosphorus occur in the form of phytic acid and are highly abundant in the bran. Phytic acid, also known as hexaphosphorylated inositol (IP6), are strong chelating agents which reduces the bioavailability of essential dietary nutrients and are therefore less desirable by rice breeders. We used the CRISPR/Cas9 system to generate mutants of a phospholipase D gene (PLDα1), which is responsible for the degradation of phospholipids into phosphatidic acid (PA). In the mutants, we found a significant reduction in the concentration of phytic acid in the grain as compared to the wild-type. The biochemical analysis of the PLDα1 mutants showed that the decrease in production of phosphatidic acid is due to reduced accumulation of CDP-diacylglycerolderived phosphatidylinositol (PI), ultimately leading to lower accumulation of phytic acid in mutants. These results showed that loss of function of PLD in rice leads to lower production of phytic acid, suggesting the potential application of Ospldα1 in breeding rice with less phytic acid.

Keywords: CRISPR/Cas9, phospholipase D, phytic acid, rice

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Authors: Samatha Ss Sutton, Kaouther Kooli

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In recent years social media influences (SMI) have become integrated into many companies marketing strategies to create buzz, target new and younger markets and further expand social media coverage in business (Lim et al 2017). SMI’s can be defined as online personalities with a substantial number of followers, across one or more social media platforms, with influence on their followers (Lou and Yuan 2018). Recently expenditure on influencer marketing has increased exponentially becoming an important area for marketing opportunities and strategies in the future (Lou and Yuan 2018). In order to market products and brands effectively through SMI’s it is important for business to understand the attributes of SMI that effect purchase intention (Lim et al 2017) of their followers and whether or not these attributes vary across generations so to market effectively to their specific segment or target market. The present study involves quantitative research to understand the attributes by which influence differs across generations namely Generation X and Millennials and its effects on purchase intentions of these generational groups. A survey will be conducted using an online questionnaire. Structural Equation Modelling and Multi group analysis will be applied. The study provides insight to marketers/decision makers on how to use influencers accordingly with their target consumer.

Keywords: social media marketing, social media influencers, attitude towards social media influencers, intention to purchase

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Authors: Ji-Young Choi, Jungjin Kim, Sang-Sun Yun, Sangmee Ahn Jo

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Intracellular adhesion molecule1 (ICAM1) is a mediator of inflammation and involved in adhesion and transmigration of leukocytes to endothelial cells, resulting in enhancement of brain inflammation. We hypothesized that increase of ICAM1 expression in endothelial cells is an early step in the pathogenesis of brain diseases such as Alzheimer’s disease. Here, we report that ICAM1 expression is regulated by pro-inflammatory cytokine TNFa in human microvascular endothelial cell (HBMVEC). TNFa significantly increased ICAM1 mRNA and protein levels at the concentrations showing no cell toxicity. This increase was also shown in micro vessels of mouse brain 24 hours after treatment with TNFa (8 mg/kg, i.v). We then investigated the epigenetic mechanism involved in the induction of ICAM1 expression. Chromatin immunoprecipitation assay revealed that TNFa reduced methylation of histone3K9 (H3K9-2me) and histone3K27 (H3K27-3me), well-known modification as gene suppression, with in the ICAM1 promoter region. However, acetylation of H3K9 and H3K14, well-known modification as gene activation, was not changed by TNFa. Treatment of BIX01294, a specific inhibitor of histone methyltransferase G9a responsible for H3K9-2me, dramatically increased in ICAM1 mRNA and protein levels and overexpression of G9a gene suppressed TNFa-induced ICAM1 expression. In contrast, GSK126, an inhibitor of histone methyltransferase EZH2 responsible for H3K27-3me and valproic acid, an inhibitor of histone deacetylase (HDAC) did not affect ICAM1 expression. These results suggested that histone3 methylation is involved in ICAM1 repression. Moreover, TNFa or BIX01294-induced ICAM induction resulted in both enhancements in adhesion and transmigration of leukocyte on endothelial cell. This study demonstrates that TNFa upregulates ICAM1 expression through H3K9-2me and H3K27-3me within the ICAM1 promoter region, in which G9a is likely to play a pivotal role in ICAM1 transcription. Our study provides a novel mechanism for ICAM1 transcription regulation in HBMVEC.

Keywords: ICAM1, TNFa, HBMVEC, H3K9-2me

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Authors: Muhammad Fiaz, Muhammad Saqlain, Bernard M. Y. Cheung, S. M. Saqlan Naqvi, Ghazala Kaukab Raja

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Background: Association of C allele of rs662799 SNP of APOA5 gene with metabolic syndrome (MetS) has been reported in different populations around the world. A case control study was conducted to explore the relationship of rs662799 variants (T/C) with the MetS and the associated risk phenotypes in a population of Pakistani origin. Methods: MetS was defined according to the IDF criteria. Blood samples were collected from the Pakistan Institute of Medical Sciences, Islamabad, Pakistan for biochemical profiling and DNA extraction. Genotyping of rs662799 was performed using mass ARRAY, iPEX Gold technology. A total of 712 unrelated case and control subjects were genotyped. Data were analyzed using Plink software and SPSS 16.0. Results: The risk allele C of rs662799 showed highly significant association with MetS (OR=1.5, Ρ=0.002). Among risk phenotypes, dyslipidemia, and obesity showed strong association with SNP (OR=1.49, p=0.03; OR =1.46, p=0.01) respectively in models adjusted for age and gender. Conclusion: The rs662799C allele is a significant risk marker for MetS in the local Pakistani population studied. The effect of the SNP is more on dyslipidemia than the other components of the MetS.

Keywords: metabolic syndrome, APOA5, rs662799, dyslipidemia, obesity

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Authors: Denis V. Axenov-Gribanov, Irina V. Voytsekhovskaya, Evgenii S. Protasov, Maxim A. Timofeyev

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Isolated ecosystems existing under specific environmental conditions have been shown to be promising sources of new strains of actinobacteria. The taiga forest of Baikal Siberia has not been well studied, and its actinobacterial population remains uncharacterized. The proximity between the huge water mass of Lake Baikal and high mountain ranges influences the structure and diversity of the plant world in Siberia. Here, we report the isolation of eighteen actinobacterial strains from male cones of Pinus sylvestris trees growing on the shore of the ancient Lake Baikal in Siberia. The actinobacterial strains were isolated on solid nutrient MS media and Czapek agar supplemented with cycloheximide and phosphomycin. Identification of actinobacteria was carried out by 16S rRNA gene sequencing and further analysis of the evolutionary history. Four different liquid and solid media (NL19, DNPM, SG and ISP) were tested for metabolite production. The metabolite extracts produced by the isolated strains were tested for antibacterial and antifungal activities. Also, antiradical activity of crude extracts was carried out. Strain Streptomyces sp. IB 2014 I 74-3 that active against Gram-negative bacteria was selected for dereplication analysis with using the high-yield liquid chromatography with mass-spectrometry. Mass detection was performed in both positive and negative modes, with the detection range set to 160–2500 m/z. Data were collected and analyzed using Bruker Compass Data Analysis software, version 4.1. Dereplication was performed using the Dictionary of Natural Products (DNP) database version 6.1 with the following search parameters: accurate molecular mass, absorption spectra and source of compound isolation. Thus, in addition to more common representative strains of Streptomyces, several species belonging to the genera Rhodococcus, Amycolatopsis, and Micromonospora were isolated. Several of the selected strains were deposited in the Russian Collection of Agricultural Microorganisms (RCAM), St. Petersburg, Russia. All isolated strains exhibited antibacterial and antifungal activities. We identified several strains that inhibited the growth of the pathogen Candida albicans but did not hinder the growth of Saccharomyces cerevisiae. Several isolates were active against Gram-positive and Gram-negative bacteria. Moreover, extracts of several strains demonstrated high antioxidant activity. The high proportion of biologically active strains producing antibacterial and specific antifungal compounds may reflect their role in protecting pollen against phytopathogens. Dereplication of the secondary metabolites of the strain Streptomyces sp. IB 2014 I 74-3 was resulted in the fact that a total of 59 major compounds were detected in the culture liquid extract of strain cultivated in ISP medium. Eight compounds were preliminarily identified based on characteristics described in the Dictionary of Natural Products database, using the search parameters Streptomyces sp. IB 2014 I 74-3 was found to produce saframycin A, Y3 and S; 2-amino-3-oxo-3H-phenoxazine-1,8-dicarboxylic acid; galtamycinone; platencin A4-13R and A4-4S; ganefromycin d1; the antibiotic SS 8201B; and streptothricin D, 40-decarbamoyl, 60-carbamoyl. Moreover, forty-nine of the 59 compounds detected in the extract examined in the present study did not result in any positive hits when searching within the DNP database and could not be identified based on available mass-spec data. Thus, these compounds might represent new findings.

Keywords: actinobacteria, Baikal Lake, biodiversity, male cones, Pinus sylvestris

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Authors: Cristian Crespo

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Conditional cash transfers (CCTs) have been targeted towards the poor. Thus, their targeting assessments check whether these schemes have been allocated to low-income households or individuals. However, CCTs have more than one goal and target group. An additional goal of CCTs is to increase school enrolment. Hence, students at risk of dropping out of school also are a target group. This paper analyses whether one of the most common targeting mechanisms of CCTs, a proxy means test (PMT), is suitable to identify the poor and future school dropouts. The PMT is compared with alternative approaches that use the outputs of a predictive model of school dropout. This model was built using machine learning algorithms and rich administrative datasets from Chile. The paper shows that using machine learning outputs in conjunction with the PMT increases targeting effectiveness by identifying more students who are either poor or future dropouts. This joint targeting approach increases effectiveness in different scenarios except when the social valuation of the two target groups largely differs. In these cases, the most likely optimal approach is to solely adopt the targeting mechanism designed to find the highly valued group.

Keywords: conditional cash transfers, machine learning, poverty, proxy means tests, school dropout prediction, targeting

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Authors: Aqsa Ali, Aleem Mushtaq, Attaullah Memon, Monna

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In this paper, we present a low cost design for a smart glove that can perform sign language recognition to assist the speech impaired people. Specifically, we have designed and developed an Assistive Hand Gesture Interpreter that recognizes hand movements relevant to the American Sign Language (ASL) and translates them into text for display on a Thin-Film-Transistor Liquid Crystal Display (TFT LCD) screen as well as synthetic speech. Linear Bayes Classifiers and Multilayer Neural Networks have been used to classify 11 feature vectors obtained from the sensors on the glove into one of the 27 ASL alphabets and a predefined gesture for space. Three types of features are used; bending using six bend sensors, orientation in three dimensions using accelerometers and contacts at vital points using contact sensors. To gauge the performance of the presented design, the training database was prepared using five volunteers. The accuracy of the current version on the prepared dataset was found to be up to 99.3% for target user. The solution combines electronics, e-textile technology, sensor technology, embedded system and machine learning techniques to build a low cost wearable glove that is scrupulous, elegant and portable.

Keywords: American sign language, assistive hand gesture interpreter, human-machine interface, machine learning, sensing glove

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Authors: M. Adamski, J. Cwiklak

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The contemporary battlefield creates a demand for more costly and highly advanced munitions. Training personnel responsible for operations, as well as an immediate execution of combat tasks, which engage real assets, is unrealistic and economically not feasible. Owing to a wide array of exploited simulators and various types of imitators, it is possible to reduce the costs. One of the effective elements of training, which can be applied in the training of all service branches, are imitators of aerial targets. This research serves as an introduction to the commencement of design analysis over a real aerial target imitator. Within the project, the basic aerodynamic calculations were made, which enabled to determine its geometry, design layout, performance, as well as the mass balance of individual components. The conducted calculations of the parameters of flight characteristics come closer to the real performance of such unmanned aerial vehicles.

Keywords: aerial target, aerodynamics, imitator, performance

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Authors: Raquel P. F. Guiné, Daniela V. T. A. Costa, Paula M. R. Correia, Moisés Castro, Luis T. Guerra, Cristina A. Costa

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The aim of this work was to characterize a potential target group of people interested in participating into a training program in organic farming in the context of mobile-learning. The information sought addressed in particular, but not exclusively, possible contents, formats and forms of evaluation that will contribute to define the course objectives and curriculum, as well as to ensure that the course meets the needs of the learners and their preferences. The sample was selected among different European countries. The questionnaires were delivered electronically for answering online and in the end 135 consented valid questionnaires were obtained. The results allowed characterizing the target group and identifying their training needs and preferences towards m-learning formats, giving valuable tools to design the training offer.

Keywords: mobile-learning, organic farming, rural development, survey

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Authors: Syed Kashif Ali, Usman Javaid, Abdullah Chohan

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In large enterprises multiple departments use different sort of information systems and databases according to their needs. These systems are independent and heterogeneous in nature and sharing information/data between these systems is not an easy task. The usage of middleware technologies have made data sharing between systems very easy. However, monitoring the exchange of data/information for verification purposes between target and source systems is often complex or impossible for maintenance department due to security/access privileges on target and source systems. In this paper, we are intended to present our experience of an end to end data monitoring approach at middle ware level implemented in Oracle BPEL for data verification without any help of monitoring tool.

Keywords: service level agreement, SOA, BPEL, oracle fusion middleware, web service monitoring

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Authors: Ahmed Khalaf Reyad Raslan

Abstract:

Cancer stem cells (CSCs) describe a class of pluripotent cancer cells that behave analogously to normal stem cells in their ability to differentiate into the spectrum of cell types observed in tumors. The de-differentiation processes, such as an epithelial-mesenchymal transition (EMT), are known to enhance cellular plasticity. Here, we demonstrate a new hypothesis to use hybrid superparamagnetic magnetite nanoparticles (Fe₃O₄)- graphene oxide functionalized surface with Collagen to target the cancer stem cell as an early detection tool for cancer. We think that with the use of magnetic resonance imaging (MRI) and the new hybrid system would be possible to track the cancer stem cells.

Keywords: hydrogel, alginate, reduced graphene oxide, collagen

Procedia PDF Downloads 145

Authors: M. J. Norashirene, Y. Zakiah, S. Nurdiana, I. Nur Hilwani, M. H. Siti Khairiyah, M. J. Muhamad Arif

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In this study, six bacterial isolates of a slightly thermophilic organism from the Sg. Klah hot spring, Malaysia were successfully isolated and designated as M7T55D1, M7T55D2, M7T55D3, M7T53D1, M7T53D2 and M7T53D3 respectively. The bacterial isolates were screened for their cellulose hydrolytic ability on Carboxymethlycellulose agar medium. The isolated bacterial strains were identified morphologically, biochemically and molecularly with the aid of 16S rDNA sequencing. All of the bacteria showed their optimum growth at a slightly alkaline pH of 7.5 with a temperature of 55°C. All strains were Gram-negative, non-spore forming type, strictly aerobic, catalase-positive and oxidase-positive with the ability to produce thermostable cellulase. Based on BLASTn results, bacterial isolates of M7T55D2 and M7T53D1 gave the highest homology (97%) with similarity to Tepidimonas ignava while isolates M7T55D1, M7T55D3, M7T53D2 and M7T53D3 showed their closest homology (97%-98%) with Tepidimonas thermarum. These cellulolytic thermophiles might have a commercial potential to produce valuable thermostable cellulase.

Keywords: cellulase, cellulolytic, thermophiles, 16S rDNA gene

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: Ali Bayram, Burak Uz, Ilhan Dolasik, Remzi Yiğiter

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The GABARAP (GABAA-receptor-associated protein) family consists of GABARAP, GABARAPL1 (GABARAP-like 1) and GABARAPL2 (GABARAP-like 2). GABARAPL1, like GABARAP, was described to interact with both GABAA receptor and tubulin, and to be involved in intracellular GABAA receptor trafficking and promoting tubulin polymerization. In addition, GABARAPL1 is thought to be involved in various physiological (autophagosome closure, regulation of circadian rhythms) and/or pathological mechanisms (cancer, neurodegeneration). Alzheimer’s disease (AD) is a progressive neuro degenerative disorder characterized with impaired cognitive functions. Disruption of the GABAergic neuro transmission as well as cholinergic and glutamatergic interactions, may also be involved in the pathogenesis of AD. GABARAPL1 presents a regulated tissue expression and is the most expressed gene among the GABARAP family members in the central nervous system. We, herein, conducted a study to investigate the GABARAPL1 mRNA expression levels in patients with AD. 50 patients with AD and 49 control patients were enrolled to the present study. Messenger RNA expression levels of GABARAPL1 were detected by real-time polymerase chain reaction. GABARAPL1 mRNA expression in AD / control patients was 0,495 (95% confidence interval: 0,404-0,607), p= 0,00000002646. Reduced activity of GABARAPL1 gene might play a role, at least partly, in the pathophysiology of AD.

Keywords: Alzheimer’s disease, GABARAPL1, mRNA expression, RT-PCR

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Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: manihot esculenta crantz, plant architecture, dartseq, snp markers, genome-wide association study

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Authors: Srijoni Banerjee

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Sequences of some of the candidate genes (e.g., CPE, CDKAL1, GCKR, HSD11B1, IGF2BP2, IRS1, LPIN1, PKLR, TNF, PPARG) implicated in some of the complex disease, e.g. Type II diabetes in man has been compared with other species to investigate phylogenetic affinity. Based on mRNA sequence of these genes of 7 to 8 species, using bioinformatics tools Mega 5, Bioedit, Clustal W, distance matrix was obtained. Phylogenetic trees were obtained by NJ and UPGMA clustering methods. The results of the phylogenetic analyses show that of the species compared: Xenopus l., Danio r., Macaca m., Homo sapiens s., Rattus n., Mus m. and Gallus g., Bos taurus, both NJ and UPGMA clustering show close affinity between clustering of Homo sapiens s. (Man) with Rattus n. (Rat), Mus m. species for the candidate genes, except in case of Lipin1 gene. The results support the functional similarity of these genes in physiological and biochemical process involving man and mouse/rat. Therefore, in understanding the complex etiology and treatment of the complex disease mouse/rate model is the best laboratory choice for experimentation.

Keywords: phylogeny, candidate gene of type-2 diabetes, CPE, CDKAL1, GCKR, HSD11B1, IGF2BP2, IRS1, LPIN1, PKLR, TNF, PPARG

Procedia PDF Downloads 321

Authors: Seonjae Lee, Sungjoo Lee

Abstract:

Excavation is necessary to remain competitive in the current business environment. The company survived the rapidly changing industry conditions by adapting new business strategy and reducing technology challenges. Traditionally, the two methods are conducted excavations for new businesses. The first method is, qualitative analysis of expert opinion, which is gathered through opportunities and secondly, new technologies are discovered through quantitative data analysis of method patents. The second method increases time and cost. Patent data is restricted for use and the purpose of discovering business opportunities. This study presents the company's characteristics (sector, size, etc.), of new business opportunities in customized form by reviewing the value chain perspective and to contributing to creating new business opportunities in the proposed model. It utilizes the trademark database of the Korean Intellectual Property Office (KIPO) and proprietary company information database of the Korea Enterprise Data (KED). This data is key to discovering new business opportunities with analysis of competitors and advanced business trademarks (Module 1) and trading analysis of competitors found in the KED (Module 2).

Keywords: value chain, trademark, trading analysis, new business opportunity

Procedia PDF Downloads 372

Authors: P. Tueku, P. Supnithi, R. Wongsathan

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Heat-Assisted Magnetic Recording (HAMR) is one of the leading technologies identified to enable areal density beyond 1 Tb/in2 of magnetic recording systems. A key challenge to HAMR designing is accuracy of positioning, timing of the firing laser, power of the laser, thermo-magnetic head, head-disk interface and cooling system. We study the effect of HAMR parameters on transition center and transition width. The HAMR is model using Thermal Williams-Comstock (TWC) and microtrack model. The target and equalizer are designed by the minimum mean square error (MMSE). The result shows that the unit energy constraint outperforms other constraints.

Keywords: heat-assisted magnetic recording, thermal Williams-Comstock equation, microtrack model, equalizer

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Authors: Hong Zeng

Abstract:

In the process of popularization of higher education, it is necessary to innovate teaching methods in order to make the students cultivated suitable for the needs of social development. This paper discusses the limitations and shortcomings of the traditional teaching method of teaching approach to a person's aptitude, personality, and interest and introduces the new teaching method of teaching approach to a person's personality. The teaching approach to a person's personality is a target teaching method that aims to develop students' potential and cultivate professional talents. Therefore, teachers should be professional and can adopt modern teaching methods from the Internet so that students can clearly understand the course and the knowledge structure. Finally, the students using new teaching methods can enhance their motivation to study and quickly acquire professional skills.

Keywords: higher education, personality, target education, student-centered

Procedia PDF Downloads 119