Search results for: transcriptome analysis

Authors: B. Atika, S. Lehmann, E. Wimmer

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The defense strategy is very common in the insect world. Defensive substances play a wide variety of functions for beetles, such as repellents, toxicants, insecticides, and antimicrobics. Beetles react to predators, invaders, and parasitic microbes with the release of toxic and repellent substances. Defensive substances are directed against a large array of potential target organisms or may function for boiling bombardment or as surfactants. Usually, Coleoptera biosynthesize and store their defensive compounds in a complex secretory organ, known as odoriferous defensive stink glands. The red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae), uses these glands to produce antimicrobial p-benzoquinones and 1-alkenes. In the past, the morphology of stink gland has been studied in detail in tenebrionid beetles; however, very little is known about the genes that are involved in the production of gland secretion. In this study, we studied a subset of genes that are essential for the benzoquinone production in red flour beetle. In the first phase, we selected 74 potential candidate genes from a genome-wide RNA interference (RNAi) knockdown screen named 'iBeetle.' All these 74 candidate genes were functionally characterized by RNAi-mediated gene knockdown. Therefore, they were selected for a subsequent gas chromatography-mass spectrometry (GC-MS) analysis of secretion volatiles in respective RNAi knockdown glands. 33 of them were observed to alter the phenotype of stink gland. In the GC-MS analysis, 7 candidate genes were noted to display a strongly altered gland, in terms of secretion color and chemical composition, upon knockdown, showing their key role in the biosynthesis of gland secretion. Morphologically altered stink glands were found for odorant receptor and protein kinase superfamily. Subsequent GC-MS analysis of secretion volatiles revealed reduced benzoquinone levels in LIM domain, PDZ domain, PBP/GOBP family knockdowns and a complete lack of benzoquinones in the knockdown of sulfatase-modifying factor enzyme 1, sulfate transporter family. Based on stink gland transcriptome data, we analyzed the function of sulfatase-modifying factor enzyme 1 and sulfate transporter family via RNAi-mediated gene knockdowns, GC-MS, in situ hybridization, and enzymatic activity assays. Morphologically altered stink glands were noted in knockdown of both these genes. Furthermore, GC-MS analysis of secretion volatiles showed a complete lack of benzoquinones in the knockdown of these two genes. In situ hybridization showed that these two genes are expressed around the vesicle of certain subgroup of secretory stink gland cells. Enzymatic activity assays on stink gland tissue showed that these genes are involved in p-benzoquinone biosynthesis. These results suggest that sulfatase-modifying factor enzyme 1 and sulfate transporter family play a role specifically in benzoquinone biosynthesis in red flour beetles.

Keywords: Red Flour Beetle, defensive stink gland, benzoquinones, sulfate transporter, sulfatase-modifying factor enzyme 1

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Authors: F. M. El-Domyati, A. Atef, S. Edris, N. O. Gadalla, M. A. Al-Kordy, A. M. Ramadan, Y. M. Saad, H. S. Al-Zahrani, A. Bahieldin

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Transcriptome retrieved from SRA database of different tissues and treatments of C. roseus was assembled in order to detect tissue-specific transcription factors (TFs) and TFs possibly related to terpenoid indole alkaloids (TIA) pathway. A number of 290 TF-like transcripts along with 12 transcripts related to TIA biosynthetic pathway were divided in terms of co-expression in the different tissues, treatments and genotypes. Three transcripts encoding peroxidases 1 and 12 were downregulated in hairy root, while upregulated in mature leaf. Eight different transcripts of the TIA pathway co-expressed with TFs either functioning downstream tryptophan biosynthesis, e.g., tdc, str1 and sgd, or upstream vindoline biosynthesis, e.g., t16h, omt, nmt, d4h and dat. The results showed no differential expression of TF transcripts in hairy roots knocked down for tdc gene (TDCi) as compared to their wild type controls. There were several evidences of tissue-specific expression of TF transcripts in flower, mature leaf, root/hairy root, stem, seedling, hairy root and immature/mature leaves. Regulation included transcription factor families, e.g., bHLH, MYB and WRKY mostly induced by ABA and/or JA (or MeJA) and regulated during abiotic or biotic stress. The information of tissue-specific regulation and co-expression of TFs and genes in the TIA pathway can be utilized in manipulating alkaloid biosynthesis in C. roseus.

Keywords: SRA database, bHLH, MYB, WRKY, co-expression

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Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu

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Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.

Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence

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Authors: Janneth Gonzalez, Andres Pinzon Velasco, Maria Angarita, Nicolas Mendoza

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Astrocytes play an important role in various processes in the brain, including pathological conditions such as neurodegenerative diseases. Recent studies have shown that the increase in saturated fatty acids such as palmitic acid (PA) triggers pro-inflammatory pathways in the brain. The use of synthetic neurosteroids such as tibolone has demonstrated neuro-protective mechanisms. However, there are few studies on the neuro-protective mechanisms of tibolone, especially at the systemic (omic) level. In this study, we performed the integration of multi-omic data (transcriptome and proteome) into a human astrocyte genomic scale metabolic model to study the astrocytic response during palmitate treatment. We evaluated metabolic fluxes in three scenarios (healthy, induced inflammation by PA, and tibolone treatment under PA inflammation). We also use control theory to identify those reactions that control the astrocytic system. Our results suggest that PA generates a modulation of central and secondary metabolism, showing a change in energy source use through inhibition of folate cycle and fatty acid β-oxidation and upregulation of ketone bodies formation.We found 25 metabolic switches under PA-mediated cellular regulation, 9 of which were critical only in the inflammatory scenario but not in the protective tibolone one. Within these reactions, inhibitory, total, and directional coupling profiles were key findings, playing a fundamental role in the (de)regulation in metabolic pathways that increase neurotoxicity and represent potential treatment targets. Finally, this study framework facilitates the understanding of metabolic regulation strategies, andit can be used for in silico exploring the mechanisms of astrocytic cell regulation, directing a more complex future experimental work in neurodegenerative diseases.

Keywords: astrocytes, data integration, palmitic acid, computational model, multi-omics, control theory

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Authors: Janneth Gonzalez, Andrés Pinzon Velasco, Maria Angarita

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Astrocytes play an important role in various processes in the brain, including pathological conditions such as neurodegenerative diseases. Recent studies have shown that the increase in saturated fatty acids such as palmitic acid (PA) triggers pro-inflammatorypathways in the brain. The use of synthetic neurosteroids such as tibolone has demonstrated neuro-protective mechanisms. However, broad studies with a systemic point of view on the neurodegenerative role of PA and the neuro-protective mechanisms of tibolone are lacking. In this study, we performed the integration of multi-omic data (transcriptome and proteome) into a human astrocyte genomic scale metabolic model to study the astrocytic response during palmitate treatment. We evaluated metabolic fluxes in three scenarios (healthy, induced inflammation by PA, and tibolone treatment under PA inflammation). We also applied a control theory approach to identify those reactions that exert more control in the astrocytic system. Our results suggest that PA generates a modulation of central and secondary metabolism, showing a switch in energy source use through inhibition of folate cycle and fatty acid β‐oxidation and upregulation of ketone bodies formation. We found 25 metabolic switches under PA‐mediated cellular regulation, 9 of which were critical only in the inflammatory scenario but not in the protective tibolone one. Within these reactions, inhibitory, total, and directional coupling profiles were key findings, playing a fundamental role in the (de)regulation of metabolic pathways that may increase neurotoxicity and represent potential treatment targets. Finally, the overall framework of our approach facilitates the understanding of complex metabolic regulation, and it can be used for in silico exploration of the mechanisms of astrocytic cell regulation, directing a more complex future experimental work in neurodegenerative diseases.

Keywords: astrocytes, data integration, palmitic acid, computational model, multi-omics

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Authors: Aoxue Yang, Weili Tian, Haikun Liu

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Brain tumor stem cells (BTSCs) are resistant to therapy and give rise to recurrent tumors. These rare and elusive cells are likely to disseminate during cancer progression, and some may enter dormancy, remaining viable but not increasing. The identification of dormant BTSCs is thus necessary to design effective therapies for glioblastoma (GBM) patients. Glucocorticoids (GCs) are used to treat GBM-associated edema. However, glucocorticoids participate in the physiological response to psychosocial stress, linked to poor cancer prognosis. This raises concern that glucocorticoids affect the tumor and BTSCs. Identifying markers specifically expressed by brain tumor stem cells (BTSCs) may enable specific therapies that spare their regular tissue-resident counterparts. By ribosome profiling analysis, we have identified that glycerol-3-phosphate dehydrogenase 1 (GPD1) is expressed by dormant BTSCs but not by NSCs. Through different stress-induced experiments in vitro, we found that only dexamethasone (DEXA) can significantly increase the expression of GPD1 in NSCs. Adversely, mifepristone (MIFE) which is classified as glucocorticoid receptors antagonists, could decrease GPD1 protein level and weaken the proliferation and stemness in BTSCs. Furthermore, DEXA can induce GPD1 expression in tumor-bearing mice brains and shorten animal survival, whereas MIFE has a distinct adverse effect that prolonged mice lifespan. Knocking out GR in NSC can block the upregulation of GPD1 inducing by DEXA, and we find the specific sequences on GPD1 promotor combined with GR, thus improving the efficiency of GPD1 transcription from CHIP-Seq. Moreover, GR and GPD1 are highly co-stained on GBM sections obtained from patients and mice. All these findings confirmed that GR could regulate GPD1 and loss of GPD1 Impairs Multiple Pathways Important for BTSCs Maintenance GPD1 is also a critical enzyme regulating glycolysis and lipid synthesis. We observed that DEXA and MIFE could change the metabolic profiles of BTSCs by regulating GPD1 to shift the transition of cell dormancy. Our transcriptome and lipidomics analysis demonstrated that cell cycle signaling and phosphoglycerides synthesis pathways contributed a lot to the inhibition of GPD1 caused by MIFE. In conclusion, our findings raise concern that treatment of GBM with GCs may compromise the efficacy of chemotherapy and contribute to BTSC dormancy. Inhibition of GR can dramatically reduce GPD1 and extend the survival duration of GBM-bearing mice. The molecular link between GPD1 and GR may give us an attractive therapeutic target for glioblastoma.

Keywords: cancer stem cell, dormancy, glioblastoma, glycerol-3-phosphate dehydrogenase 1, glucocorticoid receptor, dexamethasone, RNA-sequencing, phosphoglycerides

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Authors: Niamh Higgins, Dawn Howard

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The Irish agri-food sector is of major importance to Ireland’s manufacturing sector and to the Irish economy through employment and the exporting of animal products worldwide. Infectious diseases and parasites have an impact on farm animal health causing profitability and productivity to be affected. For the sustainability of Irish dairy farming, there must be the highest standard of animal health. There can be a lack of information in accounting for > 1% of complete microbial diversity in an environment. There is the tendency of culture-based methods of microbial identification to overestimate the prevalence of species which grow easily on an agar surface. There is a need for new technologies to address these issues to assist with animal health. Metagenomic approaches provide information on both the whole genome and transcriptome present through DNA sequencing of total DNA from environmental samples producing high determination of functional and taxonomic information. Nanopore Next Generation Technologies have the ability to be powerful sequencing technologies. They provide high throughput, low material requirements and produce ultra-long reads, simplifying the experimental process. The aim of this study is to use a metagenomics approach to analyze dairy cattle faecal samples using the Oxford Nanopore MinION Next Generation Sequencer and to establish an in-house pipeline for metagenomic characterization of complex samples. Faecal samples will be obtained from Irish dairy farms, DNA extracted and the MinION will be used for sequencing, followed by bioinformatics analysis. Of particular interest, will be the parasite Buxtonella sulcata, which there has been little research on and which there is no research on its presence on Irish dairy farms. Preliminary results have shown the ability of the MinION to produce hundreds of reads in a relatively short time frame of eight hours. The faecal samples were obtained from 90 dairy cows on a Galway farm. The results from Oxford Nanopore ‘What’s in my pot’ (WIMP) using the Epi2me workflow, show that from a total of 926 classified reads, 87% were from the Kingdom Bacteria, 10% were from the Kingdom Eukaryota, 3% were from the Kingdom Archaea and < 1% were from the Kingdom Viruses. The most prevalent bacteria were those from the Genus Acholeplasma (71 reads), Bacteroides (35 reads), Clostridium (33 reads), Acinetobacter (20 reads). The most prevalent species present were those from the Genus Acholeplasma and included Acholeplasma laidlawii (39 reads) and Acholeplasma brassicae (26 reads). The preliminary results show the ability of the MinION for the identification of microorganisms to species level coming from a complex sample. With ongoing optimization of the pipe-line, the number of classified reads are likely to increase. Metagenomics has the potential in animal health for diagnostics of microorganisms present on farms. This would support wprevention rather than a cure approach as is outlined in the DAFMs National Farmed Animal Health Strategy 2017-2022.

Keywords: animal health, buxtonella sulcata, infectious disease, irish dairy cattle, metagenomics, minION, next generation sequencing

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Authors: Chidiebere C. Agoha, Armstong C. Awuzie, Chukwuebuka N. Onwubuariri, Joy O. Njoku

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Spatial analysis is a field of study that utilizes geographic or spatial information to understand and analyze patterns, relationships, and trends in data. It is characterized by the use of geographic or spatial information, which allows for the analysis of data in the context of its location and surroundings. It is different from non-spatial or aspatial techniques, which do not consider the geographic context and may not provide as complete of an understanding of the data. Spatial analysis is applied in a variety of fields, which includes urban planning, environmental science, geosciences, epidemiology, marketing, to gain insights and make decisions about complex spatial problems. This review paper explores definitions of spatial analysis from various sources, including examples of its application and different analysis techniques such as Buffer analysis, interpolation, and Kernel density analysis (multi-distance spatial cluster analysis). It also contrasts spatial analysis with non-spatial analysis.

Keywords: aspatial technique, buffer analysis, epidemiology, interpolation

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Authors: Leszek Chybowski, Artur Bejger, Katarzyna Gawdzińska

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Subversion analysis is a tool used in the TRIZ (Theory of Inventive Problem Solving) methodology. This article introduces the history and describes the process of subversion analysis, as well as function analysis and analysis of the resources, used at the design stage when generating possible undesirable situations. The article charts the course of subversion analysis when applied to a fuel injection nozzle of a marine engine. The work describes the fuel injector nozzle as a technological system and presents principles of analysis for the causes of a cracked tip of the nozzle body. The system is modelled with functional analysis. A search for potential causes of the damage is undertaken and a cause-and-effect analysis for various hypotheses concerning the damage is drawn up. The importance of particular hypotheses is evaluated and the most likely causes of damage identified.

Keywords: complex technical system, fuel injector, function analysis, importance analysis, resource analysis, sabotage analysis, subversion analysis, TRIZ (Theory of Inventive Problem Solving)

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Authors: Debatosh Das, Moxian Chen, Jianhua Zhang, Caroline Gutjahr

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Arbuscular mycorrhiza (AM) is a mutualistic symbiosis between plant roots and Glomeromycotina fungi, which is activated under low but inhibited by high phosphate. The effect of phosphate on AM development has been observed for many years, but mechanisms regulating it under contrasting phosphate levels remain unknown. Based on previous observations that promoters of several AM functional genes contain PHR binding motifs, we hypothesized that PHR2, a master regulator of phosphate starvation response in rice, was recruited to regulate AM symbiosis development. We observed a drastic reduction in root colonization and significant AM transcriptome modulation in phr2. PHR2 targets genes required for root colonization and AM signaling. The role of PHR2 in improving root colonization, mycorrhizal phosphate uptake, and growth response was confirmed in field soil. In conclusion, rice PHR2, which is considered a master regulator of phosphate starvation responses, acts as a positive regulator of AM symbiosis between Glomeromycotina fungi and rice roots. PHR2 directly targets the transcription of plant strigolactone and AM genes involved in the establishment of this symbiosis. Our work facilitates an understanding of ways to enhance AMF propagule populations introduced in field soils (as a biofertilizer) in order to restore the natural plant-AMF networks disrupted by modern agricultural practices. We show that PHR2 is required for AM-mediated improvement of rice yield in low phosphate paddy field soil. Thus, our work contributes knowledge for rational application of AM in sustainable agriculture. Our data provide important insights into the regulation of AM by the plant phosphate status, which has a broad significance in agriculture and terrestrial ecosystems.

Keywords: biofertilizer, phosphate, mycorrhiza, rice, sustainable, symbiosis

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Authors: Aberdam Edith, Sangari Linda, Petit Isabelle, Aberdam Daniel

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Background and Rationale: Transparent avascularised cornea is essential for normal vision and depends on limbal stem cells (LSC) that reside between the cornea and the conjunctiva. Ocular burns or injuries may destroy the limbus, causing limbal stem cell deficiency (LSCD). The cornea becomes vascularised by invaded conjunctival cells, the stroma is scarring, resulting in corneal opacity and loss of vision. Grafted autologous limbus or cultivated autologous LCS can restore the vision, unless the two eyes are affected. Alternative cellular sources have been tested in the last decades, including oral mucosa or hair follicle epithelial cells. However, only partial success has been achieved by the use of these cells since they were not able to uniformly commit into corneal epithelial cells. Human pluripotent stem cells (iPSC) display both unlimited growth capacity and ability to differentiate into any cell type. Our goal was to design a standardized and reproducible protocol to produce transplantable autologous LSC from patients through cell reprogramming technology. Methodology: First, keratinocyte primary culture was established from a small number of plucked hair follicles of healthy donors. The resulting epithelial cells were reprogrammed into induced pluripotent stem cells (iPSCs) and further differentiate into corneal epithelial cells (CEC), according to a robust protocol that recapitulates the main step of corneal embryonic development. qRT-PCR analysis and immunofluorescent staining during the course of differentiation confirm the expression of stage specific markers of corneal embryonic lineage. First appear ectodermal progenitor-specific cytokeratins K8/K18, followed at day 7 by limbal-specific PAX6, TP63 and cytokeratins K5/K14. At day 15, K3/K12+-corneal cells are present. To amplify the iPSC-derived LSC (named COiPSC), intact small epithelial colonies were detached and cultivated in limbal cell-specific medium. In that culture conditions, the COiPSC can be frozen and thaw at any passage, while retaining their corneal characteristics for at least eight passages. To evaluate the potential of COiPSC as an alternative ocular toxicity model, COiPSC were treated at passage P0 to P4 with increasing amounts of SDS and Benzalkonium. Cell proliferation and apoptosis of treated cells was compared to LSC and the SV40-immortalized human corneal epithelial cell line (HCE) routinely used by cosmetological industrials. Of note, HCE are more resistant to toxicity than LSC. At P0, COiPSC were systematically more resistant to chemical toxicity than LSC and even to HCE. Remarkably, this behavior changed with passage since COiPSC at P2 became identical to LSC and thus closer to physiology than HCE. Comparative transcriptome analysis confirmed that COiPSC from P2 are similar to a mixture of LSC and CEC. Finally, by organotypic reconstitution assay, we demonstrated the ability of COiPSC to produce a 3D corneal epithelium on a stromal equivalent made of keratocytes. Conclusion: COiPSC could become valuable for two main applications: (1) an alternative robust tool to perform, in a reproducible and physiological manner, toxicity assays for cosmetic products and pharmacological tests of drugs. (2). COiPSC could become an alternative autologous source for cornea transplantation for LSCD.

Keywords: Limbal stem cell deficiency, iPSC, cornea, limbal stem cells

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Authors: Doo Byong Bae, Jae Jun Yoo, Il Gyu Park, Choi Seowon, Oh Chang Kook

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There are several wind load provisions to evaluate the wind response on tank structures such as API, Euro-code, etc. the assessment of wind action applying these provisions is made by performing the finite element analysis using both linear bifurcation analysis and geometrically nonlinear analysis. By comparing the pressure patterns obtained from the analysis with the results of wind tunnel test, most appropriate wind load criteria will be recommended.

Keywords: wind load, finite element analysis, linear bifurcation analysis, geometrically nonlinear analysis

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Authors: M. Szechynska-Hebda, M. Sobczak, E. Rozanska, J. Troczynska, Z. Banaszak, N. Hordyńska, M. Dyda, M. Wedzony

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Chloroplasts, as essential organelles for photosynthesis, play a critical role in plant development. However, disturbances in the proper functioning of chloroplasts, in the extreme case manifesting as albinism of tissues and whole plants, are a phenomenon often occurring in conditions deviating from natural (e.g., in vitro cultures applied in breeding programs). Using whole-transcriptome analysis (RNA-Seq) together with light, fluorescent and electron microscopy, it was shown, that development of chloroplasts and formation of green or albino plants in the androgenesis process are genotype-dependent; however, they could be modulated by sub-optimal temperature treatment. The reprogramming of the microspore development from gametophytic to sporophytic, and then regeneration of green plant can be positively regulated by cold stress (4 ⁰C). A high temperature stress (32 ⁰C) can induce androgenesis, but it is a factor negatively influencing green plant regeneration (promoting albinism). A similar effect on microspores, androgenesis, and subsequent chloroplast formation, is elicited as a result of postponing the date of spike collection from spring to summer in field conditions (natural temperature rise). It is determined in both environmental or genotypic manner. The delay of the sowing date (environmental effect) or growing of late genotypes (genotypic effect) result in spike maturation at higher temperatures and significantly enhance albino plant formation in androgenesis process. Such a temperature system (4 ⁰C vs. 32 ⁰C) was used to study the chloroplast biogenesis process in wheat and triticale. It was shown, that efficiency of physiological processes differentiates microspore development during cold reprograming in genotypes susceptible and resistant to androgenesis. Moreover, a great variation in developmental stages of the microspores in one anther is observed for susceptible genotypes. Microspores that are more physiologically active under cold conditions can activate signaling pathways and processes, which provide an appropriate supply of metabolites to cell compartments. This, in turn, fully correlates with the genotype-dependent efficiency of chloroplast formation (or different types of plastid) at particular steps of androgenesis. The effect obtained after applying a high temperature stress is different. High temperature causes a significant acceleration of microspore development and less variation in developmental stages at the end of the treatment. Therefore, the developmental diversity of the microspores in one anther seems to be a critical factor for subsequent cell and chloroplast differentiation. The work was financed by Ministry of Agriculture and Rural Development within Program: 'Biological Progress in Plant Production', project no HOR.hn.802.15.2018

Keywords: androgenesis, chloroplast biogenesis, temperature stress, wheat

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Authors: Liu Yao, B. T. Wan Maseri, Wan Mohd, B. T. Nurul Izzah, Mohd Shah, Wei Wei

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Effectively managing knowledge has become a vital weapon for businesses to survive or to succeed in the increasingly competitive market. But do they perform environmental analysis when managing knowledge? If yes, how is the level and significance? This paper established a conceptual framework covering the basic knowledge management activities (KMA) to examine their contribution towards organizational performance (OP). Environmental analysis (EA) was then investigated from both internal and external aspects, to identify its effects on that contribution. Data was collected from 400 Chinese SMEs by questionnaires. Cronbach's α and factor analysis were conducted. Regression results show that the external analysis presents higher level than internal analysis. However, the internal analysis mediates the effects of external analysis on the KMA-OP relation and plays more significant role in the relation comparing with the external analysis. Thus, firms shall improve environmental analysis especially the internal analysis to enhance their KM practices.

Keywords: knowledge management, environmental analysis, performance, mediating, small sized enterprises, medium sized enterprises

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Authors: Assad Maalouf, Lunjin Lu, James Lynott

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We present a taint analysis that can automatically detect when string operations result in a string that is free of taints, where all the tainted patterns have been removed. This is an improvement on the conservative behavior of previous taint analyzers, where a string operation on a tainted string always leads to a tainted string unless the operation is manually marked as a sanitizer. The taint analysis is built on top of a string analysis that uses finite state automata to approximate the sets of values that string variables can take during the execution of a program. The proposed approach has been implemented as an extension of FlowDroid and experimental results show that the resulting taint analyzer is much more precise than the original FlowDroid.

Keywords: android, static analysis, string analysis, taint analysis

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Authors: Proud Arunrangsiwed

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The part of “future direction” in the findings of meta-analysis could provide the great direction to conduct the future studies. This study, “The Documentary Analysis of Meta-Analysis Research in Violence of Media” would conclude “future directions” out of 10 meta-analysis papers. The purposes of this research are to find an appropriate research design or an appropriate methodology for the future research related to the topic, “violence of media”. Further research needs to explore by longitudinal and experimental design, and also needs to have a careful consideration about age effects, time spent effects, enjoyment effects, and ordinary lifestyle of each media consumer.

Keywords: aggressive, future direction, meta-analysis, media, violence

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Authors: Nazri Kama, Sufyan Basri, Roslina Ibrahim

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It is important to manage the changes in the software to meet the evolving needs of the customer. Accepting too many changes causes delay in the completion and it incurs additional cost. One type of information that helps to make the decision is through change impact analysis. Current impact analysis approaches assume that all classes in the class artifact are completely developed and the class artifact is used as a source of analysis. However, these assumptions are impractical for impact analysis in the software development phase as some classes in the class artifact are still under development or partially developed that leads to inaccuracy. This paper presents a novel impact analysis approach to be used in the software development phase. The significant achievements of the approach are demonstrated through an extensive experimental validation using three case studies.

Keywords: software development, impact analysis, traceability, static analysis.

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Authors: T. Padma, Jayashree S. Pillai

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Random entities are an essential component in any cryptographic application. The suitability of a number theory based novel pseudorandom sequence called Pseudorandom Partial Quotient Sequence (PPQS) generated from the continued fraction expansion of irrational numbers, in cryptographic applications, is analyzed in this paper. An approach to build the algorithm around a hard mathematical problem has been considered. The PQ sequence is tested for randomness and its suitability as a cryptographic key by performing randomness analysis, key sensitivity and key space analysis, precision analysis and evaluating the correlation properties is established.

Keywords: pseudorandom sequences, key sensitivity, correlation, security analysis, randomness analysis, sensitivity analysis

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Authors: Ho Yeon Park, Kyoung-Jae Kim

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The purpose of this study is to investigate whether friendship in social media can be an important factor in recommender system through social scientific analysis of friendship in popular social media such as Facebook and Twitter. For this purpose, this study analyzes data on friendship in real social media using component analysis and clique analysis among sub-group analysis in social network analysis. In this study, we propose an algorithm to reflect the results of sub-group analysis on the recommender system. The key to this algorithm is to ensure that recommendations from users in friendships are more likely to be reflected in recommendations from users. As a result of this study, outcomes of various subgroup analyzes were derived, and it was confirmed that the results were different from the results of the existing recommender system. Therefore, it is considered that the results of the subgroup analysis affect the recommendation performance of the system. Future research will attempt to generalize the results of the research through further analysis of various social data.

Keywords: sub-group analysis, social media, social network analysis, recommender systems

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Authors: Sannikumar Patel, Brian Nolan, Markus Hofmann, Philip Owende, Kunjan Patel

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Sentiment analysis and opinion mining have become emerging topics of research in recent years but most of the work is focused on data in the English language. A comprehensive research and analysis are essential which considers multiple languages, machine translation techniques, and different classifiers. This paper presents, a comparative analysis of different approaches for multilingual sentiment analysis. These approaches are divided into two parts: one using classification of text without language translation and second using the translation of testing data to a target language, such as English, before classification. The presented research and results are useful for understanding whether machine translation should be used for multilingual sentiment analysis or building language specific sentiment classification systems is a better approach. The effects of language translation techniques, features, and accuracy of various classifiers for multilingual sentiment analysis is also discussed in this study.

Keywords: cross-language analysis, machine learning, machine translation, sentiment analysis

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Authors: Jehan Fahim M. Alsulami

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Academic research about sentiment analysis in sentiment analysis has obtained significant advancement over recent years and is flourishing from the collection of knowledge provided by various academic disciplines. In the current study, the status and development trend of the field of sentiment analysis in social networks is evaluated through a bibliometric analysis of academic publications. In particular, the distributions of publications and citations, the distribution of subject, predominant journals, authors, countries are analyzed. The collaboration degree is applied to measure scientific connections from different aspects. Moreover, the keyword co-occurrence analysis is used to find out the major research topics and their evolutions throughout the time span. The area of sentiment analysis in social networks has gained growing attention in academia, with computer science and engineering as the top main research subjects. China and the USA provide the most to the area development. Authors prefer to collaborate more with those within the same nation. Among the research topics, newly risen topics such as COVID-19, customer satisfaction are discovered.

Keywords: bibliometric analysis, sentiment analysis, social networks, social media

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Authors: Farrah Putri Salmanida, Mei-Li Wu, Rika Wahyuningtyas, Wen-Bin Chung, Hso-Chi Chaung, Ko-Tung Chang

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Within the field of immunotherapy, oncolytic virotherapy (OVT) employs dual approaches that directly eliminate tumor cells while preserving healthy ones and indirectly reprogram the tumor microenvironment (TME) to elicit antitumor responses. Within the TME, tumor associated macrophages (TAMs) manifest characteristics akin to those of anti-inflammatory M2 macrophages, thus earning the designation of M2-like TAMs. In prior research, two antigens denoted as A1 (g6Ld10T) and A3 (ORF6L5), derived from a complete sequence of ORF5 with partial sequence of ORF6 in Porcine Reproductive and Respiratory Syndrome Virus Genotype 2 (PRRSV-2), demonstrated the capacity to repolarize M2-type porcine alveolar macrophages (PAMs) into M1 phenotypes. In this study, we sought for utilizing OVT strategies by introducing A1 or A3 on TAMs to endow them with the anti-tumor traits of M1 macrophages while retaining their capacity to target cancer cells. Upon exposing human THP-1-derived M2 macrophages to a cross-species test with 2 µg/ml of either A1 or A3 for 24 hours, real time PCR revealed that A3, but not A1, treated cells exhibited upregulated gene expressions of M1 markers (CCR7, IL-1ß, CCL2, Cox2, CD80). These cells reacted to virus-derived antigen, as evidenced by increased expression of pattern-recognition receptors TLR3, TLR7, and TLR9, subsequently providing feedback in the form of type I interferon responses like IFNAR1, IFN-ß, IRF3, IRF7, OAS1, Mx1, and ISG15. Through an MTT assay, only after 15 µg/ml of A3 treatment could the cell viability decrease, with a predicted IC50 of 16.96 µg/ml. Interestingly, A3 caused dose-dependent toxicity to a rat C6 glial cancer cell line even at doses as low as 2.5 µg/ml and reached its IC50 at 9.419 µg/ml. Using Annexin V/7AAD staining and PCR test, we deduced that a significant proportion of C6 cells were undergoing the early apoptosis phase predominantly through the intrinsic apoptosis cascade involving Bcl-2 family proteins. Following this stage, we conducted a test on A3’s repolarization ability, which revealed a significant rise in M1 gene expression markers, such as TNF, CD80, and IL-1ß, in M2-like TAMs generated in vitro from murine RAW264.7 macrophages grown with conditioned medium of 4T1 breast cancer cells. This was corroborated by the results of transcriptome analysis, which revealed that the primary subset among the top 10 to top 30 significantly upregulated differentially expressed genes (DEGs) dominantly consisted of M1 macrophages profiles, including Ccl3, Ccl4, Csf3, TNF, Bcl6b, Stc1, and Dusp2. Our findings unveiled the remarkable potential of the PRRSV-derived antigen A3 to repolarize macrophages while also being capable of selectively inducing apoptosis in cancerous cells. While further in vivo study is needed for A3, it holds promise as an adjuvant by its dual effects in cancer therapy modalities.

Keywords: cancer cell apoptosis, interferon responses, macrophage repolarization, recombinant protein

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Authors: Stefano Frassinelli, Alessandro Niccolai, Riccardo E. Zich

Abstract:

Diving is an important Olympic sport. In this sport, the effective performance of the athlete is related to his capability to interact correctly with the springboard. In fact, the elevation of the jump and the correctness of the dive are influenced by the vibrations of the board. In this paper, the vibrations of the springboard will be analyzed by means of typical tools for vibration analysis: Firstly, a modal analysis will be done on two different models of the springboard, then, these two model and another one will be analyzed with a time analysis, done integrating the equations of motion od deformable bodies. All these analyses will be compared with experimental data measured on a real springboard by means of a 6-axis accelerometer; these measurements are aimed to assess the models proposed. The acquired data will be analyzed both in frequency domain and in time domain.

Keywords: springboard analysis, modal analysis, time domain analysis, vibrations

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Authors: M. Tassi, E. Dotsika, P. Karalis, A. Trantalidou, A. Mazarakis Ainian

Abstract:

The Kythnos Island in Greece is of particular archaeological interest, as it has been inhabited from the 12th BC until the 7th AD. From island excavations, numerous faunal and human skeletal remains have been recovered. This work is the first attempt at the paleoenvironmental reconstruction of the island via stable isotope analysis. Specifically, we perform 13C and 18O isotope analysis in faunal bone apatite in order to investigate the climate conditions that prevailed in the area. Additionally, we conduct 13C and 15N isotope analysis in faunal bone collagen, which will constitute the baseline for the subsequent diet reconstruction of the ancient Kythnos population.

Keywords: stable isotopes analysis, bone collagen stable isotope analysis, bone apatite stable isotope analysis, paleodiet, palaeoclimate

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Authors: A. B. Bolkhir, A. Elshafie, T. K. Yousif

Abstract:

This paper highlights the methods of error estimation in finite element analysis (FEA) results. It indicates that the modeling error could be eliminated by performing finite element analysis with successively finer meshes or by extrapolating response predictions from an orderly sequence of relatively low degree of freedom analysis results. In addition, the paper eliminates the round-off error by running the code at a higher precision. The paper provides application in finite element analysis results. It draws a conclusion based on results of application of methods of error estimation.

Keywords: finite element analysis (FEA), discretization error, round-off error, mesh refinement, richardson extrapolation, monotonic convergence

Procedia PDF Downloads 450

Authors: Austyn Snowden

Abstract:

Aim: To examine the construct validity of the Trait Emotional Intelligence Questionnaire Short form. Background: Emotional intelligence involves the identification and regulation of our own emotions and the emotions of others. It is therefore a potentially useful construct in the investigation of recruitment and retention in nursing and many questionnaires have been constructed to measure it. Design: Secondary analysis of existing dataset of responses to TEIQue-SF using concurrent application of Rasch analysis and confirmatory factor analysis. Method: First year undergraduate nursing and computing students completed Trait Emotional Intelligence Questionnaire-Short Form. Responses were analysed by synthesising results of Rasch analysis and confirmatory factor analysis.

Keywords: emotional intelligence, rasch analysis, factor analysis, nurse recruiters

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Authors: Pingping Lin, Xudong Luo

Abstract:

Natural language often conveys emotions of speakers. Therefore, sentiment analysis on what people say is prevalent in the field of natural language process and has great application value in many practical problems. Thus, to help people understand its application value, in this paper, we survey various applications of sentiment analysis, including the ones in online business and offline business as well as other types of its applications. In particular, we give some application examples in intelligent customer service systems in China. Besides, we compare the applications of sentiment analysis on Twitter, Weibo, Taobao and Facebook, and discuss some challenges. Finally, we point out the challenges faced in the applications of sentiment analysis and the work that is worth being studied in the future.

Keywords: application, natural language processing, online comments, sentiment analysis

Procedia PDF Downloads 226

Authors: Pallavi Roe

Abstract:

Violent crime is a significant public safety concern in urban areas across the United States, and Washington, DC, is no exception. This research discusses the prevalence and types of crime, particularly violent crime, in Washington, DC, along with the factors contributing to the high rate of violent crime in the city, including poverty, inequality, access to guns, and racial disparities. The organizations working towards ensuring safety in neighborhoods are also listed. The proposal to perform spatial and temporal analysis on violent crime and the use of guns in crime analysis is presented to identify patterns and trends to inform evidence-based interventions to reduce violent crime and improve public safety in Washington, DC. The stakeholders for crime analysis are also discussed, including law enforcement agencies, prosecutors, judges, policymakers, and the public. The anticipated result of the spatial and temporal analysis is to provide stakeholders with valuable information to make informed decisions about preventing and responding to violent crimes.

Keywords: crime analysis, spatial analysis, temporal analysis, violent crime

Procedia PDF Downloads 268

Authors: Jie Liu, Xudong Luo, Pingping Lin, Yifan Fan

Abstract:

Facebook, Twitter, Weibo, and other social media and significant e-commerce sites generate a massive amount of online texts, which can be used to analyse people’s opinions or sentiments for better decision-making. So, sentiment analysis, especially fine-grained sentiment analysis, is a very active research topic. In this paper, we survey various methods for fine-grained sentiment analysis, including traditional sentiment lexicon-based methods, machine learning-based methods, and deep learning-based methods in aspect/target/attribute-based sentiment analysis tasks. Besides, we discuss their advantages and problems worthy of careful studies in the future.

Keywords: sentiment analysis, fine-grained, machine learning, deep learning

Procedia PDF Downloads 216

Authors: A. B. Robert, Adam Pramadia, Calvin Andika

Abstract:

The main purpose of this study is to explore consumer loyalty characteristic of mobile phone category in Indonesia. Second, this research attempts to identify consumer segment and to explore their profile in each segment as the basis of marketing strategy formulation. This study used some tools of multivariate analysis such as discriminant analysis and cluster analysis. Discriminate analysis used to discriminate consumer loyal and not loyal by using particular variables. Cluster analysis used to reveal various segment in mobile phone category. In addition to having better customer understanding in each segment, this study used descriptive analysis and cross tab analysis in each segment defined by cluster analysis. This study expected several findings. First, consumer can be divided into two large group of loyal versus not loyal by set of variables. Second, this study identifies customer segment in mobile phone category. Third, exploring customer profile in each segment that has been identified. This study answer a call for additional empirical research into different product categories. Therefore, a replication research is advisable. By knowing the customer loyalty characteristic, and deep analysis of their consumption behavior and profile for each segment, this study is very advisable for high impact marketing strategy development. This study contributes body of knowledge by adding empirical study of consumer loyalty, segmentation analysis in mobile phone category by multiple brand analysis.

Keywords: customer loyalty, segmentation, marketing strategy, discriminant analysis, cluster analysis, mobile phone

Procedia PDF Downloads 562