Search results for: event sequence

Authors: Salina Yahya Saddick

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Ovarian cancer remains the most lethal gynecological malignancy due to the lack of highly sensitive and specific screening tools for detection of early-stage disease. The OSE provides the progenitor cells for 90% of human ovarian cancers. Recent morphologic, immunohistochemical and molecular genetic studies have led to the development of a new paradigm for the pathogenesis and origin of epithelial ovarian cancer (EOC) based on a ualistic model of carcinogenesis that divides EOC into two broad categories designated Types I and II which are characterized by specific mutations, including KRAS, BRAF, ERBB2, CTNNB1, PTEN PIK3CA, ARID1A, and PPPR1A, which target specific cell signaling pathways. Type 1 tumors rarely harbor TP53. type I tumors are relatively genetically stable and typically display a variety of somatic sequence mutations that include KRAS, BRAF, PTEN, PIK3CA CTNNB1 (the gene encoding beta catenin), ARID1A and PPP2R1A but very rarely TP53 . The cancer stem cell (CSC) hypothesis postulates that the tumorigenic potential of CSCs is confined to a very small subset of tumor cells and is defined by their ability to self-renew and differentiate leading to the formation of a tumor mass. Potential protein biomarker miRNA, are promising biomarkers as they are remarkably stable to allow isolation and analysis from tissues and from blood in which they can be found as free circulating nucleic acids and in mononuclear cells. Recently, genomic anaylsis have identified biomarkers and potential therapeutic targets for ovarian cancer namely, FGF18 which plays an active role in controlling migration, invasion, and tumorigenicity of ovarian cancer cells through NF-κB activation, which increased the production of oncogenic cytokines and chemokines. This review summarizes update information on epithelial ovarian cancers and point out to the most recent ongoing research.

Keywords: epithelial ovarian cancers, somatic sequence mutations, cancer stem cell (CSC), potential protein, biomarker, genomic analysis, FGF18 biomarker

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Authors: Liang-Chien Lee, Chih-Hsiang Chang, Ying-Shu Tseng

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Comparing with prior studies mainly focused on the effect of a certain event (it may be the initial announcement of bad news or the repeated announcements of identical bad news) on stock price, the aim of this study is to explore how investors react to subsequent bad news with identical content. Empirical results show that as a result of behavioral pitfalls, investors underreact to the initial announcement of the bad news (i.e., unknown bad news) and overreact to the repeated announcements of the identical bad news (i.e., known bad news).

Keywords: subsequent bad news, behavioral finance, Investors’ misreaction, behavioral pitfalls

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Authors: D. P. Houhoula, J. Papaparaskevas, S. Konteles, A. Dargenta, A. Farka, C. Spyrou, M. Ziaka, S. Koussisis, E. Charvalos

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Objectives: Nanotechnology is providing revolutionary opportunities for the rapid and simple diagnosis of many infectious diseases. Staphylococcus aureus, Listeria monocytogenes and Salmonella enteritis are important human pathogens. Diagnostic assays for bacterial culture and identification are time consuming and laborious. There is an urgent need to develop rapid, sensitive, and inexpensive diagnostic tests. In this study, a gold nanoprobe strategy developed and relies on the colorimetric differentiation of specific DNA sequences based approach on differential aggregation profiles in the presence or absence of specific target hybridization. Method: Gold nanoparticles (AuNPs) were purchased from Nanopartz. They were conjugated with thiolated oligonucleotides specific for the femA gene for the identification of members of Staphylococcus aureus, the mecA gene for the differentiation of Staphylococcus aureus and MRSA Staphylococcus aureus, hly gene encoding the pore-forming cytolysin listeriolysin for the identification of Listeria monocytogenes and the invA sequence for the identification of Salmonella enteritis. DNA isolation from Staphylococcus aureus Listeria monocytogenes and Salmonella enteritis cultures was performed using the commercial kit Nucleospin Tissue (Macherey Nagel). Specifically 20μl of DNA was diluted in 10mMPBS (pH5). After the denaturation of 10min, 20μl of AuNPs was added followed by the annealing step at 58oC. The presence of a complementary target prevents aggregation with the addition of acid and the solution remains pink, whereas in the opposite event it turns to purple. The color could be detected visually and it was confirmed with an absorption spectrum. Results: Specifically, 0.123 μg/μl DNA of St. aureus, L.monocytogenes and Salmonella enteritis was serially diluted from 1:10 to 1:100. Blanks containing PBS buffer instead of DNA were used. The application of the proposed method on isolated bacteria produced positive results with all the species of St. aureus and L. monocytogenes and Salmonella enteritis using the femA, mecA, hly and invA genes respectively. The minimum detection limit of the assay was defined at 0.2 ng/μL of DNA. Below of 0.2 ng/μL of bacterial DNA the solution turned purple after addition of HCl, defining the minimum detection limit of the assay. None of the blank samples was positive. The specificity was 100%. The application of the proposed method produced exactly the same results every time (n = 4) the evaluation was repeated (100% repeatability) using the femA, hly and invA genes. Using the gene mecA for the differentiation of Staphylococcus aureus and MRSA Staphylococcus aureus the method had a repeatability 50%. Conclusion: The proposed method could be used as a highly specific and sensitive screening tool for the detection and differentiation of Staphylococcus aureus Listeria monocytogenes and Salmonella enteritis. The use AuNPs for the colorimetric detection of DNA targets represents an inexpensive and easy-to-perform alternative to common molecular assays. The technology described here, may develop into a platform that could accommodate detection of many bacterial species.

Keywords: gold nanoparticles, pathogens, nanotechnology, bacteria

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Authors: M. Amparo Nunez-Andres, Nieves Lantada

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One of the most harmful geological risks is rockfalls. They cause both economic lost, damaged in buildings and infrastructures, and personal ones. Therefore, in order to estimate the risk of the exposed elements, it is necessary to know the mechanism of this kind of events, since the characteristics of the rock walls, to the propagation of fragments generated by the initial detached rock mass. In the framework of the research RockModels project, several inventories of rockfalls were carried out along the northeast of the Spanish peninsula and the Mallorca island. These inventories have general information about the events, although the important fact is that they contained detailed information about fragmentation. Specifically, the IBSD (Insitu Block Size Distribution) is obtained by photogrammetry from drone or TLS (Terrestrial Laser Scanner) and the RBSD (Rock Block Size Distribution) from the volume of the fragment in the deposit measured by hand. In order to share all this information with other scientists, engineers, members of civil protection, and stakeholders, it is necessary a platform accessible from the internet and following interoperable standards. In all the process, open-software have been used: PostGIS 2.1., Geoserver, and OpenLayers library. In the first step, a spatial database was implemented to manage all the information. We have used the data specifications of INSPIRE for natural risks adding specific and detailed data about fragmentation distribution. The next step was to develop a WMS with Geoserver. A previous phase was the creation of several views in PostGIS to show the information at different scales of visualization and with different degrees of detail. In the first view, the sites are identified with a point, and basic information about the rockfall event is facilitated. In the next level of zoom, at medium scale, the convex hull of the rockfall appears with its real shape and the source of the event and fragments are represented by symbols. The queries at this level offer a major detail about the movement. Eventually, the third level shows all elements: deposit, source, and blocks, in their real size, if it is possible, and in their real localization. The last task was the publication of all information in a web mapping site (www.rockdb.upc.edu) with data classified by levels using libraries in JavaScript as OpenLayers.

Keywords: geological risk, web mapping, WMS, rockfalls

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Authors: Yasir Alotaibi

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The aim of this paper is to discuss the syntactic analysis of aspectual or phasal verbs in Modern Standard Arabic (MSA). Aspectual or phasal verbs refer to a class of verbs that require a verbal complement and denote the inception, duration, termination ...etc. of a state or event. This paper will discuss two groups of aspectual verbs in MSA. The first group includes verbs such as ̆gacala, tafiqa, ?akhatha, ?ansha?a, sharaca and bada?a and these verbs are used to denote the inception of an event. The second group includes verbs such as ?awshaka, kaada and karaba and the meaning of these verbs is equivalent to be near/almost . The following examples illustrate the use of the verb bada?a ‘begin’ which is from the first group: a. saalim-un bada?a yuthaakiru. Salem-NOM begin.PFV.3SGM study.IPFV.3SGM ‘Salem began to study’ b.*saalim-un bada?a ?an yuthaakiru. Salem-NOM begin.PFV.3SGM COMP study.IPFV.3SGM ‘Salem began to study’ The example in (1a) is grammatical because the aspectual verb is used with a verbal complement that is not introduced by a complementizer. In contrast, example (1b) is not grammatical because the verbal complement is introduced by the complementizer ?an ‘that’. In contrast, the following examples illustrate the use of the verb kaada ‘be almost’ which is from the second group. However, the two examples are grammatical and this means that the verbal complement of this verb can be without (as in example (2a)) or with ( as in example (2b)) a complementizer. (2) a. saalim-un kaada yuthaakiru. Salem-NOM be.almost.PFV.3SGM study.IPFV.3SGM ‘Salem was almost to study’ b. saalim-un kaada ?an yuthaakiru. Salem-NOM be.almost.PFV.3SGM COMP study.IPFV.3SGM ‘Salem was almost to study’ The salient properties of this class of verbs are that they require a verbal complement, there is no a complementizer that can introduce the complement with the first group while it is possible with the second and the aspectual verb and the embedded verb share and agree with the same subject. To the best of knowledge, aspectual verbs in MSA are discussed in traditional grammar only and have not been studied in modern syntactic theories. This paper will consider the analysis of aspectual verbs in MSA within the Lexical Functional Grammar (LFG) framework. It will use some evidence such as modifier or negation to find out whether these verbs have PRED values and head their f-structures or they form complex predicates with their complements. If aspectual verbs show the properties of heads, then the paper will explore what kind of heads they are. In particular, they should be raising or control verbs. The paper will use some tests such as agreement, selectional restrictions...etc. to find out what kind of verbs they are.

Keywords: aspectual verbs, biclausal, monoclausal, raising

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Authors: Don Anushka Sandaruwan Elvitigala, P. D. S. U. Wickramasinghe, Jehee Lee

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Cystatins are a large superfamily of proteins which act as reversible inhibitors of cysteine proteases. Papain proteases and cysteine cathepsins are predominant substrates of cystatins. Cystatin superfamily can be further clustered into three groups as Stefins, Cystatins, and Kininogens. Among them, stefines are also known as family 1 cystatins which harbors cystatin Bs and cystatin As. In this study, a homologue of family one cystatins more close to cystatin Bs was identified from Korean black rockfish (Sebastes schlegeli) using a prior constructed cDNA (complementary deoxyribonucleic acid) database and designated as RfCyt1. The full-length cDNA of RfCyt1 consisted of 573 bp, with a coding region of 294 bp. It comprised a 5´-untranslated region (UTR) of 55 bp, and 3´-UTR of 263 bp. The coding sequence encodes a polypeptide consisting of 97 amino acids with a predicted molecular weight of 11kDa and theoretical isoelectric point of 6.3. The RfCyt1 shared homology with other teleosts and vertebrate species and consisted conserved features of cystatin family signature including single cystatin-like domain, cysteine protease inhibitory signature of pentapeptide (QXVXG) consensus sequence and N-terminal two conserved neighboring glycine (⁸GG⁹) residues. As expected, phylogenetic reconstruction developed using the neighbor-joining method showed that RfCyt1 is clustered with the cystatin family 1 members, in which more closely with its teleostan orthologues. An SYBR Green qPCR (quantitative polymerase chain reaction) assay was performed to quantify the RfCytB transcripts in different tissues in healthy and immune stimulated fish. RfCyt1 was ubiquitously expressed in all tissue types of healthy animals with gill and spleen being the highest. Temporal expression of RfCyt1 displayed significant up-regulation upon infection with Aeromonas salmonicida. Recombinantly expressed RfCyt1 showed concentration-dependent papain inhibitory activity. Collectively these findings evidence for detectable protease inhibitory and immunity relevant roles of RfCyt1 in Sebastes schlegeli.

Keywords: Sebastes schlegeli, family 1 cystatin, immune stimulation, expressional modulation

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Authors: Norhidayu Muhamad Zain

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Gelatin, a purified protein derived mostly from porcine and bovine sources, is used widely in food manufacturing, pharmaceutical, and cosmetic industries. However, the presence of any porcine-related products are strictly forbidden for Muslim and Jewish consumption. Therefore, analytical methods offering reliable results to differentiate the sources of gelatin are needed. The aim of this study was to differentiate the sources of gelatin (porcine and tilapia fish) using Fourier transform infrared- attenuated total reflection (FTIR-ATR) combined with two dimensional infrared (2DIR) correlation analysis. Porcine gelatin (PG) and tilapia fish gelatin (FG) samples were diluted in distilled water at concentrations ranged from 4-20% (w/v). The samples were then analysed using FTIR-ATR and 2DIR correlation software. The results showed a significant difference in the pattern map of synchronous spectra at the region of 1000 cm⁻¹ to 1100 cm⁻¹ between PG and FG samples. The auto peak at 1080 cm⁻¹ that attributed to C-O functional group was observed at high intensity in PG samples compared to FG samples. Meanwhile, two auto peaks (1080 cm⁻¹ and 1030 cm⁻¹) at lower intensity were identified in FG samples. In addition, using 2D correlation analysis, the original broad water OH bands in 1D IR spectra can be effectively differentiated into six auto peaks located at 3630, 3340, 3230, 3065, 2950 and 2885 cm⁻¹ for PG samples and five auto peaks at 3630, 3330, 3230, 3060 and 2940 cm⁻¹ for FG samples. Based on the rule proposed by Noda, the sequence of the spectral changes in PG samples is as following: NH₃⁺ amino acid > CH₂ and CH₃ aliphatic > OH stretch > carboxylic acid OH stretch > NH in secondary amide > NH in primary amide. In contrast, the sequence was totally in the opposite direction for FG samples and thus both samples provide different 2D correlation spectra ranged from 2800 cm-1 to 3700 cm⁻¹. This method may provide a rapid determination of gelatin source for application in food, pharmaceutical, and cosmetic products.

Keywords: 2 dimensional infrared (2DIR) correlation analysis, Fourier transform infrared- attenuated total reflection (FTIR-ATR), porcine gelatin, tilapia fish gelatin

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Derya Gül Ünlü, Oguz Kuş

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The branding of a country means that the country has its own position different from other countries in its region and thus it is perceived more specifically. It is made possible by the branding efforts of a country and the uniqueness of all the national structures, by presenting it in a specific way, by creating the desired image and attracting tourists and foreign investors. Establishing a national brand involves, in a sense, the process of managing the perceptions of the citizens of the other country about the target country, by structuring the image of the country permanently and holistically. By this means, countries are not easily affected by their crisis of international relations. Therefore, within the scope of the research that will be carried out from this point, it is aimed to show how the warplane downing crisis between Turkey and Russia is perceived on social media. The Russian warplane was downed by Turkey on November 24, 2015, on the grounds that Turkey violated the airspace on the Syrian border. Whereupon the relations between the two countries have been tensed, and Russia has called on its citizens not to go to Turkey and citizens in Turkey to return to their countries. Moreover, relations between two countries have been weakened, for example, tourism tours organized in Russia to Turkey and visa-free travel were canceled and all military dialogue was cut off. After the event, various news sites on social media published plenty of news related to topic and the readers made various comments about the event and Turkey. In this context, an investigation into the perception of Turkey's national brand before and after the warplane downing crisis has been conducted. through comments fetched from the reports on the BBC World, and from Al Jazeera English news sites on Facebook accounts, which takes place widely in the social media. In order to realize study, user comments were fetched from jet downing-related news which are published on Facebook fan-page of BBC World Service, and Al Jazeera English. Regarding this, all the news published between 24.10.2015-24.12.2015 and containing Turk and Turkey keyword in its title composed data set of our study. Afterwards, comments written to these news were analyzed via text mining technique. Furthermore, by sentiment analysis, it was intended to reveal reader’s emotions before and after the crisis.

Keywords: Al Jazeera English, BBC World, country branding, social media, text mining

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Authors: Nurulhikma Md Isa, Intan Elya Suka, Nur Farhana Roslan, Chew Bee Lynn

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The evolutionarily conserved N-end rule pathway marks proteins for degradation by the Ubiquitin Proteosome System (UPS) based on the nature of their N-terminal residue. Proteins with a destabilizing N-terminal residue undergo a series of condition-dependent N-terminal modifications, resulting in their ubiquitination and degradation. Intensive research has been carried out in Arabidopsis previously. The group VII Ethylene Response Factor (ERFs) transcription factors are the first N-end rule pathway substrates found in Arabidopsis and their role in regulating oxygen sensing. ERFs also function as central hubs for the perception of gaseous signals in plants and control different plant developmental including germination, stomatal aperture, hypocotyl elongation and stress responses. However, nothing is known about the role of this pathway during fruit development and ripening aspect. The plant model system Arabidopsis cannot represent fleshy fruit model system therefore tomato is the best model plant to study. PROTEOLYSIS6 (PRT6) is an E3 ubiquitin ligase of the N-end rule pathway. Two homologs of PRT6 sequences have been identified in tomato genome database using the PRT6 protein sequence from model plant Arabidopsis thaliana. Homology search against Ensemble Plant database (tomato) showed Solyc09g010830.2 is the best hit with highest score of 1143, e-value of 0.0 and 61.3% identity compare to the second hit Solyc10g084760.1. Further homology search was done using NCBI Blast database to validate the data. The result showed best gene hit was XP_010325853.1 of uncharacterized protein LOC101255129 (Solanum lycopersicum) with highest score of 1601, e-value 0.0 and 48% identity. Both Solyc09g010830.2 and uncharacterized protein LOC101255129 were genes located at chromosome 9. Further validation was carried out using BLASTP program between these two sequences (Solyc09g010830.2 and uncharacterized protein LOC101255129) to investigate whether they were the same proteins represent PRT6 in tomato. Results showed that both proteins have 100 % identity, indicates that they were the same gene represents PRT6 in tomato. In addition, we used two different RNAi constructs that were driven under 35S and Polygalacturonase (PG) promoters to study the function of PRT6 during tomato developmental stages and ripening processes.

Keywords: ERFs, PRT6, tomato, ubiquitin

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Authors: Pranjali Sharma, Swati Neogi

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Composite pressure vessels are low weight structures mainly used in a variety of applications such as automobiles, aeronautics and chemical engineering. Fiber reinforced polymer (FRP) composite materials offer the simplicity of design and use, high fuel storage capacity, rapid refueling capability, excellent shelf life, minimal infrastructure impact, high safety due to the inherent strength of the pressure vessel, and little to no development risk. Apart from these preliminary merits, the subsidized weight of composite vessels over metallic cylinders act as the biggest asset to the automotive industry, increasing the fuel efficiency. The result is a lightweight, flexible, non-explosive, and non-fragmenting pressure vessel that can be tailor-made to attune with specific applications. The winding pattern of the composite over-wrap is a primary focus while designing a pressure vessel. The critical stresses in the system depend on the thickness, angle and sequence of the composite layers. The composite over-wrap is wound over a plastic liner, whose geometry can be varied for the ease of winding. In the present study, we aim to optimize the FRP vessel geometry that provides an ease in winding and also aids in weight reduction for enhancing the vessel performance. Finite element analysis is used to study the effect of dome geometry, yielding a design with maximum value of burst pressure and least value of vessel weight. The stress and strain analysis of different dome ends along with the cylindrical portion is carried out in ANSYS 19.2. The failure is predicted using different failure theories like Tsai-Wu theory, Tsai-Hill theory and Maximum stress theory. Corresponding to a given winding sequence, the optimum dome geometry is determined for a fixed internal pressure to identify the theoretical value of burst pressure. Finally, this geometry is used to decrease the number of layers to reach the set value of safety in accordance with the available safety standards. This results in decrease in the weight of the composite over-wrap and manufacturing cost of the pressure vessel. An improvement in the overall weight performance of the pressure vessel gives higher fuel efficiency for its use in automobile applications.

Keywords: Compressed Gas Storage, Dome geometry, Theoretical Analysis, Type-4 Composite Pressure Vessel, Improvement in Vessel Weight Performance

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Authors: Sophie Del Fa, Loup Ducol

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This presentation will focus on the discursive practices of Les Soulèvements de la Terre (hereafter SdlT), a French environmentalist group mobilized against agribusiness. More specifically, we will use, as a case study, the violently repressed demonstration that took place in Sainte-Soline on March 25, 2023 (see after for details). The SdlT embodies the renewal of anti-capitalist and environmentalist struggles that began with Occupy Wall Street in 2009 and in France with the Nuit debout in 2016 and the yellow vests movement from 2019 to 2020. These struggles have three things in common: they are self-organized without official leaders, they rely mainly on occupations to reappropriate public places (squares, roundabouts, natural territories) and they are anti-capitalist. The SdlT was created in 2021 by activists coming from the Zone-to-Defend of Notre-Dame-des-Landes, a victorious 10 yearlong occupation movement against an airport near Nantes, France (from 2009 to 2018). The SdlT is not labeled as a formal association, nor as a constituted group, but as an anti-capitalist network of local struggles at the crossroads of ecology and social issues. Indeed, although they target agro-industry, land grabbing, soil artificialization and ecology without transition, the SdlT considers ecological and social questions as interdependent. Moreover, they have an encompassing vision of ecology that they consider as a concern for the living as a whole by erasing the division between Nature and Culture. Their radicality is structured around three main elements: federative and decentralized dimensions, the rhetoric of living alliances and militant creatives strategies. The objective of this reflexion is to understand how these three dimensions are articulated through the SdlT’s discursive practices. To explore these elements, we take as a case study one specific event: the demonstration against the ‘basins’ held in Sainte-Soline on March 25, 2023, on the construction site of new water storage infrastructure for agricultural irrigation in western France. This event represents a turning point for the SdlT. Indeed, the protest was violently repressed: 5000 grenades were fired by the police, hundreds of people were injured, and one person was still in a coma at the time of writing these lines. Moreover, following Saint-Soline’s events, the Minister of Interior Affairs, Gérald Darmin, threatened to dissolve the SdlT, thus adding fuel to the fire in an already tense social climate (with the ongoing strikes against the pensions reform). We anchor our reflexion on three types of data: 1) our own experiences (inspired by ethnography) of the Sainte-Soline demonstration; 2) the collection of more than 500 000 Tweets with the #SainteSoline hashtag and 3) a press review of texts and articles published after Sainte-Soline’s demonstration. The exploration of these data from a turning point in the history of the SdlT will allow us to analyze how the three dimensions highlighted earlier (federative and decentralized dimensions, rhetoric of living alliances and creatives militant strategies) are materialized through the discursive practices surrounding the Sainte-Soline event. This will allow us to shed light on how a new contemporary movement implements contemporary environmental struggles.

Keywords: discursive practices, Sainte-Soline, Ecology, radical ecology

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Authors: Milda Nainyte, Viktoras Masevicius

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Biological methylation is a methyl group transfer from S-adenosyl-L-methionine (AdoMet) onto N-, C-, O- or S-nucleophiles in DNA, RNA, proteins or small biomolecules. The reaction is catalyzed by enzymes called AdoMet-dependent methyltransferases (MTases), which represent more than 3 % of the proteins in the cell. As a general mechanism, the methyl group from AdoMet replaces a hydrogen atom of nucleophilic center producing methylated DNA and S-adenosyl-L-homocysteine (AdoHcy). Recently, DNA methyltransferases have been used for the sequence-specific, covalent labeling of biopolymers. Two types of MTase catalyzed labeling of biopolymers are known, referred as two-step and one-step. During two-step labeling, an alkylating fragment is transferred onto DNA in a sequence-specific manner and then the reporter group, such as biotin, is attached for selective visualization using suitable chemistries of coupling. This approach of labeling is quite difficult and the chemical hitching does not always proceed at 100 %, but in the second step the variety of reporter groups can be selected and that gives the flexibility for this labeling method. In the one-step labeling, AdoMet analog is designed with the reporter group already attached to the functional group. Thus, the one-step labeling method would be more comfortable tool for labeling of biopolymers in order to prevent additional chemical reactions and selection of reaction conditions. Also, time costs would be reduced. However, effective AdoMet analog appropriate for one-step labeling of biopolymers and containing cleavable bond, required for reduction of PCR interferation, is still not known. To expand the practical utility of this important enzymatic reaction, cofactors with activated sulfonium-bound side-chains have been produced and can serve as surrogate cofactors for a variety of wild-type and mutant DNA and RNA MTases enabling covalent attachment of these chains to their target sites in DNA, RNA or proteins (the approach named methyltransferase-directed Transfer of Activated Groups, mTAG). Compounds containing hex-2-yn-1-yl moiety has proved to be efficient alkylating agents for labeling of DNA. Herein we describe synthetic procedures for the preparation of N-biotinoyl-N’-(pent-4-ynoyl)cystamine starting from the coupling of cystamine with pentynoic acid and finally attaching the biotin as a reporter group. The synthesis of the first AdoMet based cofactor containing a cleavable reporter group and appropriate for one-step labeling was developed.

Keywords: adoMet analogs, DNA alkylation, cofactor, methyltransferases

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Authors: Mustapha Kamel Mihoubi, Essadik Kerkar, Abdelhamid Hebbouche

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According to the randomness of most of the factors affecting the stability of a gravity dam, probability theory is generally used to TESTING the risk of failure and there is a confusing logical transition from the state of stability failed state, so the stability failure process is considered as a probable event. The control of risk of product failures is of capital importance for the control from a cross analysis of the gravity of the consequences and effects of the probability of occurrence of identified major accidents and can incur a significant risk to the concrete dam structures. Probabilistic risk analysis models are used to provide a better understanding the reliability and structural failure of the works, including when calculating stability of large structures to a major risk in the event of an accident or breakdown. This work is interested in the study of the probability of failure of concrete dams through the application of the reliability analysis methods including the methods used in engineering. It is in our case of the use of level II methods via the study limit state. Hence, the probability of product failures is estimated by analytical methods of the type FORM (First Order Reliability Method), SORM (Second Order Reliability Method). By way of comparison, a second level III method was used which generates a full analysis of the problem and involving an integration of the probability density function of, random variables are extended to the field of security by using of the method of Mont-Carlo simulations. Taking into account the change in stress following load combinations: normal, exceptional and extreme the acting on the dam, calculation results obtained have provided acceptable failure probability values which largely corroborate the theory, in fact, the probability of failure tends to increase with increasing load intensities thus causing a significant decrease in strength, especially in the presence of combinations of unique and extreme loads. Shear forces then induce a shift threatens the reliability of the structure by intolerable values of the probability of product failures. Especially, in case THE increase of uplift in a hypothetical default of the drainage system.

Keywords: dam, failure, limit state, monte-carlo, reliability, probability, sliding, Taylor

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Authors: H. S. Kang

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Coupled electrical and optical model for conversion of electrical energy into coherent optical energy for transmitter-receiver link by solid state device is presented. Probability distribution for travelling laser beam switching time intervals and the number of switchings in the time interval is obtained. Selector function mapping is employed to regulate optical data transmission speed. It is established that regulated laser transmission from PhotoActive Laser transmitter follows principal of invariance. This considerably simplifies design of PhotoActive Laser Transmission networks.

Keywords: computational mathematics, finite difference Markov chain methods, sequence spaces, singularly perturbed differential equations

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Authors: Sruthi Raveendran

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Developmental dyslexia, characterized by reading difficulties despite normal intelligence, presents a significant challenge for bilingual children navigating languages with varying degrees of orthographic transparency. This study bridges a critical gap in dyslexia interventions for bilingual populations in India by examining how consistency and predictability of letter-sound relationships in a writing system (orthographic transparency) influence the ability to understand and manipulate the building blocks of sound in language (phonological processing). The study employed a computerized visual rhyme-judgment task with concurrent EEG (electroencephalogram) recording. The task compared reaction times, accuracy of performance, and event-related potential (ERP) components (N170, N400, and LPC) for rhyming and non-rhyming stimuli in two orthographies: English (opaque orthography) and Kannada (transparent orthography). As hypothesized, the results revealed advantages in phonological processing tasks for transparent orthography (Kannada). Children with dyslexia were faster and more accurate when judging rhymes in Kannada compared to English. This suggests that a language with consistent letter-sound relationships (transparent orthography) facilitates processing, especially for tasks that involve manipulating sounds within words (rhyming). Furthermore, brain activity measured by event-related potentials (ERP) showed less effort required for processing words in Kannada, as reflected by smaller N170, N400, and LPC amplitudes. These findings highlight the crucial role of orthographic transparency in optimizing reading performance for bilingual children with dyslexia. These findings emphasize the need for language-specific intervention strategies that consider the unique linguistic characteristics of each language. While acknowledging the complexity of factors influencing dyslexia, this research contributes valuable insights into the impact of orthographic transparency on phonological awareness in bilingual children. This knowledge paves the way for developing tailored interventions that promote linguistic inclusivity and optimize literacy outcomes for children with dyslexia.

Keywords: developmental dyslexia, phonological awareness, rhyme judgment, orthographic transparency, Kannada, English, N170, N400, LPC

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Authors: Tomokazu Nagata, Jawid Ahmad Baktash

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The goal of this paper is to explore the use of formal methods for Electronic Identity Card System. Nowadays, one of the core research directions in a constantly growing distributed environment is the improvement of the communication process. The responsibility for proper verification becomes crucial. Formal methods can play an essential role in the development and testing of systems. The thesis presents two different methodologies for assessing correctness. Our first approach employs abstract interpretation techniques for creating a trace based model for Electronic Identity Card System. The model was used for building a semi decidable procedure for verifying the system model. We also developed the code for the eID System and can cover three parts login to system sending of Acknowledgment from user side, receiving of all information from server side and log out from system. The new concepts of impasse and spawned sessions that we introduced led our research to original statements about the intruder’s knowledge and eID system coding with respect to secrecy. Furthermore, we demonstrated that there is a bound on the number of sessions needed for the analysis of System.Electronic identity (eID) cards promise to supply a universal, nation-wide mechanism for user authentication. Most European countries have started to deploy eID for government and private sector applications. Are government-issued electronic ID cards the proper way to authenticate users of online services? We use the eID project as a showcase to discuss eID from an application perspective. The new eID card has interesting design features, it is contact-less, it aims to protect people’s privacy to the extent possible, and it supports cryptographically strong mutual authentication between users and services. Privacy features include support for pseudonymous authentication and per service controlled access to individual data items. The article discusses key concepts, the eID infrastructure, observed and expected problems, and open questions. The core technology seems ready for prime time and government projects deploy it to the masses. But application issues may hamper eID adoption for online applications.

Keywords: eID, event-B, Pro-B, formal method, message passing

Procedia PDF Downloads 237

Authors: Beatriz Martinez-Pastor, Maria Nogal, Alan O'Connor

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During the last years, the number of extreme weather events has increased. A variety of extreme weather events, including river floods, rain-induced landslides, droughts, winter storms, wildfire, and hurricanes, have threatened and damaged many different regions worldwide. These events have a devastating impact on critical infrastructure systems resulting in high social, economical and environmental costs. These events have a huge impact in transport systems. Since, transport networks are completely exposed to every kind of climatological perturbations, and its performance is closely related with these events. When a traffic network is affected by a climatological hazard, the quality of its service is threatened, and the level of the traffic conditions usually decreases. With the aim of understanding this process, the concept of resilience has become most popular in the area of transport. Transport resilience analyses the behavior of a traffic network when a perturbation takes place. This holistic concept studies the complete process, from the beginning of the perturbation until the total recovery of the system, when the perturbation has finished. Many concepts are included in the definition of resilience, such as vulnerability, redundancy, adaptability, and safety. Once the resilience of a transport network can be evaluated, in this case, the methodology used is a dynamic equilibrium-restricted assignment model that allows the quantification of the concept, the next step is its improvement. Through the improvement of this concept, it will be possible to create transport networks that are able to withstand and have a better performance under the presence of climatological hazards. Analyzing the impact of a perturbation in a traffic network, it is observed that the response of the different links, which are part of the network, can be completely different from one to another. Consequently and due to this effect, many questions arise, as what makes a link more critical before an extreme weather event? or how is it possible to identify these critical links? With this aim, and knowing that most of the times the owners or managers of the transport systems have limited resources, the identification of the critical links of a transport network before extreme weather events, becomes a crucial objective. For that reason, using the available resources in the areas that will generate a higher improvement of the resilience, will contribute to the global development of the network. Therefore, this paper wants to analyze what kind of characteristic makes a link a critical one when an extreme weather event damages a transport network and finally identify them.

Keywords: critical links, extreme weather events, hazard, resilience, transport network

Procedia PDF Downloads 287

Authors: Zinaida Shelkovnikova

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The language in science is changing and meets the demands of the society. We shall argue that in the varied modern world there are important reasons for the integration of narratives into scientific discourse. As far as nowadays scientists are faced with extremely prompt science development and progress; modern scientific society lives in the conditions of tough competition. The integration of narratives into scientific discourse is thus a good way to prompt scientific experience to different audiences and to express covert prestige of the discourse. Narratives also form the identity of the persuasive narrator. Using the narrative approach to the scientific discourse analysis we reveal the sociocultural diversity of the scientists. If you want to attract audience’s attention to your scientific research, narratives should be integrated into your scientific discourse. Those who understand this consistent pattern are considered the leading scientists. Taking into account that it is prestigious to be renowned, celebrated in science, it is a covert prestige to write narratives in science. We define a science narrative as the intentional, consequent, coherent, event discourse or a discourse fragment, which contains the author creativity, in some cases intrigue, and gives mostly qualitative information (compared with quantitative data) in order to provide maximum understanding of the research. Science narratives also allow the effective argumentation and consequently construct the identity of the persuasive narrator. However, skills of creating appropriate scientific discourse reflect the level of prestige. In order to teach postgraduate students to be successful in English scientific writing and to be prestigious in the scientific society, we have defined the science narrative and outlined its main features and characteristics. Narratives contribute to audience’s involvement with the narrator and his/her narration. In general, the way in which a narrative is performed may result in (limited or greater) contact with the audience. To gain these aim authors use emotional fictional elements; descriptive elements: adjectives; adverbs; comparisons and so on; author’s evaluative elements. Thus, the features of science narrativity are the following: descriptive tools; authors evaluation; qualitative information exceeds the quantitative data; facts take the event status; understandability; accessibility; creativity; logics; intrigue; esthetic nature; fiction. To conclude, narratives function covert prestige of the scientific discourse and shape the identity of the persuasive scientist.

Keywords: covert prestige, narrativity, scientific discourse, scientific narrative

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Authors: Mirabbos Mirkamalov, Zavkiddin Mirtoshev

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The M 1.6 class flare occurred on 6^th of September 2012. Our observations correspond to the active region NOAA 11560 with the heliographic coordinates N04W71. The event took place between 04:00 UT and 04:45 UT, and was close to the solar limb at the western region. The flare temperature correlates with flux peak, increases for a short period (between 04:08 UT and 04:12 UT), rises impulsively, attains a maximum value of about 17 MK at 04:12 UT and gradually decreases after peak value. Around the peak we observe significant emissions of X-ray sources. Flux profiles of the X-ray emission exhibit a progressively faster raise and decline as the higher energy channels are considered.

Keywords: magnetic reconnection, solar atmosphere, solar flare, X-ray emission

Procedia PDF Downloads 326

Authors: Hemant Kumar, Nilendu Das

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A study based on ANN structure gives us the information to predict the size of the future in realizing a past event. ANN, IMD (Indian meteorological department) data and remote sensing were used to enable a number of parameters for calculating the size that may occur in the future. A threshold selected specifically above the high-frequency harvest reached the area during the selected seismic activity. In the field of human and local biodiversity it remains to obtain the right parameter compared to the frequency of impact. But during the study the assumption is that predicting seismic activity is a difficult process, not because of the parameters involved here, which can be analyzed and funded in research activity.

Keywords: ANN, Bayesion class, earthquakes, IMD

Procedia PDF Downloads 126

Authors: Misbah Irshad, Faiza Sarfraz

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The problem of approximating surface to surface intersection is considered to be very important in computer aided geometric design and computer aided manufacturing. Although it is a complex problem to handle, its continuous need in the industry makes it an active topic in research. A technique for approximating intersection curves of two parametric surfaces is proposed, which extracts boundary points and turning points from a sequence of intersection points and interpolate them with the help of rational cubic spline functions. The proposed approach is demonstrated with the help of examples and analyzed by calculating error.

Keywords: approximation, parametric surface, spline function, surface intersection

Procedia PDF Downloads 270

Authors: Muhammad Haris, Syed Kamran Ali, Mubeen Islam, Tariq Mehmood, Faisal Shah

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Jacobabad Khairpur High, part of a Sukkur rift zone, is the separating boundary between Central and Southern Indus Basin, formed as a result of Post-Jurassic uplift after the deposition of Middle Jurassic Chiltan Formation. Habib Rahi Formation of Middle to Late Eocene outcrops in the vicinity of Jacobabad Khairpur High, a section at Rohri near Sukkur is measured in detail for lithofacies, microfacies, diagenetic analysis and sequence stratigraphy. Habib Rahi Formation is richly fossiliferous and consists of mostly limestone with subordinate clays and marl. The total thickness of the formation in this section is 28.8m. The bottom of the formation is not exposed, while the upper contact with the Sirki Shale of the Middle Eocene age is unconformable in some places. A section is measured using Jacob’s Staff method, and traverses were made perpendicular to the strike. Four different lithofacies were identified based on outcrop geology which includes coarse-grained limestone facies (HR-1 to HR-5), massive bedded limestone facies (HR-6 HR-7), and micritic limestone facies (HR-8 to HR-13) and algal dolomitic limestone facie (HR-14). Total 14 rock samples were collected from outcrop for detailed petrographic studies, and thin sections of respective samples were prepared and analyzed under the microscope. On the basis of Dunham’s (1962) classification systems after studying textures, grain size, and fossil content and using Folk’s (1959) classification system after reviewing Allochems type, four microfacies were identified. These microfacies include HR-MF 1: Benthonic Foraminiferal Wackstone/Biomicrite Microfacies, HR-MF 2: Foramineral Nummulites Wackstone-Packstone/Biomicrite Microfacies HR-MF 3: Benthonic Foraminiferal Packstone/Biomicrite Microfacies, HR-MF 4: Bioclasts Carbonate Mudstone/Micrite Microfacies. The abundance of larger benthic Foraminifera’s (LBF), including Assilina sp., A. spiral abrade, A. granulosa, A. dandotica, A. laminosa, Nummulite sp., N. fabiani, N. stratus, N. globulus, Textularia, Bioclasts, and Red algae indicates shallow marine (Tidal Flat) environment of deposition. Based on variations in rock types, grain size, and marina fauna Habib Rahi Formation shows progradational stacking patterns, which indicates coarsening upward cycles. The second order of sea-level rise is identified (spanning from Y-Persian to Bartonian age) that represents the Transgressive System Tract (TST) and a third-order Regressive System Tract (RST) (spanning from Bartonian to Priabonian age). Diagenetic processes include fossils replacement by mud, dolomitization, pressure dissolution associated stylolites features and filling with dark organic matter. The presence of the microfossils includes Nummulite. striatus, N. fabiani, and Assilina. dandotica, signify Bartonian to Priabonian age of Habib Rahi Formation.

Keywords: Jacobabad Khairpur High, Habib Rahi Formation, lithofacies, microfacies, sequence stratigraphy, diagenetic history

Procedia PDF Downloads 473

Authors: I. Tzoka, V. A. Chirayath, A. Brandt, J. Asaadi, Melvin J. Aviles, Stephen Clarke, Stefan Cwik, Michael R. Foley, Cole J. Hamel, Alexey Lyashenko, Michael J. Minot, Mark A. Popecki, Michael E. Stochaj, S. Shin

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Micro-channel plate photo-multiplier tubes (MCP-PMTs) have become ubiquitous and are widely considered potential candidates for next generation High Energy Physics experiments due to their picosecond timing resolution, ability to operate in strong magnetic fields, and low noise rates. A key factor that determines the applicability of MCP-PMTs in their lifetime, especially when they are used in high event rate experiments. We have developed a novel method for the investigation of the aging behavior of an MCP-PMT on an accelerated basis. The method involves exposing a localized region of the MCP-PMT to photons at a high repetition rate. This pixel-based method was inspired by earlier results showing that damage to the photocathode of the MCP-PMT occurs primarily at the site of light exposure and that the surrounding region undergoes minimal damage. One advantage of the pixel-based method is that it allows the dynamics of photo-cathode damage to be studied at multiple locations within the same MCP-PMT under different operating conditions. In this work, we use the pixel-based accelerated lifetime test to investigate the aging behavior of a 20 cm x 20 cm Large Area Picosecond Photo Detector (LAPPD) manufactured by INCOM Inc. at multiple locations within the same device under different operating conditions. We compare the aging behavior of the MCP-PMT obtained from the first lifetime test conducted under high gain conditions to the lifetime obtained at a different gain. Through this work, we aim to correlate the lifetime of the MCP-PMT and the rate of ion feedback, which is a function of the gain of each MCP, and which can also vary from point to point across a large area (400 $cm^2$) MCP. The tests were made possible by the uniqueness of the LAPPD design, which allows independent control of the gain of the chevron stacked MCPs. We will further discuss the implications of our results for optimizing the operating conditions of the detector when used in high event rate experiments.

Keywords: electron multipliers (vacuum), LAPPD, lifetime, micro-channel plate photo-multipliers tubes, photoemission, time-of-flight

Procedia PDF Downloads 180

Authors: Kiwon Yeom

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Change points are abrupt variations in a data sequence. Detection of change points is useful in modeling, analyzing, and predicting time series in application areas such as robotics and teleoperation. In this paper, a change point is defined to be a discontinuity in one of its derivatives. This paper presents a reliable method for detecting discontinuities within a three-dimensional trajectory data. The problem of determining one or more discontinuities is considered in regular and irregular trajectory data from teleoperation. We examine the geometric detection algorithm and illustrate the use of the method on real data examples.

Keywords: change point, discontinuity, teleoperation, abrupt variation

Procedia PDF Downloads 168

Authors: J. Trarbach, S. Schosser, B. Vogt

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Decision-makers tend to prefer the first alternative over subsequent alternatives which is called the primacy effect. To reliably measure this effect, we conducted an experiment with real consequences for preference statements. Therefore, we elicit preferences of subjects using a rating scale, i.e. hypothetical preferences, and willingness to pay, i.e. real preferences, for two sequences of pain. Within these sequences, both overall intensity and duration of pain are identical. Hence, a rational decision-maker should be indifferent, whereas the primacy effect predicts a stronger preference for the first sequence. What we see is a primacy effect only for hypothetical preferences. This effect vanishes for real preferences.

Keywords: decision making, primacy effect, real incentives, willingness to pay

Procedia PDF Downloads 295

Authors: F. Fekak, A. Gravouil, M. Brun, B. Depale

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During an earthquake, a bridge crane may be subjected to multiple impacts between crane wheels and rail. In order to model such phenomena, a time-history dynamic analysis with a multi-scale approach is performed. The high frequency aspect of the impacts between wheels and rails is taken into account by a Lagrange explicit event-capturing algorithm based on a velocity-impulse formulation to resolve contacts and impacts. An implicit temporal scheme is used for the rest of the structure. The numerical coupling between the implicit and the explicit schemes is achieved with a heterogeneous asynchronous time-integrator.

Keywords: bridge crane, earthquake, dynamic analysis, explicit, implicit, impact

Procedia PDF Downloads 304

Authors: Elizabeth F. Rodrigues, Julia da R. Mattos, Naira Q. Leitão, Roberta T. da Cunha

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The business strategy of many companies has two factors in common: the search for the competitive edge and its long term maintenance. The thing that differentiates the companies’ performance in their abilities to set the right strategy, which depends on their capacity to analyze and apply all sort of management support tools. In this context, the sponsorship of events stands out as an important way to increase brand awareness, especially when it is a worldwide event, such as Rio 2016 Olympic and Paralympic Games. This paper will present the case of a car maker company, which chose to invest on sponsorship as a way to reach its goals and grow in the brazilian market.

Keywords: strategy, sponsorship, events, management

Procedia PDF Downloads 500

Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

Procedia PDF Downloads 126

Authors: Hernández Eva Selene, Reyna Mary Carmen, Rivera Héctor, Barragán Irving

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We propose an approach that jointly addresses the layout of a facility and the scheduling of a sequence of jobs. In real production, these two problems are interrelated. However, they are treated separately in the literature. Our approach is an extension of the job shop problem with transportation delay, where the location of the machines is selected among possible sites. The model minimizes the makespan, using the short processing times rule with two algorithms; the first one considers all the permutations for the location of machines, and the second only a heuristic to select some specific permutations that reduces computational time. Some instances are proved and compared with literature.

Keywords: layout problem, job shop scheduling problem, concurrent scheduling and layout problem, metaheuristic

Procedia PDF Downloads 610