Search results for: hydrophobic interactions
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 2391

Search results for: hydrophobic interactions

831 Analysis of Extracellular Vesicles Interactomes of two Isoforms of Tau Protein via SHSY-5Y Cell Lines

Authors: Mohammad Aladwan

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Alzheimer’s disease (AD) is a widespread dementing illness with a complex and poorly understood etiology. An important role in improving our understanding of the AD process is the modeling of disease-associated changes in tau protein phosphorylation, a protein known to mediate events essential to the onset and progression of AD. A main feature of AD is the abnormal phosphorylation of tau protein and the presence of neurofibrillary tangles. In order to evaluate the respective roles of the microtubule-binding region (MTBR) and alternatively spliced exons in the N-terminal projection domains in AD, we have constructed SHSY-5Y cell lines that stably overexpress four different species of tau protein (4R2N, 4R0N, N(E-2), N(E+2)). Since the toxicity and spreading of tau lesions in AD depends on the interactions of tau with other proteins, we have performed a proteomic analysis of exosome-fraction interactomes for cell lysates and media samples that were isolated from SHSY-5Y cell lines. Functional analysis of tau interactomes based on gene ontology (GO) terms was performed using the String 10.5 database program. The highest number of exosomes proteomes and tau associated proteins were found with 4R2N isoform (2771 and 159) in cell lysate and they have a high strength of connectivity (78%) between proteins, while N(E-2) isoform in the media proteomes has the highest number of proteins and tau associated protein (1829 and 205). Moreover, known AD markers were significantly enriched in secreted interactomes relative to lysate interactomes in the SHSY-5Y cells of tau isoforms lacking exons 2 and 3 in the N-terminal. The lack of exon 2 (E-2) from tau protein can be mediated by tau secretion and spreading to different cells. Enriched functions in the secreted E-2 interactome include signaling and developmental pathways that have been linked to a) tau misprocessing and lesion development and b) tau secretion and which, therefore, could play novel roles in AD pathogenesis.

Keywords: Alzheimer's disease, dementia, tau protein, neurodegenration disease

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830 Intraspecific Response of the Ciliate Tetrahymena thermophila to Copper and Thermal Stress

Authors: Doufoungognon Carine Kone

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Heavy metals present in large quantities in ecosystems can alter biological and cellular functions and disrupt trophic functions. However, their toxicity can change according to thermal conditions, as toxicity depends on their bioavailability and thermal optimum of organisms. Organisms can develop different tolerance strategies to maintain themselves in a stressful environment, but these strategies are often studied in a single-stressor context. This study evaluates the responses of the ciliate Tetrahymena thermophila to copper, high temperature, and their interaction. Six genotypes were exposed to a gradient of copper concentrations ranging from 0 to 350mg/L in synthetic media at three temperatures: 15°C, 23°C, and 31°C. Cell density, cell shape and size (and their variance), swimming speed and trajectory, and copper uptake rate were measured. Depending on the genotype, swimming speed, trajectory, and cell size were highly affected by stress gradients. One gets bigger, while two genotypes get smaller and the other remain unchanged. Some genotypes swam less rapidly, while others speed up as copper and temperature increased. Concerning copper uptake, the two genotypes accumulating the best and the worst, whatever the copper concentration or temperature, were also those that had the highest densities. Finally, very few temperature x copper interactions were observed on phenotypic parameters. The diversity of phenotypic responses revealed in this study reflects the existence of divergent strategies adopted by Tetrahymena thermophila to resist to copper and thermal stress, which suggests an important role of intraspecific variability in biodiversity response to environmental stress. One general and the surprising pattern was a global absence of interactive effects between copper and high temperature exposure on the observed phenotypic responses.

Keywords: ciliate, copper, intraspecific variability, phenotype, temperature, tolerance, multiple stressors

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829 Selective Adsorption of Anionic Textile Dyes with Sustainable Composite Materials Based on Physically Activated Carbon and Basic Polyelectrolytes

Authors: Mari Carmen Reyes Angeles, Dalia Michel Reyes Villeda, Ana María Herrera González

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This work reports the design and synthesis of two composite materials based on physically activated carbon and basic polyelectrolytes useful in the adsorption of textile dyes present in aqueous solutions and wastewater. The synthesis of basic polyelectrolytes poly(2-vinylpyridine) (P2VP) and poly(4-vinylpyridine) (P4VP) was made by means of free radical polymerization. The carbon made from prickly pear peel (CarTunaF) was thermally activated in the presence of combustion gases. Composite materials CarTunaF2VP and CarTunaF4VP were obtained from CarTunaF and polybasic polyelectrolytes P2VP and P4VP with a ratio of 67:33 wt. The structure of each polyelectrolyte, P2VP, and P4VP, was elucidated by means of the FTIR and 1H NMR spectrophotometric techniques. Their thermal stability was evaluated using TGA. The characterization of CarTunaF and composite materials CarTunaF2VP and CarTunaF4VP was made by means of FTIR, TGA, SEM, and N2 adsorption. The adsorptive capacities of the polyelectrolytes and the composite materials were evaluated by adsorption of direct dyes present in aqueous solutions. The polyelectrolytes removed between 90 and 100% of the dyes, and the composite materials removed between 68 and 93% of the dyes. Using the four adsorbents P2VP, P4VP, CarTuna2VP, and CarTuna4VP, it was observed that the dyes studied, Direct Blue 80, Direct Turquoise 86, and Direct Orange 26, were adsorbed in the range between 46.1 and 188.7mg∙g-1 by means of electrostatic interactions between the anionic groups in the dyes with the cationic groups in the adsorbents. By using adsorbent materials in the treatment of wastewater from the textile industry, an improvement in the quality of the water was observed by decreasing its pH, COD, conductivity, and color considerably

Keywords: adsorption, anionic dyes, composite, polyelectrolytes

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828 Association of Brain-Derived Neurotrophic Factor (BDNF) Gene with Obesity and Metabolic Traits in Malaysian Adults

Authors: Yamunah Devi Apalasamy, Sanjay Rampal, Tin Tin Su, Foong Ming Moy, Hazreen Abdul Majid, Awang Bulgiba, Zahurin Mohamed

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Obesity is a growing global health issue. Obesity results from a combination of environmental and genetics factors. Brain-derived neurotrophic factor (BDNF), a gene encodes the BDNF protein and the BDNF gene have been linked to regulation of body weight and appetite. Genome-wide association studies have identified the BDNF variants to be related to obesity among Caucasians, East Asians, and Filipinos. However, the role of BDNF in other ethnic groups remains inconclusive. This case control study aims to investigate the associations of BDNF gene polymorphisms with obesity and metabolic parameters in Malaysian Malays. BDNF rs4074134, BDNF rs10501087 and BDNF rs6265 were genotyped using Sequenom MassARRAY. Anthropometric, body fat, fasting lipids and glucose levels were measured. A total of 663 subjects (194 obese and 469 non-obese) were included in this study. There were no significant associations association between BDNF SNPs and obesity. The allelic and genotype frequencies of the BDNF SNPs were similar in the obese and non-obese groups. After adjustment for age and sex, the BDNF variants were not associated with obesity, body fat, fasting lipids and glucose levels. Haplotypes at the BDNF gene region, were not significantly associated with obesity. The BDNF rs4074134 was in strong LD with BDNF rs10501087 (D'=0.98) and BDNF rs6265 (D'=0.87). The BDNF rs10501087 was also in strong LD with BDNF rs6265 (D'=0.91). Our findings suggest that the BDNF variants and the haplotypes of BDNF gene were not associated with obesity and metabolic traits in this study population. Further research is needed to explore other BDNF variants with a larger sample size with gene-environment interactions in multi ethnic Malaysian population.

Keywords: genomics of obesity, SNP, BMI, haplotypes

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827 Trait Anxiety, Cognitive Flexibility, Self-Efficacy and Emotion Regulation: A Moderation Model

Authors: Amina Ottozbeer, Nazanin Derakhshan

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Emotion regulation, a transdiagnostic process, is often impaired in individuals with high trait anxiety due to compromised executive functioning and attentional control. Recent research underscores the importance of studying individual differences and contextual factors in understanding the adaptability of emotion regulation processes, particularly in those with high trait anxiety. Prior studies have emphasized the role of self-efficacy in promoting positive cognitive flexibility outcomes and mitigating executive function impairments in highly anxious individuals. Accordingly, the objective of this study was to examine the moderating influence of attentional control, cognitive flexibility, and self-efficacy on the relationship between trait anxiety and emotion regulation. Using a correlational design, an online study was conducted with a sample of 82 participants (mean age: 22 years). Self-report questionnaires measured individual difference variables. The Classic Stroop Task assessed attentional control as an objective measure of cognitive flexibility . The findings revealed three significant interactions. Firstly, high cognitive flexibility and self-efficacy were linked to reduced expressive suppression in individuals with low trait anxiety. Secondly, elevations in cognitive flexibility and self-efficacy were associated with increased suppression in those with high trait anxiety. Thirdly, high trait anxiety was associated with reduced attentional control. The results suggest that typically adaptive processes can yield different outcomes in highly anxious populations, highlighting the need to explore additional variables that could alter the impact of cognitive flexibility and self-efficacy on emotion regulation in individuals with high anxiety. These findings have significant clinical implications, emphasizing the need to consider individual differences in emotion regulation and trait anxiety to inform more effective psychological treatments.

Keywords: attentional control, trait anxiety, emotional dysregulation, transdiagnostic, individual differences

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826 Unlocking the Future of Grocery Shopping: Graph Neural Network-Based Cold Start Item Recommendations with Reverse Next Item Period Recommendation (RNPR)

Authors: Tesfaye Fenta Boka, Niu Zhendong

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Recommender systems play a crucial role in connecting individuals with the items they require, as is particularly evident in the rapid growth of online grocery shopping platforms. These systems predominantly rely on user-centered recommendations, where items are suggested based on individual preferences, garnering considerable attention and adoption. However, our focus lies on the item-centered recommendation task within the grocery shopping context. In the reverse next item period recommendation (RNPR) task, we are presented with a specific item and challenged to identify potential users who are likely to consume it in the upcoming period. Despite the ever-expanding inventory of products on online grocery platforms, the cold start item problem persists, posing a substantial hurdle in delivering personalized and accurate recommendations for new or niche grocery items. To address this challenge, we propose a Graph Neural Network (GNN)-based approach. By capitalizing on the inherent relationships among grocery items and leveraging users' historical interactions, our model aims to provide reliable and context-aware recommendations for cold-start items. This integration of GNN technology holds the promise of enhancing recommendation accuracy and catering to users' individual preferences. This research contributes to the advancement of personalized recommendations in the online grocery shopping domain. By harnessing the potential of GNNs and exploring item-centered recommendation strategies, we aim to improve the overall shopping experience and satisfaction of users on these platforms.

Keywords: recommender systems, cold start item recommendations, online grocery shopping platforms, graph neural networks

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825 Development and Characterization of Cobalt Metal Loaded ZSM-5 and H-ZSM-5 Catalyst for Fischer -Tropsch Synthesis

Authors: Shashank Bahri, Divyanshu Arya, Rajni Jain, Sreedevi Upadhyayula

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Petroleum products can be obtained from syngas catalytic conversion using Fischer Tropsch Reaction. The liquid fuels obtained from FTS are sulphur and nitrogen free and thus may easily meet the increasing stringent environment regulations. In the present work we have synthesized Meso porous ZSM-5 supported catalyst. Meso structure were created in H-ZSM-5 crystallites by demetalation via subsequent base and acid treatment. Desilication through base treatment provides H-ZSM-5 with pore size and volumes similar to amorphous SiO2 (Conventional Carrier). Modifying the zeolite texture and surface chemistry by Desilication and acid washing alters its accessibility and interactions with metal phase and consequently the CO adsorption behavior and hydrocarbon product distribution. Increasing the mesoporosity via desilication provides the micro porous zeolite with essential surface area to support optimally sized metal crystallites. This improves the metal dispersion and hence improve the activity of the catalyst. Transition metal (Co) was loaded using wet impregnation method. Synthesized catalysts were characterized by Infrared Spectroscopy, Powdered X-Ray Diffraction, Scanning Electron Microscopy (SEM), BET Method analytical techniques. Acidity of the catalyst which plays an important role in FTS reaction was measured by DRIFT setup pyridine adsorption instead of NH3 Temperature Programmed Desorption. The major difference is that, Pyridine Adsorption can distinguish between Lewis acidity and Bronsted Acidity, thus giving their relative strengths in the catalyst sample, whereas TPD gives total acidity including Lewis and Bronsted ones.

Keywords: mesopourus, fischer tropsch reaction, pyridine adsorrption, drift study

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824 Kenaf MDF Panels with Soy Based Adhesive. The Influence of Preparation Parameters on Physciomechanical Properties

Authors: Imtiaz Ali, Krishnan Jayaraman, Debes Bhattacharyya

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Soybean concentrate is abundant material and renewable product that is recently been explored as an alternative to conventional formaldehyde based resins in wood based products. The main goal of this study is to evaluate the technical feasibility of manufacturing environment friendly MDF panels from renewable resources. The panels are made by using kenaf bast fibers (KB) as wood substitute and soy based adhesive as bonding material. Second order response surface regression models are used to understand the effects and interactions of resin content (RC) and pressing time (PT) on the mechanical and water soaking properties of kenaf panels. The mechanical and water soaking properties are significantly improved as the RC increased and reached at the highest level at maximum resin loading (12%). The effect of pressing time is significant in the first phase when the pressing time increased from 4 to 6 min; however the effect was not as significant when pressing time further increased to 8 min. The second order regression equations further confirm that the variation in process parameters has strong relationship with the physciomechanical properties. The MDF panels the minimum requirements of internal bond strength, modulus of rupture and modulus of elasticity as recommended by US wood MDF standard specifications for G110, G120, G130 and G140 grade MDF panels. However, the thickness swelling results are considerably poorer than the recommended values of general purpose standard requirements. This deficiency can be counterbalanced by the advantage of being formaldehyde free panels made from renewable sources and by making them suitable alternative for less humid environment applications.

Keywords: kenaf, Medium density fibreboard, soy adhesive, mechanical properties, water soaking properties

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823 Isolation and Characterisation of Novel Environmental Bacteriophages Which Target the Escherichia coli Lamb Outer Membrane Protein

Authors: Ziyue Zeng

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Bacteriophages are viruses which infect bacteria specifically. Over the past decades, phage λ has been extensively studied, especially its interaction with the Escherichia coli LamB (EcLamB) protein receptor. Nonetheless, despite the enormous numbers and near-ubiquity of environmental phages, aside from phage λ, there is a paucity of information on other phages which target EcLamB as a receptor. In this study, to answer the question of whether there are other EcLamB-targeting phages in the natural environment, a simple and convenient method was developed and used for isolating environmental phages which target a particular surface structure of a particular bacterium; in this case, the EcLamB outer membrane protein. From the enrichments with the engineered bacterial hosts, a collection of EcLamB-targeting phages (ΦZZ phages) were easily isolated. Intriguingly, unlike phage λ, an obligate EcLamB-dependent phage in the Siphoviridae family, the newly isolated ΦZZ phages alternatively recognised EcLamB or E. coli OmpC (EcOmpC) as a receptor when infecting E. coli. Furthermore, ΦZZ phages were suggested to represent new species in the Tequatrovirus genus in the Myoviridae family, based on phage morphology and genomic sequences. Most phages are thought to have a narrow host range due to their exquisite specificity in receptor recognition. With the ability to optionally recognise two receptors, ΦZZ phages were considered relatively promiscuous. Via the heterologous expression of EcLamB on the bacterial cell surface, the host range of ΦZZ phages was further extended to three different enterobacterial genera. Besides, an interesting selection of evolved phage mutants with a broader host range was isolated, and the key mutations involved in their evolution to adapt to new hosts were investigated by genomic analysis. Finally, and importantly, two ΦZZ phages were found to be putative generalised transducers, which could be exploited as tools for DNA manipulations.

Keywords: environmental microbiology, phage, microbe-host interactions, microbial ecology

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822 Online Language Tandem: Focusing on Intercultural Communication Competence and Non-Verbal Cues

Authors: Amira Benabdelkader

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Communication presents the channel by which humankind create and maintain their relationship with others, express themselves, exchange information, learn and teach etc. The context of communication plays a distinctive role in deciding about the language to be used. The term context is mainly used to refer to the interlocutors, their cultures, languages, relationship, physical surrounding that is the communication setting, type of the information to be transmitted, the topic etc. Cultures, on one hand, impose on humans certain behaviours, attitudes, gestures and beliefs. On the other hand, the focus on language is inevitable as it is with its verbal and non-verbal components, a key tool in and for communication. Moreover, each language has its particularity in how people voice, address and express their thoughts, feelings and beliefs. Being in the same setting with people from different cultures and languages and having conversations with them would call upon the intercultural communicative competence. This latter would promote the success of their conversations. Additionally, this competence could manifest in several ways during their interactions, to the extent that no one can predict when and how the interlocutors would use it. The only thing probably that could be confirmed is that the setting and culture would in a way or another intervene and often shape the flow of their communication, if not the whole communication. Therefore, this paper will look at the intercultural communicative competence of language learners when introducing their cultures to each other in an online language tandem (henceforth OLT) using their second and/or foreign language with the L1 language speakers. The participants of this study are Algerian (use L2: French, FL: English), British (L1: English, L2/FL: French). In other words, this current paper will provide a qualitative analysis of the OLT experiment by emphasising how language learners can overcome the cultural differences in an intercultural setting while communicating online using Skype (video conversations) with people from different countries, cultures and L1. The non-verbal cues will have the lion share in the analysis by focusing on how they have been used to maintain this intercultural communication or hinder it through the misinterpretation of gestures, head movements, grimaces etc.

Keywords: intercultural communicative competence, non-verbal cues, online language tandem, Skype

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821 Whole Body Vibration and Low Back Disorder among Saskatchewan Farmers: A Prospective Cohort Study

Authors: Samuel Kwaku Essien, Catherine Trask, Niels Koehncke, Brenna Bath

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Background: Low back disorder (LBD) is the most common musculoskeletal problem among farmers, with higher prevalence than other occupations. Operators of tractors and other farm machinery such as combines or all-terrain vehicles (ATV) can have considerable cumulative exposure to whole body vibration (WBV). Although there appears to be an association between LBD and WBV, lack of prospective studies makes the relationship between LBD and WBV unclear. Purpose: This study investigates the association between WBV and LBD among Saskatchewan farmers using a prospective cohort study Methods: The Saskatchewan Farm Injury Cohort Study Phase I (2007) and II (2013) data were used. Baseline data were collected via postal questionnaire on accumulated yearly tractor, combine, and ATV use as well as several covariates to support a biopsychosocial model of LBD. Follow-up data on musculoskeletal symptoms were collected for the 6-year with sample size of 1149. Questions on ‘low back trouble’ (ache, pain, discomfort) experienced in the last 12 months answered by farmer participants as ‘yes’ or ‘no’. A GEE-modified Poisson approach was performed using SPSS 22 and SAS 9.4. Results: Twelve-month Prevalence of LBD was 59.8%. In multivariate analysis of the 6-year follow-up, LBD was associated with ATV operation and tractor operation, with a dose-response relationship for annual accumulated tractor operation. Although combine operation ≥ 61 hrs/year was related to LBD in bivariate analysis, this difference did not persist after adjustment for confounder. Age was found to be a confounder in relationship between WBV and LBD and no interactions were found. Conclusion: Longer annual tractor operation and older age are important predictors of LBD symptoms in farmers. Future research involving direct measurement can help identify appropriate prevention strategies.

Keywords: agriculture, low back disorder, low back pain, occupational health

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820 Identification and Evaluation of Environmental Concepts in Paulo Coelho's "The Alchemist"

Authors: Tooba Sabir, Asima Jaffar, Namra Sabir, Mohammad Amjad Sabir

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Ecocriticism is the study of relationship between human and environment which has been represented in literature since the very beginning in pastoral tradition. However, the analysis of such representation is new as compared to the other critical evaluations like Psychoanalysis, Marxism, Post-colonialism, Modernism and many others. Ecocritics seek to find information like anthropocentrism, ecocentrism, ecofeminism, eco-Marxism, representation of environment and environmental concept and several other topics. In the current study the representation of environmental concepts, were ecocritically analyzed in Paulo Coelho’s The Alchemist, one of the most read novels throughout the world, having been translated into many languages. Analysis of the text revealed, the representations of environmental ideas like landscapes and tourism, biodiversity, land-sea displacement, environmental disasters and warfare, desert winds and sand dunes. 'This desert was once a sea' throws light on different theories of land-sea displacement, one being the plate-tectonic theory which proposes Earth’s lithosphere to be divided into different large and small plates, continuously moving toward, away from or parallel to each other, resulting in land-sea displacement. Another theory is the continental drift theory which holds onto the belief that one large landmass—Pangea, broke down into smaller pieces of land that moved relative to each other and formed continents of the present time. The cause of desertification may, however, be natural i.e. climate change or artificial i.e. by human activities. Imagery of the environmental concepts, at some instances in the novel, is detailed and at other instances, is not as striking, but still is capable of arousing readers’ imagination. The study suggests that ecocritical justifications of environmental concepts in the text will increase the interactions between literature and environment which should be encouraged in order to induce environmental awareness among the readers.

Keywords: biodiversity, ecocritical analysis, ecocriticism, environmental disasters, landscapes

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819 Viscoelastic Properties of Sn-15%Pb Measured in an Oscillation Test

Authors: Gerardo Sanjuan Sanjuan, Ángel Enrique Chavéz Castellanos

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The knowledge of the rheological behavior of partially solidified metal alloy is an important issue when modeling and simulation of die filling in semisolid processes. Many experiments for like steady state, the step change in shear rate tests, shear stress ramps have been carried out leading that semi-solid alloys exhibit shear thinning, thixotropic behavior and yield stress. More advanced investigation gives evidence some viscoelastic features can be observed. The viscoelastic properties of materials are determinate by transient or dynamic methods; unfortunately, sparse information exists about oscillation experiments. The aim of this present work is to use small amplitude oscillatory tests for knowledge properties such as G´ and G´´. These properties allow providing information about materials structure. For this purpose, we investigated tin-lead alloy (Sn-15%Pb) which exhibits a similar microstructure to aluminum alloys and is the classic alloy for semisolid thixotropic studies. The experiments were performed with parallel plates rheometer AR-G2. Initially, the liquid alloy is cooled down to the semisolid range, a specific temperature to guarantee a constant fraction solid. Oscillation was performed within the linear viscoelastic regime with a strain sweep. So, the loss modulus G´´, the storage modulus G´ and the loss angle (δ) was monitored. In addition a frequency sweep at a strain below the critical strain for characterized its structure. This provides more information about the interactions among solid particles on a liquid matrix. After testing, the sample was removed then cooled, sectioned and examined metallographically. These experiments demonstrate that the viscoelasticity is sensitive to the solid fraction, and is strongly influenced by the shape and size of particles solid.

Keywords: rheology, semisolid alloys, thixotropic, viscoelasticity

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818 Purpose in Procurement: Much Discussed, Less Conceptualized – An Exploratory Study of CPO Perceptions Based on the Gioia Methodology

Authors: Laurin Zemmrich, Nicolai Stickler

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With the ongoing debate over how to incorporate sustainability, resilience, and value creation into business strategies, many procurement departments are put under pressure by governments, consumers, non-governmental organizations, and other stakeholders to disclose more information about their supply chains. According to practitioners and experts, procurement benefits the supply chain by increasing transparency and accountability, recruiting new suppliers, and supporting sustainable and ethical sourcing strategies. While most procurement departments establish these objectives, the bulk of activities are not carried out or are not regularly monitored. With the full potential of targeted sourcing still to be realized, procurement executives, in particular, are seeking for short-term cost-cutting impacts to appease external shareholders. We overcome this limitation by using an abductive approach to research and integrating empirical data from a Gioia methodology study design with relevant literature. Our analysis demonstrates that the procurement department has six essential levers aligned with sustainability, resilience, and value creation objectives and contributes to developing a new intra- and interorganizational purpose within the supply chain. Three enablers are identified as having a value-creating effect on supply chain interactions. Additionally, we discovered two impacts that alter the power balance between buyers and suppliers during transactions and have a cost-cutting or cost-avoiding effect. While cost-cutting, cost-avoidance, and dependency-reduction impacts are desirable, redistributing power may also have negative consequences. The article establishes a first strategy framework for evaluating the influence of the procurement department on supply chain transactions, allowing managers to understand better and apply the sourcing function inside a supply chain and embed it throughout the business.

Keywords: supply chain management, resilience, sustainability, value creation, purpose

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817 Hybrid Bimodal Magnetic Force Microscopy

Authors: Fernández-Brito David, Lopez-Medina Javier Alonso, Murillo-Bracamontes Eduardo Antonio, Palomino-Ovando Martha Alicia, Gervacio-Arciniega José Juan

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Magnetic Force Microscopy (MFM) is an Atomic Force Microscopy (AFM) technique that characterizes, at a nanometric scale, the magnetic properties of ferromagnetic materials. Conventional MFM works by scanning in two different AFM modes. The first one is tapping mode, in which the cantilever has short-range force interactions with the sample, with the purpose to obtain the topography. Then, the lift AFM mode starts, raising the cantilever to maintain a fixed distance between the tip and the surface of the sample, only interacting with the magnetic field forces of the sample, which are long-ranged. In recent years, there have been attempts to improve the MFM technique. Bimodal MFM was first theoretically developed and later experimentally proven. In bimodal MFM, the AFM internal piezoelectric is used to cause the cantilever oscillations in two resonance modes simultaneously, the first mode detects the topography, while the second is more sensitive to the magnetic forces between the tip and the sample. However, it has been proven that the cantilever vibrations induced by the internal AFM piezoelectric ceramic are not optimal, affecting the bimodal MFM characterizations. Moreover, the Secondary Resonance Magnetic Force Microscopy (SR-MFM) was developed. In this technique, a coil located below the sample generates an external magnetic field. This alternating magnetic field excites the cantilever at a second frequency to apply the Bimodal MFM mode. Nonetheless, for ferromagnetic materials with a low coercive field, the external field used in SR-MFM technique can modify the magnetic domains of the sample. In this work, a Hybrid Bimodal MFM (HB-MFM) technique is proposed. In HB-MFM, the bimodal MFM is used, but the first resonance frequency of the cantilever is induced by the magnetic field of the ferromagnetic sample due to its vibrations caused by a piezoelectric element placed under the sample. The advantages of this new technique are demonstrated through the preliminary results obtained by HB-MFM on a hard disk sample. Additionally, traditional two pass MFM and HB-MFM measurements were compared.

Keywords: magnetic force microscopy, atomic force microscopy, magnetism, bimodal MFM

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816 The Crossroads of Corruption and Terrorism in the Global South

Authors: Stephen M. Magu

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The 9/11 and Christmas bombing attacks in the United States are mostly associated with the inability of intelligence agencies to connect dots based on intelligence that was already available. The 1998, 2002, 2013 and several 2014 terrorist attacks in Kenya, on the other hand, are probably driven by a completely different dynamic: the invisible hand of corruption. The World Bank and Transparency International annually compute the Worldwide Governance Indicators and the Corruption Perception Index respectively. What perhaps is not adequately captured in the corruption metrics is the impact of corruption on terrorism. The World Bank data includes variables such as the control of corruption, (estimates of) government effectiveness, political stability and absence of violence/terrorism, regulatory quality, rule of law and voice and accountability. TI's CPI does not include measures related to terrorism, but it is plausible that there is an expectation of some terrorism impact arising from corruption. This paper, by examining the incidence, frequency and total number of terrorist attacks that have occurred especially since 1990, and further examining the specific cases of Kenya and Nigeria, argues that in addition to having major effects on governance, corruption has an even more frightening impact: that of facilitating and/or violating security mechanisms to the extent that foreign nationals can easily obtain identification that enables them to perpetuate major events, targeting powerful countries' interests in countries with weak corruption-fighting mechanisms. The paper aims to model interactions that demonstrate the cost/benefit analysis and agents' rational calculations as being non-rational calculations, given the ultimate impact. It argues that eradication of corruption is not just a matter of a better business environment, but that it is implicit in national security, and that for anti-corruption crusaders, this is an argument more potent than the economic cost / cost of doing business argument.

Keywords: corruption, global south, identification, passports, terrorism

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815 Biodiversity Interactions Between C3 and C4 Plants under Agroforestry Cropping System

Authors: Ezzat Abd El Lateef

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Agroforestry means combining the management of trees with productive agricultural activities, especially in semiarid regions where crop yield increases are limited in agroforestry systems due to the fertility and microclimate improvements and the large competitive effect of trees with crops for water and nutrients, in order to assess the effect of agroforestry of some field crops with citrus trees as an approach to establish biodiversity in fruit tree plantations. Three field crops, i.e., maize, soybean and sunflower, were inter-planted with seedless orange trees (4*4 m) or were planted as solid plantings. The results for the trees indicated a larger fruit yield was obtained when soybean and sunflowers were interplant with citrus. Statistically significant effects (P<0.05) were found for maize grain and biological yields, with increased yields when grown as solid planting. There were no differences in the yields of soya bean and sunflower, where the yields were very similar between the two cropping systems. It is evident from the trials that agroforestry is an efficient concept to increase biodiversity through the interaction of trees with the interplant field crop species. Maize, unlike the other crops, was more sensitive to shade conditions under agroforestry practice and not preferred in the biodiversity system. The potential of agroforestry to improve or increase biodiversity is efficient as the understorey crops are usually C4 species, and the overstorey trees are invariably C3 species in agroforestry. Improvement in interplant species is most likely if the understorey crop is a C3 species, which are usually light saturated in the open, and partial shade may have little effect on assimilation or by a concurrent reduction in transpiration. It could be concluded that agroforestry is an efficient concept to increase biodiversity through the interaction of trees with the interplant field crop species. Some field crops could be employed successfully, like soybean or sunflowers, while others like maize are sensitive to incorporate in agroforestry system.

Keywords: agroforestry, field crops, C3 and C4 plants, yield

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814 Evaluating Seismic Earth Pressure Effects on Building Lateral Stability: Sensitivity to Retention Height Differences and Sloped Site Conditions

Authors: Rod Davis, Sara Saminfar

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Earthquakes can induce dynamic earth pressures on retaining walls, which are in addition to the static earth pressures. This raises questions about how to effectively combine the seismic lateral earth pressure with other loads on buildings, including static lateral earth pressure. When basement walls retain soil with differing exterior grades on opposite sides, the seismic increment of active earth pressure should be considered. Additionally, buildings situated on sloped sites with stepped retention may experience unique dynamic effects due to soil-structure interactions, potentially amplifying the lateral pressures exerted on the retaining walls and influencing the building's response during seismic events. To account for the dynamic effects of the retained soil on the building's responses, it is essential to interconnect the building structure with the surrounding soil to facilitate their interaction as the embedded structure and the surrounding soil move together during an earthquake. Consequently, a finite element model of the building is developed, with the rigid retaining walls and restrained to the floor diaphragms. This paper aims to explore the dynamic effects of retained soil on the lateral stability of buildings and the sensitivity of the building's responses to differences in the retained heights on opposite sides of the building basement. Furthermore, the results are compared with those from a sloped site to evaluate the impact of stepped retention on dynamic soil pressure. These findings will help establish a minimum threshold for differences in retained heights on opposite sides of a building that necessitates the inclusion of dynamic soil pressure in the building's lateral stability analysis.

Keywords: dynamic earth pressures, soil-structure interaction, stepped retention, building retention

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813 Quality Assurance for the Climate Data Store

Authors: Judith Klostermann, Miguel Segura, Wilma Jans, Dragana Bojovic, Isadora Christel Jimenez, Francisco Doblas-Reyees, Judit Snethlage

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The Climate Data Store (CDS), developed by the Copernicus Climate Change Service (C3S) implemented by the European Centre for Medium-Range Weather Forecasts (ECMWF) on behalf of the European Union, is intended to become a key instrument for exploring climate data. The CDS contains both raw and processed data to provide information to the users about the past, present and future climate of the earth. It allows for easy and free access to climate data and indicators, presenting an important asset for scientists and stakeholders on the path for achieving a more sustainable future. The C3S Evaluation and Quality Control (EQC) is assessing the quality of the CDS by undertaking a comprehensive user requirement assessment to measure the users’ satisfaction. Recommendations will be developed for the improvement and expansion of the CDS datasets and products. User requirements will be identified on the fitness of the datasets, the toolbox, and the overall CDS service. The EQC function of the CDS will help C3S to make the service more robust: integrated by validated data that follows high-quality standards while being user-friendly. This function will be closely developed with the users of the service. Through their feedback, suggestions, and contributions, the CDS can become more accessible and meet the requirements for a diverse range of users. Stakeholders and their active engagement are thus an important aspect of CDS development. This will be achieved with direct interactions with users such as meetings, interviews or workshops as well as different feedback mechanisms like surveys or helpdesk services at the CDS. The results provided by the users will be categorized as a function of CDS products so that their specific interests will be monitored and linked to the right product. Through this procedure, we will identify the requirements and criteria for data and products in order to build the correspondent recommendations for the improvement and expansion of the CDS datasets and products.

Keywords: climate data store, Copernicus, quality, user engagement

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812 A Computational Approach for the Prediction of Relevant Olfactory Receptors in Insects

Authors: Zaide Montes Ortiz, Jorge Alberto Molina, Alejandro Reyes

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Insects are extremely successful organisms. A sophisticated olfactory system is in part responsible for their survival and reproduction. The detection of volatile organic compounds can positively or negatively affect many behaviors in insects. Compounds such as carbon dioxide (CO2), ammonium, indol, and lactic acid are essential for many species of mosquitoes like Anopheles gambiae in order to locate vertebrate hosts. For instance, in A. gambiae, the olfactory receptor AgOR2 is strongly activated by indol, which accounts for almost 30% of human sweat. On the other hand, in some insects of agricultural importance, the detection and identification of pheromone receptors (PRs) in lepidopteran species has become a promising field for integrated pest management. For example, with the disruption of the pheromone receptor, BmOR1, mediated by transcription activator-like effector nucleases (TALENs), the sensitivity to bombykol was completely removed affecting the pheromone-source searching behavior in male moths. Then, the detection and identification of olfactory receptors in the genomes of insects is fundamental to improve our understanding of the ecological interactions, and to provide alternatives in the integrated pests and vectors management. Hence, the objective of this study is to propose a bioinformatic workflow to enhance the detection and identification of potential olfactory receptors in genomes of relevant insects. Applying Hidden Markov models (Hmms) and different computational tools, potential candidates for pheromone receptors in Tuta absoluta were obtained, as well as potential carbon dioxide receptors in Rhodnius prolixus, the main vector of Chagas disease. This study showed the validity of a bioinformatic workflow with a potential to improve the identification of certain olfactory receptors in different orders of insects.

Keywords: bioinformatic workflow, insects, olfactory receptors, protein prediction

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811 Large Herbivores Benefit Plant Growth via Diverse and Indirect Pathways in a Temperate Grassland

Authors: Xiaofei Li, Zhiwei Zhong, Deli Wang

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Large herbivores affect plant growth not only through their direct, consumptive effects, but also through indirect effects that alter species interactions. Indirect effects can be either positive or negative, therefore having the potential to mitigate or enhance the direct impacts of herbivores. However, until recently, we know considerably less about the indirect effects than the direct effects of large herbivores on plants, and few studies have explored multiple indirect pathways simultaneously. Here, we investigated how large domestic herbivores, cattle (Bos taurus), can shape population growth of an intermediately preferred forb species, Artemsisa scoparia, through diverse pathways in a temperate grassland of northeast China. We found that, although exposure to direct consumption of cattle, A. scoparia growth was not inhibited, but rather showed a significant increase in the grazed than ungrazed areas. This unexpected result was due to grazing-induced multiple indirect, positive effects overwhelmed the direct, negative consumption effects of cattle on plant growth. The much more intensive consumption on the dominant Leymus chinensis grass, ground litter removal, and increases in ant nest abundance induced by cattle, exerted significant indirect, positive effects on A. scoparia growth. These pathways benefited A.scoparia growth by lessening interspecific competition, mitigating negative effects of litter accumulation, and increasing soil nutrient availability, respectively. Our results highlight the need to integrate indirect effects into the traditional food web theory, which is based primary on direct, trophic linkages, to fully understand community organization and dynamics. Large herbivores are important conservation and management targets, our results suggest that these mammals should be managed with the understanding that they can affect primary producers through diverse paths.

Keywords: grasslands, large herbivores, plant growth, indirect effects

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810 An AI-generated Semantic Communication Platform in HCI Course

Authors: Yi Yang, Jiasong Sun

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Almost every aspect of our daily lives is now intertwined with some degree of human-computer interaction (HCI). HCI courses draw on knowledge from disciplines as diverse as computer science, psychology, design principles, anthropology, and more. Our HCI courses, named the Media and Cognition course, are constantly updated to reflect state-of-the-art technological advancements such as virtual reality, augmented reality, and artificial intelligence-based interactions. For more than a decade, our course has used an interest-based approach to teaching, in which students proactively propose some research-based questions and collaborate with teachers, using course knowledge to explore potential solutions. Semantic communication plays a key role in facilitating understanding and interaction between users and computer systems, ultimately enhancing system usability and user experience. The advancements in AI-generated technology, which have gained significant attention from both academia and industry in recent years, are exemplified by language models like GPT-3 that generate human-like dialogues from given prompts. Our latest version of the Human-Computer Interaction course practices a semantic communication platform based on AI-generated techniques. The purpose of this semantic communication is twofold: to extract and transmit task-specific information while ensuring efficient end-to-end communication with minimal latency. An AI-generated semantic communication platform evaluates the retention of signal sources and converts low-retain ability visual signals into textual prompts. These data are transmitted through AI-generated techniques and reconstructed at the receiving end; on the other hand, visual signals with a high retain ability rate are compressed and transmitted according to their respective regions. The platform and associated research are a testament to our students' growing ability to independently investigate state-of-the-art technologies.

Keywords: human-computer interaction, media and cognition course, semantic communication, retainability, prompts

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809 Exploring Women's Needs Referring to Health Care Centers for Doing Pap Smear Test

Authors: Arezoo Fallahi, Fateme Aslibigi, Parvaneh Taymoori, Babak Nematshahrbabaki

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Background and Aims: Cancer of the cervix, one of cancer-related death, is the second most common cancer in women worldwide. It develops over time but it is one of the most preventable types of cancer and there is the available proper screening program for its preventing. Since Pap smear test is vital to prevent and control of disease but women do not accomplish it regularly. Therefore, this study was aimed to explore women's needs referring to health care centers for doing Pap smear test. Material and methods: In this study, an inductive qualitative method with content analysis approach was used. This survey was done in varamin city (is located capital of Iran) in year 2014. Through the purposive sampling 15 women's view of point referring to health care centers of for doing Pap smear test was surveyed. Inclusion criteria were: 20-50 years old married women, having experience Pap smear test and attendance to participate in the Study. Recorded semi- structured interviews were typed and analyzed through of content analysis method. To obtain trustworthiness and rigor of the data, the criteria of credibility, dependability, confirmability and transferability was used. Results: During the data analysis, four main categories of “role of health care team”, “role of organizations”, “social support” and “policies and administration system” were developed. The participants emphasized on making motivational rules and coordination among organizations to do behaviors related to women health. Conclusion: The findings of study showed that doing Pap smear test are attributed to appropriate and intimate interactions with health professionals, family support, encouraging legislation and policies and coordination and notification of organizations. Therefore, designers and stockholders of policies and health system should more consider to growth and involve other organizations toward women's health.

Keywords: qualitative approach, pap smear test, women, health care centers

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808 Social Sustainability and Affordability of the Transitional Housing Scheme in Hong Kong

Authors: Tris Kee

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This research investigates social sustainability factors in transitional housing projects and their impact on fostering healthy living environments that promote physical activity and social interaction for residents. Social sustainability is integral to individual health and well-being, as emphasized by Goal 11 of the 2030 Agenda for Sustainable Development, which highlights the importance of safe, affordable, and accessible transport systems, green spaces, and public spaces catering to vulnerable populations' needs. Communal spaces in urban environments are essential for fostering social sustainability, as they serve as settings for physical activities and social interactions among diverse socio-economic groups. Factors such as neighborhood social atmosphere, historical context, social disparity, and mobility can influence the relationship between existing and transitional communities. Mental health effects can be measured through housing segregation, mobility and accessibility, and housing tenure. A significant research gap exists in understanding the living environment of transitional housing in Hong Kong and the social sustainability factors affecting residents' mental and physical health. To address this gap, our study employs a mixed-methods approach combining survey questionnaires and interviews to gather both quantitative and qualitative data. This methodology will provide comprehensive insights into residents' experiences and perceptions. Our research's main contribution is identifying key social sustainability factors in transitional housing and their impact on residents' well-being, informing policy-making and the creation of inclusive, healthy living environments. By addressing this research gap, we aim to provide valuable insights for future housing projects, ultimately promoting the development of socially sustainable transitional communities.

Keywords: social sustainablity, affordable housing, transitional housing, high density housing

Procedia PDF Downloads 87
807 Understanding the Interactive Nature in Auditory Recognition of Phonological/Grammatical/Semantic Errors at the Sentence Level: An Investigation Based upon Japanese EFL Learners’ Self-Evaluation and Actual Language Performance

Authors: Hirokatsu Kawashima

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One important element of teaching/learning listening is intensive listening such as listening for precise sounds, words, grammatical, and semantic units. Several classroom-based investigations have been conducted to explore the usefulness of auditory recognition of phonological, grammatical and semantic errors in such a context. The current study reports the results of one such investigation, which targeted auditory recognition of phonological, grammatical, and semantic errors at the sentence level. 56 Japanese EFL learners participated in this investigation, in which their recognition performance of phonological, grammatical and semantic errors was measured on a 9-point scale by learners’ self-evaluation from the perspective of 1) two types of similar English sound (vowel and consonant minimal pair words), 2) two types of sentence word order (verb phrase-based and noun phrase-based word orders), and 3) two types of semantic consistency (verb-purpose and verb-place agreements), respectively, and their general listening proficiency was examined using standardized tests. A number of findings have been made about the interactive relationships between the three types of auditory error recognition and general listening proficiency. Analyses based on the OPLS (Orthogonal Projections to Latent Structure) regression model have disclosed, for example, that the three types of auditory error recognition are linked in a non-linear way: the highest explanatory power for general listening proficiency may be attained when quadratic interactions between auditory recognition of errors related to vowel minimal pair words and that of errors related to noun phrase-based word order are embraced (R2=.33, p=.01).

Keywords: auditory error recognition, intensive listening, interaction, investigation

Procedia PDF Downloads 511
806 Social Networking Application: What Is Their Quality and How Can They Be Adopted in Open Distance Learning Environments?

Authors: Asteria Nsamba

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Social networking applications and tools have become compelling platforms for generating and sharing knowledge across the world. Social networking applications and tools refer to a variety of social media platforms which include Facebook, Twitter WhatsApp, blogs and Wikis. The most popular of these platforms are Facebook, with 2.41 billion active users on a monthly basis, followed by WhatsApp with 1.6 billion users and Twitter with 330 million users. These communication platforms have not only impacted social lives but have also impacted students’ learning, across different delivery modes in higher education: distance, conventional and blended learning modes. With this amount of interest in these platforms, knowledge sharing has gained importance within the context in which it is required. In open distance learning (ODL) contexts, social networking platforms can offer students and teachers the platform on which to create and share knowledge, and form learning collaborations. Thus, they can serve as support mechanisms to increase interactions and reduce isolation and loneliness inherent in ODL. Despite this potential and opportunity, research indicates that many ODL teachers are not inclined to using social media tools in learning. Although it is unclear why these tools are uncommon in these environments, concerns raised in the literature have indicated that many teachers have not mastered the art of teaching with technology. Using technological, pedagogical content knowledge (TPCK) and product quality theory, and Bloom’s Taxonomy as lenses, this paper is aimed at; firstly, assessing the quality of three social media applications: Facebook, Twitter and WhatsApp, in order to determine the extent to which they are suitable platforms for teaching and learning, in terms of content generation, information sharing and learning collaborations. Secondly, the paper demonstrates the application of teaching, learning and assessment using Bloom’s Taxonomy.

Keywords: distance education, quality, social networking tools, TPACK

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805 Sentiment Mapping through Social Media and Its Implications

Authors: G. C. Joshi, M. Paul, B. K. Kalita, V. Ranga, J. S. Rawat, P. S. Rawat

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Being a habitat of the global village, every place has established connection through the strength and power of social media piercing through the political boundaries. Social media is a digital platform, where people across the world can interact as it has advantages of being universal, anonymous, easily accessible, indirect interaction, gathering and sharing information. The power of social media lies in the intensity of sharing extreme opinions or feelings, in contrast to the personal interactions which can be easily mapped in the form of Sentiment Mapping. The easy access to social networking sites such as Facebook, Twitter and blogs made unprecedented opportunities for citizens to voice their opinions loaded with dynamics of emotions. These further influence human thoughts where social media plays a very active role. A recent incident of public importance was selected as a case study to map the sentiments of people through Twitter. Understanding those dynamics through the eye of an ordinary people can be challenging. With the help of R-programming language and by the aid of GIS techniques sentiment maps has been produced. The emotions flowing worldwide in the form of tweets were extracted and analyzed. The number of tweets had diminished by 91 % from 25/08/2017 to 31/08/2017. A boom of sentiments emerged near the origin of the case, i.e., Delhi, Haryana and Punjab and the capital showed maximum influence resulting in spillover effect near Delhi. The trend of sentiments was prevailing more as neutral (45.37%), negative (28.6%) and positive (21.6%) after calculating the sentiment scores of the tweets. The result can be used to know the spatial distribution of digital penetration in India, where highest concentration lies in Mumbai and lowest in North East India and Jammu and Kashmir.

Keywords: sentiment mapping, digital literacy, GIS, R statistical language, spatio-temporal

Procedia PDF Downloads 151
804 Calculation of Secondary Neutron Dose Equivalent in Proton Therapy of Thyroid Gland Using FLUKA Code

Authors: M. R. Akbari, M. Sadeghi, R. Faghihi, M. A. Mosleh-Shirazi, A. R. Khorrami-Moghadam

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Proton radiotherapy (PRT) is becoming an established treatment modality for cancer. The localized tumors, the same as undifferentiated thyroid tumors are insufficiently handled by conventional radiotherapy, while protons would propose the prospect of increasing the tumor dose without exceeding the tolerance of the surrounding healthy tissues. In spite of relatively high advantages in giving localized radiation dose to the tumor region, in proton therapy, secondary neutron production can have significant contribution on integral dose and lessen advantages of this modality contrast to conventional radiotherapy techniques. Furthermore, neutrons have high quality factor, therefore, even a small physical dose can cause considerable biological effects. Measuring of this neutron dose is a very critical step in prediction of secondary cancer incidence. It has been found that FLUKA Monte Carlo code simulations have been used to evaluate dose due to secondaries in proton therapy. In this study, first, by validating simulated proton beam range in water phantom with CSDA range from NIST for the studied proton energy range (34-54 MeV), a proton therapy in thyroid gland cancer was simulated using FLUKA code. Secondary neutron dose equivalent of some organs and tissues after the target volume caused by 34 and 54 MeV proton interactions were calculated in order to evaluate secondary cancer incidence. A multilayer cylindrical neck phantom considering all the layers of neck tissues and a proton beam impinging normally on the phantom were also simulated. Trachea (accompanied by Larynx) had the greatest dose equivalent (1.24×10-1 and 1.45 pSv per primary 34 and 54 MeV protons, respectively) among the simulated tissues after the target volume in the neck region.

Keywords: FLUKA code, neutron dose equivalent, proton therapy, thyroid gland

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803 Redefining Urban Sports Facilities Through Vertical Growth: An Analytical Study And Possible Solutions For Gulshan, Dhaka

Authors: Rakibul Islam Sagor, Sadia Ibnat Raisa

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Many nations across the globe, including Dhaka, are facing challenges in meeting the needs for a satisfactory quality of life due to the combination of a growing population and limited land resources. As a result, maximum spaces in modern cities are engulfed by concrete infrastructure, and there are hardly any open spaces in the urban neighborhoods. Although vertical movement has predominantly been employed for residential and commercial applications, the notion of vertical recreational and sports facilities remains unsettled. The primary objective of this study is to explore the feasibility of implementing vertical adaptations in urban recreational spaces, drawing upon the principles of high-rise theory. This article presents an analysis of the open spaces in Gulshan, Dhaka, focusing on the evaluation of the demand for open recreational and sports facilities that adequately cater to the existing population of the region. Initially, the study tried to identify and examine all potential open spaces within the designated area. Following that, an acceptable place is selected utilizing space syntax analysis, which takes into account the most conveniently accessible space for social interactions in the neighborhood. In addition, socioeconomic conditions of the area have been studied in order to determine the feasibility of the area. Finally, the study presented viable options for vertical urban sports facilities in the context of Dhaka, Bangladesh. Additionally, it seeks to develop strategies for maximizing the use of vertical expansions, thereby promoting a healthier and more active lifestyle among the city's residents. This approach aims to effectively handle the issue of limited land availability and enhance the efficiency of recreational areas around the globe.

Keywords: vertical sports, urban open spaces, social interaction, recreational activities

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802 Free Energy Computation of A G-Quadruplex-Ligand Structure: A Classical Molecular Dynamics and Metadynamics Simulation Study

Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure formed by stacked planes of four base paired guanines (G-quartet). Guanine rich DNA sequences appear in many sites of genomic DNA and can potential form G-quadruplexes, such as those occurring at 3'-terminus of the human telomeric DNA. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to down regulate oncogene expression making G-quadruplex an attractive target for anticancer therapy. Many G-quadruplex ligands have been proposed with a planar core to facilitate the pi–pi stacking and electrostatic interactions with the G-quartets. However, many drug candidates are impossibilitated to discriminate a G-quadruplex from a double helix DNA structure. In this context, it is important to investigate the site topology for the interaction of a G-quadruplex with a ligand. In this work, we determine the free energy surface of a G-quadruplex-ligand to study the binding modes of the G-quadruplex (TG4T) with the daunomycin (DM) drug. The complex TG4T-DM is studied using classical molecular dynamics in combination with metadynamics simulations. The metadynamics simulations permit an enhanced sampling of the conformational space with a modest computational cost and obtain free energy surfaces in terms of the collective variables (CV). The free energy surfaces of TG4T-DM exhibit other local minima, indicating the presence of additional binding modes of daunomycin that are not observed in short MD simulations without the metadynamics approach. The results are compared with similar calculations on a different structure (the mutated mu-G4T-DM where the 5' thymines on TG4T-DM have been deleted). The results should be of help to design new G-quadruplex drugs, and understand the differences in the recognition topology sites of the duplex and quadruplex DNA structures in their interaction with ligands.

Keywords: g-quadruplex, cancer, molecular dynamics, metadynamics

Procedia PDF Downloads 458