Search results for: cluster analysis
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 27438

Search results for: cluster analysis

27018 Excavation of Phylogenetically Diverse Bioactive Actinobacteria from Unexplored Regions of Sundarbans Mangrove Ecosystem for Mining of Economically Important Antimicrobial Compounds

Authors: Sohan Sengupta, Arnab Pramanik, Abhrajyoti Ghosh, Maitree Bhattacharyya

Abstract:

Newly emerged phyto-pathogens and multi drug resistance have been threating the world for last few decades. Actinomycetes, the most endowed group of microorganisms isolated from unexplored regions of the world may be the ultimate solution to these problems. Thus the aim of this study was to isolate several bioactive actinomycetes strains capable of producing antimicrobial secondary metabolite from Sundarbans, the only mangrove tiger land of the world. Fifty four actinomycetes were isolated and analyzed for antimicrobial activity against fifteen test organisms including three phytopathogens. Nine morphologically distinct and biologically active isolates were subjected to polyphasic identification study. 16s rDNA sequencing indicated eight isolates to reveal maximum similarity to the genus streptomyces, whereas one isolate presented only 93.57% similarity with Streptomyces albogriseolus NRRL B-1305T. Seventy-one carbon sources and twenty-three chemical sources utilization assay revealed their metabolic relatedness. Among these nine isolates three specific strains were found to have notably higher degree of antimicrobial potential effective in a broader range including phyto-pathogenic fungus. PCR base whole genome screen for PKS and NRPS genes, confirmed the occurrence of bio-synthetic gene cluster in some of the isolates for novel antibiotic production. Finally the strain SMS_SU21, which showed antimicrobial activity with MIC value of 0.05 mg ml-1and antioxidant activity with IC50 value of 0.242±0.33 mg ml-1 was detected to be the most potential one. True prospective of this strain was evaluated utilizing GC-MS and the bioactive compound responsible for antimicrobial activity was purified and characterized. Rare bioactive actinomycetes were isolated from unexplored heritage site. Diversity of the biosynthetic gene cluster for antimicrobial compound production has also been evaluated. Antimicrobial compound SU21-C has been identified and purified which is active against a broad range of pathogens.

Keywords: actinomycetes, sundarbans, antimicrobial, pks nrps, phyto-pathogens, GC-MS

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27017 Physical Activity and Nutrition Intervention for Singaporean Women Aged 50 Years and Above: A Study Protocol for a Community Based Randomised Controlled Trial

Authors: Elaine Yee Sing Wong, Jonine Jancey, Andy H. Lee, Anthony P. James

Abstract:

Singapore has a rapidly aging population, where the majority of older women aged 50 years and above, are physically inactive and have unhealthy dietary habits, placing them at ‘high risk’ of non-communicable diseases. Given the multiplicity of less than optimal dietary habits and high levels of physical inactivity among Singaporean women, it is imperative to develop appropriate lifestyle interventions at recreational centres to enhance both their physical and nutritional knowledge, as well as provide them with the opportunity to develop skills to support behaviour change. To the best of our knowledge, this proposed study is the first physical activity and nutrition cluster randomised controlled trial conducted in Singapore for older women. Findings from this study may provide insights and recommendations for policy makers and key stakeholders to create new healthy living, recreational centres with supportive environments. This 6-month community-based cluster randomised controlled trial will involve the implementation and evaluation of physical activity and nutrition program for community dwelling Singaporean women, who currently attend recreational centres to promote social leisure activities in their local neighbourhood. The intervention will include dietary education and counselling sessions, physical activity classes, and telephone contact by certified fitness instructors and qualified nutritionists. Social Cognitive Theory with Motivational Interviewing will inform the development of strategies to support health behaviour change. Sixty recreational centres located in Singapore will be randomly selected from five major geographical districts and randomly allocated to the intervention (n=30) or control (n=30) cluster. A sample of 600 (intervention n=300; control n=300) women aged 50 years and above will then be recruited from these recreational centres. The control clusters will only undergo pre and post data collection and will not receive the intervention. It is hypothesised that by the end of the intervention, the intervention group participants (n = 300) compared to the control group (n = 300), will show significant improvements in the following variables: lipid profile, body mass index, physical activity and dietary behaviour, anthropometry, mental and physical health. Data collection will be examined and compared via the Statistical Package for the Social Science version 23. Descriptive and summary statistics will be used to quantify participants’ characteristics and outcome variables. Multi-variable mixed regression analyses will be used to confirm the effects of the proposed health intervention, taking into account the repeated measures and the clustering of the observations. The research protocol was approved by the Curtin University Human Research Ethics Committee (approval number: HRE2016-0366). The study has been registered with the Australian and New Zealand Clinical Trial Registry (12617001022358).

Keywords: community based, healthy aging, intervention, nutrition, older women, physical activity

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27016 Study of Water Cluster-Amorphous Silica Collisions in the Extreme Space Environment Using the ReaxFF Reactive Force Field Molecular Dynamics Simulation Method

Authors: Ali Rahnamoun, Adri van Duin

Abstract:

The concept of high velocity particle impact on the spacecraft surface materials has been one of the important issues in the design of such materials. Among these particles, water clusters might be the most abundant and the most important particles to be studied. The importance of water clusters is that upon impact on the surface of the materials, they can cause damage to the material and also if they are sub-cooled water clusters, they can attach to the surface of the materials and cause ice accumulation on the surface which is very problematic in spacecraft and also aircraft operations. The dynamics of the collisions between amorphous silica structures and water clusters with impact velocities of 1 km/s to 10 km/s are studied using the ReaxFF reactive molecular dynamics simulation method. The initial water clusters include 150 water molecules and the water clusters are collided on the surface of amorphous fully oxidized and suboxide silica structures. These simulations show that the most abundant molecules observed on the silica surfaces, other than reflecting water molecules, are H3O+ and OH- for the water cluster impacts on suboxide and fully oxidized silica structures, respectively. The effect of impact velocity on the change of silica mass is studied. At high impact velocities the water molecules attach to the silica surface through a chemisorption process meaning that water molecule dissociates through the interaction with silica surface. However, at low impact velocities, physisorbed water molecules are also observed, which means water molecule attaches and accumulates on the silica surface. The amount of physisorbed waters molecules at low velocities is higher on the suboxide silica surfaces. The evolution of the temperatures of the water clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting water clusters increase to about 2000K, with individual molecules oocasionally reaching temperatures of over 8000K and thus will be prudent to consider the concept of electron excitation at these higher impact velocities which goes beyond the current ReaxFF ability.

Keywords: spacecraft materials, hypervelocity impact, reactive molecular dynamics simulation, amorphous silica

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27015 Research on the Conservation Strategy of Territorial Landscape Based on Characteristics: The Case of Fujian, China

Authors: Tingting Huang, Sha Li, Geoffrey Griffiths, Martin Lukac, Jianning Zhu

Abstract:

Territorial landscapes have experienced a gradual loss of their typical characteristics during long-term human activities. In order to protect the integrity of regional landscapes, it is necessary to characterize, evaluate and protect them in a graded manner. The study takes Fujian, China, as an example and classifies the landscape characters of the site at the regional scale, middle scale, and detailed scale. A multi-scale approach combining parametric and holistic approaches is used to classify and partition the landscape character types (LCTs) and landscape character areas (LCAs) at different scales, and a multi-element landscape assessment approach is adopted to explore the conservation strategies of the landscape character. Firstly, multiple fields and multiple elements of geography, nature and humanities were selected as the basis of assessment according to the scales. Secondly, the study takes a parametric approach to the classification and partitioning of landscape character, Principal Component Analysis, and two-stage cluster analysis (K-means and GMM) in MATLAB software to obtain LCTs, combines with Canny Operator Edge Detection Algorithm to obtain landscape character contours and corrects LCTs and LCAs by field survey and manual identification methods. Finally, the study adopts the Landscape Sensitivity Assessment method to perform landscape character conservation analysis and formulates five strategies for different LCAs: conservation, enhancement, restoration, creation, and combination. This multi-scale identification approach can efficiently integrate multiple types of landscape character elements, reduce the difficulty of broad-scale operations in the process of landscape character conservation, and provide a basis for landscape character conservation strategies. Based on the natural background and the restoration of regional characteristics, the results of landscape character assessment are scientific and objective and can provide a strong reference in regional and national scale territorial spatial planning.

Keywords: parameterization, multi-scale, landscape character identify, landscape character assessment

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27014 Cluster Based Ant Colony Routing Algorithm for Mobile Ad-Hoc Networks

Authors: Alaa Eddien Abdallah, Bajes Yousef Alskarnah

Abstract:

Ant colony based routing algorithms are known to grantee the packet delivery, but they su ffer from the huge overhead of control messages which are needed to discover the route. In this paper we utilize the network nodes positions to group the nodes in connected clusters. We use clusters-heads only on forwarding the route discovery control messages. Our simulations proved that the new algorithm has decreased the overhead dramatically without affecting the delivery rate.

Keywords: ad-hoc network, MANET, ant colony routing, position based routing

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27013 Multivariate Assessment of Mathematics Test Scores of Students in Qatar

Authors: Ali Rashash Alzahrani, Elizabeth Stojanovski

Abstract:

Data on various aspects of education are collected at the institutional and government level regularly. In Australia, for example, students at various levels of schooling undertake examinations in numeracy and literacy as part of NAPLAN testing, enabling longitudinal assessment of such data as well as comparisons between schools and states within Australia. Another source of educational data collected internationally is via the PISA study which collects data from several countries when students are approximately 15 years of age and enables comparisons in the performance of science, mathematics and English between countries as well as ranking of countries based on performance in these standardised tests. As well as student and school outcomes based on the tests taken as part of the PISA study, there is a wealth of other data collected in the study including parental demographics data and data related to teaching strategies used by educators. Overall, an abundance of educational data is available which has the potential to be used to help improve educational attainment and teaching of content in order to improve learning outcomes. A multivariate assessment of such data enables multiple variables to be considered simultaneously and will be used in the present study to help develop profiles of students based on performance in mathematics using data obtained from the PISA study.

Keywords: cluster analysis, education, mathematics, profiles

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27012 Evaluation of Some Trace Elements in Biological Samples of Egyptian Viral Hepatitis Patients under Nutrition Therapy

Authors: Tarek Elnimr, Reda Morsy, Assem El Fert, Aziza Ismail

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Hepatitis is an inflammation of the liver. The condition can be self-limiting or can progress to fibrosis, cirrhosis or liver cancer. Disease caused by the hepatitis virus, the virus can cause hepatitis infection, ranging in severity from a mild illness lasting a few weeks to a serious, lifelong illness. A growing body of evidence indicates that many trace elements play important roles in a number of carcinogenic processes that proceed with various mechanisms. To examine the status of trace elements during the development of hepatic carcinoma, we determined the iron, copper, zinc and selenium levels in some biological samples of patients at different stages of viral hepatic disease. We observed significant changes in the iron, copper, zinc and selenium levels in the biological samples of patients hepatocellular carcinoma, relative to those of healthy controls. The mean hair, nail, RBC, serum and whole blood copper levels in patients with hepatitis virus were significantly higher than that of the control group. In contrast the mean iron, zinc, and selenium levels in patients having hepatitis virus were significantly lower than those of the control group. On the basis of this study, we identified the impact of natural supplements to improve the treatment of viral liver damage, using the level of some trace elements such as, iron, copper, zinc and selenium, which might serve as biomarkers for increases survival and reduces disease progression. Most of the elements revealed diverse and random distribution in the samples of the donor groups. The correlation study pointed out significant disparities in the mutual relationships among the trace elements in the patients and controls. Principal component analysis and cluster analysis of the element data manifested diverse apportionment of the selected elements in the scalp hair, nail and blood components of the patients compared with the healthy counterparts.

Keywords: hepatitis, hair, nail, blood components, trace element, nutrition therapy, multivariate analysis, correlation, ICP-MS

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27011 ISSR Based Molecular Phylogeny in Naturally Growing Suaeda Populations of Saudi Arabia

Authors: Mohammed Abdullah Basahi

Abstract:

The objective of the present study was to identify the phylogenetic relationships and determine genetic diversity among Suaeda genotypes growing in Saudi Arabia and to find out whether these could be a potential source for genetic diversity. A set of nineteen genotypes was analyzed using twenty-four ISSR primers. Clear amplified polymorphic DNA products were obtained from the screening of twenty-four ISSR primers on nineteen genotypes that allowed selection of ten primers and the results were reproducible. Nineteen genotypes were revealed a unique profile with ten ISSR primers and thus it can be used for the DNA fingerprinting. Different primers produced a different level of polymorphism among the nineteen genotypes. The number of polymorphic bands per primer varied from 5 to 14 with an average of 8 bands per primer. The results revealed that the genotypes differed for ISSR markers. The genetic similarity based on Nei and Li’s ranged from 0.450 to 0.930. Cluster analysis was conducted based on ISSR data to group the Suaeda genotypes and to construct a dendrogram. Four groups can be distinguished by truncating the dendrogram at GS value of 0.54. ISSR markers showed high level of polymorphism among the genotypes examined. The present study indicates that ISSR markers could be successfully used in genetic characterization and diversity in Suaeda.

Keywords: suaeda, DNA fingerprinting, ISSR, Saudi Arabia

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27010 Re-Constructing the Research Design: Dealing with Problems and Re-Establishing the Method in User-Centered Research

Authors: Kerem Rızvanoğlu, Serhat Güney, Emre Kızılkaya, Betül Aydoğan, Ayşegül Boyalı, Onurcan Güden

Abstract:

This study addresses the re-construction and implementation process of the methodological framework developed to evaluate how locative media applications accompany the urban experiences of international students coming to Istanbul with exchange programs in 2022. The research design was built on a three-stage model. The research team conducted a qualitative questionnaire in the first stage to gain exploratory data. These data were then used to form three persona groups representing the sample by applying cluster analysis. In the second phase, a semi-structured digital diary study was carried out on a gamified task list with a sample selected from the persona groups. This stage proved to be the most difficult to obtaining valid data from the participant group. The research team re-evaluated the design of this second phase to reach the participants who will perform the tasks given by the research team while sharing their momentary city experiences, to ensure the daily data flow for two weeks, and to increase the quality of the obtained data. The final stage, which follows to elaborate on the findings, is the “Walk & Talk,” which is completed with face-to-face and in-depth interviews. It has been seen that the multiple methods used in the research process contribute to the depth and data diversity of the research conducted in the context of urban experience and locative technologies. In addition, by adapting the research design to the experiences of the users included in the sample, the differences and similarities between the initial research design and the research applied are shown.

Keywords: digital diary study, gamification, multi-model research, persona analysis, research design for urban experience, user-centered research, “Walk & Talk”

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27009 An Infinite Mixture Model for Modelling Stutter Ratio in Forensic Data Analysis

Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer

Abstract:

Forensic DNA analysis has received much attention over the last three decades, due to its incredible usefulness in human identification. The statistical interpretation of DNA evidence is recognised as one of the most mature fields in forensic science. Peak heights in an Electropherogram (EPG) are approximately proportional to the amount of template DNA in the original sample being tested. A stutter is a minor peak in an EPG, which is not masking as an allele of a potential contributor, and considered as an artefact that is presumed to be arisen due to miscopying or slippage during the PCR. Stutter peaks are mostly analysed in terms of stutter ratio that is calculated relative to the corresponding parent allele height. Analysis of mixture profiles has always been problematic in evidence interpretation, especially with the presence of PCR artefacts like stutters. Unlike binary and semi-continuous models; continuous models assign a probability (as a continuous weight) for each possible genotype combination, and significantly enhances the use of continuous peak height information resulting in more efficient reliable interpretations. Therefore, the presence of a sound methodology to distinguish between stutters and real alleles is essential for the accuracy of the interpretation. Sensibly, any such method has to be able to focus on modelling stutter peaks. Bayesian nonparametric methods provide increased flexibility in applied statistical modelling. Mixture models are frequently employed as fundamental data analysis tools in clustering and classification of data and assume unidentified heterogeneous sources for data. In model-based clustering, each unknown source is reflected by a cluster, and the clusters are modelled using parametric models. Specifying the number of components in finite mixture models, however, is practically difficult even though the calculations are relatively simple. Infinite mixture models, in contrast, do not require the user to specify the number of components. Instead, a Dirichlet process, which is an infinite-dimensional generalization of the Dirichlet distribution, is used to deal with the problem of a number of components. Chinese restaurant process (CRP), Stick-breaking process and Pólya urn scheme are frequently used as Dirichlet priors in Bayesian mixture models. In this study, we illustrate an infinite mixture of simple linear regression models for modelling stutter ratio and introduce some modifications to overcome weaknesses associated with CRP.

Keywords: Chinese restaurant process, Dirichlet prior, infinite mixture model, PCR stutter

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27008 Healthcare Big Data Analytics Using Hadoop

Authors: Chellammal Surianarayanan

Abstract:

Healthcare industry is generating large amounts of data driven by various needs such as record keeping, physician’s prescription, medical imaging, sensor data, Electronic Patient Record(EPR), laboratory, pharmacy, etc. Healthcare data is so big and complex that they cannot be managed by conventional hardware and software. The complexity of healthcare big data arises from large volume of data, the velocity with which the data is accumulated and different varieties such as structured, semi-structured and unstructured nature of data. Despite the complexity of big data, if the trends and patterns that exist within the big data are uncovered and analyzed, higher quality healthcare at lower cost can be provided. Hadoop is an open source software framework for distributed processing of large data sets across clusters of commodity hardware using a simple programming model. The core components of Hadoop include Hadoop Distributed File System which offers way to store large amount of data across multiple machines and MapReduce which offers way to process large data sets with a parallel, distributed algorithm on a cluster. Hadoop ecosystem also includes various other tools such as Hive (a SQL-like query language), Pig (a higher level query language for MapReduce), Hbase(a columnar data store), etc. In this paper an analysis has been done as how healthcare big data can be processed and analyzed using Hadoop ecosystem.

Keywords: big data analytics, Hadoop, healthcare data, towards quality healthcare

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27007 Modelling the Antecedents of Supply Chain Enablers in Online Groceries Using Interpretive Structural Modelling and MICMAC Analysis

Authors: Rose Antony, Vivekanand B. Khanapuri, Karuna Jain

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Online groceries have transformed the way the supply chains are managed. These are facing numerous challenges in terms of product wastages, low margins, long breakeven to achieve and low market penetration to mention a few. The e-grocery chains need to overcome these challenges in order to survive the competition. The purpose of this paper is to carry out a structural analysis of the enablers in e-grocery chains by applying Interpretive Structural Modeling (ISM) and MICMAC analysis in the Indian context. The research design is descriptive-explanatory in nature. The enablers have been identified from the literature and through semi-structured interviews conducted among the managers having relevant experience in e-grocery supply chains. The experts have been contacted through professional/social networks by adopting a purposive snowball sampling technique. The interviews have been transcribed, and manual coding is carried using open and axial coding method. The key enablers are categorized into themes, and the contextual relationship between these and the performance measures is sought from the Industry veterans. Using ISM, the hierarchical model of the enablers is developed and MICMAC analysis identifies the driver and dependence powers. Based on the driver-dependence power the enablers are categorized into four clusters namely independent, autonomous, dependent and linkage. The analysis found that information technology (IT) and manpower training acts as key enablers towards reducing the lead time and enhancing the online service quality. Many of the enablers fall under the linkage cluster viz., frequent software updating, branding, the number of delivery boys, order processing, benchmarking, product freshness and customized applications for different stakeholders, depicting these as critical in online food/grocery supply chains. Considering the perishability nature of the product being handled, the impact of the enablers on the product quality is also identified. Hence, study aids as a tool to identify and prioritize the vital enablers in the e-grocery supply chain. The work is perhaps unique, which identifies the complex relationships among the supply chain enablers in fresh food for e-groceries and linking them to the performance measures. It contributes to the knowledge of supply chain management in general and e-retailing in particular. The approach focus on the fresh food supply chains in the Indian context and hence will be applicable in developing economies context, where supply chains are evolving.

Keywords: interpretive structural modelling (ISM), India, online grocery, retail operations, supply chain management

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27006 Regulation of the Regeneration of Epidermal Langerhans Cells by Stress Hormone

Authors: Junichi Hosoi

Abstract:

Epidermal Langerhans cells reside in upper layer of epidermis and play a role in immune surveillance. The finding of the close association of nerve endings to Langerhans cells triggered the research on systemic regulation of Langerhans cells. They disappear from epidermis after exposure to environmental and internal stimuli and reappear about a week later. Myeloid progenitor cells are assumed to be one of the sources of Langerhans cells. We examined the effects of cortisol on the reappearance of Langerhans cells in vitro. Cord-blood derived CD34-positive cells were cultured in the medium supplemented with stem cell factor/Flt3 ligand/granulocyte macrophage-colony stimulating factor/tumor necrosis factor alpha/bone morphologic protein 7/transforming growth factor beta in the presence or absence of cortisol. Cells were analyzed by flow cytometry for CD1a (cluster differentiation 1a), a marker of Langerhans cells and dermal dendritic cells, and CD39 (cluster differentiation factor 39), extracellular adenosine triphosphatase. Both CD1a-positive cells and CD39-positive cells were decreased by treatment with cortisol (suppression by 35% and 22% compared to no stress hormone, respectively). Differentiated Langerhans cells are attracted to epidermis by chemokines that are secreted from keratinocytes. Epidermal keratinocytes were cultured in the presence or absence of cortisol and analyzed for the expression of CCL2 (C-C motif chemokine ligand 2) and CCL20 (C-C motif chemokine ligand 20), which are typical attractants of Langerhans cells, by quantitative reverse transcriptase polymerase chain reaction. The expression of both chemokines, CCL2 and CCL20, were suppressed by treatment with cortisol (suppression by 38% and 48% compared to no stress hormone, respectively). We examined the possible regulation of the suppression by cortisol with plant extracts. The extracts of Ganoderma lucidum and Iris protected the suppression of the differentiation to CD39-positive cells and also the suppression of the gene expression of LC-chemoattractants. These results suggest that cortisol, which is either systemic or locally produced, blocks the supply of epidermal Langerhans cells at 2 steps, differentiation from the precursor and attraction to epidermis. The suppression is possibly blocked by some plant extracts.

Keywords: Langerhans cell, stress, CD39, chemokine

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27005 The Relationship between Mothers’ Attachment Style, Mindful Parenting and Perception of the Child

Authors: Brigitta Szabo, Miklosi Monika

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Background/Aims: In early childhood, the context of development is the caregiver-child relationship. Maternal attachment style plays a major role in the intergenerational transmission of psychopathology. The aim of this study was to explore the relationship between the mothers’ attachment style, mindful parenting, and perception of the child. Method: Data was collected from 144 non-clinical mothers who have a child below the age of 3 years. Mothers completed self-report questionnaires, including the following scales: a demographic questionnaire, Attachment Style Questionnaire (ASQ), Interpersonal Mindfulness in Parenting Scale (IMP), and the Mothers’ Object Relations Scale (MORS-SF). K-means cluster analysis was used to identify the mothers’ attachment styles. Mediation analyses with Mothers’ Object Relations Scale (MORS-SF) positive emotions and dominance subscales as dependent variables, mothers’ attachment style (ASQ) as an independent variable, and mindful parenting (IMP) as a mediator were conducted. Results: Four attachment styles (secure, preoccupied, fearful, dismissing) were identified. The relationship between mothers’ attachment style and mindful parenting was significant (R2 = .51; F(4,139) = 36.60; p < .001). Compared to the secure attachment style as a reference group, both preoccupied and dismissing styles were related to lower levels of mindful parenting; however, this relationship was the strongest in case of fearful style. In mediation analysis the direct effects of mothers’ attachment style on the perception of the child were not significant (MORS positive emotions: R2= .29; F(5,138) = 11.22; p < .001; MORS dominance: R2= .39 F(5,138) = 17.54, p < .001). However, indirect effects through mindful parenting were significant; higher levels of mindful parenting were associated with higher levels of MORS positive emotions and lower levels of MORS dominance. Conclusions: These findings suggest that attachment styles are related to the perception of the child through mindful parenting. Mindfulness-based parenting training might be useful in case of attachment-related problems to improve the parent-child relationship.

Keywords: mindfulness, mindful parenting, attachement, perception

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27004 Analysing the Degree of Climate Risk Perception and Response Strategies of Farm Household Typologies in Northern Ghana

Authors: David Ahiamadia, Ramilan Thiagarajah, Peter Tozer

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In Sub Saharan Africa, farm typologies have been used as a practical way to address heterogeneity among farming systems which is mostly done by grouping farms into subsets with similar characteristics. Due to the complexity in farming systems among farm households, it is not possible to formulate policy recommendations for individual farmers. As a result, this study employs a multivariate statistical approach using Principal Component Analysis (PCA) coupled with cluster analysis to reduce heterogeneity in a 615-household data set from the Africa Rising Baseline Evaluation Survey for 25 farming communities in Northern Ghana. Variables selected for the study were mostly socio-economic, production potential, production intensity, production orientation, crop diversity, food security, resource endowments, and climate risk variables. To avoid making some individuals in the subpopulation worse off when aclimate risk intervention is broadly implemented, the findings of the study also account for diversity in climate risk perception among the different farm types identified and their response strategies towards climate risk. The climate risk variables used in this study involve the most severeclimate shock types perceived by the household, household response to climate shock type, and reason for crop failure (i.e., maize, rice, and groundnut). Eventually, four farm types, each with an adequate level of homogeneity in climate risk perception and response strategies, were identified. Farm type 1 and 3 were wealthy with a lower degree of climate risk perception compared to farm type 2 and 4. Also, relatively wealthy farmers used asset liquidation as a climate risk management strategy, whereas poor farmers resorted to engaging in spiritual activities such as prayers, sacrifices, and divine consultations.

Keywords: smallholder, households, climate risk, variables, typologies

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27003 The Effectiveness of Cognitive-Behavioral Group Therapy on Stress, Illness Anxiety and Obsessions-Compulsion Caused by the Coronavirus Crisis in Adolescent (14-18 Year olds) in Tehran, Iran

Authors: Maryam Mousavi Nik, Sara Pasandian

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The aim of the current research was to determine the effectiveness of Cognitive-Behavioral Group Therapy (G-CBT) on stress, illness anxiety and obsessions-compulsion caused by the coronavirus crisis in adolescents (14-18-Year-olds) in Tehran, Iran. This research was carried out in the form of a semi-experimental study with a control group and in the framework of a pre-test and post-test design for both experimental and control groups. The statistical population of this research consisted of all high schools in Tehran in 2022. The sample size includes 32 Adolescents (14-18-Year-olds) who were selected using a cluster sampling method, and then they were randomly replaced in two experimental (n=16) and control (n=16) groups. In this research, an adolescent stress questionnaire (ASQ-N) with an emphasis on the impact of Coronavirus, Coronavirus disease anxiety (CDAS) and The Children's Yale-Brown Obsessive Compulsive Symptom Scale (CY-BOCS) emphasis on the Coronavirus were used, and group therapy intervention with The cognitive-behavioral approach was conducted for 8 sessions of 90 minutes in the experimental group. The research data were analyzed by Multivariate analysis of covariance (MANCOVA) and covariance (ANCVA) tests. The results of multivariate covariance analysis showed that group therapy intervention with a cognitive-behavioral approach had a significant effect on at least one of the variables of stress, illness anxiety and obsession-compulsion at the level (P<0.01, F=94.772) in the post-test stage. Also, the results of covariance analysis of one variable showed that group therapy intervention with a cognitive-behavioral approach in the level of (P<0.01, F=106.377) stress, in the level of (P<0.01, F=48.147) disease anxiety and in the level (P>0.01, F=17.033) of obsession-compulsion had a significant effect in the post-test stage. The results showed that The treatment with GCBT can be effective in decreasing stress, illness anxiety and obsessions and compulsion caused by the coronavirus crisis in Adolescents (15-20-Year-olds) and may be considered as an alternative to either individual cognitive-behavioral therapy or medication.

Keywords: stress, disease anxiety, obsession-compulsion, coronavirus (Covid-19) crisis, and cognitive-behavioral therapy

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27002 Analysis of Determinants of Growth of Small and Medium Enterprises in Kwara State, Nigeria

Authors: Hussaini Tunde Subairu

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Small and Medium Enterprises (SMEs) sectors serve as catalyst for employment generation, national growth, poverty reduction and economic development in developing and developed countries. However, in Nigeria despite copious and plethora of government policies and stimulus schemes directed at SMEs, the sector is still characterized by high rate of failure and discontinuities. This study therefore investigated owners/managers profile, firms characteristics and external factors as possible determinants of SMEs growth from selected SMEs in Kwara State. Primary data were sourced from 200 SMEs respondents registered with the National Association of Small and Medium Enterprises (NASMES) in Kwara State Central Senatorial District. Multiple Regressions Analysis (MRA) was used to analyze the relationship between dependent and independent variables, and pair wise correlation was employed to examine the relationship among independent variables. The Analysis of Variable (ANOVA) was employed to indicate the overall significant of the model The findings revealed that Analysis of variance (ANOVA) put the value of F-statistics at 420.45 and p-value at 0.000 was significant. The values of R2 and Adjusted R2 of 0.9643 and 0.9620 respectively suggested that 96 percent of variations in employment growth were explained by the explanatory variables. The level of technical and managerial education has t- value of 24.14 and p-value of 0.001, length of managers/owners experience in similar trade with t- value of 21.37 and p-value of 0.001, age of managers/owners with t- value of 42.98 and p-value of 0.001, firm age with t- value of 25.91 and p-value of 0.001, numbers of firms in a cluster with t- value of 7.20 and p-value of 0.001, access to formal finance with t-value of 5.56 and p-value of 0.001, firm technology innovation with t- value of 25.32 and p-value of 0.01, institutional support with t- value of 18.89 and p-value of 0.01, globalization with t- value of 9.78 and p-value of 0.01, and infrastructure with t-value of 10.75 and p-value of 0.01. The result also indicated that initial size has t-value of -1.71 and p-value of 0.090 which is consistent with Gibrat’s Law. The study concluded that owners/managers profile, firm specific characteristics and external factors substantially influenced employment growths of SMEs in the study area. Therefore, policy implication should enhance human capital development of SMEs owners/managers, and strengthen fiscal policy thrust through imposition on tariff regime to minimize effect of globalization. Governments at all level must support SMEs growth radically and enhance institutional support for SMEs growth and radically and significantly upgrading key infrastructure as rail/roads, rail, telecommunications, water and power.

Keywords: external factors, firm specific characteristics, owners / manager profile, small and medium enterprises

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27001 Application of Subversion Analysis in the Search for the Causes of Cracking in a Marine Engine Injector Nozzle

Authors: Leszek Chybowski, Artur Bejger, Katarzyna Gawdzińska

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

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

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27000 Copy Number Variants in Children with Non-Syndromic Congenital Heart Diseases from Mexico

Authors: Maria Lopez-Ibarra, Ana Velazquez-Wong, Lucelli Yañez-Gutierrez, Maria Araujo-Solis, Fabio Salamanca-Gomez, Alfonso Mendez-Tenorio, Haydeé Rosas-Vargas

Abstract:

Congenital heart diseases (CHD) are the most common congenital abnormalities. These conditions can occur as both an element of distinct chromosomal malformation syndromes or as non-syndromic forms. Their etiology is not fully understood. Genetic variants such copy number variants have been associated with CHD. The aim of our study was to analyze these genomic variants in peripheral blood from Mexican children diagnosed with non-syndromic CHD. We included 16 children with atrial and ventricular septal defects and 5 healthy subjects without heart malformations as controls. To exclude the most common heart disease-associated syndrome alteration, we performed a fluorescence in situ hybridization test to identify the 22q11.2, responsible for congenital heart abnormalities associated with Di-George Syndrome. Then, a microarray based comparative genomic hybridization was used to identify global copy number variants. The identification of copy number variants resulted from the comparison and analysis between our results and data from main genetic variation databases. We identified copy number variants gain in three chromosomes regions from pediatric patients, 4q13.2 (31.25%), 9q34.3 (25%) and 20q13.33 (50%), where several genes associated with cellular, biosynthetic, and metabolic processes are located, UGT2B15, UGT2B17, SNAPC4, SDCCAG3, PMPCA, INPP6E, C9orf163, NOTCH1, C20orf166, and SLCO4A1. In addition, after a hierarchical cluster analysis based on the fluorescence intensity ratios from the comparative genomic hybridization, two congenital heart disease groups were generated corresponding to children with atrial or ventricular septal defects. Further analysis with a larger sample size is needed to corroborate these copy number variants as possible biomarkers to differentiate between heart abnormalities. Interestingly, the 20q13.33 gain was present in 50% of children with these CHD which could suggest that alterations in both coding and non-coding elements within this chromosomal region may play an important role in distinct heart conditions.

Keywords: aCGH, bioinformatics, congenital heart diseases, copy number variants, fluorescence in situ hybridization

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26999 Estimating Estimators: An Empirical Comparison of Non-Invasive Analysis Methods

Authors: Yan Torres, Fernanda Simoes, Francisco Petrucci-Fonseca, Freddie-Jeanne Richard

Abstract:

The non-invasive samples are an alternative of collecting genetic samples directly. Non-invasive samples are collected without the manipulation of the animal (e.g., scats, feathers and hairs). Nevertheless, the use of non-invasive samples has some limitations. The main issue is degraded DNA, leading to poorer extraction efficiency and genotyping. Those errors delayed for some years a widespread use of non-invasive genetic information. Possibilities to limit genotyping errors can be done using analysis methods that can assimilate the errors and singularities of non-invasive samples. Genotype matching and population estimation algorithms can be highlighted as important analysis tools that have been adapted to deal with those errors. Although, this recent development of analysis methods there is still a lack of empirical performance comparison of them. A comparison of methods with dataset different in size and structure can be useful for future studies since non-invasive samples are a powerful tool for getting information specially for endangered and rare populations. To compare the analysis methods, four different datasets used were obtained from the Dryad digital repository were used. Three different matching algorithms (Cervus, Colony and Error Tolerant Likelihood Matching - ETLM) are used for matching genotypes and two different ones for population estimation (Capwire and BayesN). The three matching algorithms showed different patterns of results. The ETLM produced less number of unique individuals and recaptures. A similarity in the matched genotypes between Colony and Cervus was observed. That is not a surprise since the similarity between those methods on the likelihood pairwise and clustering algorithms. The matching of ETLM showed almost no similarity with the genotypes that were matched with the other methods. The different cluster algorithm system and error model of ETLM seems to lead to a more criterious selection, although the processing time and interface friendly of ETLM were the worst between the compared methods. The population estimators performed differently regarding the datasets. There was a consensus between the different estimators only for the one dataset. The BayesN showed higher and lower estimations when compared with Capwire. The BayesN does not consider the total number of recaptures like Capwire only the recapture events. So, this makes the estimator sensitive to data heterogeneity. Heterogeneity in the sense means different capture rates between individuals. In those examples, the tolerance for homogeneity seems to be crucial for BayesN work properly. Both methods are user-friendly and have reasonable processing time. An amplified analysis with simulated genotype data can clarify the sensibility of the algorithms. The present comparison of the matching methods indicates that Colony seems to be more appropriated for general use considering a time/interface/robustness balance. The heterogeneity of the recaptures affected strongly the BayesN estimations, leading to over and underestimations population numbers. Capwire is then advisable to general use since it performs better in a wide range of situations.

Keywords: algorithms, genetics, matching, population

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26998 A Study of Semantic Analysis of LED Illustrated Traffic Directional Arrow in Different Style

Authors: Chia-Chen Wu, Chih-Fu Wu, Pey-Weng Lien, Kai-Chieh Lin

Abstract:

In the past, the most comprehensively adopted light source was incandescent light bulbs, but with the appearance of LED light sources, traditional light sources have been gradually replaced by LEDs because of its numerous superior characteristics. However, many of the standards do not apply to LEDs as the two light sources are characterized differently. This also intensifies the significance of studies on LEDs. As a Kansei design study investigating the visual glare produced by traffic arrows implemented with LEDs, this study conducted a semantic analysis on the styles of traffic arrows used in domestic and international occasions. The results will be able to reduce drivers’ misrecognition that results in the unsuccessful arrival at the destination, or in traffic accidents. This study started with a literature review and surveyed the status quo before conducting experiments that were divided in two parts. The first part involved a screening experiment of arrow samples, where cluster analysis was conducted to choose five representative samples of LED displays. The second part was a semantic experiment on the display of arrows using LEDs, where the five representative samples and the selected ten adjectives were incorporated. Analyzing the results with Quantification Theory Type I, it was found that among the composition of arrows, fletching was the most significant factor that influenced the adjectives. In contrast, a “no fletching” design was more abstract and vague. It lacked the ability to convey the intended message and might bear psychological negative connotation including “dangerous,” “forbidden,” and “unreliable.” The arrow design consisting of “> shaped fletching” was found to be more concrete and definite, showing positive connotation including “safe,” “cautious,” and “reliable.” When a stimulus was placed at a farther distance, the glare could be significantly reduced; moreover, the visual evaluation scores would be higher. On the contrary, if the fletching and the shaft had a similar proportion, looking at the stimuli caused higher evaluation at a closer distance. The above results will be able to be applied to the design of traffic arrows by conveying information definitely and rapidly. In addition, drivers’ safety could be enhanced by understanding the cause of glare and improving visual recognizability.

Keywords: LED, arrow, Kansei research, preferred imagery

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26997 Palyno-Morphological Characteristics of Gymnosperm Flora of Pakistan and Its Taxonomic Implications with Light Microscope and Scanning Electron Microscopy Methods

Authors: Raees Khan, Sheikh Z. Ul Abidin, Abdul S. Mumtaz, Jie Liu

Abstract:

The present study is intended to assess gymnosperms pollen flora of Pakistan using Light Microscope (LM) and Scanning Electron Microscopy (SEM) for its taxonomic significance in identification of gymnosperms. Pollens of 35 gymnosperm species (12 genera and five families) were collected from its various distributional sites of gymnosperms in Pakistan. LM and SEM were used to investigate different palyno-morphological characteristics. Five pollen types (i.e., Inaperturate, Monolete, Monoporate, Vesiculate-bisaccate, and Polyplicate) were observed. In equatorial view seven types of pollens were observed, in which ten species were sub-angular, nine species were triangular, six species were perprolate, three species were rhomboidal, three species were semi-angular, two species were rectangular and two species were prolate. While five types of pollen were observed in polar view, in which ten species were spheroidal, nine species were angular, eight were interlobate, six species were circular, and two species were elliptic. Eighteen species have rugulate and 17 species has faveolate ornamentation. Eighteen species have verrucate and 17 have gemmate type sculpturing. The data was analysed through cluster analysis. The study showed that these palyno-morphological features have significance value in classification and identification of gymnosperms. Based on these different palyno-morphological features, a taxonomic key was proposed for the accurate and fast identifications of gymnosperms from Pakistan.

Keywords: gymnosperms, palynology, Pakistan, taxonomy

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26996 Applying GIS Geographic Weighted Regression Analysis to Assess Local Factors Impeding Smallholder Farmers from Participating in Agribusiness Markets: A Case Study of Vihiga County, Western Kenya

Authors: Mwehe Mathenge, Ben G. J. S. Sonneveld, Jacqueline E. W. Broerse

Abstract:

Smallholder farmers are important drivers of agriculture productivity, food security, and poverty reduction in Sub-Saharan Africa. However, they are faced with myriad challenges in their efforts at participating in agribusiness markets. How the geographic explicit factors existing at the local level interact to impede smallholder farmers' decision to participates (or not) in agribusiness markets is not well understood. Deconstructing the spatial complexity of the local environment could provide a deeper insight into how geographically explicit determinants promote or impede resource-poor smallholder farmers from participating in agribusiness. This paper’s objective was to identify, map, and analyze local spatial autocorrelation in factors that impede poor smallholders from participating in agribusiness markets. Data were collected using geocoded researcher-administered survey questionnaires from 392 households in Western Kenya. Three spatial statistics methods in geographic information system (GIS) were used to analyze data -Global Moran’s I, Cluster and Outliers Analysis (Anselin Local Moran’s I), and geographically weighted regression. The results of Global Moran’s I reveal the presence of spatial patterns in the dataset that was not caused by spatial randomness of data. Subsequently, Anselin Local Moran’s I result identified spatially and statistically significant local spatial clustering (hot spots and cold spots) in factors hindering smallholder participation. Finally, the geographically weighted regression results unearthed those specific geographic explicit factors impeding market participation in the study area. The results confirm that geographically explicit factors are indispensable in influencing the smallholder farming decisions, and policymakers should take cognizance of them. Additionally, this research demonstrated how geospatial explicit analysis conducted at the local level, using geographically disaggregated data, could help in identifying households and localities where the most impoverished and resource-poor smallholder households reside. In designing spatially targeted interventions, policymakers could benefit from geospatial analysis methods in understanding complex geographic factors and processes that interact to influence smallholder farmers' decision-making processes and choices.

Keywords: agribusiness markets, GIS, smallholder farmers, spatial statistics, disaggregated spatial data

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26995 Spring Water Quality Appraisement for Drinking and Irrigation Application in Nigeria: A Muliti-Criteria Approach

Authors: Hillary Onyeka Abugu, Valentine Chinakwugwo Ezea, Janefrances Ngozi Ihedioha, Nwachukwu Romanus Ekere

Abstract:

The study assessed the spring water quality in Igbo-Etiti, Nigeria, for drinking and irrigation application using Physico-chemical parameters, water quality index, mineral and trace elements, pollution indices and risk assessment. Standard methods were used to determine the physicochemical properties of the spring water in rainy and dry seasons. Trace metals such as Pb, Cd, Zn and Cu were determined with atomic absorption spectrophotometer. The results showed that most of the physicochemical properties studied were within the guideline values set by Nigeria Standard for Drinking Water Quality (NSDWQ), WHO and US EPA for drinking water purposes. However, pH of all the spring water (4.27- 4.73; and 4.95- 5.73), lead (Pb) (0.01-1.08 mg/L) and cadmium (Cd) (0.01-0.15 mg/L) concentrations were above the guideline values in both seasons. This could be attributed to the lithography of the study area, which is the Nsukka formation. Leaching of lead and sulphides from the embedded coal deposits could have led to the increased lead levels and made the water acidic. Two-way ANOVA showed significant differences in most of the parameters studied in dry and rainy seasons. Pearson correlation analysis and cluster analysis showed strong significant positive and negative correlations in some of the parameters studied in both seasons. The water quality index showed that none of the spring water had excellent water status. However, one spring (Iyi Ase) had poor water status in dry season and is considered unsafe for drinking. Iyi Ase was also considered not suitable for irrigation application as predicted by most of the pollution indices, while others were generally considered suitable for irrigation application. Probable cancer and non-cancer risk assessment revealed a probable risk associated with the consumption of the spring in the Igbo-Ettiti area, Nigeria.

Keywords: water quality, pollution index, risk assessment, physico-chemical parameters

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26994 Cluster-Based Multi-Path Routing Algorithm in Wireless Sensor Networks

Authors: Si-Gwan Kim

Abstract:

Small-size and low-power sensors with sensing, signal processing and wireless communication capabilities is suitable for the wireless sensor networks. Due to the limited resources and battery constraints, complex routing algorithms used for the ad-hoc networks cannot be employed in sensor networks. In this paper, we propose node-disjoint multi-path hexagon-based routing algorithms in wireless sensor networks. We suggest the details of the algorithm and compare it with other works. Simulation results show that the proposed scheme achieves better performance in terms of efficiency and message delivery ratio.

Keywords: clustering, multi-path, routing protocol, sensor network

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26993 ICAM-2, A Protein of Antitumor Immune Response in Mekong Giant Catfish (Pangasianodon gigas)

Authors: Jiraporn Rojtinnakorn

Abstract:

ICAM-2 (intercellular adhesion molecule 2) or CD102 (Cluster of Differentiation 102) is type I trans-membrane glycoproteins, composing 2-9 immunoglobulin-like C2-type domains. ICAM-2 plays the particular role in immune response and cell surveillance. It is concerned in innate and specific immunity, cell survival signal, apoptosis, and anticancer. EST clone of ICAM-2, from P. gigas blood cell EST libraries, showed high identity to human ICAM-2 (92%) with conserve region of ICAM N-terminal domain and part of Ig superfamily. Gene and protein of ICAM-2 has been founded in mammals. This is the first report of ICAM-2 in fish.

Keywords: ICAM-2, CD102, Pangasianodon gigas, antitumor

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26992 A Brief Exploration on the Green Urban Design for Carbon Neutrality

Authors: Gaoyuan Wang, Tian Chen

Abstract:

China’s emission peak and carbon neutrality strategies lead to the transformation of development patterns and call for new green urban design thinking. This paper begins by revealing the evolution of green urban design thinking during the periods of carbon enlightenment, carbon dependency, and carbon decoupling from the perspective of the energy transition. Combined with the current energy situation, national strengths, and technological trends, the emergence of green urban design towards carbon neutrality becomes inevitable. Based on the preliminary analysis of its connotation, the characteristics of the new type of green urban design are generalized as low-carbon orientation, carbon-related objects, carbon-reduction means, and carbon-control patterns. Its theory is briefly clarified in terms of the human-earth synergism, quality-energy interconnection, and form-flow interpromotion. Then, its mechanism is analyzed combined with the core tasks of carbon neutrality, and the scope of design issues is defined, including carbon flow mapping, carbon source regulation, carbon sink construction, and carbon emission management. Finally, a multi-scale spatial response system is proposed across the region, city, cluster, and neighborhood level. The discussion aims to provide support for the innovation of green urban design theories and methods in the context of peak neutrality.

Keywords: carbon neutrality, green urban design, energy transition, theoretical exploration

Procedia PDF Downloads 151
26991 Application of Fuzzy Clustering on Classification Agile Supply Chain

Authors: Hamidreza Fallah Lajimi , Elham Karami, Fatemeh Ali nasab, Mostafa Mahdavikia

Abstract:

Being responsive is an increasingly important skill for firms in today’s global economy; thus firms must be agile. Naturally, it follows that an organization’s agility depends on its supply chain being agile. However, achieving supply chain agility is a function of other abilities within the organization. This paper analyses results from a survey of 71 Iran manufacturing companies in order to identify some of the factors for agile organizations in managing their supply chains. Then we classification this company in four cluster with fuzzy c-mean technique and with four validations functional determine automatically the optimal number of clusters.

Keywords: agile supply chain, clustering, fuzzy clustering

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26990 Cultural Landscape Planning – A Case of Chettinad Village Clusters

Authors: Adhithy Menon E., Biju C. A.

Abstract:

In the 1960s, the concept of preserving heritage monuments was first introduced. During the 1990s, the concept of cultural landscapes gained importance, highlighting the importance of culture and heritage. Throughout this paper, we examine the second category of the cultural landscape, which is an organically evolving landscape as it represents a web of tangible, intangible, and ecological heritage and the ways in which they can be rejuvenated. Cultural landscapes in various regions, such as the Chettinad Village clusters, are in serious decline, which is identified through the Heritage Passport program of this area (2007). For this reason, it is necessary to conduct a detailed analysis of the factors that contribute to this degradation to ensure its protection in the future. An analysis of the cultural landscape of the Chettinad Village clusters and its impact on the community is presented in this paper. The paper follows the first objective, which is to understand cultural landscapes and their different criteria and categories. It is preceded by the study of various methods for protecting cultural landscapes. To identify a core area of intervention based on the parameters of Cultural Landscapes and Community Based Tourism, a study and analysis of the regional context of Chettinad village clusters considering tourism development must first be conducted. Lastly, planning interventions for integrating community-based tourism in Chettinad villages for the purpose of rejuvenating the cultural landscapes of the villages as well as their communities. The major findings include the importance of the local community in protecting cultural landscapes. The parameters identified to have an impact on Chettinad Village clusters are a community (community well-being, local maintenance, and enhancement, demand, alternative income for community, public participation, awareness), tourism (location and physical access, journey time, tourist attractions), integrity (natural factors, natural disasters, demolition of structures, deterioration of materials) authenticity (sense of place, living elements, building techniques, artistic expression, religious context) disaster management (natural disasters) and environmental impact (pollution). This area can be restored to its former glory and preserved as part of the cultural landscape for future generations by focusing on and addressing these parameters within the identified core area of the Chettinad Villages cluster (Kanadukathan TP, Kothamangalam, Kottaiyur, Athangudi, Karikudi, and Palathur).

Keywords: Chettinad village clusters, community, cultural landscapes, organically evolved.

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26989 Microbial Biogeography of Greek Olive Varieties Assessed by Amplicon-Based Metagenomics Analysis

Authors: Lena Payati, Maria Kazou, Effie Tsakalidou

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Table olives are one of the most popular fermented vegetables worldwide, which along with olive oil, have a crucial role in the world economy. They are highly appreciated by the consumers for their characteristic taste and pleasant aromas, while several health and nutritional benefits have been reported as well. Until recently, microbial biogeography, i.e., the study of microbial diversity over time and space, has been mainly associated with wine. However, nowadays, the term 'terroir' has been extended to other crops and food products so as to link the geographical origin and environmental conditions to quality aspects of fermented foods. Taking the above into consideration, the present study focuses on the microbial fingerprinting of the most important olive varieties of Greece with the state-of-the-art amplicon-based metagenomics analysis. Towards this, in 2019, 61 samples from 38 different olive varieties were collected at the final stage of ripening from 13 well spread geographical regions in Greece. For the metagenomics analysis, total DNA was extracted from the olive samples, and the 16S rRNA gene and ITS DNA region were sequenced and analyzed using bioinformatics tools for the identification of bacterial and yeasts/fungal diversity, respectively. Furthermore, principal component analysis (PCA) was also performed for data clustering based on the average microbial composition of all samples from each region of origin. According to the composition, results obtained, when samples were analyzed separately, the majority of both bacteria (such as Pantoea, Enterobacter, Roserbergiella, and Pseudomonas) and yeasts/fungi (such as Aureobasidium, Debaromyces, Candida, and Cladosporium) genera identified were found in all 61 samples. Even though interesting differences were observed at the relative abundance level of the identified genera, the bacterial genus Pantoea and the yeast/fungi genus Aureobasidium were the dominant ones in 35 and 40 samples, respectively. Of note, olive samples collected from the same region had similar fingerprint (genera identified and relative abundance level) regardless of the variety, indicating a potential association between the relative abundance of certain taxa and the geographical region. When samples were grouped by region of origin, distinct bacterial profiles per region were observed, which was also evident from the PCA analysis. This was not the case for the yeast/fungi profiles since 10 out of the 13 regions were grouped together mainly due to the dominance of the genus Aureobasidium. A second cluster was formed for the islands Crete and Rhodes, both of which are located in the Southeast Aegean Sea. These two regions clustered together mainly due to the identification of the genus Toxicocladosporium in relatively high abundances. Finally, the Agrinio region was separated from the others as it showed a completely different microbial fingerprinting. However, due to the limited number of olive samples from some regions, a subsequent PCA analysis with more samples from these regions is expected to yield in a more clear clustering. The present study is part of a bigger project, the first of its kind in Greece, with the ultimate goal to analyze a larger set of olive samples of different varieties and from different regions in Greece in order to have a reliable olives’ microbial biogeography.

Keywords: amplicon-based metagenomics analysis, bacteria, microbial biogeography, olive microbiota, yeasts/fungi

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