Search results for: spatial gene

Authors: Xiaohan Gao, Kai Liu

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As essential components of urban areas, primary and secondary schools are extensively distributed throughout various regions of the city. During times of urban disturbances, these schools become direct carriers of complex disruptions. Therefore, fostering resilient schools becomes a pivotal driving force to promote high-quality urban development and a cornerstone of sustainable school growth. This paper adopts the theory of spatial resilience and focuses on primary and secondary schools in Chinese cities as the research subject. The study first explores the potential disturbance risks faced by schools and delves into the origin and concept of spatial resilience in the educational context. Subsequently, the paper conducts a meta-analysis to characterize the spatial resilience of primary and secondary schools and devises a spatial resilience planning mechanism. Drawing insights from exemplary cases both domestically and internationally, the research formulates spatial and planning resilience strategies for primary and secondary schools to cope with perturbations. These strategies encompass creating an overall layout that integrates harmoniously with nature, promoting organic growth in the planning structure, fostering ecological balance in the landscape system, and enabling dynamic adaptation in architectural spaces. By cultivating the capacity for "resistance-adaptation-transformation," these approaches support sustainable development within the school space. The ultimate goal of this project is to establish a cohesive and harmonious layout that advances the sustainable development of primary and secondary schools while contributing to the overall resilience of urban areas.

Keywords: complex disruption, primary and secondary schools, spatial resilience, sustainable development

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Authors: Sofia Barbosa, Mariana Pinto, José António Almeida, Edgar Carvalho, Catarina Diamantino

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The aim of this work was to test a methodology able to generate spatial-temporal maps that can synthesize simultaneously the trends of distinct hydrochemical indicators in an old radium-uranium tailings dam deposit. Multidimensionality reduction derived from principal component analysis and subsequent data aggregation derived from clustering analysis allow to identify distinct hydrochemical behavioural profiles and to generate synthetic evolutionary hydrochemical maps.

Keywords: Contamination plume migration, K-means of PCA scores, groundwater and mine water monitoring, spatial-temporal hydrochemical trends

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Authors: Azna Zuberi

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Biofilm is a sessile bacterial accretion in which bacteria adapts different physiological and morphological behavior from planktonic form. It is the root cause of about 80% microbial infections in human. Among them, E. coli biofilms are most prevalent in medical devices associated nosocomial infections. The objective of this study was to inhibit biofilm formation by targeting LuxS gene, involved in quorum sensing using CRISPRi. luxS is a synthase, involved in the synthesis of Autoinducer-2(AI-2), which in turn guides the initial stage of biofilm formation. To implement CRISPRi system, we have synthesized complementary sgRNA to target gene sequence and co-expressed with dCas9. Suppression of luxS was confirmed through qRT-PCR. The effect of luxS gene on biofilm inhibition was studied through crystal violet assay, XTT reduction assay and scanning electron microscopy. We conclude that CRISPRi system could be a potential strategy to inhibit bacterial biofilm through mechanism base approach.

Keywords: biofilm, CRISPRi, luxS, microbial

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Authors: Małgorzata Wrzosek, Nina Baruch, Beata Jabłonowska-Lietz

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Background: The fat mass & obesity-associated (FTO) gene is linked to an increased risk of obesity. However, the relation between rs9939609 and eating behaviors or energy expenditure is not fully elucidated. The aim of this study was to investigate the relationship between the rs9939609 polymorphism of the FTO gene and the postprandial satiety, sweets intake, physical activity and depressive symptoms in patients with obesity. Methods: The study group consisted of 585 subjects with a BMI of 42.97.0 kg/m². The rs9939609 polymorphism of the FTO gene was examined using real time – PCR method. The severity of depressive symptoms was assessed with the Beck Depression Inventory (BDI-II). Information was obtained about demographics, eating habits and lifestyle. Results: More than half (63.5%) of the patients reported consumption of sweets between main meals and 30% declared high and very high postprandial satiety and the frequency of TA/AA carriers in rs9939609 (FTO) compared with TT carriers was similar. Significantly lower BDI-II scores were found in subjects with higher level of physical activity and it was seen amongst patients with the AA and AT genotypes of the FTO rs9939609 polymorphism. Conclusion: Obesity is a highly heritable trait, but eating habits also appear as major factors affecting obesity development.

Keywords: FTO polymorphism, physical activity, obesity, depression, postprandial satiety, sugary foods, sweets

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Authors: Mehrangiz Rezaee, Zabih Charrahi

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In the last decade, with increasing tourism destinations and tourism growth, we are witnessing the widespread impacts of tourism on the economy, environment and society. Tourism and its related economy are now undergoing a transformation and as one of the key pillars of business economics, it plays a vital role in the world economy. Activities related to tourism and providing services appropriate to it in an area, like many economic sectors, require the necessary context on its origin. Given the importance of tourism industry and tourism potentials of Yazd province in Iran, it is necessary to use a proper procedure for prioritizing different areas for proper and efficient planning. One of the most important goals of planning is foresight and creating balanced development in different geographical areas. This process requires an accurate study of the areas and potential and actual talents, as well as evaluation and understanding of the relationship between the indicators affecting the development of the region. At the global and regional level, the development of tourist resorts and the proper distribution of tourism destinations are needed to counter environmental impacts and risks. The main objective of this study is the sustainable development of suitable tourism areas. Given that tourism activities in different territorial areas require operational zoning, this study deals with the evaluation of territorial tourism using concepts such as land use, fitness and sustainable development. It is essential to understand the structure of tourism development and the spatial development of tourism using land use patterns, spatial planning and sustainable development. Tourism spatial planning implements different approaches. However, the development of tourism as well as the spatial development of tourism is complex, since tourist activities can be carried out in different areas with different purposes. Multipurpose areas have great important for tourism because it determines the flow of tourism. Therefore, in this paper, by studying the development and determination of tourism suitability that is related to spatial development, it is possible to plan tourism spatial development by developing a model that describes the characteristics of tourism. The results of this research determine the suitability of multi-functional territorial tourism development in line with spatial planning of tourism.

Keywords: land use change, spatial planning, sustainability, territorial tourist, Yazd

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Authors: Karitikeya Sonker

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Religion as a discrete system through its lawful internal working produces an output in the form of realised spatial order with its social logic and a social order with its spatial logic. Thus, it appears to exhibit its duality of spatial and trans-spatial. The components of this system share a relevance forming a collective. This shared relevance creates meaning forming a group where all collectives share one identity. This group with its new social order and its spatial logic revive the already existing spatial order. These religious groups do so having a tendency to expand resulting in the production of space in a situation of encounter where they have found relevance. But an encounter without a lawful internal working of a discrete system results in anomaly because groups do not find relevance due to the absence of collective identity. Events happen all around. One of the main reasons we could say that something became an event is because of conflict. Conflict not in its definitive sense but any occurrence that happens because of an intervention that creates an event worth remembering. The unfolding of such events creates Cities and Urban spaces which exhibit their duality of spatial and trans-spatial by behaving as a discrete system. This system through its lawful internal working produces an output in the form of realized spatial order with its social logic and a social order with spatial logic. The components of this system form a collective through a shared a relevance. This shared relevance creates meaning forming a group where all collectives share one identity. This group with its new social order and its spatial logic revives the already existing spatial order. These groups do so having a tendency to expand resulting in the production of space in a situation of encounter where they have found relevance. But an encounter without a lawful internal working of the discrete system results in anomaly because groups do not find relevance due to the absence of collective identity. This paper makes an effort to explore one such even in the case of Babri Mosque and Ramjanmabhumi, Ayodhya to explain the anomaly as transposition of social and spatial. The paper through the case studies makes an attempt to generate an equation explaining the two different situations of religious encounters, former reviving the social and spatial order and the other resulting in anomaly. Through the case study, it makes an attempt to generate an equation explaining the two different situations of religious encounters, former reviving the social and spatial order and the other resulting in anomaly.

Keywords: Babri Masjid, Ayodhya, conflict, religion

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Authors: Z. Bouattou, R. Laurini, H. Belbachir

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This paper describes a new approach for the automatic generation of the visual summaries dealing with cartographic visualization methods and sensors real time data modeling. Hence, the concept of chorems seems an interesting candidate to visualize real time geographic database summaries. Chorems have been defined by Roger Brunet (1980) as schematized visual representations of territories. However, the time information is not yet handled in existing chorematic map approaches, issue has been discussed in this paper. Our approach is based on spatial analysis by interpolating the values recorded at the same time, by sensors available, so we have a number of distributed observations on study areas and used spatial interpolation methods to find the concentration fields, from these fields and by using some spatial data mining procedures on the fly, it is possible to extract important patterns as geographic rules. Then, those patterns are visualized as chorems.

Keywords: geovisualization, spatial analytics, real-time, geographic data streams, sensors, chorems

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Authors: Ahmad Ali Shahid, M Shakil Shaukat

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Agriculture is the backbone of economy of Pakistan and Cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat against the developing resistance in the target insects and combating these challenges wholesomely, a novel combination of pyramided/stacked genes was conceptualized and later realized, through the means of biotechnology i.e., transformation of three genes namely, Cry1Ac, Cry2A, and EPSP synthase (glyphosate tolerant) genes in the locally cultivated cotton variety. The progenies of the transformed plants were successfully raised and screened under the tunnel conditions for two generations and the present study focused on the screening of plants which were confirmed for containing all of these three genes and their expressions. Initially, the screening was done through glyphosate spray assay and the plants which were healthy and showed no damage on leaves were selected after 07 days of spray. In the laboratory, the DNA of these plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty were confirmed positive for Cry1Ac gene and ten out of twenty were positive for Cry2A gene and all twenty were positive for presence of EPSP synthase gene. Then, the ten plant samples which were confirmed with presence of all three genes were subjected to expression analysis of these proteins through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the expression levels of the EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes in T3 generation of the triple gene transformed cotton. These plants may be subjected to T4 generation to develop a new stable variety in due course of time.

Keywords: agriculture, cotton, transformation, cry genes, ELISA, PCR

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Authors: Rasime Kalkan, Emine Ikbal Atli, Ali Arslantaş, Muhsin Özdemir, Sevilhan Artan

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Glioblastoma (WHO grade IV), is the malignant form of brain tumor, the genetic background of the GBM is highly variable. The tumor mass of a GBM is multilayered and every tumor layer shows distinct characteristics with a different cell population. The treatment planning of GBM should be focused on the tumor genetic characteristics. We screened primary glioblastoma multiforme (GBM) in a population-based study for MGMT and RARβ methylation and IDH1 mutation correlated them with clinical data and treatment. There was no correlation between MGMT-promoter methylation and overall survival. The overall survival time of the patients with methylated RARβ was statically (OS;p<0,05) significance between the patients who were treated with chemotherapy and radiotherapy. Here we showed the status of IDH1 gene associatied with younger age. We demonstrated that the together with MGMT gene the RARβ gene should be used as a potantial treatment decision marker for GBMs.

Keywords: RARβ, primary glioblastoma multiforme, methylation, MGMT

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Authors: Xuan Zhao, Wen Jiang

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In this study, a web crawler was used to collect POI sample data from 38 districts and counties of Chongqing in 2022, and ArcGIS was combined to coordinate and projection conversion and realize data visualization. Nuclear density analysis and spatial correlation analysis were used to explore the spatial distribution characteristics of elderly care facilities in Chongqing, and K mean cluster analysis was carried out with GeoDa to study the spatial concentration degree of elderly care resources in 38 districts and counties. Finally, the driving force of spatial differentiation of elderly care facilities in various districts and counties of Chongqing is studied by using the method of geographic detector. The results show that: (1) in terms of spatial distribution structure, the distribution of elderly care facilities in Chongqing is unbalanced, showing a distribution pattern of ‘large dispersion and small agglomeration’ and the asymmetric pattern of ‘west dense and east sparse, north dense and south sparse’ is prominent. (2) In terms of the spatial matching between elderly care resources and the elderly population, there is a weak coordination between the input of elderly care resources and the distribution of the elderly population at the county level in Chongqing. (3) The analysis of the results of the geographical detector shows that the single factor influence is mainly the number of elderly population, public financial revenue and district and county GDP. The high single factor influence is mainly caused by the elderly population, public financial income, and district and county GDP. The influence of each influence factor on the spatial distribution of elderly care facilities is not simply superimposed but has a nonlinear enhancement effect or double factor enhancement. It is necessary to strengthen the synergistic effect of two factors and promote the synergistic effect of multiple factors.

Keywords: aging, elderly care facilities, spatial differentiation, geographical detector, driving force analysis, Mountain city

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Authors: Ghaleb Bin Huraib, Fahad Al Harthi, Mohammad Mustafa, Abdulrahman Al-Asmari

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Introduction: Vitiligo is an acquired pigmentary skin disorder with the regional disappearance of melanocytes. Vitiligo affects 0.1 to 2% of the global population, and the incidence varies substantially depending on ethnicity. Glutathione S-transferase (GST) is a multigene family of enzymes that detoxify oxidative stress products. The oxidative stress-related GSTM1/GSTT1 genes deletion may cause epidermal melanocytes destruction and the development of vitiligo. Hence, the present study aimed to investigate the association of GST gene polymorphisms with vitiligo in the Saudi population, if any. Materials and Methods: The present study includes 129 vitiligo cases and 130 age-matched healthy controls. The proportion of male and female patients with vitiligo is almost equal. The multiplex polymerase chain reaction (PCR) method was used for polymorphic analysis. Results: Increased odds of generalized vitiligo was observed with the null genotypes of GSTT1- gene (OR = 1.91, 95% CI = 1.07-3.42, p = 0.019). The possible genetic combinations of GSTM1/GSTT1 and their genotypic distribution showed the frequency of GSTM1+/GSTT1+ 62/130 (47.69%) and GSTM1-/GSTT1+ 52/130 (40.00%) were higher in controls than in cases 44/129 (34.11%), 43/129 (33.34%), respectively while GSTM1+/GSTT1- and GSTM1-/GSTT1- null genotypes were higher 22/129 (17.05%) and 20/129 (15.50%) in vitiligo patients as compared to controls 11/130 (8.46%), 5/130 (3.84%), respectively. The strength of association of different genetic combinations with cases have shown GSTM1+/GSTT1- (OR = 2.81, 95% CI = 1.24-6.40, p = 0.009) and GSTM1-/GSTT1- (OR = 5.63, 95% CI = 1.96 - 16.16, p = 0.0004) were significantly higher in vitiligo cases as compared to controls. We did not observe any significant association of age and gender of patients with GST gene polymorphisms. Conclusions: The GSTT1-, GSTM1+/GSTT1- and GSTM1-/GSTT1- null genotypes were significantly associated with vitiligo. These genetic polymorphisms may be the associative genetic risk factor for vitiligo among Saudis. It could be used as a genetic marker for screening vitiligo patients among Saudis. Further studies on GSTs gene polymorphism in larger sample sizes from different geographical areas and ethnicity are needed to strengthen the present findings.

Keywords: vitiligo, GSTM1, GSTT1, gene polymorphism, oxidative stress

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Authors: Sara Ramezanzadeh, Nashid Nabian

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Historically, pandemics in different periods have caused compulsory changes in human life. In the case of Covid-19, according to the limitations and established care instructions, spatial alignment with the conditions is important. Following the outbreak of Covid-19, the question raised in this study is how to do spatial design in five scales, namely object, space, architecture, city, and infrastructure, in response to the consequences created in the realms under study. From the beginning of the pandemic until now, some changes in the spatial realm have been created spontaneously or by space users. These transformations have been mostly applied in modifiable parts such as furniture arrangement, especially in work-related spaces. To implement other comprehensive requirements, flexibility and adaptation of space design to the conditions resulting from the pandemics are needed during and after the outbreak. Studying the effects of pandemics from the past to the present, this research covers eight major realms, including three categories of ramifications, solutions, and paradigm shifts, and analytical conclusions about the solutions that have been created in response to them. Finally, by the consideration of epidemiology as a modern discipline influencing the design, spatial solutions in the five scales mentioned (in response to the effects of the eight realms for spatial adaptation in the face of pandemics and their following conditions) are presented as a series of guidelines. Due to the unpredictability of possible pandemics in the future, the possibility of changing and updating the provided guidelines is considered.

Keywords: pandemics, Covid 19, spatial design, ramifications, solutions, paradigm shifts, guidelines

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Authors: Panudet Saengseedam, Nanthachai Kantanantha

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This paper proposes a linear mixed model (LMM) with spatial effects to forecast rice and cassava yields in Thailand at the same time. A multivariate conditional autoregressive (MCAR) model is assumed to present the spatial effects. A Bayesian method is used for parameter estimation via Gibbs sampling Markov Chain Monte Carlo (MCMC). The model is applied to the rice and cassava yields monthly data which have been extracted from the Office of Agricultural Economics, Ministry of Agriculture and Cooperatives of Thailand. The results show that the proposed model has better performance in most provinces in both fitting part and validation part compared to the simple exponential smoothing and conditional auto regressive models (CAR) from our previous study.

Keywords: Bayesian method, linear mixed model, multivariate conditional autoregressive model, spatial time series

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Authors: Guilan Huang

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In 2013 and 2014, the U.S. Food and Drug Administration (FDA) collected data from selected fast food restaurants and full service restaurants for tracking changes in the occurrence of foodborne illness risk factors. This paper discussed how we customized spatial random sampling method by considering financial position and availability of FDA resources, and how we enriched restaurants data with location. Location information of restaurants provides opportunity for quantitatively determining random sampling within non-government units (e.g.: 240 kilometers around each data-collector). Spatial analysis also could optimize data-collectors’ work plans and resource allocation. Spatial analytic and processing platform helped us handling the spatial random sampling challenges. Our method fits in FDA’s ability to pinpoint features of foodservice establishments, and reduced both time and expense on data collection.

Keywords: geospatial technology, restaurant, retail food risk factor study, spatially random sampling

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Authors: Yasemin İlkay

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Street is not only a crucial spatial unit in urban design and planning discipline but also the context of walking practice in urban space. Moreover, psychogeography concentrates on both ‘walking’ and, therefore, the differentiated forms of (urban) streets to examine the influence of the built environment on the feelings and attitudes of human beings. This paper focuses on ‘walking practice’ in university campuses with reference to spatial appropriation forms via a psychogeographic lens on the phenomenon of alle in two different cities of Turkey, Ankara, the capital city, and Van, in the eastern part of the country. Alle, as an extension of ‘street’ in university campuses, is the constructive spatial structure in university campuses, and as a result, it should be the (both physical and mental) spine of design policy while conceiving and constructing a university campus. The main question of the paper is: How does the interrelation of ‘campus design’ and ‘walking practice’ on alle penetrate reciprocally on the spatial representations of citizens within their urban daily lives. The body contacts with and at urban space (with other objects and subjects) via its movements and stops; this interaction occurs through the spatial pattern of occupancy and vacancy. Walking practice leads to a set of cognitive mental representations in relation to the repertoire of place attachment and spatial appropriation. University campuses are autonomous and fruitful urban spaces to investigate such an interaction. There are both physical/real and psychogeographic representations of the same urban spaces and urban spatial practices. This separation would indicate the invisible dimensions of the difference between ‘what is conceived’ and ‘what is perceived.’ This study aims to compare and contrast the role of alle in both campus design and spatial appropriation via walking at two differentiated university campuses by collecting the mental representations, doing in-depth interviews, and attending walks with the interviewees by psychogeographic techniques. Campus design and spatial appropriation will be compared [with reference to the conception and perception of alle] in three scales: (1) the historical spatial development stories and design approaches of university campuses, (2) the spatial pattern of campuses on the basis of alle, and (3) sub-behavioral regions of the alle in campuses in relation with mental representations and psychogeographic attentive walks. The sub-questions of the research are: [1] How and why do the design approaches differentiate in two university campuses in Turkey, [2] How the interrelation among alle design and spatial appropriation differs in these two cases, and [3] What do the differentiated gaps among real and psychographic maps indicate about the design and spatial appropriation interrelation. METU, as a well-designed, readable campus with its alle, promise a rich walking practice with in-depth and fruitful spatial appropriation regions; however, Van YYÜ limits both the practice and place attachment with its partial design with an alle which is later added to the campus. This research both displays the role of alle in the campus design, walking practice and spatial appropriation and opens a new methodological path to discover hidden knowledge within urban spaces.

Keywords: alle, campus design, cognitive geography, psychogeography, spatial appropriation, Turkey

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Authors: Chengming Li, Yong Yin, Peipei Guo, Xiaoli Liu

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Without taking account of the attribute richness of POI (point of interest) data and spatial distribution limited by roads, a POI generalization method considering both attribute information and spatial distribution has been proposed against the existing point generalization algorithm merely focusing on overall information of point groups. Hierarchical characteristic of urban POI information expression has been firstly analyzed to point out the measurement feature of the corresponding hierarchy. On this basis, an urban POI generalizing strategy has been put forward: POIs urban road network have been divided into three distribution pattern; corresponding generalization methods have been proposed according to the characteristic of POI data in different distribution patterns. Experimental results showed that the method taking into account both attribute information and spatial distribution characteristics of POI can better implement urban POI generalization in the mapping presentation.

Keywords: POI, road network, selection method, spatial information expression, distribution pattern

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Authors: Qiu Chen, Koji Kotani, Feifei Lee, Tadahiro Ohmi

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In this paper, we propose an improved face recognition algorithm using histogram-based features in spatial and frequency domains. For adding spatial information of the face to improve recognition performance, a region-division (RD) method is utilized. The facial area is firstly divided into several regions, then feature vectors of each facial part are generated by Binary Vector Quantization (BVQ) histogram using DCT coefficients in low frequency domains, as well as Local Binary Pattern (LBP) histogram in spatial domain. Recognition results with different regions are first obtained separately and then fused by weighted averaging. Publicly available ORL database is used for the evaluation of our proposed algorithm, which is consisted of 40 subjects with 10 images per subject containing variations in lighting, posing, and expressions. It is demonstrated that face recognition using RD method can achieve much higher recognition rate.

Keywords: binary vector quantization (BVQ), DCT coefficients, face recognition, local binary patterns (LBP)

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Authors: Taisiia Gorshkova

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Since the 1980s, spatial correlation models have been used more often to model regional indicators. An increasingly popular method for studying regional indicators is modeling taking into account spatial relationships between objects that are part of the same economic zone. In 2000s the new class of model – spatial vector autoregressions was developed. The main difference between standard and spatial vector autoregressions is that in the spatial VAR (SpVAR), the values of indicators at time t may depend on the values of explanatory variables at the same time t in neighboring regions and on the values of explanatory variables at time t-k in neighboring regions. Thus, VAR is a special case of SpVAR in the absence of spatial lags, and the spatial panel data model is a special case of spatial VAR in the absence of time lags. Two specifications of SpVAR were applied to Russian regional data for 2000-2017. The values of GRP and regional CPI are used as endogenous variables. The lags of GRP, CPI and the unemployment rate were used as explanatory variables. For comparison purposes, the standard VAR without spatial correlation was used as “naïve” model. In the first specification of SpVAR the unemployment rate and the values of depending variables, GRP and CPI, in neighboring regions at the same moment of time t were included in equations for GRP and CPI respectively. To account for the values of indicators in neighboring regions, the adjacency weight matrix is used, in which regions with a common sea or land border are assigned a value of 1, and the rest - 0. In the second specification the values of depending variables in neighboring regions at the moment of time t were replaced by these values in the previous time moment t-1. According to the results obtained, when inflation and GRP of neighbors are added into the model both inflation and GRP are significantly affected by their previous values, and inflation is also positively affected by an increase in unemployment in the previous period and negatively affected by an increase in GRP in the previous period, which corresponds to economic theory. GRP is not affected by either the inflation lag or the unemployment lag. When the model takes into account lagged values of GRP and inflation in neighboring regions, the results of inflation modeling are practically unchanged: all indicators except the unemployment lag are significant at a 5% significance level. For GRP, in turn, GRP lags in neighboring regions also become significant at a 5% significance level. For both spatial and “naïve” VARs the RMSE were calculated. The minimum RMSE are obtained via SpVAR with lagged explanatory variables. Thus, according to the results of the study, it can be concluded that SpVARs can accurately model both the actual values of macro indicators (particularly CPI and GRP) and the general situation in the regions

Keywords: forecasting, regional data, spatial econometrics, vector autoregression

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Authors: Naomi Seidu, Edward Poluyi, Chibuikem Ikwuegbuenyi, Eghosa Morgan

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The current poor prognosis of glioblastoma has called for the need for an improvement in treatment methods in order to improve its survival rate. Despite the different interventions currently available for this tumor, the average survival is still only a few months. (12-15). The aim is to create a more favorable prognosis and have a reduction in the resistance to treatment currently being experienced, even with surgical interventions and chemotherapy. From the available literature, there is a relationship between the presence of HOX genes (Homeobox genes) and glioblastoma, which could be attributable to the increasing treatment resistance. Hence silencing these genes can be a key to improving survival rates of glioblastoma. A series of studies have highlighted the role that HOX genes play in glioblastoma prognosis. Promotion of human glioblastoma initiation, aggressiveness, and resistance to Temozolomide has been associated with HOXA9. The role of HOX gene expression in cancer stem cells should be studied as it could provide a means of designing CSC-targeted therapies, as CSCs play a part in the initiation and progression of solid tumors.

Keywords: GBM- glioblastoma, HOXA gene- homeobox genes cluster, signaling pathways, temozolomide

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Authors: Sana Hamdi, Emna Bouazizi, Sami Faiz

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In recent years, real-time spatial applications, like location-aware services and traffic monitoring, have become more and more important. Such applications result dynamic environments where data as well as queries are continuously moving. As a result, there is a tremendous amount of real-time spatial data generated every day. The growth of the data volume seems to outspeed the advance of our computing infrastructure. For instance, in real-time spatial Big Data, users expect to receive the results of each query within a short time period without holding in account the load of the system. But with a huge amount of real-time spatial data generated, the system performance degrades rapidly especially in overload situations. To solve this problem, we propose the use of data partitioning as an optimization technique. Traditional horizontal and vertical partitioning can increase the performance of the system and simplify data management. But they remain insufficient for real-time spatial Big data; they can’t deal with real-time and stream queries efficiently. Thus, in this paper, we propose a novel data partitioning approach for real-time spatial Big data named VPA-RTSBD (Vertical Partitioning Approach for Real-Time Spatial Big data). This contribution is an implementation of the Matching algorithm for traditional vertical partitioning. We find, firstly, the optimal attribute sequence by the use of Matching algorithm. Then, we propose a new cost model used for database partitioning, for keeping the data amount of each partition more balanced limit and for providing a parallel execution guarantees for the most frequent queries. VPA-RTSBD aims to obtain a real-time partitioning scheme and deals with stream data. It improves the performance of query execution by maximizing the degree of parallel execution. This affects QoS (Quality Of Service) improvement in real-time spatial Big Data especially with a huge volume of stream data. The performance of our contribution is evaluated via simulation experiments. The results show that the proposed algorithm is both efficient and scalable, and that it outperforms comparable algorithms.

Keywords: real-time spatial big data, quality of service, vertical partitioning, horizontal partitioning, matching algorithm, hamming distance, stream query

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Authors: Krisada Lekdee, Sunee Sammatat, Nittaya Boonsit

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This paper proposes a GLMM with spatial and temporal effects for malaria data in Thailand. A Bayesian method is used for parameter estimation via Gibbs sampling MCMC. A conditional autoregressive (CAR) model is assumed to present the spatial effects. The temporal correlation is presented through the covariance matrix of the random effects. The malaria quarterly data have been extracted from the Bureau of Epidemiology, Ministry of Public Health of Thailand. The factors considered are rainfall and temperature. The result shows that rainfall and temperature are positively related to the malaria morbidity rate. The posterior means of the estimated morbidity rates are used to construct the malaria maps. The top 5 highest morbidity rates (per 100,000 population) are in Trat (Q3, 111.70), Chiang Mai (Q3, 104.70), Narathiwat (Q4, 97.69), Chiang Mai (Q2, 88.51), and Chanthaburi (Q3, 86.82). According to the DIC criterion, the proposed model has a better performance than the GLMM with spatial effects but without temporal terms.

Keywords: Bayesian method, generalized linear mixed model (GLMM), malaria, spatial effects, temporal correlation

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Authors: Tety Widyaningrum, Sapnah Rahmawati, Abdulmuluk Attim

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Space was a container that includes land space, sea space and air space, including space in the earth as a whole region, where humans and other living creatures, operate and maintain its survival. Whereas spatial planning was a form of the structure of space and spatial pattern. At this time, the arrangement of space became a matter of considerable concern because through spatial planning was what will determine how the future city hall, how the welfare of the population that is in it, and how space can be a comfortable space to live. This spatial arrangement became a subject that must be considered not only by the Government as policy makers but also of concern to the entire community in it. As a place to stay, this space should be able to ensure the safety and comfort of the whole community, even people with disabilities, though. For development and spatial planning in Indonesia. It was still very low which was still concerned about the disabled. The spatial arrangement made generalizations. This caused the right for disabled people was less fulfilled. In accordance with the Declaration on the Rights of Persons with Disabilities who explains that people with disabilities had the right to be able to facilitate their efforts to become self-sufficient or not depends on the other party. It was also strengthened by According to the Law of the Republic of Indonesia No. 4 of 1997 on Persons with Disabilities; disabilities were part of the Indonesian people who had the status, rights, obligations and the same role with other Indonesian community in all aspects of life and livelihood. As observed, during the disabled were still used as objects that hadn’t been involved in the formulation of development planning of space in Indonesia, so the infrastructure space was still very far from the concept of friendly to the disabled. As an example of a sidewalk in Indonesia were still in bad condition, potholes, and uneven and don’t meet the eligibility standards. In addition, there were sidewalks that abused become a trade causing run down and chaotic atmosphere. In addition, pedestrians are also disturbed because the sidewalks were often still used as a parking lot or flowers to decorate the layout of the city, so the legroom was becoming increasingly limited. The development of infrastructure for pedestrians was also still concerned with aspects of aesthetic than functional. Therefore, the participation of disabled people must be involved in spatial planning exist. It aims to achieve spatial and environmentally friendly to the disabled. These dream space activities carried out by giving questionnaires and the dream images to the disabled about how the layout of the space they want what they want and what development was also in line with the principle of their convenience. This then will be taken into consideration for government in planning layout that was friendly to the whole community.

Keywords: diffable, aspiration, spatial, planning

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Authors: Jong-Hwa Kim, Mu-Wook Pyeon, Yang-dam Eo, Ill-Woong Jang

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Construction of geo-spatial information recently tends to develop as multi-dimensional geo-spatial information. People constructing spatial information is also expanding its area to the general public from some experts. As well as, studies are in progress using a variety of devices, with the aim of near real-time update. In this paper, getting the stereo images using GoPro device used widely also to the general public as well as experts. And correcting the distortion of the images, then by using SIFT, DLT, is acquired the point clouds. It presented a possibility that on the basis of this experiment, using a video device that is readily available in real life, to create a real-time digital map.

Keywords: GoPro, SIFT, DLT, point clouds

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Authors: Khaled Khleifat, Muayyad Abboud, Ahmad Almustafa

Abstract:

The effect of metabolic inhibitor/uncoupler(s) (CCCP and NaN3) and sulfhydryl reagents (dithiothreitol, 2 mercaptoethanol glutathione) on cadmium uptake was investigated in Enterobacter aerogenes strains. They include a transformed strain bearing the Vitreoscillahemoglobin gene, vgb as well as control strains that lack this transformed gene. The vgb-harboring strains showed better uptake of cadmium than vgb-lacking strains. Under low aeration, there was 2 fold enhancement of Cd+2 uptake in vgb-harboring strains compared with 1.6-fold enhancement under high aeration. The CCCP caused 36, 40 and 58% inhibition in cadmium uptake of parental, pUC9 harboring and VHb expressing cells, respectively. Similarly, the sodium azide exerted 44, 38 and 55% inhibition in Cd+2 uptake of parental, pUC9 harboring and VHb expressing cells, respectively. Less extensive inhibition of Cd+2 uptake in the range of 11 to 39% was observed with sulfhydryl reagents.

Keywords: bacterial hemoglobin, VHb, Cd uptake, biosorption

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Authors: Tingyu Zhang

Abstract:

This paper utilizes the Super-SBM model to assess water resources green efficiency (WRGE) among provinces in China and investigate its spatial and temporal features, based on the characteristic framework of “economy-environment-society.” The social network analysis is employed to examine the network pattern and spatial interaction of WRGE. Further, the quadratic assignment procedure method is utilized for examining the influencing factors of the spatial association of WRGE regarding “relationship.” The study reveals that: (1) the spatial distribution of WRGE demonstrates a distribution pattern of Eastern>Western>Central; (2) a remarkable spatial association exists among provinces; however, no strict hierarchical structure is observed. The internal structure of the WRGE network is characterized by the feature of "Eastern strong and Western weak". The block model analysis discovers that the members of the “net spillover” and “two-way spillover” blocks are mostly in the eastern and central provinces; “broker” block, which plays an intermediary role, is mostly in the central provinces; and members of the “net beneficiary” block are mostly in the western region. (3) Differences in economic development, degree of urbanization, water use environment, and water management have significant impacts on the spatial connection of WRGE. This study is dedicated to the realization of regional linkages and synergistic enhancement of WRGE, which provides a meaningful basis for building a harmonious society of human and water coexistence.

Keywords: water resources green efficiency, super-SBM model, social network analysis, quadratic assignment procedure

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Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

Abstract:

Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

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Authors: Dina Athariah, Desriani Desriani, Bugi Ratno Budiarto, Abinawanto Abinawanto, Dwi Wulandari

Abstract:

Breast cancer is a regulated by many genes. Defect in PIK3CA gene especially at position of exon 9 (E542K and E545K), called hot spot mutation induce early transformation of breast cells. The early detection of breast cancer based on mutation profile of this hot spot region would be hampered by the existence of pseudogene, marked by its substitution mutation at base 1658 (E545A) and deletion at 1659 that have been previously proven in several cancers. To the best of the authors’ knowledge, until recently no studies have been reported about pseudogene phenomenon in breast cancer. Here, we reported PCR optimization to to obtain true exon 9 of PIK3CA gene from its pseudogene hence increasing the validity of data. Material and methods: two genomic DNA with Dev and En code were used in this experiment. Two pairs of primer were design for Standard PCR method. The size of PCR products for each primer is 200bp and 400bp. While other primer was designed for Nested-PCR followed with DNA sequencing method. For Nested-PCR, we optimized the annealing temperature in first and second run of PCR, and the PCR cycle for first run PCR (15x versus 25x). Result: standard PCR using both primer pairs designed is failed to detect the true PIK3CA gene, appearing a substitution mutation at 1658 and deletion at 1659 of PCR product in sequence chromatogram indicated pseudogene. Meanwhile, Nested-PCR with optimum condition (annealing temperature for the first round at 55oC, annealing temperatung for the second round at 60,7oC with 15x PCR cycles) and could detect the true PIK3CA gene. Dev sample were identified as WT while En sample contain one substitution mutation at position 545 of exon 9, indicating amino acid changing from E to K. For the conclusion, pseudogene also exists in breast cancer and the apllication of optimazed Nested-PCR in this study could detect the true exon 9 of PIK3CA gene.

Keywords: breast cancer, exon 9, hotspot mutation, PIK3CA, pseudogene

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Authors: Surajit Bhattacharya, Daniel Veltri, Atit A. Patel, Daniel N. Cox

Abstract:

miRNAs have emerged as key post-transcriptional regulators of gene expression, however identification of biologically-relevant target genes for this epigenetic regulatory mechanism remains a significant challenge. To address this knowledge gap, we have developed a novel tool in R, Intra-miR-ExploreR, that facilitates integrated discovery of miRNA targets by incorporating target databases and novel target prediction algorithms, using statistical methods including Pearson and Distance Correlation on microarray data, to arrive at high confidence intragenic miRNA target predictions. We have explored the efficacy of this tool using Drosophila melanogaster as a model organism for bioinformatics analyses and functional validation. A number of putative targets were obtained which were also validated using qRT-PCR analysis. Additional features of the tool include downloadable text files containing GO analysis from DAVID and Pubmed links of literature related to gene sets. Moreover, we are constructing interaction maps of intragenic miRNAs, using both micro array and RNA-seq data, focusing on neural tissues to uncover regulatory codes via which these molecules regulate gene expression to direct cellular development.

Keywords: miRNA, miRNA:mRNA target prediction, statistical methods, miRNA:mRNA interaction network

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Authors: Mehrnaz Alibeikloo, Hadi Khabbaz, Behzad Fatahi

Abstract:

The spectral random field method is one of the widely used methods to obtain more reliable and accurate results in geotechnical problems involving material variability. Karhunen-Loeve (K-L) expansion method was applied to perform random field discretization of cross-correlated creep parameters. Karhunen-Loeve expansion method is based on eigenfunctions and eigenvalues of covariance function adopting Kernel integral solution. In this paper, the accuracy of Karhunen-Loeve expansion was investigated to predict long-term settlement of soft soils adopting elastic visco-plastic creep model. For this purpose, a parametric study was carried to evaluate the effect of K-L expansion terms and spatial correlation length on the reliability of results. The results indicate that small values of spatial correlation length require more K-L expansion terms. Moreover, by increasing spatial correlation length, the coefficient of variation (COV) of creep settlement increases, confirming more conservative and safer prediction.

Keywords: Karhunen-Loeve expansion, long-term settlement, reliability analysis, spatial correlation length

Procedia PDF Downloads 159

Authors: Mehrdad Sheikhvatan, Mohammad Ali Boroumand, Mehrdad Behmanesh, Shayan Ziaee

Abstract:

Contradictory results have been obtained regarding the role of integrin, beta 3 (ITGB3) gene polymorphisms in occurrence of acute myocardial infarction (MI) in patients with coronary artery disease (CAD). Hence, we aimed to assess the association between 1565C/T polymorphism of ITGB3 gene and increased risk for acute MI in patients who suffered premature CAD in Iranian population. Our prospective study included 1000 patients (492 men and 508 women aged 21 to 55 years) referred to Tehran Heart center during a period of four years from 2008 to 2011 with the final diagnosis of premature CAD and classified into two groups with history of MI (n = 461) and without of MI (n = 539). The polymorphism variants were determined by PCR-RFLP technique by entering 10% of randomized samples and then genotyping of the polymorphism was also conducted by High Resolution Melting (HRM) method. Among study samples, 640 were followed with a median follow-up time 45.74 months for determining association of long-term major adverse cardiac events (MACE) and genotypes of polymorphisms. There was no significant difference in the frequency of 1565C/T polymorphism between the MI and non-MI groups. The frequency of wild genotype was 69.2% and 72.2%, the frequency of homozygous genotype was 21.3% and 18.4%, and the frequency of mutant genotype was 9.5% and 9.5%, respectively (p=0.505). Results were also similar when adjusted for covariates in a multivariate logistic regression model. No significant difference was also found in total-MACE free survival rate between the patients with different genotypes of 1565C/T polymorphism in both MI and non-MI group. The carriage of the 1565C/T polymorphism of ITGB3 gene seems unlikely to be a significant risk factor for the development of MI in Iranian patients with premature CAD. The presence of this ITGB3 gene polymorphism may not also predict long-term cardiac events.

Keywords: coronary artery disease, myocardial infarction, gene, integrin, beta 3, polymorphism

Procedia PDF Downloads 399