Search results for: spatial gene

Authors: Rachita Lal

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Urban sprawl is a significant contributor to land use change in developing countries, where urbanization rates are high. The most important driver of environmental changes is also considered to be the shift in land use and land cover. Our local and regional land managers must carefully analyze urbanization and its effects on cities to make the best choices. This study uses satellite imagery to examine how urbanization affects the local ecosystem through geographic expansion. The following research focuses on the effects of city growth on the local environment, land use, and Land cover. The primary focus of this research is to study, To understand the role of urbanization on city expansion. To study the impact of spatial growth of urban areas on the Land cover. In this paper, the GIS tool will be used to analyze. For this purpose, four digital images are used for the years 2000, 2005, 2011, and 2019. The use of the approach in the Bhubaneswar Urban Core, one of the fastest developing and planned cities in India, has proved that it is highly beneficial and successful for monitoring urban sprawl. It offers a helpful tool for quantitative assessment, which is crucial for determining the spatial dynamics, variations, and changes of urban sprawl patterns in quickly increasing regions.

Keywords: LULC, urbanization, environment impact assessment, spatial growth

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: adaptation, animals, evolution, genomics

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Authors: Lianxue Shi

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Urban waterfront rail transit stations exert a dual impact on both the waterfront and the transit station, resulting in a concentration of development elements in the surrounding space. In order to more effectively develop the space around the station, this study focuses on the perspective of the integration of station, city, and people. Taking Chongqing as an example, based on the Arc GIS platform, it explores the vitality of the site from the three dimensions of crowd activity heat, space facilities heat, and spatial accessibility. It conducts a comprehensive evaluation and interpretation of the vitality surrounding the waterfront rail transit station area in Chongqing. The study found that (1) the spatial vitality in the vicinity of waterfront rail transit stations is correlated with the waterfront's functional zoning and the intensity of development. Stations situated in waterfront residential and public spaces are more likely to experience a convergence of people, whereas those located in waterfront industrial areas exhibit lower levels of vitality. (2) Effective transportation accessibility plays a pivotal role in maintaining a steady flow of passengers and facilitating their movement. However, the three-dimensionality of urban space in mountainous regions is a notable challenge, leading to some stations experiencing limited accessibility. This underscores the importance of enhancing the optimization of walking space, particularly the access routes from the station to the waterfront area. (3) The density of spatial facilities around waterfront stations in old urban areas lags behind the population's needs, indicating a need to strengthen the allocation of relevant land and resources in these areas.

Keywords: rail transit station, waterfront, influence area, spatial vitality, urban vitality

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Authors: Weikang Peng

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The innovation corridor is an important spatial carrier to promote regional collaborative innovation, and its development process is the spatial re-organization process of regional innovation resources. This paper takes the Nanjing-Zhenjiang G312 Industrial Innovation Corridor, which involves seven municipal districts in Jiangsu Province, as empirical evidence. Based on multi-source spatial big data in 2010, 2016, and 2022, this paper applies triangulated irregular network (TIN), head/tail breaks, regional innovation ecosystem (RIE) niche fitness evaluation model, and social network analysis to carry out empirical research on the spatial organization and functional structural evolution characteristics of innovation corridors and their correlation with the structural evolution of collaborative innovation network. The results show, first, the development of innovation patches in the corridor has fractal characteristics in time and space and tends to be multi-center and cluster layout along the Nanjing Bypass Highway and National Highway G312. Second, there are large differences in the spatial distribution pattern of niche fitness in the corridor in various dimensions, and the niche fitness of innovation patches along the highway has increased significantly. Third, the scale of the collaborative innovation network in the corridor is expanding fast. The core of the network is shifting from the main urban area to the periphery of the city along the highway, with small-world and hierarchical levels, and the core-edge network structure is highlighted. With the development of the Innovation Corridor, the main collaborative mode in the corridor is changing from collaboration within innovation patches to collaboration between innovation patches, and innovation patches with high ecological suitability tend to be the active areas of collaborative innovation. Overall, polycentric spatial layout, graded functional structure, diversified innovation clusters, and differentiated environmental support play an important role in effectively constructing collaborative innovation linkages and the stable expansion of the scale of collaborative innovation within the innovation corridor.

Keywords: innovation corridor development, spatial structure, niche fitness evaluation model, head/tail breaks, innovation network

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Authors: Nina Doskocz, Katarzyna Affek, Magdalena Matczuk, Monika Załęska-Radziwiłł

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Wastewater treatment is a critical environmental issue, especially in the face of increasing urbanization and industrialization. One of the emerging issues related to wastewater is the presence of nanoparticles (NPs) - tiny particles with dimensions measured in nanometers. These nanoparticles are widely used in various industries, including medicine, electronics, and consumer products. With technological advances, NPs are increasingly finding their way into water and wastewater systems, posing new environmental challenges that require urgent research and regulation. Therefore, research on the impact of nanoparticles on wastewater treatment processes is critical to protect environmental health and ensure sustainable development in the face of advancing nanotechnology. Traditional ecotoxicological tests are often inadequate for routine analysis as they do not provide insight into the mechanisms of toxicity of these compounds. The development of (geno)toxicity biomarkers for nanoparticles will greatly aid in the rapid assessment and prediction of the effects of current and emerging nanomaterials on various organisms. However, despite growing interest in gene expression responses to nanoparticle-induced stress, the toxic mechanisms of action and defense responses against nanoparticle toxicity remain poorly understood. The aim of our research was to investigate the expression of several molecular biomarkers related to essential cellular functions - such as oxidative stress, xenobiotic detoxification, and mitochondrial electron transport - in Pseudomonas putida in response to Al₂O₃ nanoparticles found in wastewater, both before and after biological treatment, as well as in their native form. Real-time PCR (qPCR) was used to assess gene expression changes after 1 hour and 16 hours of exposure to Al₂O₃ NPs and wastewater containing these nanoparticles, both before and after biological treatment. In addition, gene expression measurements were performed on P. putida in the presence of bulk Al₂O₃ (pristine and in wastewater). The results showed increased expression of ahpC, katE and ctaD genes, indicating oxidative stress, increased detoxification capacity and impaired mitochondrial function. Both untreated and treated wastewater containing nanoparticles caused significant changes in gene expression, demonstrating the persistent bioactivity and potential toxicity of these nanoparticles. Nanoparticles exhibited greater reactivity and bioavailability compared to their bulk counterparts.

Keywords: nanoparticles, wastewater, gene expression, qPCR

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Authors: Bright E. Owusu, Nittaya McNeil

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Rainfall is one of the most essential quantities in meteorology and hydrology. It has important impacts on people’s daily life and excess or inadequate of it could bring tremendous losses in economy and cause fatalities. Population increase around the globe tends to have a corresponding increase in settlement and industrialization. Some countries are affected by flood and drought occasionally due to climate change, which disrupt most of the daily activities. Knowledge of trends in spatial and temporal rainfall variability and their physical explanations would be beneficial in climate change assessment and to determine erosivity. This study describes the spatial-temporal variability of daily rainfall in Australia and their corresponding long-term trend during 1950-2013. The spatial patterns were investigated by using exploratory factor analysis and the long term trend in rainfall time series were determined by linear regression, Mann-Kendall rank statistics and the Sen’s slope test. The exploratory factor analysis explained most of the variations in the data and grouped Australia into eight distinct rainfall regions with different rainfall patterns. Significant increasing trends in annual rainfall were observed in the northern regions of Australia. However, the northeastern part was the wettest of all the eight rainfall regions.

Keywords: climate change, explanatory factor analysis, Mann-Kendall and Sen’s slope test, rainfall.

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Authors: Akrem Sellami, Imed Riadh Farah

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Hyperspectral imagery (HSI) typically provides a wealth of information captured in a wide range of the electromagnetic spectrum for each pixel in the image. Hence, a pixel in HSI is a high-dimensional vector of intensities with a large spectral range and a high spectral resolution. Therefore, the semantic interpretation is a challenging task of HSI analysis. We focused in this paper on object classification as HSI semantic interpretation. However, HSI classification still faces some issues, among which are the following: The spatial variability of spectral signatures, the high number of spectral bands, and the high cost of true sample labeling. Therefore, the high number of spectral bands and the low number of training samples pose the problem of the curse of dimensionality. In order to resolve this problem, we propose to introduce the process of dimensionality reduction trying to improve the classification of HSI. The presented approach is a semi-supervised band selection method based on spatial hypergraph embedding model to represent higher order relationships with different weights of the spatial neighbors corresponding to the centroid of pixel. This semi-supervised band selection has been developed to select useful bands for object classification. The presented approach is evaluated on AVIRIS and ROSIS HSIs and compared to other dimensionality reduction methods. The experimental results demonstrate the efficacy of our approach compared to many existing dimensionality reduction methods for HSI classification.

Keywords: dimensionality reduction, hyperspectral image, semantic interpretation, spatial hypergraph

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Authors: Saima Suleman, Kalsoom Sughra, Naeem Mahmood Ashraf

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Mycobacterium tuberculosis is a communicable chronic illness. This disease is being highly focused by researchers as it is present approximately in one third of world population either in active or latent form. The genetic makeup of a person plays an important part in producing immunity against disease. And one important factor association is single nucleotide polymorphism of relevant gene. In this study, we have studied association between single nucleotide polymorphism of CD-209 gene (encode DC-SIGN receptor) and patients of tuberculosis. Dry lab (in silico) and wet lab (RFLP) analysis have been carried out. GWAS catalogue and GEO database have been searched to find out previous association data. No association study has been found related to CD-209 nsSNPs but role of CD-209 in pulmonary tuberculosis have been addressed in GEO database.Therefore, CD-209 has been selected for this study. Different databases like ENSEMBLE and 1000 Genome Project has been used to retrieve SNP data in form of VCF file which is further submitted to different software to sort SNPs into benign and deleterious. Selected SNPs are further annotated by using 3-D modeling techniques using I-TASSER online software. Furthermore, selected nsSNPs were checked in Gujrat and Faisalabad population through RFLP analysis. In this study population two SNPs are found to be associated with tuberculosis while one nsSNP is not found to be associated with the disease.

Keywords: association, CD209, DC-SIGN, tuberculosis

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Authors: Masoud Soltanialvar, Ali Bagherpour

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The aim of this study was to determinate the variety of Anaplasma species among sheep of khouzestan province, Iran. From April 2013 to June 2013, a total of 200 blood samples were collected via the jugular vein from healthy sheep (100), randomly. The extracted DNA from blood cells were amplified by Anaplasma-all primers, which amplify an approximately 1468bp DNA fragment from region of 16S rRNA gene from various members of the genus Anaplasma. For raising the test sensivity, the PCR products were amplified with the primers, which were designed from the region flanked by the first primers. The amplified nested PCR product had an expected PCR product with 345 nucleotides in length. In 100 sheep blood samples, 7 samples were Anaplasma spp. positive by first PCR and nested PCR. The results showed that 2 of total 100 blood samples (2%) were A.phagocytophilum positive by specific nested PCR based on 16S rRNA gene. The extracted DNA from positive Anaplasma spp. samples were amplified by Anaplasma ovis specific primers, which amplify an approximately 866bp DNA fragment from region of msp4 gene. 5 out of 100 sheep blood samples (5%) were positive for Anaplasma ovis. This study is the first molecular detection of A. ovis and A.phagocytophilum from sheep in Iran.

Keywords: Iran, anaplasma species, sheep, A. ovis, A. phagocytophilum, PCR

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Authors: Hui Luo, Zhenhong Li, Zhen Dong

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The analysis of multi-temporal InSAR (MTInSAR) such as persistent scatterer (PS) and small baseline subset (SBAS) techniques usually relies on temporal/spatial phase unwrapping (PU). Unfortunately, it always fails to unwrap the phase for two reasons: 1) spatial phase jump between adjacent pixels larger than π, such as layover and high discontinuous terrain; 2) temporal phase discontinuities such as time varied atmospheric delay. To overcome these limitations, a least-square based PU method is introduced in this paper, which incorporates baseline-combination interferograms and adjacent phase gradient network. Firstly, permanent scatterers (PS) are selected for study. Starting with the linear baseline-combination method, we obtain equivalent 'small baseline inteferograms' to limit the spatial phase difference. Then, phase different has been conducted between connected PSs (connected by a specific networking rule) to suppress the spatial correlated phase errors such as atmospheric artifact. After that, interval phase difference along arcs can be computed by least square method and followed by an outlier detector to remove the arcs with phase ambiguities. Then, the unwrapped phase can be obtained by spatial integration. The proposed method is tested on real data of TerraSAR-X, and the results are also compared with the ones obtained by StaMPS(a software package with 3D PU capabilities). By comparison, it shows that the proposed method can successfully unwrap the interferograms in urban areas even when high discontinuities exist, while StaMPS fails. At last, precise DEM errors can be got according to the unwrapped interferograms.

Keywords: phase unwrapping, time series, InSAR, urban areas

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Authors: Mohamed Abdalla, Ruixue Cheng, Jianyong Zhang

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In pneumatic conveying, the solids are mixed with air or gas. In industries such as coal fired power stations, blast furnaces for iron making, cement and flour processing, the mass flow rate of solids needs to be monitored or controlled. However the current gas-solids two-phase flow measurement techniques are not as accurate as the flow meters available for the single phase flow. One of the problems that the multi-phase flow meters to face is that the flow profiles vary with measurement locations and conditions of pipe routing, bends, elbows and other restriction devices in conveying system as well as conveying velocity and concentration. To measure solids flow rate or concentration with non-even distribution of solids in gas, a uniform spatial sensitivity is required for a multi-phase flow meter. However, there are not many meters inherently have such property. The circular electrostatic meter is a popular choice for gas-solids flow measurement with its high sensitivity to flow, robust construction, low cost for installation and non-intrusive nature. However such meters have the inherent non-uniform spatial sensitivity. This paper first analyses the spatial sensitivity of circular electrostatic meter in general and then by combining the effect of the sensitivity to a single particle and the sensing volume for a given electrode geometry, the paper reveals first time how a circular electrostatic meter responds to a roping flow stream, which is much more complex than what is believed at present. The paper will provide the recent research findings on spatial sensitivity investigation at the University of Tees side based on Finite element analysis using Ansys Fluent software, including time and frequency domain characteristics and the effect of electrode geometry. The simulation results will be compared tothe experimental results obtained on a large scale (14” diameter) rig. The purpose of this research is paving a way to achieve a uniform spatial sensitivity for the circular electrostatic sensor by mean of compensation so as to improve overall accuracy of gas-solids flow measurement.

Keywords: spatial sensitivity, electrostatic sensor, pneumatic conveying, Ansys Fluent software

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Authors: Vinayaka Gude Divya Sampath

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The research introduces an integrated prediction model to assess the susceptibility of roads in a future flooding event. The model consists of deep learning algorithm for forecasting gauge height data and Flood Inundation Mapper (FIM) for spatial flooding. An optimal architecture for Long short-term memory network (LSTM) was identified for the gauge located on Tangipahoa River at Robert, LA. Dropout was applied to the model to evaluate the uncertainty associated with the predictions. The estimates are then used along with FIM to identify the spatial flooding. Further geoprocessing in ArcGIS provides the susceptibility values for different roads. The model was validated based on the devastating flood of August 2016. The paper discusses the challenges for generalization the methodology for other locations and also for various types of flooding. The developed model can be used by the transportation department and other emergency response organizations for effective disaster management.

Keywords: deep learning, disaster management, flood prediction, urban flooding

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Authors: Zhuo Job Chen, Kevin Nute

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The work reported examines potential linkages between spatial and temporal prospects, and more specifically, between variations in the spatial depth and foreground obstruction of window views, and observers’ sense of connection to the future. It was found that external views from indoor spaces were strongly associated with a sense of the future, that partially obstructing such a view with foreground objects significantly reduced its association with the future, and replacing it with a pictorial representation of the same scene (with no real actual depth) removed most of its temporal association. A lesser change in the spatial depth of the view, however, had no apparent effect on association with the future. While the role of spatial depth has still to be confirmed, the results suggest that spatial prospects directly affect temporal ones. The word “prospect” typifies the overlapping of the spatial and temporal in most human languages. It originated in classical times as a purely spatial term, but in the 16th century took on the additional temporal implication of an imagined view ahead, of the future. The psychological notion of prospection, then, has its distant origins in a spatial analogue. While it is not yet proven that space directly structures our processing of time at a physiological level, it is generally agreed that it commonly does so conceptually. The mental representation of possible futures has been a central part of human survival as a species (Boyer, 2008; Suddendorf & Corballis, 2007). A sense of the future seems critical not only practically, but also psychologically. It has been suggested, for example, that lack of a positive image of the future may be an important contributing cause of depression (Beck, 1974; Seligman, 2016). Most people in the developed world now spend more than 90% of their lives indoors. So any direct link between external views and temporal prospects could have important implications for both human well-being and building design. We found that the ability to see what lies in front of us spatially was strongly associated with a sense of what lies ahead temporally. Partial obstruction of a view was found to significantly reduce that sense connection to the future. Replacing a view with a flat pictorial representation of the same scene removed almost all of its connection with the future, but changing the spatial depth of a real view appeared to have no significant effect. While foreground obstructions were found to reduce subjects’ sense of connection to the future, they increased their sense of refuge and security. Consistent with Prospect and Refuge theory, an ideal environment, then, would seem to be one in which we can “see without being seen” (Lorenz, 1952), specifically one that conceals us frontally from others, without restricting our own view. It is suggested that these optimal conditions might be translated architecturally as screens, the apertures of which are large enough for a building occupant to see through unobstructed from close by, but small enough to conceal them from the view of someone looking from a distance outside.

Keywords: foreground obstructions, prospection, spatial depth, window views

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: Mohammad Ahangari

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Schizophrenia is a psychiatric disorder with symptoms that include cognitive deficits and nicotine has been suggested to have an effect on cognition. In recent years, the advents of Genome-Wide Association Studies(GWAS) has evolved our understanding about the genetic causes of complex disorders such as schizophrenia and studying the role of genome-wide significant genes could potentially lead to the development of new therapeutic agents for treatment of cognitive deficits in schizophrenia. The current study identified six Single Nucleotide Polymorphisms (SNP) from schizophrenia and smoking GWAS that are located on or in close proximity to the nicotinic receptor gene cluster (CHRN) and studied their association with cognition in an Irish sample of 1297 cases and controls using linear regression analysis. Further on, the interaction between CHRN gene cluster and Dopamine receptor D2 gene (DRD2) during working memory was investigated. The effect of these polymorphisms on nicotinic and dopaminergic neurotransmission, which is disrupted in schizophrenia, have been characterized in terms of their effects on memory, attention, social cognition and IQ as measured by a neuropsychological test battery and significant effects in two polymorphisms were found across global IQ domain of the test battery.

Keywords: cognition, dopamine, GWAS, nicotine, schizophrenia, SNPs

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Authors: Chang Hsueh-Sheng, Chen Tzu-Ling

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Earthquake is an unpredictable natural disaster and intensive earthquakes have caused serious impacts on social-economic system, environmental and social resilience. Conventional ways to mitigate earthquake disaster are to enhance building codes and advance structural engineering measures. However, earthquake-induced ground damage such as liquefaction, land subsidence, landslide happen on places nearby earthquake prone or poor soil condition areas. Therefore, this study uses spatial statistical analysis to explore the spatial pattern of damaged buildings. Afterwards, principle components analysis (PCA) is applied to categorize the similar features in different kinds of clustered patterns. The results show that serious landslide prone area, close to fault, vegetated ground surface and mudslide prone area are common in those highly damaged buildings. In addition, the oldest building might not be directly referred to the most vulnerable one. In fact, it seems that buildings built between 1974 and 1989 become more fragile during the earthquake. The incorporation of both spatial statistical analyses and PCA can provide more accurate information to subsidize retrofit programs to enhance earthquake resistance in particular areas.

Keywords: earthquake disaster, spatial statistic analysis, principle components analysis (pca), clustered patterns

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Authors: Cenza Rhoda, Falone Sunda, Elvis Kidzeru, Nonhlanhla P. Khumalo, Afolake Arowolo

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Introduction: The human FAM111B gene mutations are associated with POIKTMP, a rare multi-organ fibrosing disease. Recent studies also reported the overexpression of FAM111B in specific cancers. However, the role of FAM111B in these pathologies, particularly fibrosarcoma, remains unknown. Materials and Methods: FAM111B RNA expression in some cancer cell lines was assessed in silico and validated in vitro in these cell lines and skin fibroblasts derived from the South African family member affected by POIKTMP with the heterozygous FAM111B gene mutation: NM_198947.4: c.1861T>G (p. Tyr621Asp or Y621D) by qPCR and western blot. The cellular function of FAM111B was also studied in HT1080 using various cell-based functional assays and a simple and cost-effective PCR-RFLP method for genotyping/screening FAM111B gene mutations described. Results: Expression studies showed upregulated FAM111B mRNA and protein in the cancer cells. High FAM111B expression with robust nuclear localization occurred in HT1080. Additionally, expression data and cell-based assays indicated that FAM111B led to the upregulation of cell migration and decreased cell apoptosis and cell proliferation modulation. FAM111B Y621D mutation showed similar effects on cell migration but minimal impact on cell apoptosis. FAM111B mRNA and protein expression were markedly downregulated (p ≤ 0.05) in the patient's skin-derived fibroblasts. Lastly, the PCR-RFLP method successfully genotyped FAM111B Y621D gene mutation. Discussion: FAM111B is a cancer-associated nuclear protein: Its modulation by mutations may enhance cell migration and proliferation and decrease apoptosis, as seen in cancers and POIKTMP/fibrosis, thus representing a viable therapeutic target in these disorders. Furthermore, the PCR-RFLP method could prove a valuable tool for FAM111B mutation validation or screening in resource-constrained laboratories.

Keywords: FAM111B, POIKTMP, cancer, fibrosis, PCR-RFLP

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Authors: Asna Anchalan, Anjana Bhagyanathan

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Urban green space plays an important role in providing health (physical and mental well-being), economic, and environmental benefits for urban residents and neighborhoods. Ensuring equitable distribution of urban green space is vital to ensure equal access to these benefits. This study is developing a methodology for assessing spatial equity of urban green spaces in the Indian context. Through a systematic literature review, the research trends, parameters, data, and tools being used are identified. After 2020, the research in this domain is increasing rapidly, where COVID-19 acted as a catalyst. Indian documents use various terminologies, definitions, and classifications of urban green spaces. The terminology, definition, and classification for this study are done after reviewing several Indian documents, master plans, and research papers. Parameters identified for assessing spatial equity are availability, proximity, accessibility, and socio-economic disparity. Criteria for evaluating each parameter were identified from diverse research papers. There is a research gap identified as a comprehensive approach encompassing all four parameters. The outcome of this study led to the development of a methodology that addresses the gaps, providing a practical tool applicable across diverse Indian cities.

Keywords: urban green space, spatial equity, accessibility, proximity, methodology

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Authors: Salwa Mohammad Alawneh

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The ongoing humanitarian crises spur rapid and unpredicted refugee influxes resulting in demographic changes in cities. Regarding different urban systems are vulnerable in refugee neighborhoods. With the consequent social, economic, and spatial challenges, cities must respond with a more durable and sustainable approach based on urban resilience. The paper systematically approaches urban resilience to contribute to refugee spaces by reflecting on the overall urban systems of their neighborhoods. The research will review the urban resilience literature to develop an evaluation framework. The developed framework applies urban resilience more holistically in refugee neighborhoods and expands to the urban systems of social, economic, and spatial. However, the main highlight of this paper is the resilient spatial structure in refugee neighborhoods to face the internal and complex stress of refugee waves and their demographic changes. Finding a set of resilient spatial measurements and focusing on urban forms at a neighborhood scale provide vulnerability reduction and enhance adaptation capacity. As a model example, the paper applies these measurements and facilitates geospatial technologies to one of the refugee neighborhoods in Amman, Jordan, namely Al-Jubilee. The application in Al-Jubilee helps to demonstrate a road map towards a developmental pattern in design and planning by different decision-makers of inter-governmental and humanitarian organizations. In this regard, urban resilience improves the humanitarian assistantship of refugee settings beyond providing the essential needs. In conclusion, urban resilience responds to the different challenges of refugee neighborhoods by supporting urban stability, improving livability, and maintaining both urban functions and security.

Keywords: urban resilience of refugee, resilient urban form, refugee neighborhoods, humanitarian assistantship, refugee in Jordan

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Authors: Ayman K. El Essawy, Amal M. Hosny, Hala M. Abu Shady

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The rapid detection of TB and drug resistance, both optimizes treatment and improves outcomes. In the current study, respiratory specimens were collected from 155 patients. Conventional susceptibility testing and MIC determination were performed for rifampicin (RIF) and isoniazid (INH). Genotype MTBDRplus assay, which is a molecular genetic assay based on the DNA-STRIP technology and specific gene sequencing with primers for rpoB, KatG, and mab-inhA genes were used to detect mutations associated with resistance to rifampicin and isoniazid. In comparison to other categories, most of rifampicin resistant (61.5%) and isoniazid resistant isolates (47.1%) were from patients relapsed in treatment. The genotypic profile (using Genotype MTBDRplus assay) of multi-drug resistant (MDR) isolates showed missing of katG wild type 1 (WT1) band and appearance of mutation band katG MUT2. For isoniazid mono-resistant isolates, 80% showed katG MUT1, 20% showed katG MUT1, and inhA MUT1, 20% showed only inhA MUT1. Accordingly, 100% of isoniazid resistant strains were detected by this assay. Out of 17 resistant strains, 16 had mutation bands for katG distinguished high resistance to isoniazid. The assay could clearly detect rifampicin resistance among 66.7% of MDR isolates that showed mutation band rpoB MUT3 while 33.3% of them were considered as unknown. One mono-resistant rifampicin isolate did not show rifampicin mutation bands by Genotype MTBDRplus assay, but it showed an unexpected mutation in Codon 531 of rpoB by DNA sequence analysis. Rifampicin resistance in this strain could be associated with a mutation in codon 531 of rpoB (based on molecular sequencing), and Genotype MTBDRplus assay could not detect the associated mutation. If the results of Genotype MTBDRplus assay and sequencing were combined, this strain shows hetero-resistance pattern. Gene sequencing of eight selected isolates, previously tested by Genotype MTBDRplus assay, could detect resistance mutations mainly in codon 315 (katG gene), position -15 in inhA promotes gene for isoniazid resistance and codon 531 (rpoB gene) for rifampicin resistance. Genotyping techniques allow distinguishing between recurrent cases of reinfection or reactivation and supports epidemiological studies.

Keywords: M. tuberculosis, rpoB, KatG, inhA, genotype MTBDRplus

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Authors: Mehrnaz Alibeikloo, Hadi Khabbaz, Behzad Fatahi

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Probabilistic analysis has become one of the most popular methods to quantify and manage geotechnical risks due to the spatial variability of soil input parameters. The correlation length is one of the key factors of quantifying spatial variability of soil parameters which is defined as a distance within which the random variables are correlated strongly. This paper aims to assess the impact of correlation length on the long-term settlement of soft soils improved with preloading. The concept of 'worst-case' spatial correlation length was evaluated by determining the probability of failure of a real case study of Vasby test fill. For this purpose, a finite difference code was developed based on axisymmetric consolidation equations incorporating the non-linear elastic visco-plastic model and the Karhunen-Loeve expansion method. The results show that correlation length has a significant impact on the post-construction settlement of soft soils in a way that by increasing correlation length, probability of failure increases and the approach to asymptote.

Keywords: Karhunen-Loeve expansion, probability of failure, soft soil settlement, 'worst case' spatial correlation length

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Authors: Sepideh Jabbari Behnam, Shadabeh Gashtasbi Iraei, Elnaz Mohsenin, MohammadAli Aghajani

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Urban neighborhoods, as important urban forming cells, play a key role in creating urban texture and integrated form. Nowadays, most of neighborhood divisions are based on urban management systems but without considering social issues and the other aspects of urban life. This can cause problems such as providing inappropriate services for city dwellers, the loss of local identity and etc. In this regard for regenerating of such neighborhoods, it is essential to locate neighborhood centers with appropriate access and services for all residents. The main objective of this article is reaching to the location of neighborhood centers in a way that, most of issues relating to the physical features (such as the form of access network and texture permeability and etc.) and other qualities such as land uses, densities and social and economic features can be done simultaneously. This paper attempts to use methods of spatial analysis in order to surveying spatial structure and space syntax of urban textures and Urban Network Analysis Systems. This can be done by one of GIS toolbars which is named UNA (Urban Network Analysis) with the use of its five functions (include: Reach, Betweenness, Gravity, Closeness, Straightness).These functions were written according to space syntax theory and offer its relating output. This paper tries to locate and evaluate the optimal location of neighborhood centers in order to create local centers. This is done through weighing of each of these functions and taking into account of spatial features.

Keywords: evaluate optimal location, Local centers, location of neighborhood centers, Spatial analysis, Urban network

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Authors: Mulata Haile Nega, Derebew Fikadu Berhe, Vera Ribeiro Marques

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There is no epidemiologic data on this gene polymorphism in several countries. Therefore, this study aimed to assess the genotype and allele frequencies of the gene variant in three countries. This study involved healthy individuals from Colombia, Mozambique, and Portugal. Genomic DNA was isolated from blood samples using the Qiamp DNA Extraction Kit (Qiagen). The isolated DNA was genotyped using Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism. Microstat and GraphPad quick cal software were used for the Chi-square test and evaluation of Hardy-Weinberg equilibrium, respectively. A total of 181 individuals’ blood sample was analyzed. Overall, TT (74.0%) genotype was the highest, and CC (7.8%) was the lowest. Country wise genotypic frequencies were Colombia 47(70.2%) TT, 12(17.9%) TC and 8(11.9%) CC; Mozambique 47(88.7%) TT, 5(9.4%) TC, and 1(1.9%) CC; and Portugal 40(65.6%) TT, 16(26.2%) TC, and 5(8.2%) CC. The reference (T) allele was highest among Mozambicans (93.4%) compared to Colombians (79.1%) and Portuguese (78.7%). Mozambicans showed statistically significant genotypic and allelic frequency differences compared to Colombians (p<0.01) and Portuguese (p <0.01). Overall and country-wise, the CC genotype was less frequent and relatively high for Colombians and Portuguese populations. This finding may imply statins risk-benefit variability associated with CC genotype among these populations that needs further understanding.

Keywords: c.521T>C, polymorphism, SLCO1B1, SNP, statins

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Rasha Ahmadi

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Glioblastoma is one of the most frequent brain malignancies, having a high mortality rate and limited survival in individuals with this malignancy. Despite different treatments and surgery, recurrence of glioblastoma cancer stem cells may arise as a subsequent tumor. For this reason, it is crucial to research the markers associated with glioblastoma stem cells and specifically their microenvironment. In this study, using bioinformatics analysis, we analyzed and nominated genes in the microenvironment pathways of glioblastoma stem cells. In this study, an appropriate database was selected for analysis by referring to the GEO database. This dataset comprised gene expression patterns in stem cells derived from glioblastoma patients. Gene clusters were divided as high and low expression. Enrichment databases such as Enrichr, STRING, and GEPIA were utilized to analyze the data appropriately. Finally, we extracted the potential genes 2700 high-expression and 1100 low-expression genes are implicated in the metabolic pathways of glioblastoma cancer progression. Cellular senescence, MAPK, TNF, hypoxia, zimosterol biosynthesis, and phosphatidylinositol metabolism pathways were substantially expressed and the metabolic pathways were downregulated. After assessing the association between protein networks, MSMP, SOX2, FGD4 ,and CNTNAP3 genes with high expression and DMKN and SBSN genes with low were selected. All of these genes were observed in the survival curve, with a survival of fewer than 10 percent over around 15 months. hsa-mir-192-5p, hsa-mir-129-5p, hsa-mir-215-5p, hsa-mir-335-5p, and hsa-mir-340-5p played key function in glioblastoma cancer stem cells microenviroments. We introduced critical genes through integrated and regular bioinformatics studies by assessing the amount of gene expression profile data that can play an important role in targeting genes involved in the energy and microenvironment of glioblastoma cancer stem cells. Have. This study indicated that hsa-mir-192-5p, and hsa-mir-129-5p are appropriate candidates for this.

Keywords: Glioblastoma, Cancer Stem Cells, Biomarker Discovery, Gene Expression Profiles, Bioinformatics Analysis, Tumor Microenvironment

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Authors: Liu Mingxin

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Streets act as the organizers of each image element on the urban spatial route, and the spatial continuity of urban streets is the basis for people to perceive the overall image of the city. This paper takes the walking space of Zhengzhou city as the research object, conducts investigation and analysis through questionnaire interviews, and selects typical walking space for in-depth study. Through the analysis of questionnaire data, the investigation and analysis of the current situation of walking space, and the analysis of pedestrian psychological behavior activities, the paper summarizes the construction suggestions of urban walking space continuity from the three aspects of the composition of walking street, the bottom interface and side interface, and the service facilities of walking space. The walking space is not only the traffic space but also the comfortable experience and the continuity of the space.

Keywords: walking space, spatial continuity, walking psychology, space reconstruction

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Authors: Leng Jian-Wei, Wang Lai-Jun, Li Ye

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In order to measure and analyze the transportation situation within the counties of Shaanxi province over a certain period of time and to promote the province's future transportation planning and development, this paper proposes a reasonable layout plan and compares model rationality. The study uses entropy weight method to measure the transportation advantages of 107 counties in Shaanxi province from three dimensions: road network density, trunk line influence and location advantage in 2013 and 2021, and applies spatial autocorrelation analysis method to analyze the spatial layout and development trend of county-level transportation, and conducts ordinary least square (OLS)regression on transportation impact factors and other influencing factors. The paper also compares the regression fitting degree of the Geographically weighted regression(GWR) model and the OLS model. The results show that spatially, the transportation advantages of Shaanxi province generally show a decreasing trend from the Weihe Plain to the surrounding areas and mainly exhibit high-high clustering phenomenon. Temporally, transportation advantages show an overall upward trend, and the phenomenon of spatial imbalance gradually decreases. People's travel demands have changed to some extent, and the demand for rapid transportation has increased overall. The GWR model regression fitting degree of transportation advantages is 0.74, which is higher than the OLS regression model's fitting degree of 0.64. Based on the evolution of transportation advantages, it is predicted that this trend will continue for a period of time in the future. To improve the transportation advantages of Shaanxi province increasing the layout of rapid transportation can effectively enhance the transportation advantages of Shaanxi province. When analyzing spatial heterogeneity, geographic factors should be considered to establish a more reliable model

Keywords: traffic dominance, GWR model, spatial autocorrelation analysis, temporal and spatial evolution

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Authors: Emrehan Ozcan, Dilek Beyazlı

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The development of tourism depends on an accurate planning approach as well as on the right planning process. This dependency is also a key factor in ensuring sustainability of tourism. The types of tourism, social expectations, planning practice, the socio-economic and the cultural structure of the region are determinants of planning approaches for tourism development. The tourism plans prepared for the historic city centers are usually based on the revitalization of cultural and historical values. The preservation and development of the tourism potentials of the historic city centers are important for providing an economic contribution to the locality, creating livable solutions for local residents and also the sustainability of tourism. This research is about experiencing and discussing a planning approach that will provide tourism development based on historical and cultural values. Historical and cultural values in the historical city center of Trabzon -which has a settlement history of approximately 4000 years, is located on the Black Sea coast of Turkey- wear out over years and lose their tourism potential. A planning study has been experienced with strategic spatial planning approach for Trabzon, which has not done a tourism-oriented planning study until now. The stages of the planning process provided by strategic spatial planning approach are an assessment of the current situation; vision, strategies, and actions; action planning; designing and implementation of actions and monitoring-evaluation. In the discussion section, the advantages, planning process, methods and techniques of the approach are discussed for the possibilities and constraints in terms of tourism planning. In this context, it is aimed to put forth tourism planning process, stages, and implementation tools within the scope of strategic spatial planning approach by comparing approaches used in the tourism-oriented/priority planning of historical city centers. Suggestions on the position and effect of the preferred planning approach in the existing spatial planning practice are the outputs of the study.

Keywords: cultural heritage, tourism oriented planning, Trabzon, strategic spatial Planning

Procedia PDF Downloads 258

Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Chi V. Phan, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le

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Wilson’s disease is an autosomal recessive disorder of copper metabolism, which is caused by mutation in copper- transporting P-type ATPase (ATP7B). The mechanism of this disease is a failure of hepatic excretion of copper to the bile, and it leads to copper deposits in the liver and other organs. Most clinical symptoms of Wilson’s disease can present as liver disease and/or neurologic disease. Objective: The goal of the study is prenatal diagnosis for pregnant women at high risk of Wilson’s disease in Northern Vietnam. Material and method: Three probands with clinically diagnosed liver disease were detected in the mutations of 21 exons and exon-intron boundaries of the ATP7B gene by direct Sanger-sequencing. Prenatal diagnoses were performed by amniotic fluid sampling from pregnant women in the 16th-18th weeks of pregnancy after the genotypes of parents with the probands were identified. Result: A total of three different mutations of the probands, including of S105*, P1052L, P1273G, were detected. Among three fetuses which underwent prenatal genetic testing, one fetus was homozygote; two fetuses were carriers. Conclusion: Genetic testing provided a useful method for prenatal diagnosis, and is a basis for genetic counseling.

Keywords: ATP7B gene, genetic testing, prenatal diagnosis, pedigree, Wilson disease

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Authors: Salina Y. Saddick

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Mild gestational hyperglycemia (MGH) is a very common complication of pregnancy that is characterized by intolerance to glucose. The association of angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism to MGH has been previously reported. In this study, we evaluated the association between ACE polymorphism and the risk of MGH in a Saudi population. We conducted a case-control study in a population of 100 MGH patients and 100 control subjects. ACE gene polymorphism was analyzed by the novel approach of tetraprimer amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR). The frequency of ACE polymorphism was not associated with either alleles or genotypes in MGH patients. Glucose concentration was found to be significantly associated with the MGH group. Our study suggests that ACE genotypes were not associated with ACE polymorphism in a Saudi population.

Keywords: MGH, ACE, insertion polymorphism, deletion polymorphism

Procedia PDF Downloads 319