Search results for: spatial gene

Authors: Ali Aydin, Mert Sudagidan, Aysen Coban, Alparslan Kadir Devrim

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Pseudomonas spp. (specifically, P. fluorescens and P. fragi) are considered the principal spoilage microorganisms of refrigerated poultry meats. The higher the level psychrophilic spoilage Pseudomonas spp. on carcasses at the end of processing lead to decrease the shelf life of the refrigerated product. The aim of the study was the identification of psychrophilic Pseudomonas spp. having proteolytic and lipolytic activities from poultry meats by 16S rRNA and rpoB gene sequencing, investigation of protease and lipase related genes and determination of proteolytic activity of Pseudomonas spp. In the of isolation procedure, collected chicken meat samples from local markets and slaughterhouses were homogenized and the lysates were incubated on Standard method agar and Skim Milk agar for selection of proteolytic bacteria and tributyrin agar for selection of lipolytic bacteria at +4 °C for 7 days. After detection of proteolytic and lipolytic colonies, the isolates were firstly analyzed by biochemical tests such as Gram staining, catalase and oxidase tests. DNA gene sequencing analysis and comparison with GenBank revealed that 126 strong enzyme Pseudomonas spp. were identified as predominantly P. fluorescens (n=55), P. fragi (n=42), Pseudomonas spp. (n=24), P. cedrina (n=2), P. poae (n=1), P. koreensis (n=1), and P. gessardi (n=1). Additionally, protease related aprX gene was screened in the strains and it was detected in 69/126 strains, whereas, lipase related lipA gene was found in 9 Pseudomonas strains. Protease activity was determined using commercially available protease assay kit and 5 strains showed high protease activity. The results showed that psychrophilic Pseudomonas strains were present in chicken meat samples and they can produce important levels of proteases and lipases for food spoilage to decrease food quality and safety.

Keywords: Pseudomonas, chicken meat, protease, lipase

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Authors: Jarmila Bernasovska, Pavel Ružbarský, Ivan Bernasovsky, Regina Lohajová Behulová

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The paper presents the results of the application of molecular genetics methods in sport research, with special emphasis on the most advanced methods and trends in diagnosing of motoric predispositions for the sake of identifying talented children. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. Genetics is important in determining the capacity of an individual and for professional sport level. Genetic information can be used for individual genetic predispositions in early childhood. The phenotypes are influenced by a combination of genetic and environmental factors. The aim of the presented study was to examine physical condition, coordination skills, motoric docility and to determine the frequency of ACTN3 (R577X) gene in Romany children from Eastern Slovakia and compared their motoric performance with non-Romany children. This paper is not looking just for a performance, but also its association to genetic predispositions in relation to ACTN3 gene and its R577X polymorphism. Genotype data were obtained from 175 Romany children from 6 to 15 years old and 218 non-Romany children at the same age from Eastern Slovakia. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor Gene 6000 Corbett and LightCycler 480 Roche). Romany children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in children was different from controls. The frequency of XX genotype was 11,45% which is comparable to a frequency of an Indian population. Data were analysed with the ANOVA statistical programme and parametric and nonparametric tests. This work was supported by grants APVV-0716-10, ITMS 26220120023 and ITMS 26220120041.

Keywords: ACTN3 gene, R577X polymorphism, Romany children, sport performance, Slovakia

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Authors: Lazhar Belkhiri, Ammar Tiri, Lotfi Mouni

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In this research, we analyzed the groundwater quality index in the El Milia plain, Kebir Rhumel Basin, Algeria. Thirty-three groundwater samples were collected from wells in the El Milia plain during April 2015. In this study, pH and electrical conductivity (EC) were conducted at each sampling well. Eight hydrochemical parameters such as calcium (Ca), magnesium (Mg), sodium (Na), potassium (K), chlorid (Cl), sulfate (SO4), bicarbonate (HCO3), and Nnitrate (NO3) were analysed. The entropy water quality index (EWQI) method was employed to evaluate the groundwater quality in the study area. Moran’s I and the ordinary kriging (OK) interpolation technique were used to examine the spatial distribution pattern of the hydrochemical parameters in the groundwater. It was found that the hydrochemical parameters Ca, Cl, and HCO3 showed strong spatial autocorrelation in the El Milia plain, indicating a spatial dependence and clustering of these parameters in the groundwater. The groundwater quality was evaluated using the entropy water quality index (EWQI). The results showed that approximately 86% of the total groundwater samples in the study area fall within the moderate groundwater quality category. The spatial map of the EWQI values indicated an increasing trend from the south-west to the northeast, following the direction of groundwater flow. The highest EWQI values were observed near El Milia city in the center of the plain. This spatial pattern suggests variations in groundwater quality across the study area, with potentially higher risks near the city center. Therefore, the results obtained in this research provide very useful information to decision-makers.

Keywords: entropy water quality index (EWQI), moran’s i, ordinary kriging interpolation, el milia plain

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Authors: Emanuela Chiarella, Annamaria Aloisio, Nisticò Clelia, Maria Mesuraca

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ZNF521 is a stem cell-associated transcription co-factor, that plays a crucial role in the homeostatic regulation of the stem cell compartment in the hematopoietic, osteo-adipogenic, and neural system. In normal hematopoiesis, primary human CD34+ hematopoietic stem cells display typically a high expression of ZNF521, while its mRNA levels rapidly decrease when these progenitors progress towards erythroid, granulocytic, or B-lymphoid differentiation. However, most acute myeloid leukemias (AMLs) and leukemia-initiating cells keep high ZNF521 expression. In particular, AMLs are often characterized by chromosomal translocations involving the Mixed Lineage Leukemia (MLL) gene, which MLL gene includes a variety of fusion oncogenes arisen from genes normally required during hematopoietic development; once they are fused, they promote epigenetic and transcription factor dysregulation. The chromosomal translocation t(9;11)(p21-22;q23), fusing the MLL gene with AF9 gene, results in a monocytic immune phenotype with an aggressive course, frequent relapses, and a short survival time. To better understand the dysfunctional transcriptional networks related to genetic aberrations, AML gene expression profile datasets were queried for ZNF521 expression and its correlations with specific gene rearrangements and mutations. The results showed that ZNF521 mRNA levels are associated with specific genetic aberrations: the highest expression levels were observed in AMLs involving t(11q23) MLL rearrangements in two distinct datasets (MILE and den Boer); elevated ZNF521 mRNA expression levels were also revealed in AMLs with t(7;12) or with internal rearrangements of chromosome 16. On the contrary, relatively low ZNF521 expression levels seemed to be associated with the t(8;21) translocation, that in turn is correlated with the AML1-ETO fusion gene or the t(15;17) translocation and in AMLs with FLT3-ITD, NPM1, or CEBPα double mutations. Invitro, we found that the enforced co-expression of ZNF521 in cord blood-derived CD34+ cells induced a significant proliferative advantage, improving MLL-AF9 effects on the induction of proliferation and the expansion of leukemic progenitor cells. Transcriptome profiling of CD34+ cells transduced with either MLL-AF9, ZNF521, or a combination of the two transgenes highlighted specific sets of up- or down-regulated genes that are involved in the leukemic phenotype, including those encoding transcription factors, epigenetic modulators, and cell cycle regulators as well as those engaged in the transport or uptake of nutrients. These data enhance the functional cooperation between ZNF521 and MA9, resulting in the development, maintenance, and clonal expansion of leukemic cells. Finally, silencing of ZNF521 in MLL-AF9-transformed primary CD34+ cells inhibited their proliferation and led to their extinction, as well as ZNF521 silencing in the MLL-AF9+ THP-1 cell line resulted in an impairment of their growth and clonogenicity. Taken together, our data highlight ZNF521 role in the control of self-renewal and in the immature compartment of malignant hematopoiesis, which, by altering the gene expression landscape, contributes to the development and/or maintenance of AML acting in concert with the MLL-AF9 fusion oncogene.

Keywords: AML, human zinc finger protein 521 (hZNF521), mixed lineage leukemia gene (MLL) AF9 (MLLT3 or LTG9), cord blood-derived hematopoietic stem cells (CB-CD34+)

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Authors: Rima Hleiss, Elie Bitar, Mahmoud Hassan, Mohamad Khalil

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A comprehensive study of object recognition in the human brain requires combining both spatial and temporal analysis of brain activity. Here, we are mainly interested in three issues: the time perception of visual objects, the ability of discrimination between two particular categories (objects vs. animals), and the possibility to identify a particular spatial representation of visual objects. Our experiment consisted of acquiring dense electroencephalographic (EEG) signals during a picture-naming task comprising a set of objects and animals’ images. These EEG responses were recorded from nine participants. In order to determine the time perception of the presented visual stimulus, we analyzed the Event Related Potentials (ERPs) derived from the recorded EEG signals. The analysis of these signals showed that the brain perceives animals and objects with different time instants. Concerning the discrimination of the two categories, the support vector machine (SVM) was applied on the instantaneous EEG (excellent temporal resolution: on the order of millisecond) to categorize the visual stimuli into two different classes. The spatial differences between the evoked responses of the two categories were also investigated. The results showed a variation of the neural activity with the properties of the visual input. Results showed also the existence of a spatial pattern of electrodes over particular regions of the scalp in correspondence to their responses to the visual inputs.

Keywords: brain activity, categorization, dense EEG, evoked responses, spatio-temporal analysis, SVM, time perception

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Authors: Syed M. Shahid, Rozeena Shaikh, Syeda N. Nawab, Abid Azhar

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Diabetes mellitus (DM) is a prevalent non-communicable disease worldwide. DM may lead to many vascular complications like hypertension, nephropathy, retinopathy, neuropathy and foot infections. Pathogenesis of diabetic nephropathy (DN) is implicated by the polymorphisms in genes encoding the specific components of renin angiotensin aldosterone system (RAAS) which include angiotensinogen (AGT), angiotensin-II receptor and angiotensin converting enzyme (ACE) genes. This study was designed to explore the possible association of AG (M268T) polymorphism in the patients of diabetes and nephropathy in Pakistan. Study subjects included 100 controls, 260 diabetic patients without renal insufficiency and 190 diabetic nephropathy patients with persistent albuminuria. Fasting blood samples were collected from all the subjects after getting institutional ethical approval and informed consent. The biochemical estimations, PCR amplification and direct sequencing for the specific region of AGT gene was carried out. A significantly high frequency of TT genotype and T allele of AGT (M268T) was observed in the patients of diabetes with nephropathy as compared to controls and diabetic patients without any known renal impairment. The TT genotype and T allele of AGT (M268T) polymorphism may be considered as a genetic risk factor for the development and progression of nephropathy in diabetes. Further cross sectional population studies would be of help to establish and confirm the observed possible association of AGT gene variations with development of nephropathy in diabetes.

Keywords: RAAS, AGT (M268T), diabetes, nephropathy

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Authors: Mahbuba Rahman, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Darawan Rinchai, Damien Chaussabel, Nico Marr

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Collections of large-scale datasets made available in public repositories can be used to identify and fill gaps in biomedical knowledge. But first, these data need to be made readily accessible to researchers for analysis and interpretation. Here a collection of transcriptome datasets was made available to investigate the functional programming of human hematopoietic cells in early life. Thirty two datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom, interactive web application called the Gene Expression browser (GXB), designed for visualization and query of integrated large-scale data. Multiple sample groupings and gene rank lists were created based on the study design and variables in each dataset. Web links to customized graphical views can be generated by users and subsequently be used to graphically present data in manuscripts for publication. The GXB tool also enables browsing of a single gene across datasets, which can provide information on the role of a given molecule across biological systems. The dataset collection is available online. As a proof-of-principle, one of the datasets (GSE25087) was re-analyzed to identify genes that are differentially expressed by regulatory T cells in early life. Re-analysis of this dataset and a cross-study comparison using multiple other datasets in the above mentioned collection revealed that PMCH, a gene encoding a precursor of melanin-concentrating hormone (MCH), a cyclic neuropeptide, is highly expressed in a variety of other hematopoietic cell types, including neonatal erythroid cells as well as plasmacytoid dendritic cells upon viral infection. Our findings suggest an as yet unrecognized role of MCH in immune regulation, thereby highlighting the unique potential of the curated dataset collection and systems biology approach to generate new hypotheses which can be tested in future mechanistic studies.

Keywords: early-life, GEO datasets, PMCH, interactive query, systems biology

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Authors: Nan Deng, Zhenqiu Liu

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Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

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Authors: K. R. Thabethe, G. A. Adefolaju, M. J. Hosie

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Cervical cancer is the third most commonly diagnosed cancer globally and it is one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs and has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. The aim of this study was to investigate the relationship between cervical cancer and HAART. This was achieved by studying the expression of two signalling molecules expressed in cervical cancer; MUC1 and P65. Following the 24 hour treatment of a cervical cancer cell line, HCS-2, with drugs which are commonly used as part of HAART at their clinical plasma concentrations, real-time qPCR and immunofluorescence were used in order to study gene and protein expression. A one way ANOVA followed by a Tukey Kramer Post Hoc test was conducted using JMP 11 software on both sets of data. The drug classified as a protease inhibitor (PI) (i.e. LPV/r) reduced MUC1 and P65 gene and protein expression more than the other drug tested. PIs are known to play a significant role in cell death, therefore the cells were thought to be more susceptible to cell death following treatment with PIs. In conclusion, the drugs used, especially the PI showed some anticancer effects by facilitating cell death through decreased gene and protein expression of MUC1 and P65 and present promising agents for cancer treatment.

Keywords: cervical cancer, haart, MUC1, P65

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Authors: Ningfei Xiao, Simon Twose, Hannah Hopewell

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In urban settings worldwide, artists and researchers have drawn from shamanic healing, providing insightful responses to the environment. This project is a transdisciplinary creative research project where architecture and art practice draw from shamanic healing and provide the potential to expand knowledge of public space and inspire more aesthetic explorations of public spatial visions. The research started from the encounters with the Ewengki/Evenki shaman tribe in settlement areas of northern China in 2019 and extended through the partnerships with Maori artists in Poneke Aotearoa, New Zealand, in 2023. Based on the learnings and collaborations with female indigenous tradition practitioners and the healing that the researcher received from the land, a spatial installation exhibition was developed in this project. Indigenous practices are intricately woven with contemporary technology, merging visuals, soundscapes, and other non-visual aesthetics influenced by the researcher's personal experiences of embodied shamanic healing with brainwave generative technology. This synthesis seeks to ritualize and reimagine future public spaces, encompassing streetscapes and greenscapes from China to Aotearoa, and fostering connections between urbanized human body, mind, spirit, and land. In doing so, the project presents a feminist posthuman inquiry into how individuals perceive materiality within the context of a future city. Grounded in creative research and embodied methodologies, this paper focuses on the conceptual and autoethnographic aspects of visual-non-visual aesthetics and their creative representation. Through the exploration of aesthetics beyond the visual realm within urban and spatial contexts, this project showcases the spatial installation exhibition as an example of shamanic influence and related response to public space through embodied artistry and transdisciplinary creative inquiry.

Keywords: aesthetic, embodiment, visual and/or non-visual, spatial installation, shamanic healing, public space

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

Procedia PDF Downloads 141

Authors: Nanjiang Chen

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In the backdrop of expanding urban landscapes, accurately assessing spatial openness is critical. Traditional visibility analysis methods grapple with discretization errors and inefficiencies, creating a gap in truly capturing the human experi-ence of space. Addressing these gaps, this paper introduces a distinct continuous visibility algorithm, a leap in measuring urban spaces from a human-centric per-spective. This study presents a methodological breakthrough by applying this algorithm to urban visibility analysis. Unlike conventional approaches, this tech-nique allows for a continuous range of visibility assessment, closely mirroring hu-man visual perception. By eliminating the need for predefined subdivisions in ray casting, it offers a more accurate and efficient tool for urban planners and architects. The proposed algorithm not only reduces computational errors but also demonstrates faster processing capabilities, validated through a case study in Bei-jing's urban setting. Its key distinction lies in its potential to benefit a broad spec-trum of stakeholders, ranging from urban developers to public policymakers, aid-ing in the creation of urban spaces that prioritize visual openness and quality of life. This advancement in urban analysis methods could lead to more inclusive, comfortable, and well-integrated urban environments, enhancing the spatial experience for communities worldwide.

Keywords: visual openness, spatial continuity, ray-tracing algorithms, urban computation

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Authors: Alina Smalinskiene Janina Petkeviciene, Jurate Klumbiene, Vilma Kriaucioniene, Vaiva Lesauskaite

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The worldwide prevalence of obesity has been increasing dramatically in the last few decades, and Lithuania is no exception. In 2012, every fifth adult (19% of men and 20.5 % of women) was obese and every third was overweight Association studies have highlighted the influence of SNPs in obesity, with particular focus on FTO rs9939609. Thus far, no data on the possible association of this SNP to obesity in the adult Lithuanian population has been reported. Here, for the first time, we demonstrate an association between the FTO rs9939609 homozygous AA genotype and increased BMI when compared to homozygous TT. Furthermore, a positive association was determined between the FTO rs9939609 variant and risk of metabolic syndrome. Background: This study aimed to examine the associations between the fat mass and obesity associated (FTO) gene rs9939609 variant with obesity and metabolic syndrome in Lithuanian adult population. Materials and Methods: A cross-sectional health survey was carried out in randomly selected municipalities of Lithuania. The random sample was obtained from lists of 25–64 year-old inhabitants. The data from 1020 subjects were analysed. The rs9939609 SNP of the FTO gene was assessed using TaqMan assays (Applied Biosystems, Foster City, CA, USA). The Applied Biosystems 7900HT Real-Time Polymerase Chain Reaction System was used for detecting the SNPs. Results: The carriers of the AA genotype had the highest mean values of BMI and waist circumference (WC) and the highest risk of obesity. Interactions ‘genotype x age’ and ‘genotype x physical activity’ in determining BMI and WC were shown. Neither lipid and glucose levels, nor blood pressure were associated with the rs9939609 independently of BMI. In the age group of 25-44 years, association between the FTO genotypes and metabolic syndrome was found. Conclusion: The FTO rs9939609 variant was significantly associated with BMI and WC, and with the risk of obesity in Lithuanian population. The FTO polymorphism might have a greater influence on weight status in younger individuals and in subjects with a low level of physical activity.

Keywords: obesity metabolic syndrome, FTO gene, polymorphism, Lithuania

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Authors: C. Agrawal, R. Kumar, A. Gupta, B. Chatterjee

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An experimental investigation has been carried out to study the cooling of a hot horizontal Stainless Steel surface of 3 mm thickness, which has 800±10 °C initial temperature. A round water jet of 22 ± 1 °C temperature was injected over the hot surface through straight tube type nozzles of 2.5-4.8 mm diameter and 250 mm length. The experiments were performed for the jet exit to target surface spacing of 4 times of jet diameter and jet Reynolds number of 5000-24000. The effect of change in jet Reynolds number on the surface quenching has been investigated form the stagnation point to 16 mm spatial location.

Keywords: hot-surface, jet impingement, quenching, stagnation point

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Authors: Yu Pan, Jing Wu, Lingwan Shen

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Since the reform and opening, China's cities have developed rapidly, and the industrial structure has been constantly adjusted and optimized. A large number of industrial plants have lost their production functions and become idle buildings. The renovation projects for the old factory buildings are important parts of the urban renewal, and most of them are the cultural and creative industrial park projects. In this paper, a statistical analysis of renovation projects of the representative cultural and creative industrial parks in recent years was conducted. According to the user's spatial experience satisfaction survey, the physical and spatial factors affecting the space regeneration of the old factory were concluded. Thus the relationship between space regeneration and material, structure, internal and external space design has been derived. Finally, we summarized the general spatial processing model in which the contradiction between ‘new’ and ‘old’ can be grafted and transformed.

Keywords: renovation of factory buildings, urban renewal, the cultural and creative industrial park, space regeneration, reconstruction mode

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Authors: T. C. C. Soo, S. Bhassu

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Unlike the common presence of both innate and adaptive immunity in vertebrates, crustaceans, in particular, shrimps, have been discovered to possess only innate immunity. This further emphasizes the importance of innate immunity within shrimps in pathogenic resistance. Under the study of pathogenic immune challenge, different shrimp species actually exhibit varying degrees of immune resistance towards the same pathogen. Furthermore, even within the same shrimp species, different batches of challenged shrimps can have different strengths of immune defence. Several important pathways are activated within shrimps during pathogenic infection. One of them is JAK-STAT pathway that is activated during bacterial, viral and fungal infections by which STAT(Signal Transducer and Activator of Transcription) gene is the core element of the pathway. Based on theory of Central Dogma, the genomic information is transmitted in the order of DNA, RNA and protein. This study is focused in uncovering the important evolutionary patterns present within the DNA (non-coding region) and RNA (coding region). The three shrimp species involved are Macrobrachium rosenbergii, Penaeus monodon and Litopenaeus vannamei which all possess commercial significance. The shrimp species were challenged with a famous penaeid shrimp virus called white spot syndrome virus (WSSV) which can cause serious lethality. Tissue samples were collected during time intervals of 0h, 3h, 6h, 12h, 24h, 36h and 48h. The DNA and RNA samples were then extracted using conventional kits from the hepatopancreas tissue samples. PCR technique together with designed STAT gene conserved primers were utilized for identification of the STAT coding sequences using RNA-converted cDNA samples and subsequent characterization using various bioinformatics approaches including Ramachandran plot, ProtParam and SWISS-MODEL. The varying levels of immune STAT gene activation for the three shrimp species during WSSV infection were confirmed using qRT-PCR technique. For one sample, three biological replicates with three technical replicates each were used for qRT-PCR. On the other hand, DNA samples were important for uncovering the structural variations within the genomic region of STAT gene which would greatly assist in understanding the STAT protein functional variations. The partially-overlapping primers technique was used for the genomic region sequencing. The evolutionary inferences and event predictions were then conducted through the Bayesian Inference method using all the acquired coding and non-coding sequences. This was supplemented by the construction of conventional phylogenetic trees using Maximum likelihood method. The results showed that adaptive evolution caused STAT gene sequence mutations between different shrimp species which led to evolutionary divergence event. Subsequently, the divergent sites were correlated to the differing expressions of STAT gene. Ultimately, this study assists in knowing the shrimp species innate immune variability and selection of disease resistant shrimps for breeding purpose. The deeper understanding of STAT gene evolution from the perspective of both purifying and adaptive approaches not only can provide better immunological insight among shrimp species, but also can be used as a good reference for immunological studies in humans or other model organisms.

Keywords: gene evolution, JAK-STAT pathway, immunology, STAT gene

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Authors: Sisi Xia, Dezhuan Tao, Junyan Yang, Weiting Xiong

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Under the background of Chinese urbanization changing from incremental development to stock development, the completion of urban public service facilities is essential to urban spatial quality. As public services facilities is a huge and complicated system, clarifying the various types of internal rules associated with the land market price is key to optimizing spatial layout. This paper takes Wuxi City as a representative sample location and establishes the digital analysis platform using urban price and several high-precision big data acquisition methods. On this basis, it analyzes the coupling relationship between different public service categories and land price, summarizing the coupling patterns of urban public facilities distribution and urban land price fluctuations. Finally, the internal mechanism within each of the two elements is explored, providing the reference of the optimum layout of urban planning and public service facilities.

Keywords: public service facilities, land price, urban spatial morphology, big data

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Authors: Lin Li, P. G. R. N. I. Pussella

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When representing spatial data and their attributes on different types of maps, the scale plays a key role in the process of map generalization. The process is consisted with two main operators such as selection and omission. Once some data were selected, they would undergo of several geometrical changing processes such as elimination, simplification, smoothing, exaggeration, displacement, aggregation and size reduction. As a result of these operations at different levels of data, the geometry of the spatial features such as length, sinuosity, orientation, perimeter and area would be altered. This would be worst in the case of preparation of small scale maps, since the cartographer has not enough space to represent all the features on the map. What the GIS users do is when they wanted to analyze a set of spatial data; they retrieve a data set and does the analysis part without considering very important characteristics such as the scale, the purpose of the map and the degree of generalization. Further, the GIS users use and compare different maps with different degrees of generalization. Sometimes, GIS users are going beyond the scale of the source map using zoom in facility and violate the basic cartographic rule 'it is not suitable to create a larger scale map using a smaller scale map'. In the study, the effect of map generalization for GIS analysis would be discussed as the main objective. It was used three digital maps with different scales such as 1:10000, 1:50000 and 1:250000 which were prepared by the Survey Department of Sri Lanka, the National Mapping Agency of Sri Lanka. It was used common features which were on above three maps and an overlay analysis was done by repeating the data with different combinations. Road data, River data and Land use data sets were used for the study. A simple model, to find the best place for a wild life park, was used to identify the effects. The results show remarkable effects on different degrees of generalization processes. It can see that different locations with different geometries were received as the outputs from this analysis. The study suggests that there should be reasonable methods to overcome this effect. It can be recommended that, as a solution, it would be very reasonable to take all the data sets into a common scale and do the analysis part.

Keywords: generalization, GIS, scales, spatial analysis

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Authors: Wen-Yan Chiau

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Taiwan passed the 'Basic Ocean Act' in November 2019, and in accordance with Article 4 of its provisions, the government should draft a decree on ocean space planning (MSP). In the past few years, although Taiwan has passed the 'Coastal Zone Management Act' and the 'Spatial Planning Act', in the face of multiple use of marine areas, it still lacks a comprehensive marine area use blueprint and a fundamental mechanism for multi-purpose use planning management. In particular, Taiwan's active development of offshore wind power is facing this problem, and it is impossible to fully reconcile the use of each domain and the public welfare through a holistic system, highlighting the urgency of the establishment of MSP system. Therefore, this article will review relevant Taiwan laws and regulations, refer to important international initiatives and experiences, and participate in the exchange of practical experience in international conference(s), and propose adequate framework, principles, procedures, and promotion strategies on MSP. Possible solutions to promote sustainable and wise use in Taiwan's waters will also be suggested for comments.

Keywords: basic ocean act, coastal zone management act, marine spatial planning, spatial planning act, Taiwan

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Authors: Danna Jia, Bin Li

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Background: Atopic dermatitis (AD) is a chronic and refractory inflammatory skin disease characterized by relapsing eczematous and pruritic skin lesions. The global prevalence of AD ranges from 1~ 20%, and its incidence rates are increasing. It affects individuals from infancy to adulthood, significantly impacting their daily lives and social activities. Despite its major health burden, the precise mechanisms underlying AD remain unknown. Understanding the genetic differences associated with AD is crucial for advancing diagnosis and targeted treatment development. This study aims to identify candidate genes of AD by using bioinformatics analysis. Methods: We conducted a comprehensive analysis of four pooled transcriptomic datasets (GSE16161, GSE32924, GSE130588, and GSE120721) obtained from the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed using the R statistical language. The differentially expressed genes (DEGs) between AD patients and normal individuals were functionally analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, a protein-protein interaction (PPI) network was constructed to identify candidate genes. Results: Among the patient-level gene expression datasets, we identified 114 shared DEGs, consisting of 53 upregulated genes and 61 downregulated genes. Functional analysis using GO and KEGG revealed that the DEGs were mainly associated with the negative regulation of transcription from RNA polymerase II promoter, membrane-related functions, protein binding, and the Human papillomavirus infection pathway. Through the PPI network analysis, we identified eight core genes: CD44, STAT1, HMMR, AURKA, MKI67, and SMARCA4. Conclusion: This study elucidates key genes associated with AD, providing potential targets for diagnosis and treatment. The identified genes have the potential to contribute to the understanding and management of AD. The bioinformatics analysis conducted in this study offers new insights and directions for further research on AD. Future studies can focus on validating the functional roles of these genes and exploring their therapeutic potential in AD. While these findings will require further verification as achieved with experiments involving in vivo and in vitro models, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.

Keywords: atopic dermatitis, bioinformatics, biomarkers, genes

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Authors: Ali̇ Bayram, Semih Dalkilic, Remzi Yigiter

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N-methyl-D-aspartate (NMDA) receptor is a subtype of glutamate receptor and plays a pivotal role in learning, memory, neuronal plasticity, neurotoxicity and synaptic mechanisms. Animal experiments were suggested that glutamate-induced excitotoxic injuriy and NMDA receptor blockage lead to amnesia and other neurodegenerative diseases including Alzheimer’s disease (AD), Huntington’s disease, amyotrophic lateral sclerosis. Aim of this study is to investigate association between NMDA receptor coding gene GRIN2B expression level and Alzheimer disease. The study was approved by the local ethics committees, and it was conducted according to the principles of the Declaration of Helsinki and guidelines for the Good Clinical Practice. Peripheral blood was collected 50 patients who diagnosed AD and 49 healthy control individuals. Total RNA was isolated with RNeasy midi kit (Qiagen) according to manufacturer’s instructions. After checked RNA quality and quantity with spectrophotometer, GRIN2B expression levels were detected by quantitative real time PCR (QRT-PCR). Statistical analyses were performed, variance between two groups were compared with Mann Whitney U test in GraphpadInstat algorithm with 95 % confidence interval and p < 0.05. After statistical analyses, we have determined that GRIN2B expression levels were down regulated in AD patients group with respect to control group. But expression level of this gene in each group was showed high variability. İn this study, we have determined that NMDA receptor coding gene GRIN2B expression level was down regulated in AD patients when compared with healthy control individuals. According to our results, we have speculated that GRIN2B expression level was associated with AD. But it is necessary to validate these results with bigger sample size.

Keywords: Alzheimer’s disease, N-methyl-d-aspartate receptor, NR2B, GRIN2B, mRNA expression, RT-PCR

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Authors: Chenchen Liu, Jacques Audran

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Using tablet apps with a certain educational purpose to promote young children’s cognitive development, is quite common now. Developing an educational app on an Ipad like tablet, especially for a young child (age 3-5) requires an optimal level of challenge to continuously attract children’s attention and obtain an educational effect. Adaptive difficulty adjustment, which could dynamically set the difficulty in the challenge according to children’s performance, seems to be a good solution. Since space concept plays an important role in young children’s cognitive development, we made an experimental comparison in a French kindergarten between one group of 23 children using an educational app ‘Debout Ludo’ with adaptive difficulty settings and another group of 20 children using the previous version of ‘Debout Ludo’ with a classic incremental difficulty adjustment. The experiment results of spatial problem solving indicated that a significantly higher learning outcome was acquired by the young children who used the adaptive version of the app.

Keywords: adaptive difficulty, spatial problem solving, tactile tablet, young children

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Authors: Melkamu A. Zeru, Aweke A. Mitiku, Endashaw Amuka

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Background: Under-five mortality is the likelihood that a baby will pass away before turning exactly 5 years old, represented as a percentage per 1,000 live births. Exploring the spatial distribution and identifying the temporal pattern is important to reducing under-five child mortality globally, including in Ethiopia. Thus, this study aimed to identify the risk factors of under-five mortality and the spatiotemporal variation in Ethiopian administrative zones. Method: This study used the 2000-2016 Ethiopian Demographic and Health Survey (EDHS) data, which were collected using a two-stage sampling method. A total of 43,029 (10,873 in 2000, 9,861 in 2005, 11,654 in 2011, and 10,641 in 2016) weighted sample under-five child mortality was used. The space-time dynamic model was employed to account for spatial and time effects in 65 administrative zones in Ethiopia. Results: From the result of a general nesting spatial-temporal dynamic model, there was a significant space-time interaction effect [γ = -0.1444, 95 % CI (-0.6680, -0.1355)] for under-five mortality. The increase in the percentages of mothers illiteracy [𝛽 = 0.4501, 95% CI (0.2442, 0.6559)], not vaccinated[𝛽= 0.7681, 95% CI (0.5683, 0.9678)], unimproved water[𝛽= 0.5801, CI (0.3793, 0.7808)] were increased death rates for under five children while increased percentage of contraceptive use [𝛽= -0.6609, 95% CI (-0.8636, -0.4582)] and ANC visit > 4 times [𝛽= -0.1585, 95% CI(-0.1812, -0.1357)] were contributed to the decreased under-five mortality rate at the zone in Ethiopia. Conclusions: Even though the mortality rate for children under five has decreased over time, still there is still higher in different zones of Ethiopia. There exists spatial and temporal variation in under-five mortality among zones. Therefore, it is very important to consider spatial neighbourhoods and temporal context when aiming to avoid under-five mortality.

Keywords: under-five children mortality, space-time dynamic, spatiotemporal, Ethiopia

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Authors: Seung-Hwa Baek, In-Jung Nam, Sang-Han Lee

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The development of anti-melanogenic agents is important for the prevention of serious esthetic problem like a melasma, freckle, age spots, and chloasma. The aim of this study was to investigate the anti-melanogenic effect of sesamol, an active lignan isolated from sesame seed, by mushroom and cellular tyrosinase assay, melanin content and the analysis of melanogensis-related mRNA expressions in melana cells. Sesamol showed strong inhibitory activity against the mushroom tyrosinase in a dose-dependent manner. Intracellular tyrosinase inhibition activity was also confirmed by zymography. At a concentration of 50 μM, sesamol inhibited melanin production in melan-a cells with no cytoxicity while those of phenylthiourea (PTU) as a positive control were the same condition. Sesamol significantly inhibited the expression of melanogensis-related genes, such as tyrosinase, tyrosinase-related protein-1 (TRP-1), dopachrome tautomerase (Dct), microphthalmia-associated transcription factor (MITF) and melanocortin 1 receptor (MC1R). These findings indicate that sesamol could reduce melanin biosynthesis via the downregulation of tyrosinase activity and melanin production via subsequent gene expression of melanogenesis-related proteins. Together, these results suggest that the sesamol have strong potential in inhibiting melanin biosynthesis, in that the substance may be used as a new skin-whitening agent of cosmetic materials.

Keywords: sesamol, sesame seed, melanin biosynthesis, melanogenesis-related gene, skin-whitening agent

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Authors: Jiayue Yang

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Based on an analysis of China's database of certified disabled persons in 2021, this study reveals several key findings. Firstly, the proportion of certified mentally disabled persons among China's certified disabled population (Certification rate 1) shows a decreasing distribution from the East to the West and from the South to the North. Secondly, the spatial distribution of the number of mentally disabled persons per 1,000 people holding certificates (certification rate 2) shows a relatively scattered pattern, with significant variations observed between cities in the eastern region. However, on an overall scale, a south-north gradient can still be observed, with higher rates in the North and lower rates in the west, while the central region demonstrates higher rates compared to the western region. The variation in the rate of mentally handicapped certificates among regions is influenced not only by traditional culture and welfare level but also exhibits a certain correlation with the level of economic development.

Keywords: certified disabled persons, mentally disabled persons, spatial distribution, China

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Ramazan Özbey

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The basic criteria which determine durum wheat quality is its suitability for pasta processing that is pasta making quality. Bright yellow color is a desired property in pasta products. Durum wheat pasta making quality is affected by grain pigment content and oxidative enzymes which affect adversely bright yellow color. Of the oxidative enzymes, lipoxygenase LOX is the most effective one on oxidative bleaching of yellow pigments in durum wheat products. Thus, wheat cultivars that are high in yellow pigments but low in LOX enzyme activity should be preferred for the production of pasta with high color quality. The aim of this study was to reduce lipoxygenase activities of the backcross durum wheat lines that were previously improved for their protein quality. For this purpose, two advanced lines with different parents (TMB2 and TMB3) were used recurrent parents. Also, Gediz-75 wheat with low LOX enzyme activity was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region (Lpx-B1.1) were selected using SSR markers by marker assisted selection method. As a result, the study will be completed in three years instead of six years required in a classical backcross breeding study, leading to the development of high-quality candidate varieties. This research has been financially supported by TÜBİTAK (Project No: 112T910).

Keywords: durum wheat, lipoxygenase, LOX, Lpx-B1.1, MAS, Triticum durum

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Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

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Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

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Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

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Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs

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Authors: Sun fang, Zhang Wenxin

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This paper establishes an evaluation index system for spatio-temporal patterns of urbanization, with the county as research unit. We use the Entropy Weight method, coefficient variance, the Theil index and ESDA-GIS to analyze spatial patterns and evolutionary characteristics of New-Type Urbanization in the Central Plains Economic Region (CPER) between 2000 and 2011. Results show that economic benefit, non-agricultural employment level and level of market development are the most important factors influencing the level of New-Type Urbanization in the CPER; overall regional differences in New-Type Urbanization have declined while spatial correlations have increased from 2000 to 2011. The overall spatial pattern has changed little, however; differences between the western and eastern areas of the CPER are clear, and the pattern of a strong west and weak east did not change significantly over the study period. Areas with high levels of New-Type Urbanization were mostly distributed along the Beijing-Guangzhou and LongHai Railways on both sides, a new influx of urbanization was tightly clustered around ZhengZhou in the Central Henan Urban Agglomeration, but this trend was found to be weakening slightly. The level of New-Type Urbanization in municipal districts was found to be much higher than it was in the county generally. Provincial borders experienced a lower rate of growth and a lower level of New-Type Urbanization than did any other areas, consistently forming clusters of cold spots and sub-cold spots. The analysis confirms that historical development, location, and diffusion effects of urban agglomeration are the main drivers of changes in New-Type Urbanization patterns in CPER.

Keywords: new-type urbanization, spatial pattern, central plains economic region, spatial evolution

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Authors: Yelbek B. Utepov, Assel T. Mukhamejanova, Aliya K. Aldungarova, Aida G. Nazarova, Sabit A. Karaulov, Nurgul T. Alibekova, Aigul K. Kozhas, Dias Kazhimkanuly, Akmaral K. Tleubayeva

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This research focuses on enhancing geotechnical surveying for foundation design through the spatial interpolation of intermediate soil properties. Traditional geotechnical practices rely on discrete data from borehole drilling, soil sampling, and laboratory analyses, often neglecting the continuous nature of soil properties and disregarding values in intermediate locations. This study challenges these omissions by emphasizing interpolation techniques such as Kriging, Inverse Distance Weighting, and Spline interpolation to capture the nuanced spatial variations in soil properties. The methodology is applied to geotechnical survey data from two construction sites in Astana, Kazakhstan, revealing continuous representations of Young's Modulus, Cohesion, and Friction Angle. The spatial heatmaps generated through interpolation offered valuable insights into the subsurface environment, highlighting heterogeneity and aiding in more informed foundation design decisions for considered cites. Moreover, intriguing patterns of heterogeneity, as well as visual clusters and transitions between soil classes, were explored within seemingly uniform layers. The study bridges the gap between discrete borehole samples and the continuous subsurface, contributing to the evolution of geotechnical engineering practices. The proposed approach, utilizing open-source software geographic information systems, provides a practical tool for visualizing soil characteristics and may pave the way for future advancements in geotechnical surveying and foundation design.

Keywords: soil mechanical properties, spatial interpolation, inverse distance weighting, heatmaps

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