Search results for: spatial gene

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 re-investigate 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 However, the use of bootstrap support has become outdated for large-scale phylogenomic data.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 internode certainty, relative gene support, and high gene concordance factor. The evidence stems from 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 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, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Mediha B. Sılaydın Aydın, Emine D. Kahraman

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One of the important impacts of climate change is the sea level rise. Turkey is a peninsula, so the coastal areas of the country are threatened by the problem of sea level rise. Therefore, the urbanized coastal areas are highly vulnerable to climate change. At the aim of enhancing spatial resilience of urbanized areas, this question arises: What should be the priority intervention subject in the urban planning process for a given city. To answer this question, by focusing on the problem of sea level rise, this study aims to determine spatial vulnerability typologies and levels of Turkey coastal cities based on morphological, physical and social characteristics. As a method, spatial vulnerability of coastal cities is determined by two steps as level and type. Firstly, physical structure, morphological structure and social structure were examined in determining spatial vulnerability levels. By determining these levels, most vulnerable areas were revealed as a priority in adaptation studies. Secondly, all parameters are also used to determine spatial typologies. Typologies are determined for coastal cities in order to use as a base for urban planning studies. Adaptation to climate change is crucial for developing countries like Turkey so, this methodology and created typologies could be a guide for urban planners as spatial directors and an example for other developing countries in the context of adaptation to climate change. The results demonstrate that the urban settlements located on the coasts of the Marmara Sea, the Aegean Sea and the Mediterranean respectively, are more vulnerable than the cities located on the Black Sea’s coasts to sea level rise.

Keywords: climate change, coastal cities, vulnerability, urban land use planning

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Authors: M. Kalyuga

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Prepositions have long been considered to be one of the major challenges for second language learners, since they have multiple uses that differ greatly from one language to another. The traditional approach to second language teaching supplies students with a list of uses of a preposition that they have to memorise and no explanation is provided. Contrary to the traditional grammar approach, the cognitive linguistic approach offers an explanation for the use of prepositions and provides strategies to comprehend and learn prepositions that would be otherwise seem obscure. The present paper demonstrates the use of the cognitive approach for the explanation of prepositions through the example of the Russian preposition 'за'. The paper demonstrates how various spatial and non-spatial uses of this preposition are linked together through metaphorical and metonymical mapping. The diversity of expressions with за is explained by the range of spatial scenes this preposition is associated with.

Keywords: language teaching, Russian, preposition 'за', cognitive approach

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Leyla Gündüz

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Durum wheat quality is defined as its suitability for pasta processing, that is pasta making quality. Another factor that determines the quality of durum wheat is the nutritional value of wheat or its final products. Wheat is a basic source of calories, proteins and minerals for humans in many countries of the world. For this reason, improvement of wheat nutritional value is of great importance. In recent years, deficiencies in protein and micronutrients, particularly in iron and zinc, have seriously increased. Therefore, basic foods such as wheat must be improved for micronutrient content. The effects of some major genes for grain quality established. Gpc-B1 locus is one of the genes increased protein and micronutrients content, and used in improvement studies of durum wheat nutritional value. The aim of this study was to increase the protein content and the micronutrient (Fe, Zn ve Mn) contents of an advanced durum wheat line (TMB 1) that was previously improved for its protein quality. For this purpose, TMB1 advanced durum wheat line were used as the recurrent parent and also, UC1113-Gpc-B1 line containing the Gpc-B1 gene was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region were selected by marker assisted selection (MAS). BC4F1 plants MAS method was employed in combination with embryo culture and rapid plant growth in a controlled greenhouse conditions in order to shorten the duration of the transition between generations in backcross breeding. The Gpc-B1 gene was selected specific molecular markers. Since Yr-36 gene associated with Gpc-B1 allele, it was also transferred to the Gpc-B1 transferred lines. Thus, the backcrossed plants selected by MAS are resistance to yellow rust disease. This research has been financially supported by TÜBİTAK (112T910).

Keywords: Durum wheat, Gpc-B1, MAS, Triticum durum, Yr-36

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Authors: Siyamthanda Makhwabe

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Tourism development and spatial planning within the broader spectrum of the Eastern Cape needs to be strategically integrated to give effectiveness to development planning within the province. Tourism was severely affected and limited by policies of the previous regime. Tourism development in the Eastern Cape has been identified as one of the underdeveloped sectors that have the potential to improve the province’s local economic development trajectory The proposed study reviews literature on tourism development in an urban/rural and regional context in the Eastern Cape province. The proposed study will therefore offer an in-depth literature review on issues pertaining to spatial planning, land use management policies and tourism development within the Eastern Cape using the scoping review method. The intention of the proposed study is to identify synergies between the intertwined municipalities within the Wild Coast region in order to create a tourism belt that would yield benefit from Coffee Bay to East London.

Keywords: development, Eastern Cape, policies, spatial planning, tourism

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Authors: M. Chukhryaeva, R. Skhalyakho, J. Kagazegeva, E. Pocheshkhova, L. Yepiskopossyan, O. Balanovsky, E. Balanovska

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The Middle East is crossroad of different populations at different times. The Kurds are of particular interest in this region. Historical sources suggested that the origin of the Kurds is associated with Medes. Therefore, it was especially interesting to compare gene pool of Kurds with other supposed descendants of Medes-Tats. Yezidis are ethno confessional group of Kurds. Yezidism as a confessional teaching was formed in the XI-XIII centuries in Iraq. Yezidism has caused reproductively isolation of Yezidis from neighboring populations for centuries. Also, isolation helps to retain Yezidian caste system. It is unknown how the history of Yezidis affected its genу pool because it has never been the object of researching. We have examined the Y-chromosome variation in Yezidis and Kurdish males to understand their gene pool. We collected DNA samples from 90 Yezidi males and 24 Kurdish males together with their pedigrees. We performed Y-STR analysis of 17 loci in the samples collected (Yfiler system from Applied Biosystems) and analysis of 42 Y-SNPs by real-time PCR. We compared our data with published data from other Kurdish groups and from European, Caucasian, and West Asian populations. We found that gene pool of Yezidis contains haplogroups common in the Middle East (J-M172(xM67,M12)- 24%, E-M35(xM78)- 9%) and in South Western Asia (R-M124- 8%) and variant with wide distribution area - R-M198(xM458- 9%). The gene pool of Kurdish has higher genetic diversity than Yezidis. Their dominants haplogroups are R-M198- 20,3 %, E-M35- 9%, J-M172- 9%. Multidimensional scaling also shows that the Kurds and Yezidis are part of the same frontier Asian cluster, which, in addition, included Armenians, Iranians, Turks, and Greeks. At the same time, the peoples of the Caucasus and Europe form isolated clusters that do not overlap with the Asian clusters. It is noteworthy that Kurds from our study gravitate towards Tats, which indicates that most likely these two populations are descendants of ancient Medes population. Multidimensional scaling also reveals similarity between gene pool of Yezidis, Kurds with Armenians and Iranians. The analysis of Yezidis pedigrees and their STR variability did not reveal a reliable connection between genetic diversity and caste system. This indicates that the Yezidis caste system is a social division and not a biological one. Thus, we showed that, despite many years of isolation, the gene pool of Yezidis retained a common layer with the gene pool of Kurds, these populations have common spectrum of haplogroups, but Yezidis have lower genetic diversity than Kurds. This study received primary support from the RSF grant No. 16-36-00122 to MC and grant No. 16-06-00364 to EP.

Keywords: gene pool, haplogroup, Kurds, SNP and STR markers, Yezidis

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Authors: Peter. M. Kusen, Georg Wandrey, Christopher Probst, Dietrich Kohlheyer, Jochen Buchs, Jorg Pietruszkau

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Light as a stimulus provides the capability to develop regulation techniques for customizable gene expression. A great advantage is the extremely flexible and accurate dosing that can be performed in a non invasive and sterile manner even for high throughput technologies. Therefore, light regulation in a multiwell microbioreactor system was realized providing the opportunity to control gene expression with outstanding complexity. A light-regulated gene expression system in Saccharomyces cerevisiae was designed applying the strategy of caged compounds. These compounds are photo-labile protected and therefore biologically inactive regulator molecules which can be reactivated by irradiation with certain light conditions. The “caging” of a repressor molecule which is consumed after deprotection was essential to create a flexible expression system. Thereby, gene expression could be temporally repressed by irradiation and subsequent release of the active repressor molecule. Afterwards, the repressor molecule is consumed by the yeast cells leading to reactivation of gene expression. A yeast strain harboring a construct with the corresponding repressible promoter in combination with a fluorescent marker protein was applied in a Photo-BioLector platform which allows individual irradiation as well as online fluorescence and growth detection. This device was used to precisely control the repression duration by adjusting the amount of released repressor via different irradiation times. With the presented screening platform the regulation of complex expression procedures was achieved by combination of several repression/derepression intervals. In particular, a stepwise increase of temporally-constant expression levels was demonstrated which could be used to study concentration dependent effects on cell functions. Also linear expression rates with variable slopes could be shown representing a possible solution for challenging protein productions, whereby excessive production rates lead to misfolding or intoxication. Finally, the very flexible regulation enabled accurate control over the expression induction, although we used a repressible promoter. Summing up, the continuous online regulation of gene expression has the potential to synchronize gene expression levels to optimize metabolic flux, artificial enzyme cascades, growth rates for co cultivations and many other applications addicted to complex expression regulation. The developed light-regulated expression platform represents an innovative screening approach to find optimization potential for production processes.

Keywords: caged-compounds, gene expression regulation, optogenetics, photo-labile protecting group

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Authors: Hao-Hsi Tseng, Hsin-Yun Lee

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In the process of building design, the designers have to complete the spatial design and consider the evacuation performance at the same time. It is usually difficult to combine the two planning processes and it results in the gap between spatial design and evacuation performance. Then the designers cannot complete an integrated optimal design solution. In addition, the evacuation routing models proposed by previous researchers is different from the practical evacuation decisions in the real field. On the other hand, more and more building design projects are executed by Building Information Modeling (BIM) in which the design content is formed by the object-oriented framework. Thus, the integration of BIM and evacuation simulation can make a significant contribution for designers. Therefore, this research plan will establish a model that integrates spatial design and evacuation planning. The proposed model will provide the support for the spatial design modifications and optimize the evacuation planning. The designers can complete the integrated design solution in BIM. Besides, this research plan improves the evacuation routing method to make the simulation results more practical. The proposed model will be applied in a building design project for evaluation and validation when it will provide the near-optimal design suggestion. By applying the proposed model, the integration and efficiency of the design process are improved and the evacuation plan is more useful. The quality of building spatial design will be better.

Keywords: building information modeling, evacuation, design, floor plan

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Authors: Eric Bang

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Interactions between receptors and ligands are crucial for many essential biological processes, including neurotransmission and metabolism. Ligand-receptor analyses that examine cell behavior and interactions often utilize cell type-specific RNA expressions from single-cell RNA sequencing (scRNA-seq) data. Using CellPhoneDB, a public repository consisting of ligands, receptors, and ligand-receptor interactions, the cell-cell interactions were explored in a specific scRNA-seq dataset from kidney tissue and portrayed the results with dot plots and heat maps. Depending on the type of cell, each ligand-receptor pair was aligned with the interacting cell type and calculated the positori probabilities of these associations, with corresponding P values reflecting average expression values between the triads and their significance. Using single-cell data (sample kidney cell references), genes in the dataset were cross-referenced with ones in the existing CellPhoneDB dataset. For example, a gene such as Pleiotrophin (PTN) present in the single-cell data also needed to be present in the CellPhoneDB dataset. Using the single-cell transcriptomics data via slide-seq and reference data, the CellPhoneDB program defines cell types and plots them in different formats, with the two main ones being dot plots and heat map plots. The dot plot displays derived measures of the cell to cell interaction scores and p values. For the dot plot, each row shows a ligand-receptor pair, and each column shows the two interacting cell types. CellPhoneDB defines interactions and interaction levels from the gene expression level, so since the p-value is on a -log10 scale, the larger dots represent more significant interactions. By performing an interaction analysis, a significant interaction was discovered for myeloid and T-cell ligand-receptor pairs, including those between Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1), which is consistent with previous findings. It was proposed that an effective protocol would involve a filtration step where cell types would be filtered out, depending on which ligand-receptor pair is activated in that part of the tissue, as well as the incorporation of the CellPhoneDB data in a streamlined workflow pipeline. The filtration step would be in the form of a Python script that expedites the manual process necessary for dataset filtration. Being in Python allows it to be integrated with the CellPhoneDB dataset for future workflow analysis. The manual process involves filtering cell types based on what ligand/receptor pair is activated in kidney cells. One limitation of this would be the fact that some pairings are activated in multiple cells at a time, so the manual manipulation of the data is reflected prior to analysis. Using the filtration script, accurate sorting is incorporated into the CellPhoneDB database rather than waiting until the output is produced and then subsequently applying spatial data. It was envisioned that this would reveal wherein the cell various ligands and receptors are interacting with different cell types, allowing for easier identification of which cells are being impacted and why, for the purpose of disease treatment. The hope is this new computational method utilizing spatially explicit ligand-receptor association data can be used to uncover previously unknown specific interactions within kidney tissue.

Keywords: bioinformatics, Ligands, kidney tissue, receptors, spatial transcriptome

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Raden Suhartono, Alexander Jayadi Utama, Patrianef Darwis, S. Dwi Anita, Luluk Yunaini, Kemas Dahlan

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Introduction: Vascular endothelial growth factor (VEGF) gene shows association with various angiogenesis conditions including Diabetic Foot Ulcer (DFU) disease. In this study, we performed this study to examine VEGF gene polymorphism associated with DFU. Methods: Case-control study of polymorphism of VEGF gene +405 C>G and -460 T>C, of diabetes mellitus (DM) type 2 with Diabetic Foot Ulcer (DFU) in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. Results: There were 203 patients, 102 patients with DFU and 101 patients without DFU. Forty-nine point 8 percent of total samples is male and 50,2% female with mean age 56,06 years. Distribution of the wild-type genotype VEGF +405 C>G wild type CC was found in 6,9% of respondents, the number of mutant heterozygote CG was 69,5% and mutant homozygote GG was 19,7%. Cumulatively, there were 6,9% wild-type and 85,2% mutant and 3,9% of total blood samples could not be detected on PCR-RFLP. Distribution of VEGF allele +405 C>G C alleles were 43% and G alleles were 57%. Distribution of genotype from VEGF gene -460 T>C is wild type TT 42,9%, mutant heterozygote TC 37,9% and mutant homozygote CC 13,3%. Cumulatively, there were 42,9% wild-type and 51% mutant type. Distribution of VEGF -460 T>C were 62% T allele and 38% C allele. Conclusion: In this study we found the distribution of alleles from VEGF +405 C>G is C 43% and G 57% and from VEGF -460 T>C; T 62% and C 38%. We propose that G allele in VEGF +405 C>G can act as a protective allele and on the other hands T allele in VEGF -460 T>C could be acted as a risk factor for DFU in diabetic patients.

Keywords: diabetic foot ulcer, diabetes mellitus, polymorphism, VEGF

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Authors: Tariq Abbas, Younus Muhammad, Sayyad Aun Muhammad

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Background : Crimean Congo hemorrhagic fever (CCHF) is a tick born viral zoonotic disease that has been notified from almost all regions of Pakistan. The aim of this study was to investigate spatial distribution of CCHF cases reported to National Institue of Health , Islamabad during year 2013. Methods : Spatial statistics tools were applied to detect extent spatial auto-correlation and clusters of the disease based on adjusted cumulative incidence per million population for each district. Results : The data analyses revealed a large multi-district cluster of high values in the uplands of Balochistan province near Afghanistan border. Conclusion : The cluster included following districts: Pishin; Qilla Abdullah; Qilla Saifullah; Quetta, Sibi; Zhob; and Ziarat. These districts may be given priority in CCHF surveillance, control programs, and further epidemiological research . The location of the cluster close to border of Afghanistan and Iran highlight importance of the findings for organizations dealing with disease at national, regional and global levels.

Keywords: Crimean Congo hemorrhagic fever, Pakistan, spatial autocorrelation, clusters , adjusted cumulative incidence

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Authors: Natasha Petrovska, Mirjana Pavlovic, Maria M. Larrondo-Petrie

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Neural stem cells (NSCs) are multi-potent, self-renewing cells that generate new neurons. Three subtypes of NSCs can be separated regarding the stages of NSC lineage: quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs), but their gene expression signatures are not utterly understood yet. Single-cell examinations have started to elucidate the complex structure of NSC populations. Nevertheless, there is a lack of thorough molecular interpretation of the NSC lineage heterogeneity and an increasing need for tools to analyze and improve the efficiency and correctness of single-cell sequencing data. Feature selection and ordering can identify and classify the gene expression signatures of these subtypes and can discover novel subpopulations during the NSCs activation and differentiation processes. The aim here is to review the implementation of the feature selection technique on NSC subtypes and the classification techniques that have been used for the identification of gene expression signatures.

Keywords: feature selection, feature similarity, neural stem cells, genes, feature selection methods

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Authors: Orhun Aydin, Mark V. Janikas, Rodrigo Alves, Renato Assuncao

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In this paper, a tree-based perturbation methodology for regionalization inference is presented. Regionalization is a constrained optimization problem that aims to create groups with similar attributes while satisfying spatial contiguity constraints. Similar to any constrained optimization problem, the spatial constraint may hinder convergence to some global minima, resulting in spatially contiguous members of a group with dissimilar attributes. This paper presents a general methodology for rigorously perturbing spatial constraints through the use of random spanning trees. The general framework presented can be used to quantify the effect of the spatial constraints in the overall regionalization result. We compare several types of stochastic spanning trees used in inference problems such as fuzzy regionalization and determining the number of regions. Performance of stochastic spanning trees is juxtaposed against the traditional permutation-based hypothesis testing frequently used in spatial statistics. Inference results for fuzzy regionalization and determining the number of regions is presented on the Local Area Personal Incomes for Texas Counties provided by the Bureau of Economic Analysis.

Keywords: regionalization, constrained clustering, probabilistic inference, fuzzy clustering

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Authors: Liuhui Zhu, Peng Zeng

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The rural revitalization strategy means to take the country and the city on the same level, and achieve urban-rural integration and comprehensive development of rural areas. Beijing-Tianjin-Hebei rural areas have always been the weak links in the region, with prominently uneven development between urban and rural areas. The rural areas need to join the overall regional synergy. Based on the analysis of the characteristics and problems of rural development in the region from the perspective of production-living-ecology space, the paper proposes the township as the basic unit for rural revitalization according to the overall requirements of the rural revitalization strategy. The basic unit helps to realize resource arrangement, functional organization, and collaborative governance organized by the production-living-ecology spatial network. The paper summarizes the planning strategies for the basic unit. Through spatial cognition and spatial reconstruction, the three space is networked through the base, nodes, and connections to improve the comprehensive value of rural areas and achieve the multiple goals of rural revitalization.

Keywords: rural revitalization, Beijing-Tianjin-Hebei region, township level, production-living-ecology spatial network

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Authors: Aleksandr Nagay, Gulnoz Khamidullayeva

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It is known that an unbalanced intake of salt (NaCI), lifestyle and genetic predisposition to pathology is a key component of the risk and the development of essential hypertension (EH). Purpose: To study the relationship between salt-sensitivity and blood pressure (BP) on systolic (SBP) and diastolic (DBP) blood pressure, depending on the C825T polymorphism of GNB3 in individuals of Uzbek nationality with EH. Method: studied 148 healthy and 148 patients with EH with I-II degree (WHO/ISH, 2003) with disease duration 6,5±1,3 years. Investigation of the gene GNB3 was produced by PCR-RFLP method. Determination of salt-sensitivity was performed by the method of R. Henkin. Results: For a comparative analysis of BP, the groups with carriage of CТ and TT genotypes were combined. The analysis showed that carriers of CC genotype and low salt-sensitivity were determined by higher levels of SBP compared with carriers of CT and TT genotypes, and low salt-sensitivity of SBP: 166,2±4,3 against 158,2±9,1 mm Hg (p=0,000). A similar analysis on the values of DBP also showed significantly higher values of blood pressure in carriers of CC genotype DBP: 105,8±10,6 vs. 100,5±7,2 mm Hg, respectively (p=0,001). The average values of SBP and DBP in groups with carriers of CC genotype at medium or high salt-sensitivity in comparison with carriers of CT or TT genotype did not differ statistically SBP: 165,0±0,1 vs. 160,0±8,6 mm Hg (p=0,275) and DBP: 100,1±0,1 vs. 101,6±7,6 mm Hg (p=0,687), respectively. Conclusion: It is revealed that in patients with EH CC genotype of the gene GNB3 given salt-sensitivity has a negative effect on blood pressure profile. Since patients with EH with the CC genotype of GNB3 gene with low-salt taste sensitivity is determined by a higher level of blood pressure, both on SBP and DBP.

Keywords: salt sensitivity, essential hypertension EH, blood pressure BP, genetic predisposition

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Authors: Zhuoran Shan, Li Wan, Xianchun Zhang

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With an increasing trend of regionalization and polycentricity in Chinese contemporary big cities, “sub-region life circle” turns to be an effective method on rational organization of urban function and spatial structure. By the method of questionnaire, network big data, route inversion on internet map, GIS spatial analysis and logistic regression, this article makes research on characteristic and formation mechanism of “sub-region life circle” based on human high-probability daily activity in Chinese big cities. Firstly, it shows that “sub-region life circle” has been a new general spatial sphere of residents' high-probability daily activity and mobility in China. Unlike the former analysis of the whole metropolitan or the micro community, “sub-region life circle” has its own characteristic on geographical sphere, functional element, spatial morphology and land distribution. Secondly, according to the analysis result with Binary Logistic Regression Model, the research also shows that seven factors including land-use mixed degree and bus station density impact the formation of “sub-region life circle” most, and then analyzes the index critical value of each factor. Finally, to establish a smarter “sub-region life circle”, this paper indicates that several strategies including jobs-housing fit, service cohesion and space reconstruction are the keys for its spatial organization optimization. This study expands the further understanding of cities' inner sub-region spatial structure based on human daily activity, and contributes to the theory of “life circle” in urban's meso-scale.

Keywords: sub-region life circle, characteristic, formation mechanism, human activity, spatial structure

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Authors: Elizelle Juaneé Cilliers

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The green hype is becoming stronger within various disciplines, modern practices and academic thinking, enforced by concepts such as eco-health, eco-tourism, eco-cities, and eco-engineering. There is currently also an expanded scientific understanding regarding the value and benefits relating to green infrastructure, for both communities and their host cities, linked to broader sustainability and resilience thinking. The integration and implementation of green infrastructure as part of spatial planning approaches and municipal planning, are, however, more complex, especially in South Africa, inflated by limitations of budgets and human resources, development pressures, inequities in terms of green space availability and political legacies of the past. The prevailing approach to spatial planning is further contributing to complexity, linked to misguided perceptions of the function and value of green infrastructure. As such, green spaces are often considered a luxury, and green infrastructure a costly alternative, resulting in green networks being susceptible to land-use changes and under-prioritized in local authority decision-making. Spatial planning, in this sense, may well be a valuable tool to realise the green agenda, encapsulating various initiatives of sustainability as provided by a range of disciplines. This paper aims to clarify the importance and value of green infrastructure planning as a component of spatial planning approaches, in order to inform and encourage local authorities to embed sustainability thinking into city planning and decision-making approaches. It reflects on the decisive role of land-use management to guide the green agenda and refers to some recent planning initiatives. Lastly, it calls for trans-disciplinary planning approaches to build a case towards green(er) cities.

Keywords: green infrastructure, spatial planning, transdisciplinary, integrative

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Authors: Jose Funes, Jeff Sauer, Laixiang Sun

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This research examines determinants of multifamily housing development and spillovers in the District of Columbia. A range of socioeconomic factors related to income distribution, productivity, and land use policies are thought to influence the development in contemporary U.S. multifamily housing markets. The analysis leverages data from the American Community Survey to construct panel datasets spanning from 2010 to 2019. Using spatial regression, we identify several socioeconomic measures and land use policies both positively and negatively associated with new housing supply. We contextualize housing estimates related to race in relation to uneven development in the contemporary D.C. housing supply.

Keywords: neighborhood effect, sorting, spatial spillovers, multifamily housing

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Authors: Bououden Soraya

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This paper aims to study the existence of the change of coordinates which permits to transform a class of nonlinear dynamical systems into the so-called nonlinear observer canonical form (NOCF). Moreover, an algorithm to construct such a change of coordinates is given. Based on this form, we can design an observer with a linear error dynamic. This enables us to estimate the state of a nonlinear dynamical system. A concrete example (biological model) is provided to illustrate the feasibility of the proposed results.

Keywords: nonlinear observer canonical form, observer, design, gene regulation, gene expression

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Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule

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Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.

Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity

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Authors: Aisling De Paor

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Scientific and technological developments are driving genetics and genetic technologies into the public sphere. Scientists are making genetic discoveries as to the make up of the human body and the cause and effect of disease, diversity and disability amongst individuals. Technological innovation in the field of genetics is also advancing, with the development of genetic testing, and other emerging genetic technologies, including gene editing (which offers the potential for genetic modification). In addition to the benefits for medicine, health care and humanity, these genetic advances raise a range of ethical, legal and societal concerns. From an ethical perspective, such advances may, for example, change the concept of humans and what it means to be human. Science may take over in conceptualising human beings, which may push the boundaries of existing human rights. New genetic technologies, particularly gene editing techniques create the potential to stigmatise disability, by highlighting disability or genetic difference as something that should be eliminated or anticipated. From a disability perspective, use (and misuse) of genetic technologies raise concerns about discrimination and violations to the dignity and integrity of the individual. With an acknowledgement of the likely future orientation of genetic science, and in consideration of the intersection of genetics and disability, this paper highlights the main concerns raised as genetic science and technology advances (particularly with gene editing developments), and the consequences for disability and human rights. Through the use of traditional doctrinal legal methodologies, it investigates the use (and potential misuse) of gene editing as creating the potential for a unique form of discrimination and stigmatization to develop, as well as a potential gateway to a form of new, subtle eugenics. This article highlights the need to maintain caution as to the use, application and the consequences of genetic technologies. With a focus on the law and policy position in Europe, it examines the need to control and regulate these new technologies, particularly gene editing. In addition to considering the need for regulation, this paper highlights non-normative approaches to address this area, including awareness raising and education, public discussion and engagement with key stakeholders in the field and the development of a multifaceted genetics advisory network.

Keywords: disability, gene-editing, genetics, law, regulation

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Authors: Yue Hao

Abstract:

COVID-19 vaccines not only protect individuals but society as a whole. In this case, having an understanding of the change and trend of vaccination conditions may shed some light on revising and making up-to-date policies regarding large-scale public health promotions and calls in order to lead and encourage the adoption of COVID-19 vaccines. However, vaccination status change over time and vary from place to place hidden patterns that were not fully explored in previous research. In our research, we took advantage of the spatial-temporal analytical methods in the domain of geographic information science and captured the spatial-temporal changes regarding COVID-19 vaccination status in the United States during 2020 and 2021. After conducting the emerging hot spots analysis on both the state level data of the US and county level data of California we found that: (1) at the macroscopic level, there is a continuously increasing trend of the vaccination rate in the US, but there is a variance on the spatial clusters at county level; (2) spatial hotspots and clusters with high vaccination amount over time were clustered around the west and east coast in regions like California and New York City where are densely populated with considerable economy conditions; (3) in terms of the growing trend of the daily vaccination among, Los Angeles County alone has very high statistics and dramatic increases over time. We hope that our findings can be valuable guidance for supporting future decision-making regarding vaccination policies as well as directing new research on relevant topics.

Keywords: COVID-19 vaccine, GIS, space time cube, spatial-temporal analysis

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Authors: Yu Liang, Wei Wei

Abstract:

Spatial representation of numbers and numerical magnitude are important for preschoolers’ mathematical ability. Mental number line, a typical index to measure numbers spatial representation, and numerical comparison are both related to arithmetic obviously. However, they seem to rely on different mechanisms and probably influence arithmetic through different mechanisms. In line with this idea, preschool children were trained with two tasks to investigate which one is more important for approximate arithmetic. The training of numerical processing and number line estimation were proved to be effective. They both improved the ability of approximate arithmetic. When the difficulty of approximate arithmetic was taken into account, the performance in number line training group was not significantly different among three levels. However, two harder levels achieved significance in numerical comparison training group. Thus, comparing spatial representation ability, symbolic approximation arithmetic relies more on numerical magnitude. Educational implications of the study were discussed.

Keywords: approximate arithmetic, mental number line, numerical magnitude, preschooler

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Authors: Kirill D. Kapustin, Mikhail B. Krasilnikov, Anatoly A. Kudryavtsev

Abstract:

Physical formation mechanisms of differential electron fluxes is high pressure positive column gas discharge are discussed. It is shown that the spatial differential fluxes of the electrons are directed both inward and outward depending on the energy relaxation law. In some cases the direction of energy differential flux at intermediate energies (5-10eV) in whole volume, except region near the wall, appeared to be down directed, so electron in this region dissipate more energy than gain from axial electric field. Paradoxical behaviour of electron flux in spatial-energy space is presented.

Keywords: plasma kinetics, electron distribution function, excitation and radiation rates, local and nonlocal EDF

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Authors: Chao Sima, Shanaz Ghandhi, Sally A. Amundson, Michael L. Bittner, David J. Brenner

Abstract:

In a large-scale radiologic emergency, potentially affected population need to be triaged efficiently using various biomarkers where personal dosimeters are not likely worn by the individuals. It has long been established that radiation injury can be estimated effectively using panels of genetic biomarkers. Furthermore, the rate of radiation, in addition to dose of radiation, plays a major role in determining biological responses. Therefore, a better and more accurate triage involves estimating both the dose level of the exposure and the length of time of that exposure. To that end, a large in vivo study was carried out on mice with internal emitter caesium-137 (¹³⁷Cs). Four different injection doses of ¹³⁷Cs were used: 157.5 μCi, 191 μCi, 214.5μCi, and 259 μCi. Cohorts of 6~7 mice from the control arm and each of the dose levels were sacrificed, and blood was collected 2, 3, 5, 7 and 14 days after injection for microarray RNA gene expression analysis. Using a generalized linear model with penalized maximum likelihood, a panel of 244 genes was established and both the doses of injection and the number of days after injection were accurately predicted for all 155 subjects using this panel. This has proven that microarray gene expression can be used effectively in radiation biodosimetry in predicting both the dose levels and the length of exposure time, which provides a more holistic view on radiation exposure and helps improving radiation damage assessment and treatment.

Keywords: caesium-137, gene expression microarray, multivariate responses prediction, radiation biodosimetry

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Authors: Jake Gonzalez, Tommy Dang

Abstract:

This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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Authors: Mohammad Rahim Rahnama, Lia Shaddel

Abstract:

Today, along with the development of urbanism, its negative consequences on the health of citizens are emerging. Mental disorders are common in the big cities, while mental health enables individuals to become active citizens. Meanwhile, women have a larger share of mental problems. Depression and anxiety disorders have a higher prevalence rate among women and these disorders affect the health of future generations, too. Therefore, improving women’s mental health through the potentials offered by urban spaces are of paramount importance. The present study aims to first, evaluate the spatial autocorrelation of women’s mental health and walkable spaces and then present solutions, based on the findings, to improve the walkability index. To determine the spatial distribution of women’s mental health in Mashhad, Moran's I was used and 1000 questionnaire were handed out in various sub-districts of Mashhad. Moran's I was calculated to be 0.18 which indicates a cluster distribution pattern. The walkability index was calculated using the four variables pertaining to the length of walkable routes, mixed land use, retail floor area ratio, and household density. To determine spatial autocorrelation of mental health and the walkability index, bivariate Moran’s I was calculated. Moran's I was determined to be 0.37 which shows a direct spatial relationship between variables; 4 clusters in 9 sub-districts of Mashhad were created. In High-Low cluster, there was a negative spatial relationship and hence, to identify factors affecting walkability in urban spaces semi-structures interviews were conducted with 21 women in this cluster. The findings revealed that security is the major factor influencing women’s walking behavior in this cluster. In accordance with the findings, some suggestions are offered to improve the presence of women in this sub-district.

Keywords: Mashhad, spatial autocorrelation, women’s mental health, walkability index

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Authors: Olesya Bolkhovskaya, Alexander Maltsev

Abstract:

Antenna arrays are widely used in modern radio systems in sonar and communications. The solving of the detection problems of a useful signal on the background of noise is based on the GLRT method. There is a large number of problem which depends on the known a priori information. In this work, in contrast to the majority of already solved problems, it is used only difference spatial properties of the signal and noise for detection. We are analyzing the influence of the degree of non-coherence of signal and noise unhomogeneity on the performance characteristics of different GLRT statistics. The description of the signal and noise is carried out by means of the spatial covariance matrices C in the cases of different number of known information. The partially coherent signal is simulated as a plane wave with a random angle of incidence of the wave concerning a normal. Background noise is simulated as random process with uniform distribution function in each element. The results of investigation of degradation of performance characteristics for different cases are represented in this work.

Keywords: GLRT, Neumann-Pearson’s criterion, Test-statistics, degradation, spatial processing, multielement antenna array

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Authors: Mohamed A. Almoghalis, Osman M. Hegazy, Ibrahim F. Imam, Ali H. Elbastawessy

Abstract:

This paper presents a new hyperspectral image segmentation scheme with respect to both spatial and spectral contexts. The scheme uses the 8-pixels spatial pattern to build a weight structure that holds the number of outlier bands for each pixel among its neighborhood windows in different directions. The number of outlier bands for a pixel is obtained using bands quartile box plots profile among spatial 8-pixels pattern windows. The quartile box plot weight structure represents the spatial-spectral context in the image. Instead of starting segmentation process by single pixels, the proposed methodology starts by pixels groups that proved to share the same spectral features with respect to their spatial context. As a result, the segmentation scheme starts with Jigsaw pieces that build a mosaic image. The following step builds a model for each Jigsaw piece in the mosaic image. Each Jigsaw piece will be merged with another Jigsaw piece using KNN applied to their bands' quartile box plots profiles. The scheme iterates till required number of segments reached. Experiments use two data sets obtained from Earth Observer 1 (EO-1) sensor for Egypt and France. Initial results qualitative analysis showed encouraging results compared with ground truth. Quantitative analysis for the results will be included in the final paper.

Keywords: hyperspectral image segmentation, image processing, remote sensing, box plot

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Authors: Kumaran Narayanan, Andrew N. Osahor

Abstract:

E. coli has been engineered by our group and by others as a vector to deliver DNA into cultured human and animal cells. However, so far conditions to improve gene delivery using this vector have not been investigated, resulting in a major gap in our understanding of the requirements for this vector to function optimally. Our group recently published novel data showing that simple addition of the DNA transfection reagent Lipofectamine increased the efficiency of the E. coli vector by almost 3-fold, providing the first strong evidence that further optimization of bactofection is possible. This presentation will discuss advances that demonstrate the effects of several intracellular strategies that improve the efficiency of this vector. Conditions that promote endosomal escape of internalized bacteria to evade lysosomal destruction after entry in the cell, a known obstacle limiting this vector, are elucidated. Further, treatments that increase bacterial lysis so that the vector can release its transgene into the mammalian environment for expression will be discussed. These experiments will provide valuable new insight to advance this E. coli system as an important class of vector technology for genetic correction of human disease models in cells and whole animals.

Keywords: DNA, E. coli, gene expression, vector

Procedia PDF Downloads 329