Search results for: spatial gene

Authors: Okolie Pius Ifeanyi, Emerenini Emilymary Chima

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Aims: The study investigated the diversity and identities of Lactic Acid Bacteria (LAB) isolated from different fresh fruits using Molecular Nested PCR analysis and the efficacy of cell free supernatants from Lactic Acid Bacteria (LAB) isolated from fresh fruits for in vitro control of some tomato pathogens. Study Design: Nested PCR approach was used in this study employing universal 16S rRNA gene primers in the first round PCR and LAB specific Primers in the second round PCR with the view of generating specific Nested PCR products for the LAB diversity present in the samples. The inhibitory potentials of supernatant obtained from LAB isolates of fruits origin that were molecularly characterized were investigated against some tomato phytopathogens using agar-well method with the view to develop biological agents for some tomato disease causing organisms. Methodology: Gram positive, catalase negative strains of LAB were isolated from fresh fruits on Man Rogosa and Sharpe agar (Lab M) using streaking method. Isolates obtained were molecularly characterized by means of genomic DNA extraction kit (Norgen Biotek, Canada) method. Standard methods were used for Nested Polymerase Chain Reaction (PCR) amplification targeting the 16S rRNA gene using universal 16S rRNA gene and LAB specific primers, agarose gel electrophoresis, purification and sequencing of generated Nested PCR products (Macrogen Inc., USA). The partial sequences obtained were identified by blasting in the non-redundant nucleotide database of National Center for Biotechnology Information (NCBI). The antimicrobial activities of characterized LAB against some tomato phytopathogenic bacteria which include (Xanthomonas campestries, Erwinia caratovora, and Pseudomonas syringae) were obtained by using the agar well diffusion method. Results: The partial sequences obtained were deposited in the database of National Centre for Biotechnology Information (NCBI). Isolates were identified based upon the sequences as Weissella cibaria (4, 18.18%), Weissella confusa (3, 13.64%), Leuconostoc paramensenteroides (1, 4.55%), Lactobacillus plantarum (8, 36.36%), Lactobacillus paraplantarum (1, 4.55%) and Lactobacillus pentosus (1, 4.55%). The cell free supernatants of LAB from fresh fruits origin (Weissella cibaria, Weissella confusa, Leuconostoc paramensenteroides, Lactobacillus plantarum, Lactobacillus paraplantarum and Lactobacillus pentosus) can inhibits these bacteria by creating clear zones of inhibition around the wells containing cell free supernatants of the above mentioned strains of lactic acid bacteria. Conclusion: This study shows that potentially LAB can be quickly characterized by molecular methods to specie level by nested PCR analysis of the bacteria isolate genomic DNA using universal 16S rRNA primers and LAB specific primer. Tomato disease causing organisms can be most likely biologically controlled by using extracts from LAB. This finding will reduce the potential hazard from the use of chemical herbicides on plant.

Keywords: nested pcr, molecular characterization, 16s rRNA gene, lactic acid bacteria

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Authors: Yun Zhang, Zhu Wang

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Renewing ancient residential areas is an integral part of the sustainable development of modern cities. Compared with a metropolis, the old areas of small and medium-sized cities is more complicated to update, as the spatial form is more fragmented. In this context, the author takes as the research object, the ancient town of Changshu City, which is a small city representative in China with a history of more than 1,200 years. Through the analysis of urban research and update projects, the spatial evolution characteristics and renewal strategies of small ancient urban settlements are studied. On this basis, it is proposed to protect the residential area from the perspective of integrity and sustainability, strengthen the core public part, control the district building, and reshape the important interface. Renewing small and medium-sized urban areas should respect the rhythm of their own urban development and gradually complete the update, not blindly copying the experience of large cities.

Keywords: ancient residential area, Changshu, city renewal strategy, small and medium-sized cities

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Authors: Katerina Balounova, Jiri Pacha, Peter Ergang, Martin Vodicka, Pavlina Kvapilova

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MicroRNAs are small non-coding RNAs involved in a wide range of physiological processes. Post-transcriptional regulation of gene expression by microRNAs gives the organism a further level of control of the gene-expression program and the disruption of this microRNA regulatory mechanism seems to increase the risk of various pathophysiological conditions including tumorigenesis. To the present day, microRNAs were shown to participate in the mayor signalization pathways leading to tumorigenesis, including proliferation, cell cycle, apoptosis and metastasis formation. In addition, microRNAs have been found to play important roles in the generation and maintenance of circadian clock. These clocks generate circadian rhythms, which participate in a number of regulatory pathways. Disruption of the circadian signals seems to be associated with the development and the progression of tumours including colorectal cancer. We investigated therefore whether the diurnal profiles of miRNAs linked to tumorigenesis and regulation of circadian clock are changed during tumorigenesis. Based on published data we chose 10 microRNAs linked to tumorigenesis or circadian clock (let-7b-5p, miR 1 3p, miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p, miR 29a 3p, miR 34a 5p and miR 93 5p) and compared their 24-hr expression profiles in healthy and in chemically induces primary colorectal tumours of 52week-old mice. Using RT-qPCR we proved circadian rhythmicity in let-7b-5p, miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p, miR 29a 3p and miR 93 5p in healthy colon but not in tumours. The acrophases of miR 106b 5p, miR 141 3p, miR 191 5p, miR 20a 5p, miR 25 3p and miR 93 5p were reached around CT 24, the acrophases of let-7b-5p and miR-29a-3p were slightly shifted and reached around CT 21. In summary, our results show that circadian regulation of some colonic microRNAs is greatly affected by neoplastic transformation.

Keywords: circadian rhythm, colon, colorectal cancer, microRNA, tumorigenesis

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Authors: Yu Bingqing

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Research on the meteorological observation data of conventional meteorological stations in Jiangnan area from 2001 to 2020 and digital elevation DEM, the "golden section" comfort index calculation method was used to refine the spatial estimation of climate comfort in Jiangnan area under undulating terrain on the Gis platform, and its spatiotemporal distribution characteristics in the region were analyzed. The results can provide reference for the development and utilization of climate resources in Jiangnan area.The results show that: ① there is a significant spatial difference between winter and summer climate comfort from low latitude to high latitude. ②There is a significant trend of decreasing climate comfort from low altitude to high altitude in winter, but the opposite is true in summer. ③There is a trend of decreasing climate comfort from offshore to inland in winter, but the difference is not significant in summer. The climate comfort level in the natural lake area is higher in summer than in the surrounding areas, but not in winter. ⑤ In winter and summer, altitude has the greatest influence on the difference in comfort level.

Keywords: vernacular courtyards, thermal environment, depth-to-height ratio, climate adaptability，Southeast China

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Authors: Salina Saddick, Mohamed Afifi, Osama Abuznadah

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This study was carried out to determine the median lethal concentrations (LC50) of Zinc nanoparticles (ZnNPs) on Oreochromis niloticus and Tilapia zillii. The biochemical and molecular potential effects of ZnNPs (500 and 2000 μg L−1) on the antioxidant system in the brain tissue of O. niloticus and T. zillii were investigated. Four hundred fish were used for acute and sub-acute studies. ZnNP LC50 concentrations were investigated in O. niloticus and T. zillii. The effect of 500 and 2000 μg L−1 ZnNPs on brain antioxidants of O. niloticus and T. zillii was investigated. The result indicated that 69 h LC50 was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. Fish exposed to 500 μg L−1 ZnNPs showed a significant increase in reduced glutathione (GSH), total glutathione (tGSH) levels, superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) activity and gene expression. On the contrary, malondialdehyde (MDA) levels significantly decreased. Meanwhile, fish exposed to 2000 μg L−1 ZnNPs showed a significant decrease of GSH, tGSH levels, SOD, CAT, GR, GPx and GST activity and gene expression. On the contrary, MDA levels significantly increased. It was concluded that, the 96 h LC50 of ZnNPs was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. ZnNPs in exposure concentrations of 2000 μg/L induced a deleterious effect on the brain antioxidant system of O. nilotica and T. zillii. In contrast, ZnNPs in exposure concentrations of 500 μg L−1 produced an inductive effect on the brain antioxidant system of O. nilotica and T. zillii.

Keywords: ZnNPs, LC50, antioxidants, O. nilotica

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Authors: Mojeed A. Oladele

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The original zoning system in Louisville promoted social segregation among groups and remained a tool for social exclusion that strengthened preexisting inequalities. The current residential zoning system in Louisville is predominantly single-family residential housing. Of the 75% of total land allocated for residential purposes, 55% comprises single-family housing, constituting one form of development and ruminant problems of social segregation within the city. The zoning reform initiative birthed the spatial improvement and development of additional middle housing as a more generic and inclusive housing form. The paper investigates the basis of zoning reform relative to the interconnectedness amongst the discursive objects of analysis and the extensiveness as a strategic tool of structural adjustment. Qualitative methodological assessment generated by collective planning professionals reflects the effectiveness of the new zoning design in strengthening the socio-spatial interactions within the city. The zoning reform is currently at the early stage of implementation and requires more professional/public inputs and constant iterative processes for a more promising urban planning outcome.

Keywords: zoning reform, viability, urban inequality, housing affordability, Louisville

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Mustafa Mutahari, Nao Sugiki, Kojiro Matsuo

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The four decades of war, lack of job opportunities, poverty, lack of services, and natural disasters in different provinces of Afghanistan have contributed to a rapid increase in the population of Kabul, the capital city of Afghanistan. Population census has not been conducted since 1979, the first and last population census in Afghanistan. However, according to population estimations by Afghan authorities, the population of Kabul has been estimated at more than 4 million people, whereas the city was designed for two million people. Although the major transport mode of Kabul residents is public transport, responsible authorities within the country failed to supply the required means of transportation systems for the city. Besides, informal resettlement, lack of intersection control devices, presence of illegal vendors on streets, presence of illegal and unstandardized on-street parking and bus stops, driver`s unprofessional behavior, weak traffic law enforcement, and blocked roads and sidewalks have contributed to the extreme traffic congestion of Kabul. In 2018, the government of Afghanistan approved the Kabul city Urban Design Framework (KUDF), a vision towards the future of Kabul, which provides strategies and design guidance at different scales to direct urban development. Considering traffic congestion of the city and its budget limitations, the KUDF proposes a BRT route network with seven lines to reduce the traffic congestion, and it is said to facilitate more than 50% of Kabul population to benefit from this service. Based on the KUDF, it is planned to increase the BRT mode share from 0% to 17% and later to 30% in medium and long-term planning scenarios, respectively. Therefore, a detailed research study is needed to evaluate the proposed system before the implementation stage starts. The integrated land-use transport model is an effective tool to evaluate the Kabul BRT because of its future assessment capabilities that take into account the interaction between land use and transportation. This research aims to analyze and evaluate the proposed BRT route network with the application of an integrated land-use and transportation model. The research estimates the population distribution and travel behavior of Kabul within small boundary scales. The actual road network and land-use detailed data of the city are used to perform the analysis. The BRT corridors are evaluated not only considering its impacts on the spatial interactions in the city`s transportation system but also on the spatial developments. Therefore, the BRT are evaluated with the scenarios of improving the Kabul transportation system based on the distribution of land-use or spatial developments, planned development typology and population distribution of the city. The impacts of the new improved transport system on the BRT network are analyzed and the BRT network is evaluated accordingly. In addition, the research also focuses on the spatial accessibility of BRT stops, corridors, and BRT line beneficiaries, and each BRT stop and corridor are evaluated in terms of both access and geographic coverage, as well.

Keywords: accessibility, BRT, integrated land-use and transport model, travel behavior, spatial development

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Authors: N. David, H. O. Gao

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Air pollution is a serious environmental threat on a global scale and can cause harm to human health, morbidity and premature mortality. Reliable monitoring and control systems are therefore necessary to develop coping skills against the hazards associated with this phenomenon. However, existing environmental monitoring means often do not provide a sufficient response due to practical and technical limitations. Commercial microwave links that form the infrastructure for transmitting data between cell phone towers can be harnessed to map rain at high tempo-spatial resolution. Rainfall causes a decrease in the signal strength received by these wireless communication links allowing it to be used as a built-in sensor network to map the phenomenon. In this study, we point to the potential that lies in this system to indirectly monitor areas where air pollution is reduced. The relationship between pollutant wash-off and rainfall provides an opportunity to acquire important spatial information about air quality using existing cell-phone tower signals. Since the density of microwave communication networks is high relative to any dedicated sensor arrays, it could be possible to rely on this available observation tool for studying precipitation scavenging on air pollutants, for model needs and more.

Keywords: air pollution, commercial microwave links, rainfall, washout

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Authors: Seyed Davar Siadat, Samira Tarashi, Abolfazl Fateh, Arfa Moshiri

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Background: The global health issue of tuberculosis (TB) still affects patients in every country. TB control may not be as effective as it should be, especially when resistant strains are involved. In this regard, mycobacterial MTases play a major role in tuberculosis, but the mechanisms underlying their function have yet to be fully deciphered. Methods: Five resistant isolates of M.tb were accumulated. As a reference strain, M.tb H37Rv (ATCC 27249) was used. For this analysis, seven putative mycobacterial MTase genes (Rv0645c, Rv1694, Rv2966c, Rv3919c, Rv2756c, Rv1988, and Rv3263), as well as Rv1392 as SAM synthase, were selected. Comparing mutations and expression levels of MTases in different strains was accomplished by PCR-sequencing and qRT-PCR. The relative expression levels of these genes were calculated using the 2 -ΔΔCt method. Results: The Rv3919c gene (T to G in codon 341) and Rv1392 gene (G to A in codon 97) were the only mutations found in the INHR strain. In all sensitive and resistant isolates, Rv0645c, Rv3263, Rv2756c, and Rv2966c were overexpressed. However, the expression of Rv1988 and Rv3919c decreased in the sensitive strains, whereas the expression of Rv1694 increased. There was also a decreased expression of Rv1392 in the INHR isolate. Conclusion: The presence of mycobacterial MTases as well as resistance to antibiotics were found to be correlated in M.tb strains. Undoubtedly, there are some MTases that are associated with the virulence process. It is necessary to conduct additional studies to fully explore the impact of mycobacterial MTases within specific strains of M.tb to develop novel diagnostic and treatment strategies.

Keywords: mycobacterium tuberculosis, drug resistance, methyltransferases, s-adenosylmethionine

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Authors: Raeesa Moolla, Ryan S. Johnson

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Air travel, and the use of airports, has experienced proliferative growth in the past few decades, resulting in the concomitant release of air pollutants. Air pollution needs to be monitored because of the known relationship between exposure to air pollutants and increased adverse effects on human health. This study monitored a group of volatile organic compounds (VOCs); specifically BTEX (viz. benzene, toluene, ethyl-benzene and xylenes), as many are detrimental to human health. Through the use of passive sampling methods, the spatial variability of BTEX within an international airport was investigated, in order to determine ‘hotspots’ where occupational exposure to BTEX may be intensified. The passive sampling campaign revealed BTEX_total concentrations ranged between 12.95–124.04 µg m^-3. Furthermore, BTEX concentrations were dispersed heterogeneously within the airport. Due to the slow wind speeds recorded (1.13 m.s^-1); the hotspots were located close to their main BTEX sources. The main hotspot was located over the main apron of the airport. Employees working in this area may be chronically exposed to these emissions, which could be potentially detrimental to their health.

Keywords: air pollution, air quality, hotspot monitoring, volatile organic compounds

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Authors: M. A. Wanzala, L. A. Ogallo, F. J. Opijah, J. N. Mutemi

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The usefulness and limitations in climate information are due to uncertainty inherent in the climate system. For any given region to have sustainable development it is important to apply climate information into its socio-economic strategic plans. The overall objective of the study was to assess the performance of the Coupled Model Inter-comparison Project (CMIP5) over the Lake Victoria Basin. The datasets used included the observed point station data, gridded rainfall data from Climate Research Unit (CRU) and hindcast data from eight CMIP5. The methodology included trend analysis, spatial analysis, correlation analysis, Principal Component Analysis (PCA) regression analysis, and categorical statistical skill score. Analysis of the trends in the observed rainfall records indicated an increase in rainfall variability both in space and time for all the seasons. The spatial patterns of the individual models output from the models of MPI, MIROC, EC-EARTH and CNRM were closest to the observed rainfall patterns.

Keywords: categorical statistics, coupled model inter-comparison project, principal component analysis, statistical downscaling

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Authors: Seo-Hee Kim, Kee-Won Kim, Seung-Hoon Kim

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The most important elements of a novel are the characters, events and background. The background represents the time, place and situation that character appears, and conveys event and atmosphere more realistically. If readers have the proper knowledge about background of novels, it may be helpful for understanding the atmosphere of a novel and choosing a novel that readers want to read. In this paper, we are targeting Korean historical novels because spatio-temporal background especially performs an important role in historical novels among the genre of Korean novels. To the best of our knowledge, we could not find previous study that was aimed at Korean novels. In this paper, we build a Korean historical national dictionary. Our dictionary has historical places and temple names of kings over many generations as well as currently existing spatial words or temporal words in Korean history. We also present a method for recognizing spatio-temporal background based on patterns of phrasal words in Korean sentences. Our rules utilize postposition for spatial background recognition and temple names for temporal background recognition. The knowledge of the recognized background can help readers to understand the flow of events and atmosphere, and can use to visualize the elements of novels.

Keywords: data mining, Korean historical novels, Korean linguistic feature, spatio-temporal background

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Authors: Mukta Singh, Ratan Kumar Saha, Himadri Saha, Paramveer Singh

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The present study evaluated the effect of sub-lethal doses of antifungal drug miconazole nitrate (MCZ) on immunological responses including immune-related gene expression and its role as a prophylactic drug against S. parasitica in Labeo rohita fingerlings. Fish were fed with sub lethal doses of MCZ i.e., T1- 6.30 mg MCZ kgBW⁻¹, T2- 12.61 mg MCZ kgBW⁻¹ and T3- 25.22 mg MCZ kgBW⁻¹ and sampling was done at different time intervals for 240 h. Immunological parameters viz. lysozyme activity, oxygen radical production and plasma anti-protease activity showed significant enhancement (p < 0.05) in fish fed with T2 and T3 doses. Significant reduction in plasma protein content was observed in all the dietary groups as compared to control. Expression of immune-relevant genes like TLR-22 and β2-M showed significantly higher expression at six h and 24 h of sampling in both liver and head-kidney. However, these genes showed a down-regulation after 120 h of sampling in both the tissues. Preventive efficacy study showed that single dose of MCZ provides protection against oomycetes up to the fourth day of infection. Significantly higher mortality was observed in control diet-fed fish as compared to fish fed with MCZ medicated diet. Thus, from the study, it can be concluded that the MCZ can act as a potent antifungal agent for preventing oomycetes infection as well as to enhance the immune response.

Keywords: antifungal, immune gene, immunological, miconazole nitrate, prophylactic

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Authors: Mahmoodreza Tahamtan

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Background: Malignant surface epithelial ovarian tumors (SEOT) account for approximately 90% of primary ovarian cancer. Wilms tumor gene (WT1) product was defined as a tumor suppressor gene, but today it is considered capable of performing oncogenic functions. There seems to be differences in WT1 expression patterns among SEOT subtypes. We evaluate the immunohistochemical expression of WT1 protein among different histologic subtypes of SEOT. Materials and Methods: Immunohistochemistry for WT1 was done on 35 serous cystadenocarcinomas, 9 borderline serous tumors, 3 mucinous cystadenocarcinomas, 10 borderline mucinous tumors, 7 endometrioid ovarian carcinomas, 3 clear cell carcinomas, 1 malignant Brenner tumor, 2 metastatic adenocarcinomas, and 6 endometrial adenocarcinomas. A tumor was considered negative if < 1% of tumor cells were stained.Positive reactions were graded as follows:1+,1%-24%; 2+,25%-49%; 3+,50%-74%; 4+,75%-100%. Results: Of the 35 cases of ovarian serous cystadenocarcinoma, 30(85.7%) were diffusely positive (3+,4+),4 showed reactivity of < 50% of the tumor cells (1+,2+), and one were negative. All 9 borderline serous tumors showed immunoreactivity with WT1. All the mucinous tumors(n:13), endometrioid carcinomas (n: 7), clear cell carcinomas (n: 3), metastatic adenocarcinomas (n: 2) and primary endometrial carcinomas (n:6) were negative. The single malignant Brenner tumor showed a positive reaction for WT1(4+) Conclusion: WT1 is a good marker to distinguish primary ovarian serous carcinomas from other surface epithelial tumors (especially endometrioid subtype) and metastatic carcinomas (especially endometrial serous carcinoma), other than malignant mesothelioma. We cannot rely to the degree of expression inorder to separate high grade borderline serous tumors from low grade ones.

Keywords: WT1, ovary, epithelial tumors, malignant

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Authors: Liu Danping

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Walking space has very important historical and cultural value in ancient and even modern urban development. As far as the footpath itself is concerned, it reflects the spatial organization mode and traditional architectural construction characteristics of mountain cities. In terms of the spatial nature of streets, traditional streets contain the history of urban development and the most primitive urban life. The slow walking speed allows people to carefully perceive the space and scenery along the way. The real city life in the streets often makes people feel the cultural connotation and unique charm of the city. According to the regional characteristics of pedestrian traffic in the main urban area of Chongqing, the charm of chongqing is discussed. Based on the study of chongqing characteristic walking space elements, this paper summarizes the characteristics of Chongqing urban walking traffic, analyzes the existing problems of mountain city walking traffic, and takes Yuzhong Peninsula as an example to analyze the charm promotion strategy of urban walking traffic.

Keywords: mountain city, walking space, urban charm, urban renewal, regional culture

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Authors: M. Al Zallouha, Y. Landkocz, J. Brunet, R. Cousin, J. M. Halket, E. Genty, P. J. Martin, A. Verdin, D. Courcot, S. Siffert, P. Shirali, S. Billet

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Toluene is one of the most used Volatile Organic Compounds (VOCs) in the industry. Amongst VOCs, Benzene, Toluene, Ethylbenzene and Xylenes (BTEX) emitted into the atmosphere have a major and direct impact on human health. It is, therefore, necessary to minimize emissions directly at source. Catalytic oxidation is an industrial technique which provides remediation efficiency in the treatment of these organic compounds. However, during operation, the catalysts can release some compounds, called byproducts, more toxic than the original VOCs. The catalytic oxidation of a gas stream containing 1000ppm of toluene on Pd/α-Al2O3 can release a few ppm of benzene, according to the operating temperature of the catalyst. The development of new catalysts must, therefore, include chemical and toxicological validation phases. In this project, A549 human lung cells were exposed in air/liquid interface (Vitrocell®) to gas mixtures derived from the oxidation of toluene with a catalyst of Pd/α-Al2O3. Both exposure concentrations (i.e. 10 and 100% of catalytic emission) resulted in increased gene expression of Xenobiotics Metabolising Enzymes (XME) (CYP2E1 CYP2S1, CYP1A1, CYP1B1, EPHX1, and NQO1). Some of these XMEs are known to be induced by polycyclic organic compounds conventionally not searched during the development of catalysts for VOCs degradation. The increase in gene expression suggests the presence of undetected compounds whose toxicity must be assessed before the adoption of new catalyst. This enhances the relevance of toxicological validation of such systems before scaling-up and marketing.

Keywords: BTEX toxicity, air/liquid interface cell exposure, Vitrocell®, catalytic oxidation

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Authors: S. Hannah Elizabeth, A. Panneerselvam

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Objective: The main objective was to evaluate the degradative properties of Bacillus cereus sp TUHP2 isolated from TNT-Polluted soils in the Vellore District, Tamil Nadu, India. Methods: Among the 3 bacterial genera isolated from different soil samples, one potent TNT degrading strain Bacillus cereus sp TUHP2 was identified. The morphological, physiological and the biochemical properties of the strain Bacillus cereus sp TUHP2 was confirmed by conventional methods and genotypic characterization was carried out using 16S r-DNA partial gene amplification and sequencing. The broken down by products of DNT in the extract was determined by Gas Chromatogram- Mass spectrometry (GC-MS). Supernatant samples from the broth studied at 24 h interval were analyzed by HPLC analysis and the effect on various nutritional and environmental factors were analysed and optimized for the isolate. Results: Out of three isolates one strain TUHP2 were found to have potent efficiency to degrade TNT and revealed the genus Bacillus. 16S rDNA gene sequence analysis showed highest homology (98%) with Bacillus cereus and was assigned as Bacillus cereus sp TUHP2. Based on the energy of the predicted models, the secondary structure predicted by MFE showed the more stable structure with a minimum energy. Products of TNT Transformation showed colour change in the medium during cultivation. TNT derivates such as 2HADNT and 4HADNT were detected by HPLC chromatogram and 2ADNT, 4ADNT by GC/MS analysis. Conclusion: Hence this study presents the clear evidence for the biodegradation process of TNT by strain Bacillus cereus sp TUHP2.

Keywords: bioremediation, biodegradation, biotransformation, sequencing

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Authors: Sankaran Rajendran

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Remote sensing plays a vital role in mapping of resources and monitoring of environments of the earth. In the present research study, mapping and monitoring of clay siltations occurred in the Alkhod Dam of Muscat, Sultanate of Oman are carried out using low-cost multispectral Landsat and ASTER data. The dam is constructed across the Wadi Samail catchment for ground water recharge. The occurrence and spatial distribution of siltations in the dam are studied with five years of interval from the year 1987 of construction to 2014. The deposits are mainly due to the clay, sand, and silt occurrences derived from the weathering rocks of ophiolite sequences occurred in the Wadi Samail catchment. The occurrences of clays are confirmed by minerals identification using ASTER VNIR-SWIR spectral bands and Spectral Angle Mapper supervised image processing method. The presence of clays and their spatial distribution are verified in the field. The study recommends the technique and the low-cost satellite data to similar region of the world.

Keywords: Alkhod Dam, ASTER siltation, Landsat, remote sensing, Oman

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Authors: Catharina Dwi Astuti Depari, Gregorius Agung Setyonugroho

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In concern for human safety, living in disaster-prone areas is twofold: it is profoundly cataclysmic yet perceptibly contributive. This paradox could be identified in Kalitengah Lor Sub-village community who inhabit Mount Merapi’s most hazardous area, putting them to the highest exposure to eruptions’ cataclysmic impacts. After the devastating incident in 2010, through the Action Plan for Rehabilitation and Reconstruction, the National Government with immediate aid from humanitarian agencies initiated a relocation program by establishing nearly 2,613 temporary shelters throughout the mountain’s region. The problem arose as some of the most affected communities including those in Kalitengah Lor Sub-village, persistently refused to relocate. The obnoxious experience of those living in temporary shelters resulted from the program’s failure to support a long-term living was assumed to instigate the rejection. From the psychological standpoint, this phenomenon reflects the emotional bond between the affected communities with their former dwellings. Regarding this, the paper aims to reveal the factors influencing the emotional attachment of Kalitengah Lor community to their former dwellings including the dwellings’ spatial design transformation prior and post the eruption in 2010. The research adopted Likert five scale-questionnaire comprising a wide range of responses from strongly agree to strongly disagree. The responses were then statistically measured, leading to consensus that provides bases for further interpretations toward the local’s characteristics. Using purposive unit sampling technique, 50 respondents from 217 local households were randomly selected. Questions in the questionnaire were developed with concerns on the aspects of place attachment concept: affection, cognitive, behavior, and perception. Combined with quantitative method, the research adopted diachronic method which was aimed to analyze the spatial design transformation of each dwelling in relation to the inhabitant’s daily activities and personal preferences. The research found that access to natural resources like sand mining, agricultural farms and wood forests, social relationship and physical proximity from house to personal asset like cattle shed, are the dominant factors encouraging the locals to emotionally attached to their former dwellings. Consequently, each dwelling’s spatial design is suffered from changes in which the current house is typically larger in dimension and the bathroom is replaced by public toilet located outside the house’s backyard. Relatively unchanged, the cattle shed is still located in front of the house, the continuous visual relationship, particularly between the living and family room, is maintained, as well as the main orientation of the house towards the local street.

Keywords: diachronic method, former dwellings, local’s characteristics, place attachment, spatial design transformation

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Authors: Pei-Ying Lo, Jing-Hao Ciou, Kai-Cheng Yang, Jia-Huei Zheng, Shih-Hsiang Huang, Kuen-Chan Lee, Er-Chieh Cho

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As-produced CNTs are insoluble in all organic solvents and aqueous solutions have imposed limitations to the use of CNTs. Therefore, how to debundle carbon nanotubes and to modify them for further uses is an important issue. There are several methods for the dispersion of CNTs in water using covalent attachment of hydrophilic groups to the surface of tubes. These methods, however, alter the electronic structure of the nanotubes by disrupting the network of sp2 hybridized carbons. In order to keep the nanotubes’ intrinsic mechanical and electrical properties intact, non-covalent interactions are increasingly being explored as an alternative route for dispersion. Apart from conventional surfactants such as sodium dodecylsulfate (SDS) or sodium dodecylbenzenesulfonate (SDBS) which are highly effective in dispersing CNTs, biopolymers have received much attention as dispersing agents due to the anticipated biocompatibility of the dispersed CNTs. Also, The pyrenyl group is known to interact strongly with the basal plane of graphene via π-stacking. In this study, a highly re-dispersible biopolymer is reported for the synthesis of pyrene-modified poly-L-lysine (PBPL) and poly(D-Glu, D-Lys) (PGLP). To provide the evidence of the safety of the PBPL/CNT & PGLP/CNT materials we use in this study, H1299 and HCT116 cells were incubated with PBPL/CNT & PGLP/CNT materials for toxicity analysis, MTS assays. The results from MTS assays indicated that no significant cellular toxicity was shown in H1299 and HCT116 cells. Furthermore, the fluorescence marker fluorescein isothiocyanate (FITC) was added to PBPL & PGLP dispersions. From the fluorescent measurements showed that the chemical functionalisation of the PBPL/CNT & PGLP/CNT conjugates with the fluorescence marker were successful. The fluorescent PBPL/CNT & PGLP/CNT conjugates could find application in medical imaging. In the next step, the GFP gene is immobilized onto PBPL/CNT conjugates by introducing electrostatic interaction. GFP-transfected cells that emitted fluorescence were imaged and counted under a fluorescence microscope. Due to the unique biocompatibility of PBPL modified CNTs, the GFP gene could be transported into H1299 cells without using antibodies. The applicability of such soluble and chemically functionalised polypeptide/CNT conjugates in biomedicine is currently investigated. We expect that this polypeptide/CNT system will be a safe and multi-functional nanomedical delivery platform and contribute to future medical therapy.

Keywords: carbon nanotube, nanotoxicology, GFP transfection, polypeptide/CNT hybrids

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Authors: Ratneev Kaur, Tajinder Kaur, Anupam Kaur

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Introduction: Polycystic Ovary Syndrome (PCOS) is a heterogenous disorder of endocrine system among women of reproductive age. PCOS is characterized by hyperandrogenism, anovulation, polycystic ovaries, hirsutism, obesity, and hyperinsulinemia. Several pathways are implicated in its etiology including the metabolic pathway of steroid hormone synthesis regulatory pathways. PCOS is an androgen excess disorder, genes operating in steroidogenesis may alter pathogenesis of PCOS. The cytochrome P450scc is a cholesterol side chain cleavage enzyme coded by CYP11A1 gene and catalyzes conversion of cholesterol to pregnenolone, the initial and rate-limiting step in steroid hormone synthesis. It is postulated that polymorphisms in this gene may play an important role in the regulation of CYP11A1 expression and leading to increased or decreased androgen production. The present study will be the first study from north India to best of our knowledge, to analyse the association of CYP11A1 (rs11632698) polymorphism in women suffering from PCOS. Methodology: The present study was approved by ethical committee of Guru Nanak Dev University in consistent with declaration of Helsinki. A total of 300 samples (150 PCOS cases and 150 controls) were recruited from Hartej hospital, for the present study. Venous blood sample (3ml) was withdrawn from women diagnosed with PCOS by doctor, according to Rotterdam 2003 criteria and from healthy age matched controls only after informed consent and detailed filled proforma. For molecular genetics analysis, blood was stored in EDTA vials. After DNA isolation by organic method, PCR-RFLP approach was used for genotyping and association analysis of rs11632698 polymorphism. Statistical analysis was done to check for significance of selected polymorphism with PCOS. Results: In 150 PCOS cases, the frequency of AA, AG and GG genotype was found to be 48%, 35%, and 13% compared to 62%, 27% and 8% in 150 controls. The major allele (A) and minor allele (G) frequency was 68% and 32% in cases and 78% and 22% in controls. Minor allele frequency was higher in cases as compared to controls, as well as the distribution of genotype was observed to be statistically significant (ᵡ²=6.525, p=0.038). Odds ratio in dominant, co-dominant and recessive models observed was 1.81 (p=0.013), 1.54 (p=0.012) and 1.77 (p=0.132) respectively. Conclusion: The present study showed statistically significant association of rs11632698 with PCOS (p=0.038) in North Indian women.

Keywords: polycystic ovary syndrome, CYP11A1, rs11632698, hyperandrogenism

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Authors: Ajay Kumar

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Using data from census of India, sample registration system and national family health survey (NFHS-3), this paper traces spatial pattern, trends and the factors which have played their role differently in fertility transition in Uttar Pradesh and Tamil Nadu. For the purpose spatial variation analysis, trend line and binary logistic regression analysis has been carried out. There exist considerable regional disparities in terms of fertility decline in northern and southern states. The pace of fertility decline has been faster in southern and coastal regions, and at a slow pace in backward northern state. In Tamil Nadu fertility declined substantially among the women of lower and higher age groups in comparison to Uttar Pradesh characterized by low literacy, low female age at marriage, poor health infrastructure and low status of women. The Study shows that Fertility rates have been higher among the most vulnerable and deprived sections of the society like Illiterate women, women belong to scheduled caste, scheduled tribe and women residing in rural areas.

Keywords: age specific fertility rate, fertility transition, replacement level, total fertility rate

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Authors: Iacopo Testi, Diego Pajarito, Nicoletta Roberto, Carmen Greco

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Today, a consistent segment of the world’s population lives in urban areas, and this proportion will vastly increase in the next decades. Therefore, understanding the key trends in urbanization, likely to unfold over the coming years, is crucial to the implementation of sustainable urban strategies. In parallel, the daily amount of digital data produced will be expanding at an exponential rate during the following years. The analysis of various types of data sets and its derived applications have incredible potential across different crucial sectors such as healthcare, housing, transportation, energy, and education. Nevertheless, in city development, architects and urban planners appear to rely mostly on traditional and analogical techniques of data collection. This paper investigates the prospective of the data science field, appearing to be a formidable resource to assist city managers in identifying strategies to enhance the social, economic, and environmental sustainability of our urban areas. The collection of different new layers of information would definitely enhance planners' capabilities to comprehend more in-depth urban phenomena such as gentrification, land use definition, mobility, or critical infrastructural issues. Specifically, the research results correlate economic, commercial, demographic, and housing data with the purpose of defining the youth economic discomfort index. The statistical composite index provides insights regarding the economic disadvantage of citizens aged between 18 years and 29 years, and results clearly display that central urban zones and more disadvantaged than peripheral ones. The experimental set up selected the city of Rome as the testing ground of the whole investigation. The methodology aims at applying statistical and spatial analysis to construct a composite index supporting informed data-driven decisions for urban planning.

Keywords: data science, spatial analysis, composite index, Rome, urban planning, youth economic discomfort index

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Authors: Samira Khalaji, , Fenneke Klein Jan, Kay-E. Gottschalk, Eugenia Makrantonaki, Karin Scharffetter-Kochanek

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Biological aging is a multi-dimensional process that takes place over a whole range of scales from the nanoscopic alterations within individual cells, over transformations in tissues and organs and to changes of the whole organism. On the single cell level, aging involves mutation of genes, differences in gene expression levels as well as altered posttranslational modifications of proteins. A variety of proteins is affected, including proteins of the cell cytoskeleton and migration machinery. Previous work quantified the expression of cytoskeleton proteins on the gene and protein levels in senescent and young fibroblasts. Their results show that senescent skin fibroblasts have an upregulated expression of the intermediate filament (IF) protein vimentin in contrast to actin and tubulin, which are downregulated. IFs play an important role in providing mechanical stability of cells. However, the mechanical properties of IFs depending on cellular senescence or age of the donor has not been studied so far. Hence, we employed passive microrheology on primary human dermal fibroblasts from female donors with age of 28 years (young) and 86 years (old) as model of in vivo aging and human normal dermal fibroblast from 11-year old male with CPD 17-35 (young) and CPD 58-59 (senescence) as a model of in vitro replicative senescence. In contrast to the expectations, our primary results show no significant differences in the viscoelastic properties of fibroblasts depending on age of the donor or cellular replicative senescence.

Keywords: aging, cytoskeleton, fibroblast, mechanical properties

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Authors: Pedro Martinez-Santos, Víctor Gómez-Escalonilla, Silvia Díaz-Alcaide, Esperanza Montero, Miguel Martín-Loeches

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Groundwater monitoring networks are critical in evaluating the vulnerability of groundwater resources to depletion and contamination, both in space and time. Groundwater monitoring networks typically grow over decades, often in organic fashion, with relatively little overall planning. The groundwater monitoring networks in the Madrid area, Spain, were reviewed for the purpose of identifying gaps and opportunities for improvement. Spatial analysis reveals the presence of various monitoring networks belonging to different institutions, with several hundred observation wells in an area of approximately 4000 km2. This represents several thousand individual data entries, some going back to the early 1970s. Major issues included overlap between the networks, unknown screen depth/vertical distribution for many observation boreholes, uneven time series, uneven monitored species, and potentially suboptimal locations. Results also reveal there is sufficient information to carry out a spatial and temporal analysis of groundwater vulnerability based on machine learning applications. These can contribute to improve the overall planning of monitoring networks’ expansion into the future.

Keywords: groundwater monitoring, observation networks, machine learning, madrid

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Authors: Devansh Desai, Rahul Nigam

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Crop water stress (W) at a given growth stage starts to set in as moisture availability (M) to roots falls below 75% of maximum. It has been found that ratio of crop evapotranspiration (ET) and reference evapotranspiration (ET0) is an indicator of moisture adequacy and is strongly correlated with ‘M’ and ‘W’. The spatial variability of ET0 is generally less over an agricultural farm of 1-5 ha than ET, which depends on both surface and atmospheric conditions, while the former depends only on atmospheric conditions. Solutions from surface energy balance (SEB) and thermal infrared (TIR) remote sensing are now known to estimate latent heat flux of ET. In the present study, ET and moisture adequacy index (MAI) (=ET/ET0) have been estimated over two contrasting western India agricultural farms having rice-wheat system in semi-arid climate and arid grassland system, limited by moisture availability. High-resolution multi-band TIR sensing observations at 65m from ECOSTRESS (ECOsystemSpaceborne Thermal Radiometer Experiment on Space Station) instrument on-board International Space Station (ISS) were used in an analytical SEB model, STIC (Surface Temperature Initiated Closure) to estimate ET and MAI. The ancillary variables used in the ET modeling and MAI estimation were land surface albedo, NDVI from close-by LANDSAT data at 30m spatial resolution, ET0 product at 4km spatial resolution from INSAT 3D, meteorological forcing variables from short-range weather forecast on air temperature and relative humidity from NWP model. Farm-scale ET estimates at 65m spatial resolution were found to show low RMSE of 16.6% to 17.5% with R2 >0.8 from 18 datasets as compared to reported errors (25 – 30%) from coarser-scale ET at 1 to 8 km spatial resolution when compared to in situ measurements from eddy covariance systems. The MAI was found to show lower (<0.25) and higher (>0.5) magnitudes in the contrasting agricultural farms. The study showed the potential need of high-resolution high-repeat spaceborne multi-band TIR payloads alongwith optical payload in estimating farm-scale ET and MAI for estimating consumptive water use and water stress. A set of future high-resolution multi-band TIR sensors are planned on-board Indo-French TRISHNA, ESA’s LSTM, NASA’s SBG space-borne missions to address sustainable irrigation water management at farm-scale to improve crop water productivity. These will provide precise and fundamental variables of surface energy balance such as LST (Land Surface Temperature), surface emissivity, albedo and NDVI. A synchronization among these missions is needed in terms of observations, algorithms, product definitions, calibration-validation experiments and downstream applications to maximize the potential benefits.

Keywords: thermal remote sensing, land surface temperature, crop water stress, evapotranspiration

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Authors: Renata Checiches, Thierry Coche, Nicolas F. Delahaye, Albert Linder, Fernando Ulloa Montoya, Olivier Gruselle, Karen Langfeld, An de Creus, Bart Spiessens, Vincent G. Brichard, Jamila Louahed, Frédéric F. Lehmann

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Background: The RNA-expression levels of cancer-testis antigens MAGE A3 and PRAME were determined in resected tissue from patients with primary non-small-cell lung cancer (NSCLC) and related to clinical outcome. EGFR, KRAS and BRAF mutation status was determined in a subset to investigate associations with MAGE A3 and PRAME expression. Methods: We conducted a single-centre, uncontrolled, retrospective study of 1260 tissue-bank samples from stage IA-III resected NSCLC. The prognostic value of antigen expression (qRT-PCR) was determined by hazard-ratio and Kaplan-Meier curves. Results: Thirty-seven percent (314/844) of tumours expressed MAGE-A3, 66% (723/1092) expressed PRAME and 31% (239/839) expressed both. Respective frequencies in squamous-cell tumours and adenocarcinomas were 43%/30% for MAGE A3 and 80%/44% for PRAME. No correlation with stage, tumour size or patient age was found. Overall, no prognostic value was identified for either antigen. A trend to poorer overall survival was associated with MAGE-A3 in stage IIIB and with PRAME in stage IB. EGFR and KRAS mutations were found in 10.1% (28/311) and 33.8% (97/311) of tumours, respectively. EGFR (but not KRAS) mutation status was negatively associated with PRAME expression. Conclusion: No clear prognostic value for either PRAME or MAGE A3 was observed in the overall population, although some observed trends may warrant further investigation.

Keywords: MAGE A3, PRAME, cancer-testis gene, NSCLC, survival, EGFR

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Authors: Gizaw Mamo Gebeyehu, Marianna Pap, Geza Makkai, Tibor Z. Janosi, Shima Rashidian, Tibor A. Rauch

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Sepsis poses a significant global health threat, necessitating extensive exploration of indicators tied to its pathological mechanisms and multi-organ dysfunction. While murine studies have shed light on sepsis, the intricate cellular and molecular landscape in human sepsis remains enigmatic. Exploring the influence of activated monocyte-derived exosomes in sepsis sheds light on a promising pathway for understanding the intricate cellular and molecular mechanisms involved in this condition in humans. In sepsis, exosome-borne mRNA and miRNA orchestrate immune response gene expression in recipient cells. Yet, the specifics of exosome-mediated cell-to-cell communication, especially how mRNA cargoes modulate gene expression in recipient cells, remain poorly understood. This study aims to elucidate the precise molecular pathways through which exosomal mRNA cargo, particularly MAFB, contributes to the developing sepsis-induced molecular aberrations in liver tissues, employing rigorously defined cell culture conditions. THP-1 cells were treated with LPS to induce changes in exosomal RNA profiles. Exosomes were isolated and characterized using microscopy and mass spectrometry. RNA was extracted from exosomes and sequenced. The most abundant exosomal mRNAs were subjected to GO analysis for functional annotation analysis and KEGG database analysis to identify the involved enriched pathways. PCR (Polymerase Chain Reaction), RNA sequencing, and Western blotting were involved to analyze changes in gene expression, protein levels, and signaling pathways within the liver cells( HepG2) after exposure to exosomal MAFB. This study pinpoints exosomal MAFB as a potential key regulator linked to liver cell damage during sepsis, along with associated genes (miR155HG, H3F3A, and possibly JARD2) forming a crucial molecular pathway contributing to liver cell injury, Together, these elements indicate a vital molecular pathway that plays a significant role in the emergence of liver cell injury during sepsis.. These findings suggest the importance of further research on these components for potential therapeutic interventions in managing acute liver damage in sepsis.

Keywords: sepsis, exososome, exosomal MAFB, LPS-induced THP-1 cells, RNA profiles, sepsis-triggered liver injury

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Authors: Nawaf Alotaibi, Andy Evans, Alison Heppenstall, Nick Malleson

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Throughout the last two decades, motor vehicle theft (MVT) has accounted for the largest proportion of property crime incidents in Saudi Arabia (SA). However, to date, few studies have investigated SA’s MVT problem. Those that have are primarily focused on the characteristics of car thieves, and most have overlooked any spatial-temporal distribution of MVT incidents and the characteristics of victims. This paper represents the first step in understanding this problem by reviewing the existing MVT studies contextualised within the theoretical frameworks developed in environmental criminology theories – originating in the West – and exploring to what extent they are relevant to the SA context. To achieve this, the paper has identified a range of key features in SA that are different from typical Western contexts, that could limit the appropriateness and capability of applying existing environmental criminology theories. Furthermore, despite these Western studies reviewed so far having introduced a number of explanatory variables for MVT rates, a range of significant elements are apparently absent in the current literature and this requires further analysis. For example, almost no attempts have been made to quantify the associations between the locations of vehicle theft, recovery of stolen vehicles, joyriding and traffic volume.

Keywords: environmental criminology theories, motor vehicle theft, Saudi Arabia, spatial analysis

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