Search results for: spatial gene

Authors: Ceyda Okudu, Secil Eroglu, Khandakar A. S. M. Saadat, Sibel O. Balci

Abstract:

Ring Finger Protein 2 (RNF2) is a member of polycomb repressive complex 1 (PRC1), which is one of the epigenetic regulators in the genome. When RNF2 combines with other PRC1 members, it mediates the mono-ubiquitination of Histon2A (H2A). In breast cancer, RNF2 is commonly overexpressed, and also it promotes metastasis and invasion in other aggressive tumors like melanoma, prostate, and hepatocarcinoma. The role of RNF2 in the metastasis and invasion of breast cancer has not yet been elucidated. Our aim is to observe the role of RNF2 in metastasis and invasion in this study by miRNA mediated RNF2 gene silencing in breast cancer cell lines. We selected miRNAs, targeting to RNF2 by searching online databases. miR-17-5p, miR20a-5p, and miR-106b-5p were transfected to breast cancer cell lines (MCF-7, MDA-MB-231, SK-BR-3, and ZR-75-1), and also we used normal breast epithelial cell line (hTERT-HME1) to compare RNF2 gene expression level. After 48-72 hours post-transfection, mRNAs were isolated from the cells, and gene expressions were measured by RT-qPCR after from cDNA syntheses. We observed that RNF2 was highly expressed in SK-BR-3 and MDA-MB-231 cell lines opposite to MCF-7 and ZR-75-1 cell lines. RNF2 was downregulated 5, 5 and 7 fold by miR17-5p, miR20a-5p and miR106b-5p respectively in MCF-7. However, in SK-BR-3 and ZR-75-1 cell lines, miRNAs did not affect significantly RNF2 gene expression level. miR20a-5p decreased RNF2 3 fold and miR17-5p and miR106b-5p did not affect MDA-MB-231. After gene expression analysis, we performed metastasis and invasion assay in MCF-7 cells. For metastasis, we used both wound healing assay and Transwell Cell Migration Assay, and we used Transwell Cell Invasion Assay for invasion. The data of this assay showed that miR17-5p and miR20a-5p decreased both invasion and metastasis level, but miR106b-5p has no effect. We would like to conclude that RNF2 can be targeted by miR17-5p, miR20a-5p and miR106b-5p in MCF-7 cells and also RNF2, which is one of the upregulated genes in aggressive tumor, can be decreased by using these miRNAs. In future, we would like to confirm these results at the protein level and also whether these miRNAs are direct target of RNF2 or not.

Keywords: breast cancer, epigenetic, microRNAs, RNF2

Procedia PDF Downloads 180

Authors: Yessi Rahmawati, Andiga Kusuma Nur Ichsan, Fitria Nur Anggraeni

Abstract:

Climate change is one of the focus studies that many researchers focus on in the present world, either in the emerging countries or developed countries which is one of the main pillars on Sustainable Development Goals (SDGs). There is on-going discussion that climate change can affect natural disaster, namely drought, storm, flood, and many others; and also the impact on human life. East Java is the best performances and has economic potential that should be utilized. Despite the economic performance and high agriculture productivity, East Java has the highest number of people under the poverty line. The present study is to measuring the contribution of drought and productivity of agriculture to the poverty in East Java, Indonesia, using spatial econometrics analysis. The authors collect data from 2008 – 2015 from Indonesia’s Ministry of Agriculture, Natural Disaster Management Agency (BNPB), and Official Statistic (BPS). First, the result shows the existence of spatial autocorrelation between drought and poverty. Second, the present research confirms that there is strong relationship between drought and poverty. the majority of farmer in East Java are still relies on the rainfall and traditional irrigation system. When the drought strikes, mostly the farmer will lose their income; make them become more vulnerable household, and trap them into poverty line. The present research will give empirical studies regarding drought and poverty in the academics world.

Keywords: SDGs, drought, poverty, Indonesia, spatial econometrics, spatial autocorrelation

Procedia PDF Downloads 154

Authors: Yoshino Murakami, Takeshi Hashimoto, Steve Cole

Abstract:

The autonomic nervous system (ANS), particularly the sympathetic (SNS) and parasympathetic (PNS) branches, plays a vital role in modulating immune function and physiological homeostasis. In recent years, the Conserved Transcriptional Response to Adversity (CTRA) has emerged as a key marker of the body's response to chronic stress. This gene expression profile is characterized by SNS-mediated upregulation of pro-inflammatory genes (such as IL1B and TNF) and downregulation of antiviral response genes (e.g., IFI and MX families). CTRA has been observed in individuals exposed to prolonged stressors like loneliness, social isolation, and bereavement. Some research suggests that PNS activity, as indicated by heart rate variability (HRV), may help counteract the CTRA. However, previous PNS-CTRA studies have focused on Western populations, raising questions about the generalizability of these findings across different cultural and ethnic backgrounds. This study aimed to examine the relationship between HRV and CTRA gene expression in young, healthy adults in Japan. We hypothesized that HRV would be inversely related to CTRA gene expression, similar to patterns observed in previous Western studies. A total of 49 participants aged 20 to 39 were recruited, and after data exclusions, 26 participants' HRV and CTRA data were analyzed. HRV was measured using an electrocardiogram (ECG), and two time-domain indices were utilized: the root mean square of successive differences (RMSSD) and the standard deviation of NN intervals (SDNN). Blood samples were collected for gene expression analysis, focusing on a standard set of 47 CTRA indicator gene transcripts. it findings revealed a significant inverse relationship between HRV and CTRA gene expression, with higher HRV correlating with reduced pro-inflammatory gene activity and increased antiviral response. These results are consistent with findings from Western populations and demonstrate that the relationship between ANS function and immune response generalizes to an East Asian population. The study highlights the importance of HRV as a biomarker for psychophysiological health, reflecting the body's ability to buffer stress and maintain immune balance. These findings have implications for understanding how physiological systems interact across different cultures and ethnicities. Given the influence of chronic stress in promoting inflammation and disease risk, interventions aimed at improving HRV, such as mindfulness-based practices or physical exercise, could provide significant health benefits. Future research should focus on larger sample sizes and experimental interventions to better understand the causal pathways linking HRV to CTRA gene expression, and determine whether improving HRV may help mitigate the harmful effects of stress on health by reducing inflammation.

Keywords: autonomic nervous activity, neuroendocrine system, inflammation, Japan

Procedia PDF Downloads 20

Authors: Jonas Hamann, Siavash Saki, Tobias Hagen

Abstract:

Discretization of urban areas is a crucial aspect in many spatial analyses. The process of discretization of space into subspaces without overlaps and gaps is called tessellation. It helps understanding spatial space and provides a framework for analyzing geospatial data. Tessellation methods can be divided into two groups: regular tessellations and irregular tessellations. While regular tessellation methods, like squares-grids or hexagons-grids, are suitable for addressing pure geometry problems, they cannot take the unique characteristics of different subareas into account. However, irregular tessellation methods allow the border between the subareas to be defined more realistically based on urban features like a road network or Points of Interest (POI). Even though Python is one of the most used programming languages when it comes to spatial analysis, there is currently no library that combines different tessellation methods to enable users and researchers to compare different techniques. To close this gap, we are proposing TessPy, an open-source Python package, which combines all above-mentioned tessellation methods and makes them easily accessible to everyone. The core functions of TessPy represent the five different tessellation methods: squares, hexagons, adaptive squares, Voronoi polygons, and city blocks. By using regular methods, users can set the resolution of the tessellation which defines the finesse of the discretization and the desired number of tiles. Irregular tessellation methods allow users to define which spatial data to consider (e.g., amenity, building, office) and how fine the tessellation should be. The spatial data used is open-source and provided by OpenStreetMap. This data can be easily extracted and used for further analyses. Besides the methodology of the different techniques, the state-of-the-art, including examples and future work, will be discussed. All dependencies can be installed using conda or pip; however, the former is more recommended.

Keywords: geospatial data science, geospatial data analysis, tessellations, urban studies

Procedia PDF Downloads 128

Authors: Yin-Yee Leong, Jack C. Yue, Hsin-Chung Wang

Abstract:

Human longevity has been experiencing its largest increase since the end of World War II, and modeling the mortality rates is therefore often the focus of many studies. Among all mortality models, the Lee–Carter model is the most popular approach since it is fairly easy to use and has good accuracy in predicting mortality rates (e.g., for Japan and the USA). However, empirical studies from several countries have shown that the age parameters of the Lee–Carter model are not constant in time. Many modifications of the Lee–Carter model have been proposed to deal with this problem, including adding an extra cohort effect and adding another period effect. In this study, we propose a spatial modification and use clusters to explain why the age parameters of the Lee–Carter model are not constant. In spatial analysis, clusters are areas with unusually high or low mortality rates than their neighbors, where the “location” of mortality rates is measured by age and time, that is, a 2-dimensional coordinate. We use a popular cluster detection method—Spatial scan statistics, a local statistical test based on the likelihood ratio test to evaluate where there are locations with mortality rates that cannot be described well by the Lee–Carter model. We first use computer simulation to demonstrate that the cluster effect is a possible source causing the problem of the age parameters not being constant. Next, we show that adding the cluster effect can solve the non-constant problem. We also apply the proposed approach to mortality data from Japan, France, the USA, and Taiwan. The empirical results show that our approach has better-fitting results and smaller mean absolute percentage errors than the Lee–Carter model.

Keywords: mortality improvement, Lee–Carter model, spatial statistics, cluster detection

Procedia PDF Downloads 171

Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

Abstract:

The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

Procedia PDF Downloads 389

Authors: Kyere Vincent Nartey, Klaus Greve, Atiemo Sampson

Abstract:

E-waste is discarded electrical electronic equipment inclusive of all components, sub-assemblies and consumables which are part of the product at the time of discarding and known to contain both hazardous and valuable fractions. E-waste is recycled within the proposed ecological restoration of the Agbogbloshie enclave using crude and rudimental recycling procedures such as open burning and manual dismantling which result in pollution and contamination of soil, water and air. Using GIS, this study was conducted to examine the spatial distribution and extent of soil contamination by heavy metals from the e-waste recycling site in Agbogbloshie. From the month of August to November 2013, 146 soil samples were collected in addition to their coordinates using GPS. Elemental analysis performed on the collected soil samples using X-Ray fluorescence revealed over 30 elements including, Ni, Cr, Zn, Cu, Pb and Mn. Using geostatistical techniques in ArcGIS 10.1 spatial assessment and distribution maps were generated. Mathematical models or equations were used to estimate the degree of contamination and pollution index. Results from soil analysis from the Agbogbloshie enclave showed that levels of measured or observed elements were significantly higher than the Canadian EPA and Dutch environmental standards.

Keywords: e-waste, geostatistics, soil contamination, spatial distribution

Procedia PDF Downloads 515

Authors: M. Habibi

Abstract:

The angular distribution of ion beam emission from the APF plasma focus device (15kV, 40μf, 115nH) filled with nitrogen gas has been examined through investigating the effect of ion beams on aluminum thin foils in different angular positions. The samples are studied in different distances from the anode end with different shots. The optimum pressure that would be obtained at the applied voltages of 12kV was 0.7 torr. The ions flux declined as the pressure inclined and the maximum ion density at 0.7 torr was about 10.26 × 1022 ions/steradian. The irradiated foils were analyzed with SEM method in order to study their surface and morphological changes. The results of the analysis showed melting and surface evaporation effects and generation of some cracks in the specimens. The result of ion patterns on the samples obtained in this study can be useful in determining ion spatial distributions on the top of anode.

Keywords: plasma focus, spatial distribution, high energy ions, ion angular distribution

Procedia PDF Downloads 458

Authors: Xiaoping Su, Gabriel G. Malouf

Abstract:

Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

Procedia PDF Downloads 105

Authors: Prami Sengupta, Randall A. Cantrell, Tracy Johns

Abstract:

A typical US household consumes more energy than households in other countries and is directly responsible for a considerable proportion of the atmospheric concentration of the greenhouse gases. This makes U.S. household a vital target group for energy conservation studies. Positive household behavior is central to residential energy conservation. However, for individuals to conserve energy they must not only know how to conserve energy but be also willing to do so. That is, a positive attitude towards residential conservation and an intention to conserve energy are two of the most important psychological determinants for energy conservation behavior. Most social science studies, to date, have studied the relationships between attitude, intention, and behavior by building upon socio-psychological theories of behavior. However, these frameworks, including the widely used Theory of Planned Behavior and Social Cognitive Theory, lack a spatial component. That is, these studies fail to capture the impact of the geographical locations of homeowners’ residences on their residential energy consumption and conservation practices. Therefore, the purpose of this study is to explore geospatial relationships between homeowners’ residential energy conservation-attitudes, conservation-intentions, and consumption behavior. The study analyzes residential conservation-attitudes and conservation-intentions of homeowners across 63 counties in Florida and compares it with quantifiable measures of residential energy consumption. Empirical findings revealed that the spatial distribution of high and/or low values of homeowners’ mean-score values of conservation-attitudes and conservation-intentions are more spatially clustered than would be expected if the underlying spatial processes were random. On the contrary, the spatial distribution of high and/or low values of households’ carbon footprints was found to be more spatially dispersed than assumed if the underlying spatial process were random. The study also examined the influence of potential spatial variables, such as urban or rural setting and presence of educational institutions and/or extension program, on the conservation-attitudes, intentions, and behaviors of homeowners.

Keywords: conservation-attitude, conservation-intention, geospatial analysis, residential energy consumption, spatial autocorrelation

Procedia PDF Downloads 191

Authors: Ankan Roy, Niharika, Samir Kumar Patra

Abstract:

Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

Procedia PDF Downloads 128

Authors: Jung-Hong Hong, Jing-Cen Yang, Cai-Yu Ou

Abstract:

The analysis of geographic inequality heavily relies on the use of location-enabled statistical data and quantitative measures to present the spatial patterns of the selected phenomena and analyze their differences. To protect the privacy of individual instance and link to administrative units, point-based datasets are spatially aggregated to area-based statistical datasets, where only the overall status for the selected levels of spatial units is used for decision making. The partition of the spatial units thus has dominant influence on the outcomes of the analyzed results, well known as the Modifiable Areal Unit Problem (MAUP). A new spatial reference framework, the Taiwan Geographical Statistical Classification (TGSC), was recently introduced in Taiwan based on the spatial partition principles of homogeneous consideration of the number of population and households. Comparing to the outcomes of the traditional township units, TGSC provides additional levels of spatial units with finer granularity for presenting spatial phenomena and enables domain experts to select appropriate dissemination level for publishing statistical data. This paper compares the results of respectively using TGSC and township unit on the mortality data and examines the spatial characteristics of their outcomes. For the mortality data between the period of January 1^st, 2008 and December 31^st, 2010 of the Taitung County, the all-cause age-standardized death rate (ASDR) ranges from 571 to 1757 per 100,000 persons, whereas the 2^nd dissemination area (TGSC) shows greater variation, ranged from 0 to 2222 per 100,000. The finer granularity of spatial units of TGSC clearly provides better outcomes for identifying and evaluating the geographic inequality and can be further analyzed with the statistical measures from other perspectives (e.g., population, area, environment.). The management and analysis of the statistical data referring to the TGSC in this research is strongly supported by the use of Geographic Information System (GIS) technology. An integrated workflow that consists of the tasks of the processing of death certificates, the geocoding of street address, the quality assurance of geocoded results, the automatic calculation of statistic measures, the standardized encoding of measures and the geo-visualization of statistical outcomes is developed. This paper also introduces a set of auxiliary measures from a geographic distribution perspective to further examine the hidden spatial characteristics of mortality data and justify the analyzed results. With the common statistical area framework like TGSC, the preliminary results demonstrate promising potential for developing a web-based statistical service that can effectively access domain statistical data and present the analyzed outcomes in meaningful ways to avoid wrong decision making.

Keywords: mortality map, spatial patterns, statistical area, variation

Procedia PDF Downloads 258

Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

Abstract:

Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

Procedia PDF Downloads 422

Authors: Adrien Marque, Daniel Delahaye, Pierre Maréchal, Isabelle Berry

Abstract:

Wind direction and uncertainty are crucial in aircraft or unmanned aerial vehicle trajectories. By computing wind covariance matrices on each spatial grid point, these spatial grids can be defined as images with symmetric positive definite matrix elements. A data pre-processing step, a specific convolution, a specific max-pooling, and a specific flatten layers are implemented to process such images. Then, the neural network is applied to spatial grids, whose elements are wind covariance matrices, to solve classification problems related to the feasibility of unmanned aerial vehicles based on wind direction and wind uncertainty.

Keywords: wind direction, uncertainty level, unmanned aerial vehicle, convolution neural network, SPD matrices

Procedia PDF Downloads 51

Authors: Jung-Hun Cho, Tae-Heon Moon, Jin-Hak Lee

Abstract:

Land price contains the comprehensive characteristics of urban space, representing the social and economic features of the city. Accordingly, land price can be utilized as an indicator, which can identify the changes of spatial structure and socioeconomic variations caused by urban development. This study attempted to explore the changes in land price by a new road construction. Methodologically, it adopted Space Syntax, which can interpret urban spatial structure comprehensively, to identify the relationship between the forms of road networks and land price. The result of the regression analysis showed the ‘integration index’ of Space Syntax is statistically significant and has a strong correlation with land price. If the integration value is high, land price increases proportionally. Subsequently, using regression equation, it tried to predict the land price changes of each of the lots surrounding the roads that are newly opened. The research methods or study results have the advantage of predicting the changes in land price in an easy way. In addition, it will contribute to planners and project managers to establish relevant polices and smoothing urban regeneration projects through enhancing residents’ understanding by providing possible results and advantages in their land price before the execution of urban regeneration and development projects.

Keywords: space syntax, urban regeneration, spatial structure, official land price

Procedia PDF Downloads 328

Authors: Ali Bayram, Remzi Yiğiter

Abstract:

Objective: Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disease. At present, diagnosis of AD is rather late in the disease. Therefore, we attempted to find peripheral biomarkers for the early diagnosis of AD. Herein, we conducted a study to investigate the unc-51 like autophagy activating kinase-1 (ULK1) mRNA expression levels in human peripheral blood mononuclear cells from patients with Alzheimer's disease. Method: To determine whether ULK1 gene expression are altered in AD patients, we measured their gene expression in human peripheral blood cell in 50 patients with AD and 50 age and gender matched healthy controls by quantitative real-time PCR technique. Results: We found that both ULK1 gene expression in peripheral blood cell were significantly decreased in patients with AD as compared with controls (p <0.05). Lower levels of ULK1 gene expression were significantly associated with the increased risk for AD. Conclusions: Serine/threonine-protein kinase involved in autophagy in response to starvation. Acts upstream of phosphatidylinositol 3-kinase PIK3C3 to regulate the formation of autophagophores, the precursors of autophagosomes. Part of regulatory feedback loops in autophagy: acts both as a downstream effector and negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK and also acts as a regulator of AMPK by mediating phosphorylation of AMPK subunits PRKAA1, PRKAB2, and PRKAG1, leading to negatively regulate AMPK activity. May phosphorylate ATG13/KIAA0652 and RPTOR; however such data need additional evidences. Plays a role early in neuronal differentiation and is required for granule cell axon formation. Alzheimer is the most common neurodegenerative disease. Our results provide useful information that the ULK1 gene expression is decreased in the neurodegeneration and AD patients with, indicating their possible systemic involvement in AD.

Keywords: Alzheimer’s sisease, ULK1, mRNA expression, RT-PCR

Procedia PDF Downloads 398

Authors: Jae Woong Sull, Sun Ha Jee

Abstract:

High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

Procedia PDF Downloads 286

Authors: Debjani Chakraborty, Abhijit Chatterjee, Aishwaryaprajna

Abstract:

Posynomials, a special type of polynomials, having singularities, pose difficulties while solving geometric programming problems. In this paper, a methodology has been proposed and used to obtain extreme values for geometric programming problems by nth degree polynomial interpolation technique. Here the main idea to optimise the posynomial is to fit a best polynomial which has continuous gradient values throughout the range of the function. The approximating polynomial is smoothened to remove the discontinuities present in the feasible region and the objective function. This spatial interpolation method is capable to optimise univariate and multivariate geometric programming problems. An example is solved to explain the robustness of the methodology by considering a bivariate nonlinear geometric programming problem. This method is also applicable for signomial programming problem.

Keywords: geometric programming problem, multivariate optimisation technique, posynomial, spatial interpolation

Procedia PDF Downloads 371

Authors: Robert Christopher Hamilton

Abstract:

This research examined the effects of reflexive cosmopolitanism on the competition for sexual territoriality. By adopting Michel De Certeau’s (1984) spatial didactic model, the article maps out the key elements at play and the dynamics explaining how gays gay place in the backdrop of rapid modernization. It found that heterosexual space and heteronormative assumptions helped to create temporal and spatial opportunities that allow for sexual performativity of gay males. Moreover, using data collected from multiple semi-controlled one-on-one interviews over 13 months, this article illustrates how spatial competition culminates in non-zero sum game outcomes and particularly to compromise of sexual territoriality while further demonstrating the need to understand the sexual coping tactics used in cultures with similar backgrounds. The findings enable researchers to better understand how gay men gay space, and how space performatively embodies gay men.

Keywords: South Korea, coffee bean, sexual territoriality, reflexive cosmopolitanism

Procedia PDF Downloads 327

Authors: Jorge Urrutia-Mosquera, Luz Flórez-Calderón, Yasna Cortés

Abstract:

We assessed the state of progress in terms of urban sustainability indicators and studied the impact of current land use conditions and the level of spatial accessibility to basic urban amenities on travel patterns and sustainable mobility in Santiago de Chile. We determined the spatial impact of urban facilities on sustainable travel patterns through the statistical analysis, data visualisation, and weighted regression models. The results show a need to diversify land use in more than 60% of the communes, although in 85% of the communes, accessibility to public spaces is guaranteed. The findings also suggest improving access to early education facilities, as only 26% of the communes meet the sustainability standard, negatively impacting travel in sustainable modes. It is also observed that the level of access to urban facilities generates spatial heterogeneity in the city, which negatively affects travel patterns in terms of time over 60 minutes and modes of travel in private vehicles. The results obtained allow us to identify opportunities for public policy intervention to promote and adopt sustainable mobility.

Keywords: land use, urban sustainability, travel patterns, spatial heterogeneity, GWR model, sustainable mobility

Procedia PDF Downloads 81

Authors: Dipanshu Sur, Ratnabali Chakravorty

Abstract:

Background: Polycystic ovary syndrome (PCOS) is the most common metabolic abnormality such as changes in lipid profile, diabetes, hypertension and metabolic syndrome occurring in young women of reproductive age. Low vitamin D levels were found to be associated with the development of obesity and insulin resistance in women with PCOS. Variants on vitamin D receptor (VDR) gene have also been related to metabolic comorbidities in general population. Aim: The aim of this case-control study was to investigate whether the VDR gene polymorphisms are associated with susceptibility to PCOS. Methods: Women with PCOS and a control group, all aged 16-40 years, were enrolled. Genotyping of VDR Fok-I (rs2228570), VDR Apa-I (rs7975232) as well as GC (rs2282679), DHCR7 (rs12785878) SNPs between groups were determined by using direct sequencing. Serum 25-hydroxyvitamin D [25(OH)] levels were measured by ELISA. Results: Mean serum 25(OH)D in the PCOS and control samples were 19.08±7 and 23.27±6.03 (p=0.048) which were significantly lower in PCOS patients compared with controls. CC genotype of the VDR Apa-I SNP was same frequent in PCOS (25.6%) and controls (25.6%) (OR: 0.9995; 95%CI: 0.528 to 1.8921; p= 0.9987). The CC genotype was also significantly associated with both lower E2 (p=0.031) and Androstenedione levels (p=0.062). We observed a significant association of GC polymorphism with 25(OH)D levels. PCOS women carrying the GG genotype (in GC genes) had significantly higher risk for vitamin D deficiency than women carrying the TT genotype. Conclusions: In conclusion, data from this study indicate that vitamin D levels are lower, and vitamin D deficiency more frequent, in PCOS than in controls. The present findings suggest that the Apa-I, Fok-I polymorphism of the VDR gene is associated with PCOS and seems to modulate ovarian steroid secretion. Further studies are needed to better clarify the biological mechanisms by which the polymorphism influences PCOS risk.

Keywords: vitamin D receptor, polymorphism, vitamin D, polycystic ovary syndrome

Procedia PDF Downloads 305

Authors: Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Teklehaimanot Hailesslasie

Abstract:

The advancement of target-specific genome editing tools, including clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), mega-nucleases, base editing (BE), prime editing (PE), transcription activator-like endonucleases (TALENs), and zinc-finger nucleases (ZFNs), have paved the way for a modern era of gene editing. CRISPR/Cas9, as a versatile, simple, cost-effective and robust system for genome editing, has dominated the genome manipulation field over the last few years. The application of CRISPR/Cas9 in sorghum improvement is particularly vital in the context of ecological, environmental and agricultural challenges, as well as global climate change. In this context, gene editing using CRISPR/Cas9 can improve nutritional value, yield, resistance to pests and disease and tolerance to different abiotic stress. Moreover, CRISPR/Cas9 can potentially perform complex editing to reshape already available elite varieties and new genetic variations. However, existing research is targeted at improving even further the effectiveness of the CRISPR/Cas9 genome editing techniques to fruitfully edit endogenous sorghum genes. These findings suggest that genome editing is a feasible and successful venture in sorghum. Newer improvements and developments of CRISPR/Cas9 techniques have further qualified researchers to modify extra genes in sorghum with improved efficiency. The fruitful application and development of CRISPR techniques for genome editing in sorghum will not only help in gene discovery, creating new, improved traits in sorghum regulating gene expression sorghum functional genomics, but also in making site-specific integration events.

Keywords: CRISPR/Cas9, genome editing, quality, sorghum, stress, yield

Procedia PDF Downloads 59

Authors: Ali Essam El Shazly

Abstract:

The Haussmannization plan of Cairo in 1867 formed a regular network of roundabout spaces, though deteriorated at present. The method of identifying the spatial structure of roundabout Cairo for conservation matches the voronoi diagram with the space syntax through their geometrical property of spatial convexity. In this initiative, the primary convex hull of first-order voronoi adopts the integral and control measurements of space syntax on Cairo’s roundabout generators. The functional essence of royal palaces optimizes the roundabout structure in terms of spatial measurements and the symbolic voronoi projection of 'Tahrir Roundabout' over the Giza Nile and Pyramids. Some roundabouts of major public and commercial landmarks surround the pole of 'Ezbekia Garden' with a higher control than integral measurements, which filter the new spatial structure from the adjacent traditional town. Nevertheless, the least integral and control measures correspond to the voronoi contents of pollutant workshops and the plateau of old Cairo Citadel with the visual compensation of new royal landmarks on top. Meanwhile, the extended suburbs of infinite voronoi polygons arrange high control generators of chateaux housing in 'garden city' environs. The point pattern of roundabouts determines the geometrical characteristics of voronoi polygons. The measured lengths of voronoi edges alternate between the zoned short range at the new poles of Cairo and the distributed structure of longer range. Nevertheless, the shortest range of generator-vertex geometry concentrates at 'Ezbekia Garden' where the crossways of vast Cairo intersect, which maximizes the variety of choice at different spatial resolutions. However, the symbolic 'Hippodrome' which is the largest public landmark forms exclusive geometrical measurements, while structuring a most integrative roundabout to parallel the royal syntax. Overview of the symbolic convex hull of voronoi with space syntax interconnects Parisian Cairo with the spatial chronology of scattered monuments to conceive one universal Cairo structure. Accordingly, the approached methodology of 'voronoi-syntax' prospects the future conservation of roundabout Cairo at the inferred city-level concept.

Keywords: roundabout Cairo, first-order Voronoi, space syntax, spatial structure

Procedia PDF Downloads 501

Authors: Abdullah M. Alzahrani

Abstract:

Our physiopathological assumption is that u-PA, t-PA, and PAI-1 are released by calcified aortic valves and play a role in the calcification of these valves. Sixty-five calcified aortic valves were collected from patients suffering from aortic stenosis. Each valve was incubated for 24 hours in culture medium. The supernatants were used to measure u-PA, t-PA, and PAI-1 concentrations; the valve calcification was evaluated using biphotonic absorptiometry. Aortic stenosis valves expressed normal plasminogen activators concentrations and overexpressed PAI-1 (u-PA, t-PA, and PAI-1 mean concentrations were, resp., 1.69 ng/mL ± 0.80, 2.76 ng/mL ± 1.33, and 53.27 ng/mL ± 36.39). There was no correlation between u-PA and PAI-1 (r = 0.3) but t-PA and PAI-1 were strongly correlated with each other (r = 0.6). Over expression of PAI-1 was proportional to the calcium content of theAS valves. Our results demonstrate a consistent increase of PAI-1 proportional to the calcification. The over expression of PAI-1 may be useful as a predictive indicator in patients with aortic stenosis.

Keywords: aortic valve, PAI-1, tPA gene, uPA gene

Procedia PDF Downloads 474

Authors: Omneya M. Helmy, Mona T. Kashef

Abstract:

Aminoglycosides are used in treating a wide range of infections caused by both Gram-negative and Gram positive bacteria. The presence of 16S rRNA methyl transferases (16S-RMTase) is among the newly discovered resistance mechanisms that confer high resistance to clinically useful aminoglycosides. Cephalosporins are the most commonly used antimicrobials in Egypt; therefore, this study was conducted to determine the isolation frequency of 16S rRNA methyl transferases among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycoside resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In Conclusion, the isolation frequency of 16S-RMTase was low among the tested cephalosporin-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.

Keywords: aminoglcosides, armA gene, β lactmases, 16S rRNA methyl transferases

Procedia PDF Downloads 282

Authors: Katie Kilgour, Brendan Turner, Carly Catella, Michael Daniele, Stefano Menegatti

Abstract:

In vivo, the extracellular matrix (ECM) provides biochemical and mechanical properties that are instructional to resident cells to form complex tissues with characteristics to develop and support vascular networks. In vitro, the development of vascular networks can be guided by biochemical patterning of substrates via spatial distribution and display of peptides and growth factors to prompt cell adhesion, differentiation, and proliferation. We have developed a technique utilizing peptide ligands that specifically bind vascular endothelial growth factor (VEGF), erythropoietin (EPO), or angiopoietin-1 (ANG1) to spatiotemporally distribute growth factors to cells. This allows for the controlled release of each growth factor, ultimately enhancing the formation of a vascular network. Our engineered tissue constructs (ETCs) are fabricated out of gelatin methacryloyl (GelMA), which is an ideal substrate for tailored stiffness and bio-functionality, and covalently patterned with growth factor specific peptides. These peptides mimic growth factor receptors, facilitating the non-covalent binding of the growth factors to the ETC, allowing for facile uptake by the cells. We have demonstrated in the absence of cells the binding affinity of VEGF, EPO, and ANG1 to their respective peptides and the ability for each to be patterned onto a GelMA substrate. The ability to organize growth factors on an ETC provides different functionality to develop organized vascular networks. Our results demonstrated a method to incorporate biochemical cues into ETCs that enable spatial and temporal control of growth factors. Future efforts will investigate the cellular response by evaluating gene expression, quantifying angiogenic activity, and measuring the speed of growth factor consumption.

Keywords: growth factor, hydrogel, peptide, angiogenesis, vascular, patterning

Procedia PDF Downloads 164

Authors: Mohammad Ahmad Ahmad Odah

Abstract:

Aging is a complex biological process characterized by the progressive decline of physiological functions and increased vulnerability to age-related diseases. Epigenetic changes, particularly DNA methylation alterations, play a critical role in the aging process by influencing gene expression and genomic stability. This study explores the potential of epigenetic reprogramming as a strategy to reverse aging phenotypes in human fibroblasts. Using CRISPR-Cas9 gene editing and small molecule inhibitors targeting DNA methylation and histone acetylation, we successfully induced significant changes in DNA methylation and gene expression profiles. Our results demonstrate a global reduction in DNA methylation levels and the identification of differentially methylated regions (DMRs) associated with cellular senescence and DNA repair. Additionally, treated fibroblasts exhibited enhanced proliferative capacity, reduced cellular senescence, and improved differentiation potential. These findings suggest that epigenetic reprogramming could be a promising approach for regenerative medicine, offering potential therapeutic strategies to counteract age-related decline and extend healthy lifespan.

Keywords: epigenetic reprogramming, aging, regenerative medicine, DNA methylation, cellular rejuvenation, CRISPR-Cas9, senescence

Procedia PDF Downloads 36

Authors: Melkamu A. Zeru, Yamral M. Warkaw, Aweke A. Mitku, Muluwerk Ayele

Abstract:

Introduction: Malaria is a severe health threat in the World, mainly in Africa. It is the major cause of health problems in which the risk of morbidity and mortality associated with malaria cases are characterized by spatial variations across the county. This study aimed to investigate the spatial patterns and predictors of malaria distribution in Ethiopia. Methods: A weighted sample of 15,239 individuals with rapid diagnosis tests was obtained from the Central Statistical Agency and Ethiopia malaria indicator survey of 2015. Global Moran's I and Moran scatter plots were used in determining the distribution of malaria cases, whereas the local Moran's I statistic was used in identifying exposed areas. In data manipulation, machine learning was used for variable reduction and statistical software R, Stata, and Python were used for data management and analysis. The auto logistics spatial binary regression model was used to investigate the predictors of malaria. Results: The final auto logistics regression model reported that male clients had a positive significant effect on malaria cases as compared to female clients [AOR=2.401, 95 % CI: (2.125 - 2.713)]. The distribution of malaria across the regions was different. The highest incidence of malaria was found in Gambela [AOR=52.55, 95%CI: (40.54-68.12)] followed by Beneshangul [AOR=34.95, 95%CI: (27.159 - 44.963)]. Similarly, individuals in Amhara [AOR=0.243, 95% CI:(0.1950.303],Oromiya[AOR=0.197,95%CI:(0.1580.244)],DireDawa[AOR=0.064,95%CI(0.049-0.082)],AddisAbaba[AOR=0.057,95%CI:(0.044-0.075)], Somali[AOR=0.077,95%CI:(0.059-0.097)], SNNPR[OR=0.329, 95%CI: (0.261- 0.413)] and Harari [AOR=0.256, 95%CI:(0.201 - 0.325)] were less likely to had low incidence of malaria as compared with Tigray. Furthermore, for a one-meter increase in altitude, the odds of a positive rapid diagnostic test (RDT) decrease by 1.6% [AOR = 0.984, 95% CI :( 0.984 - 0.984)]. The use of a shared toilet facility was found as a protective factor for malaria in Ethiopia [AOR=1.671, 95% CI: (1.504 - 1.854)]. The spatial autocorrelation variable changes the constant from AOR = 0.471 for logistic regression to AOR = 0.164 for auto logistics regression. Conclusions: This study found that the incidence of malaria in Ethiopia had a spatial pattern that is associated with socio-economic, demographic, and geographic risk factors. Spatial clustering of malaria cases had occurred in all regions, and the risk of clustering was different across the regions. The risk of malaria was found to be higher for those who live in soil floor-type houses as compared to those who live in cement or ceramics floor type. Similarly, households with thatched, metal and thin, and other roof-type houses have a higher risk of malaria than ceramic tiles roof houses. Moreover, using a protected anti-mosquito net reduced the risk of malaria incidence.

Keywords: malaria, Ethiopia, auto logistics, spatial model, spatial clustering

Procedia PDF Downloads 34

Authors: İsmail İnce, Mustafa Fener, Sair Kahraman

Abstract:

The uniaxial compressive strength (UCS) of rocks is an important input parameter for the design of rock engineering project. Compressive strength can be determined in the laboratory using the uniaxial compressive strength (UCS) test. Although the test is relatively simple, the method is time consuming and expensive. Therefore many researchers have tried to assess the uniaxial compressive strength values of rocks via relatively simple and indirect tests (e.g. point load strength test, Schmidt Hammer hardness rebound test, P-wave velocity test, etc.). Pyroclastic rocks are widely exposed in the various regions of the world. Cappadocia region located in the Central Anatolia is one of the most spectacular cite of these regions. It is important to determine the mechanical behaviour of the pyroclastic rocks due to their ease of carving, heat insulation properties and building some civil engineering constructions in them. The purpose of this study is to estimate a widely varying uniaxial strength of pyroclastic rocks from Cappadocia region by means of point load strength, porosity, dry density and saturated density tests utilizing gene expression programming.

Keywords: pyroclastic rocks, uniaxial compressive strength, gene expression programming (GEP, Cappadocia region

Procedia PDF Downloads 341

Authors: Carlo Stephen O. Moneva, Sharon Rose M. Tabugo

Abstract:

The present study aims to assess polymorphism in the prolactin (C576A) gene and determine the influence of different prolactin (PRL) genotypes to milk yield performance in crossbred Anglo-Nubian dairy goats raised from Awang, Opol, Misamis Oriental and Talay, Dumaguete City, Negros Oriental. Genomic DNA was extracted from hair follicles and Polymerase Chain Reaction – Restriction Fragment Length Polymorphism (PCR-RFLP) was performed for the genotyping of the C576A polymorphism located in exon 5 of goats’ prolactin gene using Eco241 restriction enzyme. Genotypic and allelic frequencies of 0.56 for AA, 0.44 for AB, 0.78 for A, and 0.22 for B were recorded. Observed heterozygosity values were higher than the expected heterozygosity. All populations followed the Hardy–Weinberg principle at p>0.05, except for dairy goats from Farm A located in Opol, Misamis Oriental. A two-way factorial (2 x 4) in a Randomized Complete Block Design was used to be able to evaluate the relationship between genotypes and milk yield performance. PRL genotypes and parity were used as main factors and farm as the blocking factor. AB genotype goats produced significantly higher average daily milk yield and total milk production than AA genotype (p<0.05), an indication that the polymorphism in the caprine PRL (C576A) gene influenced milk yield performance in the population of crossbred Anglo-Nubian goats from Opol, Misamis Oriental and Dumaguete City, Negros Oriental. However, these results have to be validated in other dairy goat breeds.

Keywords: polymorphism, prolactin, milk yield, Anglo-Nubian, PCR-RFLP

Procedia PDF Downloads 106