Search results for: spatial gene

Authors: Ramin Mehdiabadi, Neda Menbari, Mohammad Nazir Menbari

Abstract:

As a pressing public health concern, breast cancer stands as the predominant oncological diagnosis and principal cause of cancer-related mortality among women globally, accounting for 11.7% of new cancer incidences and 6.9% of cancer-related deaths. The annual figures indicate that approximately 230,480 women are diagnosed with breast cancer in the United States alone, with 39,520 succumbing to the disease. While developed economies have reported a deceleration in both incidence and mortality rates across various forms of cancer, including breast cancer, emerging and low-income economies manifest a contrary escalation, largely attributable to lifestyle-mediated risk factors such as tobacco usage, physical inactivity, and high caloric intake. Breast cancer is distinctly characterized by molecular heterogeneity, manifesting in specific subtypes delineated by biomarkers—Estrogen Receptors (ER), Progesterone Receptors (PR), and Human Epidermal Growth Factor Receptor 2 (HER2). These subtypes, comprising Luminal A, Luminal B, HER2-enriched, triple-negative/basal-like, and normal-like, necessitate nuanced, subtype-specific therapeutic regimens, thereby challenging the applicability of generalized treatment protocols. Within this molecular complexity, the transcription factor Forkhead Box M1 (FoxM1) has garnered attention as a significant driver of cellular proliferation, tumorigenesis, metastatic progression, and treatment resistance in a spectrum of human malignancies, including breast cancer. Concurrently, microRNAs (miRs), specifically miR-216b-5p, have been identified as post-transcriptional gene expression regulators and potential tumor suppressors. The overarching objective of this academic investigation is to explicate the multifaceted interrelationship between FoxM1 and miR-216b-5p across the disparate molecular subtypes of breast cancer. Employing a methodologically rigorous, interdisciplinary research design that incorporates cutting-edge molecular biology techniques, sophisticated bioinformatics analytics, and exhaustive meta-analyses of extant clinical data, this scholarly endeavor aims to unveil novel biomarker-specific therapeutic pathways. By doing so, this research is positioned to make a seminal contribution to the advancement of personalized, efficacious, and minimally toxic treatment paradigms, thus profoundly impacting the global efforts to ameliorate the burden of breast cancer.

Keywords: breast cancer, fox m1, microRNAs, mir-216b-5p, gene expression

Procedia PDF Downloads 56

Authors: Yi H. Wong, Li L. Chan, Chee O. Leong, Stephen Ambu, Joon W. Mak, Priyadashi S. Sahu

Abstract:

Background: Acanthamoeba is a free-living opportunistic protist which is ubiquitously distributed in the environment. Virulent Acanthamoeba can cause fatal encephalitis in immunocompromised patients and potential blinding keratitis in immunocompetent contact lens wearers. Approximately 24 species have been identified but only the A. castellanii, A. polyphaga and A. culbertsoni are commonly associated with human infections. Until to date, the precise molecular basis for Acanthamoeba pathogenesis remains unclear. Previous studies reported that Acanthamoeba virulence can be diminished through prolonged axenic culture but revived through serial mouse passages. As no clear explanation on this reversible pathogenesis is established, hereby, we postulate that the epigenetic regulators, DNA-methyltransferases (DNMT) and histone-deacetylases (HDAC), could possibly be involved in granting the virulence plasticity of Acanthamoeba spp. Methods: Four rounds of mouse passages were conducted to revive the virulence potential of the virulence-attenuated Acanthamoeba castellanii strain (ATCC 50492). Briefly, each mouse (n=6/group) was inoculated intraperitoneally with Acanthamoebae cells (2x 105 trophozoites/mouse) and incubated for 2 months. Acanthamoebae cells were isolated from infected mouse organs by culture method and subjected to subsequent mouse passage. In vitro cytopathic, encystment and gelatinolytic assays were conducted to evaluate the virulence characteristics of Acanthamoebae isolates for each passage. PCR primers which targeted on the 2 members (DNMT1 and DNMT2) and 5 members (HDAC1 to 5) of the DNMT and HDAC gene families respectively were custom designed. Quantitative real-time PCR (qPCR) was performed to detect and quantify the relative expression of the two gene families in each Acanthamoeba isolates. Beta-tubulin of A. castellanii (Genbank accession no: XP_004353728) was included as housekeeping gene for data normalisation. PCR mixtures were also analyzed by electrophoresis for amplicons detection. All statistical analyses were performed using the paired one-tailed Student’s t test. Results: Our pathogenicity tests showed that the virulence-reactivated Acanthamoeba had a higher degree of cytopathic effect on vero cells, a better resistance to encystment challenge and a higher gelatinolytic activity which was catalysed by serine protease. qPCR assay showed that DNMT1 expression was significantly higher in the virulence-reactivated compared to the virulence-attenuated Acanthamoeba strain (p ≤ 0.01). The specificity of primers which targeted on DNMT1 was confirmed by sequence analysis of PCR amplicons, which showed a 97% similarity to the published DNA-methyltransferase gene of A. castellanii (GenBank accession no: XM_004332804.1). Out of the five primer pairs which targeted on the HDAC family genes, only HDAC4 expression was significantly difference between the two variant strains. In contrast to DNMT1, HDAC4 expression was much higher in the virulence-attenuated Acanthamoeba strain. Conclusion: Our mouse passages had successfully restored the virulence of the attenuated strain. Our findings suggested that DNA-methyltransferase (DNMT1) and histone deacetylase (HDAC4) expressions are associated with virulence potential of Acanthamoeba spp.

Keywords: acanthamoeba, DNA-methyltransferase, histone deacetylase, virulence-associated proteins

Procedia PDF Downloads 281

Authors: Thanh Van Hoang, Tien Yin Chou, Yao Min Fang, Yi Min Huang, Xuan Linh Nguyen

Abstract:

Reliable information on the spatial distribution of annual rainfall and temperature is essential in research projects relating to urban and regional planning. This research presents results of a classification of temperature and rainfall in the Red River Delta of northern Vietnam based on measurements from seven meteorological stations (Ha Nam, Hung Yen, Lang, Nam Dinh, Ninh Binh, Phu Lien, Thai Binh) in the river basin over a thirty-years period from 1982-2011. The average accumulated rainfall trends in the delta are analysed and form the basis of research essential to weather and climate forecasting. This study employs interpolation based on the Kriging Method for daily rainfall (min and max) and daily temperature (min and max) in order to improve the understanding of sources of variation and uncertainly in these important meteorological parameters. To the Kriging method, the results will show the different models and the different parameters based on the various precipitation series. The results provide a useful reference to assist decision makers in developing smart agriculture strategies for the Red River Delta in Vietnam.

Keywords: spatial interpolation method, ArcGIS, temperature variability, rainfall variability, Red River Delta, Vietnam

Procedia PDF Downloads 321

Authors: T. J. B. van Niekerk, J. Viviers, E. J. Cilliers

Abstract:

Substantial efforts were made in South Africa, stemming from a historic political change in 1994, to remedy the inequality and injustice, resulting from a dispensation where spatial patterns were largely based on racial segregation. Spatially distorted patterns predominantly originated from colonialism in the beginning of the twentieth century, ensuing a physical imprint on South African cities relating to architecture, urban layout and planning, frequently reflecting European norms and standards. As a consequence of physical and land use barriers, and well-established dual cities, attempts to address spatial injustices, apart from limited occurrences in metropolitan areas, gravely failed. Interception of incessant segregated growth, combined with urban sprawl is becoming increasingly evident. Intervention is a prerequisite to duly address the impact of colonial planning and its legacy still prevalent in most urban areas. During 1998, the National Department of Transport prepared the “Moving South Africa” strategy; presenting the Corridor Densification Option Model for the first time, as it was deemed more fitting to the existing South African urban tenure patterns than more familiar planning approaches. Urban planners are progressively contemplating the Corridor Densification Option Model and its attributes, besides its transportation emphasis, as an alternative approach to address spatial imbalances and to attain the physical integration of contemporary urban forms. In attaining a clearer understanding of the Corridor Densification Option Model, its rationale was analysed in greater detail. This research further investigated the provisional applications of the model in spatially segregated cities and illustrated that viable options are present to effectively employ it. Research revealed that the application of the model will, however, be dependent on the occurrence of specific characteristics in spatially segregated cities to warrant augmentation thereof.

Keywords: corridor densification option model, spatially segregated settlements, integration, urban restructuring

Procedia PDF Downloads 213

Authors: Zenebu Adere Tola

Abstract:

Informal settlements behave dynamically over space and time and the number of people living in such housing areas is growing worldwide. In the cities of developing countries especially in sub-Saharan Africa, poverty, unemployment rate, poor living condition, lack transparency and accountability, lack of good governance are the major factors to contribute for the people to hold land informally and built houses for residential or other purposes. In most of Ethiopian cities informal settlement is highly seen in peripheral areas this is because people can easily to hold land for housing from local farmers, brokers, speculators without permission from concerning bodies. In Adama informal settlement has created risky living conditions and led to environmental problems in natural areas the main reason for this was the lack of sufficient knowledge about informal settlement development. On the other side there is a strong need to transform informal into formal settlements and to gain more control about the actual spatial development of informal settlements. In another hand to tackle the issue it is at least very important to understand the scale of the problem. To understand the scale of the problem it is important to use up-to-date technology. For this specific problem, it is good to use high-resolution imagery to detect informal settlement in Adama city. The main objective of this study is to assess the spatiotemporal dynamics and environmental impacts of informal settlement using OBIA. Specifically, the objective of this study is to; identify informal settlement in the study area, determine the change in the extent and pattern of informal settlement and to assess the environmental and social impacts of informal settlement in the study area. The methods to be used to detect the informal settlement is object-oriented image analysis. Consequently, reliable procedures for detecting the spatial behavior of informal settlements are required in order to react at an early stage to changing housing situations. Thus, obtaining spatial information about informal settlement areas which is up to date is vital for any actions of enhancement in terms of urban or regional planning. Using data for this study aerial photography for growth and change of informal settlements in Adama city. Software ECognition software for classy to built-up and non-built areas. Thus, obtaining spatial information about informal settlement areas which is up to date is vital for any actions of enhancement in terms of urban or regional planning.

Keywords: informal settlement, change detection, environmental impact, object based analysis

Procedia PDF Downloads 69

Authors: Laetitia Lemiere, Marie Gosme, Gerard Subsol, Marc Jaeger

Abstract:

Agroforestry is recognized as a way of developing sustainable and resilient agriculture that can fight against climate change. However, the number of species combinations, spatial configurations, and management options for trees and crops is vast. These choices must be adapted to the pedoclimatic and socio-economic contexts and to the objectives of the farmer, who therefore needs support in designing his system. Participative design workshops are a good way to integrate the knowledge of several experts in order to design such complex systems. The design of agroforestry systems should take into account both spatial aspects (e.g., spacing of trees within the lines and between lines, tree line orientation, tree-crop distance, species spatial patterns) and temporal aspects (e.g., crop rotations, tree thinning and pruning, tree planting in the case of successional agroforestry). Furthermore, the interactions between trees and crops evolve as the trees grow. However, agroforestry design workshops generally emphasize the spatial aspect only through the use of static tokens to represent the different species when designing the spatial configuration of the system. Augmented reality (AR) may overcome this limitation, allowing to visualize dynamic representations of trees and crops, and also their interactions, while at the same time retaining the possibility to physically interact with the system being designed (i.e., move trees, add or remove species, etc.). We propose an ergonomic digital solution capable of assisting a group of agroforestry experts to design an agroforestry system and to represent it. We investigated the use of web-based marker-based AR that does not require specific hardware and does not require specific installation so that all users could use their own smartphones right out of the pocket. We developed a prototype mobilizing the AR.js, ArToolKit.js, and Three.js open source libraries. In our implementation, we gradually build a virtual agroforestry system pattern scene from the users' interactions. A specific set of markers initialize the scene properties, and the various plant species are added and located during the workshop design session. The full virtual scene, including the trees positions with their neighborhood, are saved for further uses, such as virtual, augmented instantiation in the farmer fields. The number of tree species available in the application is gradually increasing; we mobilize 3D digital models for walnut, poplar, wild cherry, and other popular species used in agroforestry systems. The prototype allows shadow computations and the representation of trees at various growth stages, as well as different tree generations, and is thus able to visualize the dynamics of the system over time. Future work will focus on i) the design of complex patterns mobilizing several tree/shrub organizations, not restricted to lines; ii) the design of interfaces related to cultural practices, such as clearing or pruning; iii) the representation of tree-crop interactions. Beside tree shade (light competition), our objective is to represent also below-ground competitions (water, nitrogen) or other variables of interest for the design of agroforestry systems (e.g., predicted crop yield).

Keywords: agroforestry system design, augmented reality, marker-based AR, participative design, web-based AR

Procedia PDF Downloads 163

Authors: Meng-Cong Zheng

Abstract:

When the public space is in an emergency, how to quickly establish spatial cognition and emergency shelter in the closed underground space is the urgent task. This study takes Taipei Station as the research base and aims to apply the use of Internet of things (IoT) application for underground evacuation mobility design. The first experiment identified passengers' evacuation behaviors and spatial cognition in underground spaces by wayfinding tasks and thinking aloud, then defined the design conditions of User Interface (UI) and proposed the UI design.  The second experiment evaluated the UI design based on passengers' evacuation behaviors by wayfinding tasks and think aloud again as same as the first experiment. The first experiment found that the design conditions that the subjects were most concerned about were "map" and hoping to learn the relative position of themselves with other landmarks by the map and watch the overall route. "Position" needs to be accurately labeled to determine the location in underground space. Each step of the escape instructions should be presented clearly in "navigation bar." The "message bar" should be informed of the next or final target exit. In the second experiment with the UI design, we found that the "spatial map" distinguishing between walking and non-walking areas with shades of color is useful. The addition of 2.5D maps of the UI design increased the user's perception of space. Amending the color of the corner diagram in the "escape route" also reduces the confusion between the symbol and other diagrams. The larger volume of toilets and elevators can be a judgment of users' relative location in "Hardware facilities." Fire extinguisher icon should be highlighted. "Fire point tips" of the UI design indicated fire with a graphical fireball can convey precise information to the escaped person. "Fire point tips" of the UI design indicated fire with a graphical fireball can convey precise information to the escaped person. However, "Compass and return to present location" are less used in underground space.

Keywords: evacuation behaviors, IoT application, map UI design, underground station

Procedia PDF Downloads 194

Authors: Eun-Ji Lee, Hye-Sung Park, Chan-Jung Lee, Won-Sik Kong

Abstract:

We analyzed the DNA sequence of the ITS (Internal Transcribed Spacer) region of the 18S ribosomal gene and compared it with the gene sequence of T. fuciformis and Hypoxylon sp. in the BLAST database. The sequences of collected T. fuciformis and Hypoxylon sp. have over 99% homology in the T. fuciformis and Hypoxylon sp. sequence BLAST database. In order to select the optimal medium for T. fuciformis, five kinds of a medium such as Potato Dextrose Agar (PDA), Mushroom Complete Medium (MCM), Malt Extract Agar (MEA), Yeast extract (YM), and Compost Extract Dextrose Agar (CDA) were used. T. fuciformis showed the best growth on PDA medium, and Hypoxylon sp. showed the best growth on MCM. So as to investigate the optimum pH and temperature, the pH range was set to pH4 to pH8 and the temperature range was set to 15℃ to 35℃ (5℃ degree intervals). Optimum culture conditions for the T. fuciformis growth were pH5 at 25℃. Hypoxylon sp. were pH6 at 25°C. In order to confirm the most suitable carbon source, we used fructose, galactose, saccharose, soluble starch, inositol, glycerol, xylose, dextrose, lactose, dextrin, Na-CMC, adonitol. Mannitol, mannose, maltose, raffinose, cellobiose, ethanol, salicine, glucose, arabinose. In the optimum carbon source, T. fuciformis is xylose and Hypoxylon sp. is arabinose. Using the column test, we confirmed sawdust a suitable for T. fuciformis, since the composition of sawdust affects the growth of fruiting bodies of T. fuciformis. The sawdust we used is oak tree, pine tree, poplar, birch, cottonseed meal, cottonseed hull. In artificial cultivation of T. fuciformis with sawdust medium, T. fuciformis and Hypoxylon sp. showed fast mycelial growth on mixture of oak tree sawdust, cottonseed hull, and wheat bran.

Keywords: cultivation, optimal condition, tremella fuciformis, nutritional source

Procedia PDF Downloads 198

Authors: Muhammad Zubair Khan, Yugyung Lee

Abstract:

Deep learning has recently achieved enormous response in semantic image segmentation. The previously developed U-Net inspired architectures operate with continuous stride and pooling operations, leading to spatial data loss. Also, the methods lack establishing long-term pixels connection to preserve context knowledge and reduce spatial loss in prediction. This article developed encoder-decoder architecture with bi-directional LSTM embedded in long skip-connections and densely connected convolution blocks. The network non-linearly combines the feature maps across encoder-decoder paths for finding dependency and correlation between image pixels. Additionally, the densely connected convolutional blocks are kept in the final encoding layer to reuse features and prevent redundant data sharing. The method applied batch-normalization for reducing internal covariate shift in data distributions. The empirical evidence shows a promising response to our method compared with other semantic segmentation techniques.

Keywords: deep learning, semantic segmentation, image analysis, pixels connection, convolution neural network

Procedia PDF Downloads 93

Authors: Sachin Jain, Daniel Perez-Astudillo, Dunia A. Bachour, Antonio P. Sanfilippo

Abstract:

The future of solar energy in Qatar is evolving steadily. Hence, high-quality spatial solar radiation data is of the uttermost requirement for any planning and commissioning of solar technology. Generally, two types of solar radiation data are available: satellite data and ground observations. Satellite solar radiation data is developed by the physical and statistical model. Ground data is collected by solar radiation measurement stations. The ground data is of high quality. However, they are limited to distributed point locations with the high cost of installation and maintenance for the ground stations. On the other hand, satellite solar radiation data is continuous and available throughout geographical locations, but they are relatively less accurate than ground data. To utilize the advantage of both data, a product has been developed here which provides spatial continuity and higher accuracy than any of the data alone. The popular satellite databases: National Solar radiation Data Base, NSRDB (PSM V3 model, spatial resolution: 4 km) is chosen here for merging with ground-measured solar radiation measurement in Qatar. The spatial distribution of ground solar radiation measurement stations is comprehensive in Qatar, with a network of 13 ground stations. The monthly average of the daily total Global Horizontal Irradiation (GHI) component from ground and satellite data is used for error analysis. The normalized root means square error (NRMSE) values of 3.31%, 6.53%, and 6.63% for October, November, and December 2019 were observed respectively when comparing in-situ and NSRDB data. The method is based on the Empirical Bayesian Kriging Regression Prediction model available in ArcGIS, ESRI. The workflow of the algorithm is based on the combination of regression and kriging methods. A regression model (OLS, ordinary least square) is fitted between the ground and NSBRD data points. A semi-variogram is fitted into the experimental semi-variogram obtained from the residuals. The kriging residuals obtained after fitting the semi-variogram model were added to NSRBD data predicted values obtained from the regression model to obtain the final predicted values. The NRMSE values obtained after merging are respectively 1.84%, 1.28%, and 1.81% for October, November, and December 2019. One more explanatory variable, that is the ground elevation, has been incorporated in the regression and kriging methods to reduce the error and to provide higher spatial resolution (30 m). The final GHI maps have been created after merging, and NRMSE values of 1.24%, 1.28%, and 1.28% have been observed for October, November, and December 2019, respectively. The proposed merging method has proven as a highly accurate method. An additional method is also proposed here to generate calibrated maps by using regression and kriging model and further to use the calibrated model to generate solar radiation maps from the explanatory variable only when not enough historical ground data is available for long-term analysis. The NRMSE values obtained after the comparison of the calibrated maps with ground data are 5.60% and 5.31% for November and December 2019 month respectively.

Keywords: global horizontal irradiation, GIS, empirical bayesian kriging regression prediction, NSRDB

Procedia PDF Downloads 82

Authors: Bojana Horvat, Barbara Karleusa, Goran Volf, Nevenka Ozanic, Ivica Kisic

Abstract:

Forest fire is a major threat in many regions in Croatia, especially in coastal areas. Although they are often caused by natural processes, the most common cause is the human factor, intentional or unintentional. Forest fires drastically transform landscapes and influence natural processes. The main goal of the presented research is to analyse and quantify the impact of the forest fire on hydrological processes and propose the model that best describes changes in hydrological patterns in the analysed catchments. Keeping in mind the spatial component of the processes, geospatial analysis is performed to gain better insight into the spatial variability of the hydrological response to disastrous events. In that respect, two catchments that experienced severe forest fire were delineated, and various hydrological and meteorological data were collected both attribute and spatial. The major drawback is certainly the lack of hydrological data, common in small torrential karstic streams; hence modelling results should be validated with the data collected in the catchment that has similar characteristics and established hydrological monitoring. The event chosen for the modelling is the forest fire that occurred in July 2019 and burned nearly 10% of the analysed area. Surface (land use/land cover) conditions before and after the event were derived from the two Sentinel-2 images. The mapping of the burnt area is based on a comparison of the Normalized Burn Index (NBR) computed from both images. To estimate and compare hydrological behaviour before and after the event, curve number (CN) values are assigned to the land use/land cover classes derived from the satellite images. Hydrological modelling resulted in surface runoff generation and hence prediction of hydrological responses in the catchments to a forest fire event. The research was supported by the Croatian Science Foundation through the project 'Influence of Open Fires on Water and Soil Quality' (IP-2018-01-1645).

Keywords: Croatia, forest fire, geospatial analysis, hydrological response

Procedia PDF Downloads 126

Authors: Sezen Aslan, N. Aydan Sat

Abstract:

The society of 21st century constantly faces with complex otherness that emerges in various forms and justifications. Otherness caused by class, race or ethnicity inevitably reflects to urban areas, and in this way, cities are diversified into totally self-centered and closed-off urban enclaves. One of the most important dynamics that creates otherness in contemporary society is migration. Immigration on an international scale is one of the most important events that have reshaped the world, and the number of immigrants in the world is increasing day by day. Forced migration and refugee statements constitute the major part of countries' immigration policies and practices. Domestic problems such as racism, violence, war, censorship and silencing, attitudes contrary to human rights, different cultural or religious identities cause populations to migrate. Immigration is one of the most important reasons for the formation of urban enclaves within cities. Turkey, which was used to face a higher rate of outward migration, has begun to host immigrant groups from foreign countries. 1980s is the breaking point about the issue as a result of internal disturbances in the Middle East. After Iranian, Iraqi and Afghan immigrants, Turkey faces the largest external migration in its story with Syrian population. Turkey has been hosting approximate three million Syrian people after Syrian Civil War which started in 2011. 92% of Syrian refugees are currently living in different urban areas in Turkey instead of camps. Syrian refugees are experiencing a spontaneous spatiality due to the lack of specific settlement and housing policies of the country. This spontaneity is one of the most important factors in the creation of urban enclaves. From this point of view, the aim of this study is to clarify processes that lead the creation of urban enclaves and to explain socio-spatial effects of these urban enclaves to the other parts of the cities. Ankara, which is one of the most registered Syrian hosting Province in Turkey, is selected as a case study area. About 55% of the total Syrian population lives in the Altındağ district in Ankara. They settled specifically in two neighborhoods in Altındağ district, named as Önder and Ulubey. These neighborhoods are old slum areas, and they were evacuated due to urban renewal on the same dates with the migration of the Syrians. Before demolition of these old slums, Syrians are settled into them as tenants. In the first part of the study, a brief explanation of the concept of urban enclave, its occurrence parameters and possible socio-spatial threats, examples from previous immigrant urban enclaves caused internal migration will be given. Emergence of slums, planning history and social processes in the case study area will be described in the second part of the study. The third part will be focused on the Syrian refugees and their socio-spatial relationship in the case study area and in-depth interviews with refugees and spatial analysis will be realized. Suggestions for the future of the case study area and recommendations to prevent immigrant groups from social and spatial exclusion will be discussed in the conclusion part of the study.

Keywords: migration, immigration, Syrian refugees, urban enclaves, Ankara

Procedia PDF Downloads 195

Authors: Kazi Md. Shifun Newaz, S. Miaji, Shahnewaz Hazanat-E-Rabbi

Abstract:

In this study, the kernel density estimation tool has been used to identify most crash prone locations in a national highway of Bangladesh. Like other developing countries, in Bangladesh road traffic crashes (RTC) have now become a great social alarm and the situation is deteriorating day by day. Today’s black spot identification process is not based on modern technical tools and most of the cases provide wrong output. In this situation, characteristic analysis and black spot identification by spatial analysis would be an effective and low cost approach in ensuring road safety. The methodology of this study incorporates a framework on the basis of spatial-temporal study to identify most RTC occurrence locations. In this study, a very important and economic corridor like Dhaka to Sylhet highway has been chosen to apply the method. This research proposes that KDE method for identification of Hazardous Road Location (HRL) could be used for all other National highways in Bangladesh and also for other developing countries. Some recommendations have been suggested for policy maker to reduce RTC in Dhaka-Sylhet especially in black spots.

Keywords: hazardous road location (HRL), crash, GIS, kernel density

Procedia PDF Downloads 303

Authors: Kamal, J. P. Narayan

Abstract:

In the present wok the effects of basin-shape-ratio on the frequency content and spectral amplitudes of the basin-generated surface waves and the associated spatial variation of ground motion amplification and differential ground motion in a 3D semi-spherical basin has been studied. A recently developed 3D fourth-order spatial accurate time-domain finite-difference (FD) algorithm based on the parsimonious staggered-grid approximation of the 3D viscoelastic wave equations was used to estimate seismic responses. The simulated results demonstrated the increase of both the frequency content and the spectral amplitudes of the basin-generated surface waves and the duration of ground motion in the basin with the increase of shape-ratio of semi-spherical basin. An increase of the average spectral amplification (ASA), differential ground motion (DGM) and the average aggravation factor (AAF) towards the centre of the semi-spherical basin was obtained.

Keywords: 3D viscoelastic simulation, basin-generated surface waves, basin-shape-ratio effects, average spectral amplification, aggravation factors and differential ground motion

Procedia PDF Downloads 493

Authors: Christoph Opperer

Abstract:

Space syntax is a theory and method for analyzing the spatial layout of buildings and urban environments to understand how they can influence patterns of human movement, social interaction, and behavior. While direct visibility is a key factor in space syntax research, important visual information such as light, color, texture, etc., are typically not considered, even though psychological studies have shown a strong correlation to the human perceptual experience within physical space – with light and color, for example, playing a crucial role in shaping the perception of spaciousness. Furthermore, these surface properties are often the visual features that are most salient and responsible for drawing attention to certain elements within the environment. This paper explores the potential of integrating these factors into general space syntax methods and visibility-based analysis of space, particularly for architectural spatial layouts. To this end, we use a combination of geometric (isovist) and topological (visibility graph) approaches together with image-based methods, allowing a comprehensive exploration of the relationship between spatial geometry, visual aesthetics, and human experience. Custom-coded ray-tracing techniques are employed to generate spherical panorama images, encoding three-dimensional spatial data in the form of two-dimensional images. These images are then processed through computer vision algorithms to generate saliency-maps, which serve as a visual representation of areas most likely to attract human attention based on their visual properties. The maps are subsequently used to weight the vertices of isovists and the visibility graph, placing greater emphasis on areas with high saliency. Compared to traditional methods, our weighted visibility analysis introduces an additional layer of information density by assigning different weights or importance levels to various aspects within the field of view. This extends general space syntax measures to provide a more nuanced understanding of visibility patterns that better reflect the dynamics of human attention and perception. Furthermore, by drawing parallels to traditional isovist and VGA analysis, our weighted approach emphasizes a crucial distinction, which has been pointed out by Ervin and Steinitz: the difference between what is possible to see and what is likely to be seen. Therefore, this paper emphasizes the importance of including surface properties in visibility-based analysis to gain deeper insights into how people interact with their surroundings and to establish a stronger connection with human attention and perception.

Keywords: space syntax, visibility analysis, isovist, visibility graph, visual features, human perception, saliency detection, raytracing, spherical images

Procedia PDF Downloads 60

Authors: Elif Coskun Daggecen, Seyma Dokucu, Yekta Gezginc, Ismail Akyol

Abstract:

Fermented dairy food quality is mainly determined by the sensory perception and influenced by many factors. Today, starter cultures for fermented foods are being developed to have a constant quality in these foods. Streptococcus thermophilus is one of the main species of most a starter cultures of yogurt fermentation. This species produces lactate by lactose fermentation from pyruvate. On the other hand, a small amount of pyruvate can alternatively be converted to various typical yoghurt flavor compounds such as diacetyl, acetoin, acetaldehyde, or acetic acid, for which the activity of three genes are shown to be especially important; ldh, nox and als. Up to date, commercially produced yoghurts have not yet met the desired aromatic properties that Turkish consumers find in traditional homemade yoghurts. Therefore, it is important to select starters carrying favorable metabolic characteristics from natural isolates. In this study, 30 strains of Str. Thermophilus were isolated from traditional Turkish yoghurts obtained from different regions of the country. In these strains, transcriptional levels of ldh, nox and als genes were determined via a newly developed qPCR protocol, which is a more reliable and precision method for analyzing the quantitative and qualitative expression of specific genes in different experimental conditions or in different organisms compared to conventional analytical methods. Additionally, the metabolite production potentials of the isolates were measured. Of all the strains examined, 60% were found to carry the metabolite production potential and the gene activity which appeared to be suitable to be used as a starter culture. Probable starter cultures were determined according to real-time PCR results.

Keywords: gene expression, RT-PCR, starter culture, Streptococcus thermophilus

Procedia PDF Downloads 178

Authors: Olusegun Oguntoke, Aramide Y. Tijani, Olayide R. Adetunji

Abstract:

Environmental noise has become a major threat to the quality of human life, and it is generally more severe in cities. This study assessed the level of environmental noise, mapped the spatial pattern at different times of the day and examined the association with morbidity of auditory ailments in Abeokuta metropolis. The entire metropolis was divided into 80 cells (areas) of 1000 m by 1000 m; out of which 33 were randomly selected for noise levels assessment. Portable noise meter (AR824) was used to measure noise level, and Global Positioning System (Garmin GPS-72H) was employed to take the coordinates of the sample sites for mapping. Risk map of the noise levels was produced using Kriging interpolation techniques based on the spatial spread of measured noise values across the study area. Data on cases of hearing impairments were collected from four major hospitals in the city. Data collected from field measurements and medical records were subjected to descriptive (frequency and percentage) and inferential (mean, ANOVA and correlation) statistics using SPSS (version 20.0). ArcMap 10.1 was employed for spatial analysis and mapping. Results showed mean noise levels range at morning (42.4 ± 4.14 – 88.2 ± 15.1 dBA), afternoon (45.0 ± 6.72– 86.4 ± 12.5 dBA) and evening (51.0 ± 6.55–84.4 ± 5.19 dBA) across the study area. The interpolated maps identified Kuto, Okelowo, Isale-Igbein, and Sapon as high noise risk areas. These are the central business district and nucleus of Abeokuta metropolis where commercial activities, high traffic volume, and clustered buildings exist. The monitored noise levels varied significantly among the sampled areas in the morning, afternoon and evening (p < 0.05). A significant correlation was found between diagnosed cases of auditory ailments and noise levels measured in the morning (r=0.39 at p < 0.05). Common auditory ailments found across the metropolis included impaired hearing (25.8%), tinnitus (16.4%) and otitis (15.0%). The most affected age groups were between 11-30 years while the male gender had more cases of hearing impairments (51.2%) than the females. The study revealed that environmental noise levels exceeded the recommended standards in the morning, afternoon and evening in 60.6%, 61% and 72.7% of the sampled areas respectively. Summarily, environmental noise in the study area is high and contributes to the morbidity of auditory ailments. Areas identified as hot spots of noise pollution should be avoided in the location of noise sensitive activities while environmental noise monitoring should be included as part of the mandate of the regulatory agencies in Nigeria.

Keywords: noise pollution, associative analysis, auditory impairment, urban, human exposure

Procedia PDF Downloads 131

Authors: Rabia Munsaf Khan, Eshrat Fatima

Abstract:

The analysis of the spatial extent and temporal change of vegetation cover using remotely sensed data is of critical importance to agricultural sciences. Pakistan, being an agricultural country depends on this resource as it makes 70% of the GDP. The case study is of Lal Suhanra National Park, which is not only the biggest forest reserve of Pakistan but also of Asia. The study is performed using different temporal images of Landsat. Also, the results of Landsat are cross-checked by using Sentinel-2 imagery as it has both higher spectral and spatial resolution. Vegetation can easily be detected using NDVI which is a common and widely used index. It is an important vegetation index, widely applied in research on global environmental and climatic change. The images are then classified to observe the change occurred over 15 years. Vegetation cover maps of 2000 and 2016 are used to generate the map of vegetation change detection for the respective years and to find out the changing pattern of vegetation cover. Also, the NDVI values aided in the detection of percentage decrease in vegetation cover. The study reveals that vegetation cover of the area has decreased significantly during the year 2000 and 2016.

Keywords: Landsat, normalized difference vegetation index (NDVI), sentinel 2, Greenland monitoring

Procedia PDF Downloads 298

Authors: Yingchen Yang

Abstract:

In the present work, development of a new vertical-axis unidirectional wave rotor is reported. The wave rotor is a key component of a wave energy converter (WEC), which harvests energy from ocean waves. Differing from the huge majority of WEC designs that perform reciprocating motions (heaving up and down, swaying back and forth, etc.), our wave rotor performs unidirectional rotation about a vertical axis when directly exposed in waves. The unidirectional feature of the rotor makes the rotor respond well in a wide range of the wave frequency. The vertical axis arrangement of the rotor makes the rotor insensitive to the wave propagation direction. The rotor employs blades with a cross-section in an airfoil shape and a span curled into a semi-oval shape. Two sets of blades, with one nested inside the other, constitute the rotor. In waves, water particles perform an omnidirectional motion that constantly changes in both spatial and temporal domains. The blade nesting permits a compact rotor configuration that ‘sees’ a relatively uniform local flow in the spatial domain. The rotor was experimentally tested in simulated waves in a wave flume under various conditions. The testing results show a promising unidirectional rotor that is capable of extracting energy from waves at a capture width ratio of 0.08 to 0.15, depending on detailed wave conditions.

Keywords: unidirectional, vertical axis, wave energy converter, wave rotor

Procedia PDF Downloads 229

Authors: S. M. M. Syairah, M. H. Rajikin, A. R. Sharaniza

Abstract:

Several embryonic cellular mechanism including cell cycle, growth and apoptosis are regulated by phosphatidylinositol-3-kinase (PI3K)/Akt signaling pathway. The goal of present study is to determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol (δ-TCT) on the regulations of PI3K/Akt genes in murine morula. Twenty four 6-8 week old (23-25g) female balb/c mice were randomly divided into four groups (G1-G4; n=6). Those groups were subjected to the following treatments for 7 consecutive days: G1 (control) received tocopherol stripped corn oil, G2 was given 60 mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity) and G4 received 60 mg/kg/day α-TOC. On Day 8, females were superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin (PMSG) for 48 hours followed with 5 IU human Chorionic Gonadotropin (hCG) before mated with males at the ratio of 1:1. Females were sacrificed by cervical dislocation for embryo collection 48 hours post-coitum. About fifty morula from each group were used in the gene expression analyses using Affymetrix QuantiGene Plex 2.0 Assay. Present data showed a significant increase (p<0.05) in the average number (mean + SEM) of morula produced in G2 (26.0 + 0.45), G3 (23.0 + 0.63) and G4 (25.0 + 0.73) compared to control group (G1 – 16.0 + 0.63). This is parallel with the high expression of PDK1 gene with increase of 2.75-fold (G2), 3.07-fold (G3) and 3.59-fold (G4) compared to G1 (1.78-fold). From the present data, it can be concluded that supplementation with δ-TCT(s) and α-TOC induced high expression of PDK1 in G2-G4 which enhanced the PI3K/Akt signaling activity, resulting in the increased number of morula.

Keywords: delta-tocotrienol, embryonic development, nicotine, vitamin E

Procedia PDF Downloads 420

Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

Abstract:

Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

Procedia PDF Downloads 69

Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

Abstract:

Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

Procedia PDF Downloads 115

Authors: Nodi Islam

Abstract:

This paper critically reads Richard Powers’ novel The Echo Maker to read and understand the personal traumas of the characters in the novel depending on the various situations they face throughout the story. Also, the paper attempts to read different traumas and disorders due to their different situations. With a focus on the individual experiences, this paper addresses the core issues of trauma, which triggers their reactions and reads the novel through theories of Freud, Caruth, and other critics in this field. While transcending the boundary of personal and collective trauma, this paper suggests that traumas not only arise from the core mental issues, from both past or present memories; it also depends on places too which can be called, according to Yi-Fu Tuan, topophobia. Intimate places such as home provoke not only attachment and expectation but also produce fear in a person. Failure in identifying with such places means losing a central piece of identity of the individual. In order to analyse the traumas in the novel, the characters’ association with homes and places has been provided. This paper attempts to suggest that people are not traumatised because of what Freud explained as unpleasant memories of the past but also intimacy and lost identities related to a place can trigger trauma.

Keywords: spatial trauma, traumatic stress disorder, identity and place, core mental issues

Procedia PDF Downloads 138

Authors: Varsha Shinde, Belle Damodara Shenoy

Abstract:

Tarballs are crude oil remnants found in oceans after long term weathering process and are a global concern since several decades as potential marine pollutant. Being complicated in structure microbial remediation of tarballs in natural environment is a slow process. They are rich in high molecular weight alkanes and poly aromatic hydrocarbons which are resistant to microbial attack and other environmental factors, therefore remain in environment for long time. However, it has been found that many bacteria and fungi inhabit on tarballs for nutrients and shelter. Many of them are supposed to be oil degraders, while others are supposed to be getting benefited by byproducts formed during hydrocarbon metabolism. Thus tarballs are forming special interesting ecological niche of microbes. This work aimed to study diversity of bacteria and fungi from tarballs and to see their potential application in crude oil degradation. The samples of tarballs were collected from Betul beach of south Goa (India). Different methods were used to isolate culturable fraction of bacteria and fungi from it. Those were sequenced for 16S rRNA gene and ITS for molecular level identification. The 16S rRNA gene sequence analysis revealed the presence of 13 bacterial genera/clades (Alcanivorax, Brevibacterium, Bacillus, Cellulomonas, Enterobacter, Klebsiella, Marinobacter, Nitratireductor, Pantoea, Pseudomonas, Pseudoxanthomonas, Tistrella and Vibrio), while the ITS sequence analysis placed the fungi in 8 diverse genera/ clades (Aspergillus, Byssochlamys, Monascus, Paecilomyces, Penicillium, Scytalidium/ Xylogone, Talaromyces and Trichoderma). All bacterial isolates were screened for oil degradation capacity. Potential strains were subjected to crude oil degradation experiment for quantification. Results were analyzed by GC-MS-MS.

Keywords: bacteria, biodegradation, crude oil, diversity, fungi, tarballs

Procedia PDF Downloads 215

Authors: Syed Khurram Mahmud, Athar Naveed, Shoaib Arif

Abstract:

Beamforming is a signal processing technique extensively utilized in wireless communications and radars for desired signal intensification and interference signal minimization through spatial selectivity. In this paper, we present a method for calculation of optimal weight vectors for smart antenna array, to achieve a directive pattern during transmission and selective reception in interference prone environment. In proposed scheme, Mutual Information (MI) extrema are evaluated through an energy constrained objective function, which is based on a-priori information of interference source and desired array factor. Signal to Interference plus Noise Ratio (SINR) performance is evaluated for both transmission and reception. In our scheme, MI is presented as an index to identify trade-off between information gain, SINR, illumination time and spatial selectivity in an energy constrained optimization problem. The employed method yields lesser computational complexity, which is presented through comparative analysis with conventional methods in vogue. MI based beamforming offers enhancement of signal integrity in degraded environment while reducing computational intricacy and correlating key performance indicators.

Keywords: beamforming, interference, mutual information, wireless communications

Procedia PDF Downloads 271

Authors: Priti Saha, Biswajit Paul

Abstract:

Rapid urbanization and industrialization have increased the demand of groundwater. However, the present era has evident an enormous level of groundwater pollution. Therefore, water quality assessment is paramount importance to evaluate its suitability for drinking, irrigation and industrial use. This study focus to evaluate the groundwater quality of an industrial city in eastern India through interdisciplinary techniques. The multi-purpose Water Quality Index (WQI) assess the suitability for drinking as well as irrigation of forty sampling locations, where 2.5% and 15% of sampling locations have excellent water quality (WQI:0-25) as well as 15% and 40% have good quality (WQI:25-50), which represents its suitability for drinking and irrigation respectively. However, the industrial water quality was assessed through Ryznar Stability Index (LSI), which affirmed that only 2.5% of sampling locations have neither corrosive nor scale forming properties (RSI: 6.2-6.8). These techniques with the integration of geographical information system (GIS) for spatial assessment indorsed its effectiveness to identify the regions where the water bodies are suitable to use for drinking, irrigation as well as industrial activities. Further, the sources of these contaminants were identified through factor analysis (FA), which revealed that both the geogenic as well as anthropogenic sources were responsible for groundwater pollution. This research demonstrates the effectiveness of statistical and GIS techniques for the analysis of environmental contaminants.

Keywords: groundwater, water quality analysis, water quality index, WQI, factor analysis, FA, spatial assessment

Procedia PDF Downloads 186

Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

Abstract:

Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

Procedia PDF Downloads 99

Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

Abstract:

The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

Procedia PDF Downloads 238

Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

Abstract:

The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

Procedia PDF Downloads 514

Authors: Vijay Kumar Singh, Pooja Kushwaha, Prabhat Ranjan, Krishna Kumar Ojha, Jitendra Kumar

Abstract:

Present day high-throughput genomic technologies, NGS/microarrays, are producing large volume of data that require improved analysis methods to make sense of the data. The correlation between genes and samples has been regularly used to gain insight into many biological phenomena including, but not limited to, co-expression/co-regulation, gene regulatory networks, clustering and pattern identification. However, presence of outliers and violation of assumptions underlying Pearson correlation is frequent and may distort the actual correlation between the genes and lead to spurious conclusions. Here, we report a method to measure the strength of association between genes. The method assumes that the expression values of a gene are Bernoulli random variables whose outcome depends on the sample being probed. The method considers the two genes as uncorrelated if the number of sample with same outcome for both the genes (Ns) is equal to certainly expected number (Es). The extent of correlation depends on how far Ns can deviate from the Es. The method does not assume normality for the parent population, fairly unaffected by the presence of outliers, can be applied to qualitative data and it uses the binomial distribution to assess the significance of association. At this stage, we would not claim about the superiority of the method over other existing correlation methods, but our method could be another way of calculating correlation in addition to existing methods. The method uses binomial distribution, which has not been used until yet, to assess the significance of association between two variables. We are evaluating the performance of our method on NGS/microarray data, which is noisy and pierce by the outliers, to see if our method can differentiate between spurious and actual correlation. While working with the method, it has not escaped our notice that the method could also be generalized to measure the association of more than two variables which has been proven difficult with the existing methods.

Keywords: binomial distribution, correlation, microarray, outliers, transcriptome

Procedia PDF Downloads 402