Search results for: spatial gene

Authors: Karthik Mittal

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This study performs an unsupervised machine learning analysis to find clusters of related SNPs which highlight biological pathways that are important for the biological mechanisms of breast cancer. Studying genetic variations in isolation is illogical because these genetic variations are known to modulate protein production and function; the downstream effects of these modifications on biological outcomes are highly interconnected. After extracting the SNPs and their effect on different types of breast cancer using the MRBase library, two unsupervised machine learning clustering algorithms were implemented on the genetic variants: a k-means clustering algorithm and a hierarchical clustering algorithm; furthermore, principal component analysis was executed to visually represent the data. These algorithms specifically used the SNP’s beta value on the three different types of breast cancer tested in this project (estrogen-receptor positive breast cancer, estrogen-receptor negative breast cancer, and breast cancer in general) to perform this clustering. Two significant genetic pathways validated the clustering produced by this project: the MAPK signaling pathway and the connection between the BRCA2 gene and the ESR1 gene. This study provides the first proof of concept showing the importance of unsupervised machine learning in interpreting GWAS summary statistics.

Keywords: breast cancer, computational biology, unsupervised machine learning, k-means, PCA

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Authors: Chitresh Kumar, Santanu Gupta

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The research work intends to understand the process of initiation, planning and development of capital-intensive urban area level infrastructure development in East Asian Cities (specific to Indian Cities). With the onset of emphasis on sustainable urban transport, self-financed urban local bodies, it has become of utmost important to identify infrastructure and projects on a priority basis, which provide optimal utility to the urban area. Through identification of Spatial, Demographic and Socio-Economic and Political Instability Parameters and their trends for the past 60 years at the urban area and state level, the paper attempts to identify the most suitable time period when initiation of the project would become economically and demographically viable for the city.

Keywords: urban planning, regional planning, mass transit, infrastructure development, spatial planning

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Authors: Alemaw Kefale, Aramde Fetene, Hayal Desta

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Monitoring the amount of green space in urban areas is important for ensuring sustainable development and proper management. The study analyzed changes in urban green space coverage over the past 20 years in two rapidly urbanizing cities in Ethiopia, Debre Berhan and Debre Markos, using GIS and remote sensing. The researchers used Landsat 5 and 8 data with a spatial resolution of 30 m to determine different land use and land cover classes, including urban green spaces, barren and croplands, built-up areas, and water bodies. The classification accuracy ranged between 90% and 91.4%, with a Kappa Statistic of 0.85 to 0.88. The results showed that both cities experienced significant decreases in vegetation cover in their urban cores between 2000 and 2020, with radical changes observed from green spaces and croplands to built-up areas. In Debre Berhan, barren and croplands decreased by 32.96%, while built-up and green spaces increased by 357.9% and 37.4%, respectively, in 2020. In Debre Markos, built-up areas increased by 224.2%, while green spaces and barren and croplands decreased by 41% and 5.71%, respectively. The spatial structure of cities and planning policies were noticed as the major factors for big green cover change. Thus it has an implication for other rapidly urbanized cities in Africa and Asia. Overall, rapid urbanization threatens green spaces and agricultural areas, highlighting the need for ecological-based spatial planning in rapidly urbanizing cities.

Keywords: green space coverage, GIS and remote sensing, Landsat, LULC, Ethiopia

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Authors: A. Abdullah, S. Abushalmat, A. Bakshwain, A. Basuhail, A. Aslam

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GIS (Geographic Information System) applications require geo-referenced data, this data could be available as databases or in the form of digital or hard-copy agro-meteorological maps. These parameter maps are color-coded with different regions corresponding to different parameter values, converting these maps into a database is not very difficult. However, text and different planimetric elements overlaid on these maps makes an accurate image to database conversion a challenging problem. The reason being, it is almost impossible to exactly replace what was underneath the text or icons; thus, pointing to the need for inpainting. In this paper, we propose a probabilistic inpainting approach that uses the probability of spatial locality of colors in the map for replacing overlaid elements with underlying color. We tested the limits of our proposed technique using non-textual simulated data and compared text removing results with a popular image editing tool using public domain data with promising results.

Keywords: noise, image, GIS, digital map, inpainting

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Authors: Pei-Chih Wu, Hsin-Chih Lai, Yung-Lung Lee, Yun-Yao Chi, Ching-Yi Horng, Hsien-Chang Wang

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The impact of climate change to health has always been well documented. Amongst them, water-borne infectious diseases, chronic adverse effects or cancer risks due to chemical contamination in flooding or drought events are especially important in river basin. This study therefore utilizes GIS and different models to integrate demographic, land use, disaster prevention, social-economic factors, and human health assessment in the Erren River basin. Therefore, through the collecting of climatic, demographic, health surveillance, water quality and other water monitoring data, potential risks associated with the Erren River Basin are established and to understand human exposure and vulnerability in response to climate extremes. This study assesses the temporal and spatial patterns of melioidosis (2000-2015) and various cancer incidents in Tainan and Kaohsiung cities. The next step is to analyze the spatial association between diseases incidences, climatic factors, land uses, and other demographic factors by using ArcMap and GeoDa. The study results show that amongst all melioidosis cases in Taiwan, 24% cases (115) residence occurred in the Erren River basin. The relationship between the cases and in Tainan and Kaohsiung cities are associated with population density, aging indicator, and residence in Erren River basin. Risks from flooding due to heavy rainfall and fish farms in spatial lag regression are also related. Through liver cancer, the preliminary analysis in temporal and spatial pattern shows an increases pattern in annual incidence without clusters in Erren River basin. Further analysis of potential cancers connected to heavy metal contamination from water pollution in Erren River is established. The final step is to develop an assessment tool for human exposure from water contamination and vulnerability in response to climate extremes for the second year.

Keywords: climate change, health impact, health adaptation, Erren River Basin

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Authors: Arash Rahmani, Ahmad Ghanbari, Abbas Baghernezhad, Babak Safaei

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In the design of parallel manipulators, usually mean value of a dexterity measure over the workspace volume is considered as the objective function to be used in optimization algorithms. The mentioned indexes in a hybrid parallel manipulator (HPM) are quite complicated to solve thanks to infinite solutions for every point within the workspace of the redundant manipulators. In this paper, spatial isotropic design axioms are extended as a well-known method for optimum design of manipulators. An upper limit for the isotropy measure of HPM is calculated and instead of computing and minimizing isotropy measure, minimizing the obtained limit is considered. To this end, two different objective functions are suggested which are obtained from objective functions of comprising modules. Finally, by using genetic algorithm (GA), the best geometric parameters for a specific hybrid parallel robot which is composed of two modified Gough-Stewart platforms (MGSP) are achieved.

Keywords: hybrid manipulator, spatial isotropy, genetic algorithm, optimum design

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Authors: Lin Dong, Fei Shi

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Based on the railway network and the principles of space syntax, the study attempts to reconstruct the spatial relationship of the passenger network connections from space and time perspective. According to the travel time data of main stations in the Yangtze River Delta urban agglomeration obtained by the Internet, the topological drawing of railway network under different time sections is constructed. With the comprehensive index composed of connection and integration, the accessibility and network operation efficiency of the railway network in different time periods is calculated, while the fairness of the network is analyzed by the fairness indicators constructed with the integration and location entropy from the perspective of horizontal and vertical fairness respectively. From the analysis of the efficiency and fairness of the railway passenger transport network, the study finds: (1) There is a strong regularity in regional system accessibility change; (2) The problems of efficiency and fairness are different in different time periods; (3) The improvement of efficiency will lead to the decline of horizontal fairness to a certain extent, while from the perspective of vertical fairness, the supply-demand situation has changed smoothly with time; (4) The network connection efficiency of Shanghai, Jiangsu and Zhejiang regions is higher than that of the western regions such as Anqing and Chizhou; (5) The marginalization of Nantong, Yancheng, Yangzhou, Taizhou is obvious. The study explores the application of spatial syntactic theory in regional traffic analysis, in order to provide a reference for the development of urban agglomeration transportation network.

Keywords: spatial syntax, the Yangtze River Delta, railway passenger time, efficiency and fairness

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Authors: Khen Cohen, Daniel Yankelevich, David Mendlovic, Dan Raviv

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We present a 3D stereo system for high-resolution sensing in both the spatial and the temporal domains by combining a frame-based camera and an event-based camera. We establish a method to merge both devices into one unite system and introduce a calibration process, followed by a correspondence technique and interpolation algorithm for 3D reconstruction. We further provide quantitative analysis about our system in terms of depth resolution and additional parameter analysis. We show experimentally how our system performs temporal super-resolution up to effectively 1ms and can detect fast-moving objects and human micro-movements that can be used for micro-expression analysis. We also demonstrate how our method can extract colored events for an event-based camera without any degradation in the spatial resolution, compared to a colored filter array.

Keywords: DVS-CIS stereo vision, micro-movements, temporal super-resolution, 3D reconstruction

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Authors: David Sarpong, Waleed Khursheed, Ernest Danquah, Erin Murphy

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Shigella is a pathogenic bacterium responsible for shigellosis, a severe diarrheal disease that claims the lives of immunocompromised individuals worldwide. To develop therapeutics against this disease, an understanding of the molecular mechanisms underlying the pathogen’s physiology is crucial. Small non-coding RNAs (sRNAs) have emerged as important regulators of bacterial physiology, including as components of toxin-antitoxin systems. In this study, we investigated the role of RyfA in S. flexneri physiology and virulence. RyfA, originally identified as an sRNA in Escherichia coli, is conserved within the Enterobacteriaceae family, including Shigella. Whereas two copies of ryfA are present in S. dysenteriae, all other Shigella species contain only one copy of the gene. Additionally, we identified a putative open reading frame within the RyfA transcript, suggesting that it may be a dual-functioning gene encoding a small protein in addition to its sRNA function. To study ryfA in vitro, we cloned the gene into an inducible plasmid and observed the effect on bacterial growth. Here, we report that RyfA production inhibits the growth of S. flexneri, and this inhibition is dependent on the contained open reading frame. In-silico analyses have revealed the presence of two divergently transcribed sRNAs, RyfB1 and RyfB2, which share nucleotide complementarity with RyfA and thus are predicted to function as anti-toxins. Our data demonstrate that RyfB2 has a stronger antitoxin effect than RyfB1. This regulatory pattern suggests a novel form of a toxin-antitoxin system in which the activity of a single toxin is inhibited to varying degrees by two sRNA antitoxins. Studies are ongoing to investigate the regulatory mechanism(s) of the antitoxin genes, as well as the downstream targets and mechanism of growth inhibition by the RyfA toxin. This study offers distinct insights into the regulatory mechanisms underlying Shigella physiology and may inform the development of new anti-Shigella therapeutics.

Keywords: sRNA, shigella, toxin-antitoxin, Type 1 toxin antitoxin

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Authors: Narjes Abbasabadi

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As the world continues to urbanize and suburbanize, where suburbanization associated with mass sprawl has been the dominant form of this expansion, sustainable development challenges will be more concerned. Sprawling, characterized by low density and automobile dependency, presents significant environmental issues regarding energy consumption and Co2 emissions. This paper examines the vertical expansion of suburbs integrated into mass transit nodes as a planning strategy for boosting density, intensification of land use, conversion of single family homes to multifamily dwellings or mixed use buildings and development of viable alternative transportation choices. It analyzes the spatial patterns of tall building transit-oriented development (TB-TOD) of suburban regions in Sydney (Australia), Toronto (Canada), and Washington D.C. (United States). The main objectives of this research seek to understand the effect of the new morphology of suburban tall, the physical dimensions of individual buildings and their arrangement at a larger scale with energy efficiency. This study aims to answer these questions: 1) why and how can the potential phenomenon of vertical expansion or high-rise development be integrated into suburb settings? 2) How can this phenomenon contribute to an overall denser development of suburbs? 3) Which spatial pattern or typologies/ sub-typologies of the TB-TOD model do have the greatest energy efficiency? It addresses these questions by focusing on 1) energy, heat energy demand (excluding cooling and lighting) related to design issues at two levels: macro, urban scale and micro, individual buildings—physical dimension, height, morphology, spatial pattern of tall buildings and their relationship with each other and transport infrastructure; 2) Examining TB-TOD to provide more evidence of how the model works regarding ridership. The findings of the research show that the TB-TOD model can be identified as the most appropriate spatial patterns of tall buildings in suburban settings. And among the TB-TOD typologies/ sub-typologies, compact tall building blocks can be the most energy efficient one. This model is associated with much lower energy demands in buildings at the neighborhood level as well as lower transport needs in an urban scale while detached suburban high rise or low rise suburban housing will have the lowest energy efficiency. The research methodology is based on quantitative study through applying the available literature and static data as well as mapping and visual documentations of urban regions such as Google Earth, Microsoft Bing Bird View and Streetview. It will examine each suburb within each city through the satellite imagery and explore the typologies/ sub-typologies which are morphologically distinct. The study quantifies heat energy efficiency of different spatial patterns through simulation via GIS software.

Keywords: energy efficiency, spatial pattern, suburb, tall building transit-oriented development (TB-TOD)

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Authors: Qi Kan, Xiaoyu Ying

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With a rapid urbanization in China, the high-density new urban-center districts have already changed the microclimate in the city. Because of the using characters of building the commercial pedestrian streets which have emerged massively making a large number of pedestrians appear in there, pedestrian comfort in the commercial streets of the new urban-center districts requires more attention. The different street spatial layout will change the wind environment in the street and then influence the pedestrian comfort. Computational fluid dynamics (CFD) models are used to study the correlation between the street aspect ratio and wind environment, under the simulation with relevant weather conditions. The results show that the wind speed in the city streets is inversely proportional to the street aspect ratio. The conclusion will provide an evaluation basis for urban planners and architects at the beginning stage of the design to effectively avoid the potential poor physical environment.

Keywords: street spatial layout, wind environment, street aspect ratio, pedestrian comfort

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Authors: B. Hekner, J. Myalski, P. Wrzesniowski

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This study presents aluminum matrix composites reinforced by glassy carbon (GC) and titanium (Ti). In the first step, the heterophase (GC+Ti), spatial form (similar to skeleton) of reinforcement was obtained via own method. The polyurethane foam (with spatial, open-cells structure) covered by suspension of Ti particles in phenolic resin was pyrolyzed. In the second step, the prepared heterogeneous foams were infiltrated by aluminium alloy. The manufactured composites are designated to industrial application, especially as a material used in tribological field. From this point of view, the glassy carbon was applied to stabilise a coefficient of friction on the required value 0.6 and reduce wear. Furthermore, the wear can be limited due to titanium phase application, which reveals high mechanical properties. Moreover, fabrication of thin titanium layer on the carbon skeleton leads to reduce contact between aluminium alloy and carbon and thus aluminium carbide phase creation. However, the main modification involves the manufacturing of reinforcement in the form of 3D, skeleton foam. This kind on reinforcement reveals a few important advantages compared to classical form of reinforcement-particles: possibility to control homogeneity of reinforcement phase in composite material; low-advanced technique of composite manufacturing- infiltration; possibility to application the reinforcement only in required places of material; strict control of phase composition; High quality of bonding between components of material. This research is founded by NCN in the UMO-2016/23/N/ST8/00994.

Keywords: metal matrix composites, MMC, glassy carbon, heterophase composites, tribological application

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Authors: Amani Ashari, Julia Omar, Arif Hashim, Shahrul Hamid

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Apolipoprotein E (APOE) gene polymorphism has influence on serum lipids which relates to cardiovascular risk. The purpose of this study was to determine the frequency distribution of APOE alleles among Malaysian Type 2 Diabetes Mellitus (DM) patients with and without coronary artery disease (CAD) and their association with serum lipid profiles. A total of 115 patients were recruited in which 78 patients had Type 2 DM without CAD and 37 patients had Type 2 DM with CAD. The APOE polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The APOE ɛ3 allele was the most common one in both groups. There was no significant association between the APOE genotypes and the CAD status in Type 2 DM using Pearson χ² test. Further analysis indicated there were no significant differences in all lipid parameters between E2, E3 and E4 subgroups in both groups. The study showed that the E4 allele carriers of Type 2 DM with CAD patients had higher LDL-C level and lower HDL-C level compared to the other allele carriers. However, analyses showed these levels were not statistically different. The study also showed that the Type 2 DM with CAD group with E2 allele had higher triglyceride (TG). In conclusion, further study with larger sample size is needed to confirm role of E4 as a marker of CAD among Type 2 DM patients in Malaysian population.

Keywords: Apolipoprotein E, diabetes mellitus, cardiovascular disease, lipids

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Authors: S. J. Sirima, C. Thirawan, R.Puntharikorn, K. Ungsumalin, J. Kaemwich

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Acinetobacter spp. is a gram negative bacterium causing the high incidence of multi-drug resistance in patients admitted to an intensive care unit. A hundred isolates of Imipenem-resistant Acinetobacter spp. isolated from patients admitted at tertiary health care center, Northeastern region, Ubon Ratchathani, Thailand, were subjected to modified Hodge test and combined disc test in order to evaluate the production of carbapenemases. The results revealed that about 35% of isolates were found to be carbapenemases producers. In addition, multiplex polymerase chain reactions were performed to detect blaOXA-like genes. It showed that 92% of isolates possess blaOXA-51-like and blaOXA-23-like genes. However, blaOXA-58-like gene was detected in only 8 isolates. No detection of blaOXA-24-like gene was observed in all isolates. In conclusion, an ability to produce carbepenemases would be an important mechanism of multi-drug resistance among clinical isolates of Acinetobacter spp. at tertiary health care center, Northeastern region, Ubon Ratchathani, Thailand. Furthermore, it was likely that the class D carbapenemases genes, blaOXA-51-like and blaOXA-23-like, might contribute to imipenem-resistance exhibiting among isolates.

Keywords: Acinetobacter spp., blaOXA-like genes, carbapenemases, tertiary health care center

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Authors: Komal Vig, Syamala Soumyakrishnan, Yadav Baral

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Bypass surgery, using the autologous vein has been one of the most effective treatments for cardiovascular diseases (CVD). More recently tissue engineering including engineered vascular grafts to synthesize blood vessels is gaining usage. Dacron and ePTFE has been employed for vascular grafts, however, these does not work well for small diameter grafts (<6 mm) due to intimal hyperplasia and thrombosis. In the present study PTFE was treated with LTP to improve the endothelialization of intimal surface of graft. Scaffolds were also modified with polyvinylpyrrolidone coated silver nanoparticles (Ag-PVP) and the antimicrobial peptides, p753 and p359. Human umbilical vein endothelial cells (HUVEC) were plated on the developed scaffolds and cell proliferation was determined by the MTT assay. Cells attachment on scaffolds was visualized by microscopy. mRNA expressions levels of different cell markers were investigated using quantitative real-time PCR (qPCR). X ray photoelectron spectroscopic confirmed the introduction of oxygenated functionalities from LTP air plasma. Microscopic and MTT assays indicated increase in cell viability in LTP treated scaffolds. Gene expression studies shows enhanced expression of cell adhesion marker Integrin- α 5 gene after LTP treatment. The KB test displayed a zone of inhibition for Ag-PVP, p753 and p359 of 19mm, 14mm, and 12mm respectively. To determine toxicity of antimicrobial agents to cells, MTT Assay was performed using HEK293 cells. MTT Assay exhibited that Ag-PVP and the peptides were non-toxic to cells at 100μg/mL and 50μg/mL, respectively. Live/dead analysis and plate count of treated bacteria exhibited bacterial inhibition on develop scaffold compared to non-treated scaffold. SEM was performed to analyze the structural changes of bacteria after treatment with antimicrobial agents. Gene expression studies were conducted on RNA from bacteria treated with Ag-PVP and peptides using qRT-PCR. Based on our initial results, more scaffolds alternatives will be developed and investigated for cell growth and vascularization studies.

Keywords: low temperature plasma, vascular graft, HUVEC cells, antimicrobial

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Authors: Saima Saleem, Zubair Abbasi, Abdul Hameed, Mansoor Ahmed Khan, Navid Rashid Qureshi, Abid Azhar

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Oral Squamous Cell Carcinoma (OSCC) is the leading cause of death in the developing countries like Pakistan. This problem aggravates because of the excessive use of available chewing products. In spite of widespread information on their use and purported legislations against their use the Pakistani markets are classical examples of selling chewable carcinogenic mutagens. Reported studies indicated that these products are rich in reactive oxygen species (ROS) and polyphenols. TP53 gene is involved in the suppression of tumor. It has been reported that somatic mutations caused by TP53 gene are the foundation of the cancer. This study aims to find the loss of TP53 functions due to mutation/polymorphism caused by genomic alteration and interaction with tobacco and its related ingredients. Total 260 tissues and blood specimens were collected from OSCC patients and compared with age and sex matched controls. Mutations in exons 2-11 of TP53 were examined by PCR-SSCP. Samples showing mobility shift were directly sequenced. Two mutations were found in exon 4 at nucleotide position 108 and 215 and one in exon 7 at nucleotide position 719 of the coding sequences in patient’s tumor samples. These results show that substitution of proline with arginine at codon 72 and serine with threonine at codon 240 of p53 protein. These polymorphic changes, found in tumor samples of OSCC, could be involved in loss of heterozygocity and apoptotic activity in the binding domain of TP53. The model of the mutated TP53 gene elaborated a nonfunctional unfolded p53 protein, suggesting an important role of these mutations in p53 protein inactivation and malfunction. This nonfunctional 3D model also indicates that exogenous tobacco related carcinogens may act as DNA-damaging agents affecting the structure of DNA. The interpretations could be helpful in establishing the pathways responsible for tumor formation in OSCC patients.

Keywords: TP53 mutation/polymorphism, OSCC, PCR-SSCP, direct DNA sequencing, 3D structure

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Authors: Rachel Hetherington, Chad Deering, Ann Maclean, Snehamoy Chatterjee

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The U.S. Geological Survey conducted a soil survey and subsequent mineralogical and geochemical analyses of over 4800 samples taken across the contiguous United States between the years 2007 and 2013. At each location, samples were taken from the top 5 cm, the A-horizon, and the C-horizon. Many studies have looked at the correlation between the mineralogical and geochemical content of soils and influencing factors such as parent lithology, climate, soil type, and age, but it seems little has been done in relation to quantifying and assessing the correlation between elements in the soil on a national scale. GIS was used for the mapping and multivariate interpolation of over 40 major and trace elements for surficial soils (0-5 cm depth). Qualitative analysis of the spatial distribution across the U.S. shows distinct patterns amongst elements both within the same periodic groups and within different periodic groups, and therefore with different behavioural characteristics. Results show the emergence of 4 main patterns of high concentration areas: vertically along the west coast, a C-shape formed through the states around Utah and northern Arizona, a V-shape through the Midwest and connecting to the Appalachians, and along the Appalachians. The Band Collection Statistics tool in GIS was used to quantitatively analyse the geochemical raster datasets and calculate a correlation matrix. Patterns emerged, which were not identified in qualitative analysis, many of which are also amongst elements with very different characteristics. Preliminary results show 41 element pairings with a strong positive correlation ( ≥ 0.75). Both qualitative and quantitative analyses on this scale could increase knowledge on the relationships between element distribution and behaviour in surficial soils of the U.S.

Keywords: correlation matrix, geochemical analyses, spatial distribution of elements, surficial soils

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Authors: Batul Kagalwala

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The nervous system is made up of complex delicate structures such as the spinal cord, peripheral nerves and the brain. These are prone to various types of injury ranging from neurodegenerative diseases to trauma leading to diseases like Parkinson's, Alzheimer's, multiple sclerosis, amyotrophic lateral sclerosis (ALS), multiple system atrophy etc. Unfortunately, because of the complicated structure of nervous system, spontaneous regeneration, repair and healing is seldom seen due to which brain damage, peripheral nerve damage and paralysis from spinal cord injury are often permanent and incapacitating. Hence, innovative and standardized approach is required for advance treatment of neurological injury. Nigella sativa (N. sativa), an annual flowering plant native to regions of southern Europe and Asia; has been suggested to have neuroprotective and anti-seizures properties. Neuroregeneration is found to occur in damaged cells when treated using extract of N. sativa. Due to its proven health benefits, lots of experiments are being conducted to extract all the benefits from the plant. The flowers are delicate and are usually pale blue and white in color with small black seeds. These seeds are the source of active components such as 30–40% fixed oils, 0.5–1.5% essential oils, pharmacologically active components containing thymoquinone (TQ), ditimoquinone (DTQ) and nigellin. In traditional medicine, this herb was identified to have healing properties and was extensively used Middle East and Far East for treating diseases such as head ache, back pain, asthma, infections, dysentery, hypertension, obesity and gastrointestinal problems. Literature studies have confirmed the extract of N. sativa seeds and TQ have inhibitory effects on inducible nitric oxide synthase and production of nitric oxide as well as anti-inflammatory and anticancer activities. Experimental investigation will be conducted to understand which ingredient of N. sativa causes neuroregeneration and roots to its healing property. An aqueous/ alcoholic extract of N. sativa will be made. Seed oil is also found to have used by researchers to prepare such extracts. For the alcoholic extracts, the seeds need to be powdered and soaked in alcohol for a period of time and the alcohol must be evaporated using rotary evaporator. For aqueous extracts, the powder must be dissolved in distilled water to obtain a pure extract. The mobile phase will be the extract while the suitable stationary phase (substance that is a good adsorbent e.g. silica gels, alumina, cellulose etc.) will be selected. Different ingredients of N. sativa will be separated using High Performance Liquid Chromatography (HPLC) for treating damaged cells. Damaged brain cells will be treated individually and in different combinations of 2 or 3 compounds for different intervals of time. The most suitable compound or a combination of compounds for the regeneration of cells will be determined using DOE methodology. Later the gene will also be determined and using Polymerase Chain Reaction (PCR) it will be replicated in a plasmid vector. This plasmid vector shall be inserted in the brain of the organism used and replicated within. The gene insertion can also be done by the gene gun method. The gene in question can be coated on a micro bullet of tungsten and bombarded in the area of interest and gene replication and coding shall be studied. Investigation on whether the gene replicates in the organism or not will be examined.

Keywords: black cumin, brain cells, damage, extract, neuroregeneration, PCR, plasmids, vectors

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Authors: Ashraf Y. Z. Khalifa, Mohammed A. Almalki

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Medicago sativa (Alfalfa) is an important forage crop legume worldwide including Saudia Arabia due to its high nutritive value. Soil bacteria exist in root or root-nodules of Medicago sativa in either symbiotic relationships or in associations. The aim of the present study was to isolate and characterize endophytic bacteria that live in association with non-nodulated roots of Medicago sativa growing in Al-Ahsaa region, Saudia Arabia. Several bacterial strains were isolated from sterilized roots of Medicago sativa. Strains were characterized using 16S rRNA gene sequences, phylogenetic relationships analysis, morphological and biochemical characteristics. The strains utilized 50% (10 out of 20) of the different chemical substrates contained in the API20E strip. In general, many strains had the ability to ferment/oxidise all the carbohydrate tested except for rhamnose and the polyol carbohydrate, inositol. Comparative sequence analysis of the 16S rDNA gene indicated that the strains were closely related to the genus Bacillus. Furthermore, the growth parameters of Vigna sinensis were enhanced upon single-inoculation of the isolated strains, compared to the uninoculated control plants. The results highlighted that the root-nodules of Medicago sativa harbor non-nodulating bacterial strains that could have significant agricultural applications.

Keywords: Medicago sativa, endophytic bacteria, Pisum sativum, Vigna sinensis

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Authors: Michael Aupetit, Mahmoud Al-ismail, Khaled Mohamed

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Cancer is a major public health problem all over the world. Breast cancer has the highest incidence rate over all cancers for women in Qatar making its study a top priority of the country. Human cancer is a dynamic disease that develops over an extended period through the accumulation of a series of genetic alterations. A Darwinian process drives the tumor cells toward higher malignancy growing the branches of a progression tree in the space of genes expression. Although it is not possible to track these genetic alterations dynamically for one patient, it is possible to reconstruct the progression tree from the aggregation of thousands of tumor cells’ genetic profiles from thousands of different patients at different stages of the disease. Analyzing the progression tree is a way to detect pivotal molecular events that drive the malignant evolution and to provide a guide for the development of cancer diagnostics, prognostics and targeted therapeutics. In this work we present the development of a Visual Analytic web platform CanVis enabling users to upload gene-expression data and analyze their progression tree. The server computes the progression tree based on state-of-the-art techniques and allows an interactive visual exploration of this tree and the gene-expression data along its branching structure helping to discover potential driver genes.

Keywords: breast cancer, progression tree, visual analytics, web platform

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Authors: Min-Shiuan Liou, Yi Shan Yang, Yang-Zhan Huang, Chia-Wen Hsieh

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A high speed growing and butanol-tolerant Clostridium acetobutylicum HOL1 mutant was screened throughout continuous adaption culture with C. acetobutylicum ATCC 824. The HOL1 strain can grow well in 10 g/L butanol contained CGM medium and can produce about 12.8 g /L butanol during 24 hrs. The C. acetobutylicum HOL1 strain was able to produce 166 mM butanol with 21 mM acetone at pH 4.8, resulting in a butanol selectivity (a molar ratio of butanol to total solvents) of 0.79, which is much higher than that (0.6) of the wild-type strain C. acetobutylicum ATCC 824. The acetate and butyrate accumulation were not observed during fermentation of the HOL1 strain. A hyper-butanol producing C. acetobutylicum HOL1 (pBPHS-3), which was created to overexpress the Bacillus psychrosaccharolyticus originated specific heat-shock protein gene, hspX, from a clostridial phosphotransbutyrylase promoter, was studied for its potential to produce a high titer of butanol. Overexpression of hspX resulted in increased final butanol yield 47% and 30% higher than those of the the ATCC824 and the HOL1 strains, respectively. The remarkable high-speed growth and butanol tolerance of strain HOL1 (pBPHS-3) demonstrates that overexpression of heterogeneous stress protein-encoding gene, hspX, could help C. acetobutylicum to effectively produce a high concentration of butanol.

Keywords: Clostridium acetobutylicum, butanol, heat-shock protein, resistance

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Authors: Yassir Abdelrazig, Ren Moses

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Roadway planning and design is a very complex process involving five key phases before a project is completed; planning, project development, final design, right-of-way, and construction. The planning phase for a new roadway transportation project is a very critical phase as it greatly affects all latter phases of the project. A location study is usually performed during the preliminary planning phase in a new roadway project. The objective of the location study is to develop alignment alternatives that are cost efficient considering land acquisition and construction costs. This paper describes a methodology to develop optimal preliminary roadway alignments utilizing spatial-data. Four optimization criteria are taken into consideration; roadway length, land cost, land slope, and environmental impacts. The basic concept of the methodology is to convert the proposed project area into a grid, which represents the search space for an optimal alignment. The aforementioned optimization criteria are represented in each of the grid’s cells. A spatial-data optimization technique is utilized to find the optimal alignment in the search space based on the four optimization criteria. Two case studies for new roadway projects in Duval County in the State of Florida are presented to illustrate the methodology. The optimization output alignments are compared to the proposed Florida Department of Transportation (FDOT) alignments. The comparison is based on right-of-way costs for the alignments. For both case studies, the right-of-way costs for the developed optimal alignments were found to be significantly lower than the FDOT alignments.

Keywords: gemoetric design, optimization, planning, roadway planning, roadway design

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Authors: Bin Wang, Yong Xu, Honggang Qu, Rongmei Liu, Zhenji Gao

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Today's mining industry is advancing gradually toward digital and visual direction. The three dimensional visualization geological modeling of mine is the digital characterization of mineral deposit, and is one of the key technology of digital mine. The three-dimensional geological modeling is a technology that combines the geological spatial information management, geological interpretation, geological spatial analysis and prediction, geostatistical analysis, entity content analysis and graphic visualization in three-dimensional environment with computer technology, and is used in geological analysis. In this paper, the three-dimensional geological modeling of an iron mine through the use of Surpac is constructed, and the weight difference of the estimation methods between distance power inverse ratio method and ordinary kriging is studied, and the ore body volume and reserves are simulated and calculated by using these two methods. Compared with the actual mine reserves, its result is relatively accurate, so it provided scientific bases for mine resource assessment, reserve calculation, mining design and so on.

Keywords: three-dimensional geological modeling, geological database, geostatistics, block model

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Authors: (Ted) Edward Holmberg, Mahdi Abdelguerfi, Elias Ioup

Abstract:

This research details a coverage measure for evaluating the effectiveness of observer node placements in a spatial bipartite network. This coverage measure can be used to optimize the configuration of stationary or mobile spatially oriented observer nodes, or a hybrid of the two, over time in order to fully utilize their capabilities. To demonstrate the practical application of this approach, we construct a SpatioTemporal Bipartite Network (STBN) using real-time crime center (RTCC) camera nodes and NOPD calls for service (CFS) event nodes from New Orleans, La (NOLA). We use the coverage measure to identify optimal placements for moving mobile RTCC camera vans to improve coverage of vulnerable areas based on temporal patterns.

Keywords: coverage measure, mobile node dynamics, Monte Carlo simulation, observer nodes, observable nodes, spatiotemporal bipartite knowledge graph, temporal spatial analysis

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Authors: Chansheng He, Lanhui Zhang, Baoqing Zhang

Abstract:

Spatial heterogeneity of landscape significantly affects watershed hydrological processes, particularly in high elevation and cold mountainous watersheds such as the inland river (terminal lake) basins in Northwest China, where the upper reach mountainous areas are the main source of streamflow for the downstream agricultural oases and desert ecosystems. Thus, it is essential to take into account spatial variations of hydrological processes in streamflow allocation at the watershed scale. This paper adapts the Distributed Large Basin Runoff Model (DLBRM) to the Heihe River Watershed, the second largest inland river with a drainage area of about 128,000 km2 in Northwest China, for understanding the transfer and partitioning mechanism among the glacier and snowmelt, surface runoff, evapotranspiration, and groundwater recharge among the upper, middle, and lower reaches in the study area. Results indicate that the upper reach Qilian Mountain area is the main source of streamflow for the middle reach agricultural oasis and downstream desert areas. Large withdrawals for agricultural irrigation in the middle reach had significantly depleted river flow for the lower reach desert ecosystems. Innovative conservation and enforcement programs need to be undertaken to ensure the successful implementation of water allocation plan of delivering 0.95 x 109 m3 of water downstream annually by the State Council in the Heihe River Watershed.

Keywords: DLBRM, Northwestern China, spatial variation, water allocation

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Authors: Danjuma Bawa

Abstract:

This paper aimed at exploring the capabilities of Location-Allocation model in complementing the strides of the existing physical planning models in the location and distribution of facilities for regional consumption. The paper was designed to provide a blueprint to the Nigerian government and other donor agencies especially the Fertilizer Distribution Initiative (FDI) by the federal government for the revitalization of the terrorism ravaged regions. Theoretical underpinnings of central place theory related to spatial distribution, interrelationships, and threshold prerequisites were reviewed. The study showcased how Location-Allocation Model (L-AM) alongside Central Place Theory (CPT) was applied in Geographic Information System (GIS) environment to; map and analyze the spatial distribution of settlements; exploit their physical and economic interrelationships, and to explore their hierarchical and opportunistic influences. The study was purely spatial qualitative research which largely used secondary data such as; spatial location and distribution of settlements, population figures of settlements, network of roads linking them and other landform features. These were sourced from government ministries and open source consortium. GIS was used as a tool for processing and analyzing such spatial features within the dictum of CPT and L-AM to produce a comprehensive spatial digital plan for equitable and judicious location and distribution of fertilizer deports in the study area in an optimal way. Population threshold was used as yardstick for selecting suitable settlements that could stand as service centers to other hinterlands; this was accomplished using the query syntax in ArcMapTM. ArcGISTM’ network analyst was used in conducting location-allocation analysis for apportioning of groups of settlements around such service centers within a given threshold distance. Most of the techniques and models ever used by utility planners have been centered on straight distance to settlements using Euclidean distances. Such models neglect impedance cutoffs and the routing capabilities of networks. CPT and L-AM take into consideration both the influential characteristics of settlements and their routing connectivity. The study was undertaken in two terrorism ravaged Local Government Areas of Adamawa state. Four (4) existing depots in the study area were identified. 20 more depots in 20 villages were proposed using suitability analysis. Out of the 300 settlements mapped in the study area about 280 of such settlements where optimally grouped and allocated to the selected service centers respectfully within 2km impedance cutoff. This study complements the giant strides by the federal government of Nigeria by providing a blueprint for ensuring proper distribution of these public goods in the spirit of bringing succor to these terrorism ravaged populace. This will ardently at the same time help in boosting agricultural activities thereby lowering food shortage and raising per capita income as espoused by the government.

Keywords: central place theory, GIS, location-allocation, network analysis, urban and regional planning, welfare economics

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Authors: Vinay C. Doranalu, Amba Shetty

Abstract:

In recent days due to climate change, there is a large variation in spatial distribution of daily rainfall within a small region. Rainfall is one of the main end climatic variables which affect spatio-temporal patterns of water availability. The real task postured by the change in climate is identification, estimation and understanding the uncertainty of rainfall. This study intended to analyze the spatial variations and temporal trends of daily precipitation using high resolution (0.25º x 0.25º) gridded data of Indian Meteorological Department (IMD). For the study, 38 grid points were selected in the study area and analyzed for daily precipitation time series (113 years) over the period 1901-2013. Grid points were divided into two zones based on the elevation and situated location of grid points: Low Land (exposed to sea and low elevated area/ coastal region) and High Land (Interior from sea and high elevated area/western Ghats). Time series were applied to examine the spatial analysis and temporal trends in each grid points by non-parametric Mann-Kendall test and Theil-Sen estimator to perceive the nature of trend and magnitude of slope in trend of rainfall. Pettit-Mann-Whitney test is applied to detect the most probable change point in trends of the time period. Results have revealed remarkable monotonic trend in each grid for daily precipitation of the time series. In general, by the regional cluster analysis found that increasing precipitation trend in shoreline region and decreasing trend in Western Ghats from recent years. Spatial distribution of rainfall can be partly explained by heterogeneity in temporal trends of rainfall by change point analysis. The Mann-Kendall test shows significant variation as weaker rainfall towards the rainfall distribution over eastern parts of the Western Ghats region of Karnataka.

Keywords: change point analysis, coastal region India, gridded rainfall data, non-parametric

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Authors: Roudabeh Vakil Monfared, Farhad Mashayekhi

Abstract:

Breast cancer is the most common malignancy type among women with about 1 million new cases each year. The immune system plays an important role in the breast cancer development. OX40L (also known as TNFSF4), a membrane protein, which is a member of the tumor necrosis factor super family binds to its receptor OX40 and this co-stimulation has a crucial role in T-cell proliferation, survival and cytokine release. Due to the importance of the T-cells in anti-tumor activities of OX40L we studied the association of rs3850641 (T→C) polymorphism of OX40L gene with breast cancer. The study included 123 women with breast cancer and 126 healthy volunteers with no signs of cancer. Genomic DNA was extracted from blood leucocytes. Genotype and allele frequencies were determined in patients and control cases with the method of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and the analysis was performed by Med Calc. The prevalence of genotype frequencies of TT, CT and CC were 60.9%, 30.08% and 8.9 % in patients with breast cancer and 74.6 %, 18.25 % and 7.14 % in healthy volunteers while the T and C allelic frequency was 76.01% and 23.98 % in patients and 83.73% and 16.26% in healthy controls. Respectively Statistical analysis has shown no significant difference from the comparison of either genotype (P=0.06). According to these results, the rs3850641 SNP has no association with the susceptibility of breast cancer in a population in northern Iran. However, further studies in larger populations including other genetic and environmental factors are required to achieve conclusion.

Keywords: OX40L, gene, polymorphism, breast cancer

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Authors: Sergey Ermolin, Olga Ermolin

Abstract:

A Deep Convolution Neural Network with Triplet Loss is used to identify duplicate images in real-estate advertisements in the presence of image artifacts such as watermarking, cropping, hue/brightness adjustment, and others. The effects of batch normalization, spatial dropout, and various convergence methodologies on the resulting detection accuracy are discussed. For comparative Return-on-Investment study (per industry request), end-2-end performance is benchmarked on both Nvidia Titan GPUs and Intel’s Xeon CPUs. A new real-estate dataset from San Francisco Bay Area is used for this work. Sufficient duplicate detection accuracy is achieved to supplement other database-grounded methods of duplicate removal. The implemented method is used in a Proof-of-Concept project in the real-estate industry.

Keywords: visual recognition, convolutional neural networks, triplet loss, spatial batch normalization with dropout, duplicate removal, advertisement technologies, performance benchmarking

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

Abstract:

We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae

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