Search results for: spatial differentiation pattern

Authors: Atsuko Okazaki, Jurg Ott

Abstract:

Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

Procedia PDF Downloads 115

Authors: Jaishree Ranganathan, MuthuPriya Shanmugakani Velsamy, Shamika Kulkarni, Angelina Tzacheva

Abstract:

Emotions play an important role in everyday life. An-alyzing these emotions or feelings from social media platforms like Twitter, Facebook, blogs, and forums based on user comments and reviews plays an important role in various factors. Some of them include brand monitoring, marketing strategies, reputation, and competitor analysis. The opinions or sentiments mined from such data helps understand the current state of the user. It does not directly provide intuitive insights on what actions to be taken to benefit the end user or business. Actionable Pattern Mining method provides suggestions or actionable recommendations on what changes or actions need to be taken in order to benefit the end user. In this paper, we propose automatic classification of emotions in Twitter data using Recurrent Neural Network - Gated Recurrent Unit. We achieve training accuracy of 87.58% and validation accuracy of 86.16%. Also, we extract action rules with respect to the user emotion that helps to provide actionable suggestion.

Keywords: emotion mining, twitter, recurrent neural network, gated recurrent unit, actionable pattern mining

Procedia PDF Downloads 159

Authors: Nguyen Tien Thanh, Günter Meon

Abstract:

Precipitation plays a key role in water cycle, defining the local climatic conditions and in ecosystem. It is also an important input parameter for water resources management and hydrologic models. With spatial continuous data, a certainty of discharge predictions or other environmental factors is unquestionably better than without. This is, however, not always willingly available to acquire for a small basin, especially for coastal region in Vietnam due to a low network of meteorological stations (30 stations) on long coast of 3260 km2. Furthermore, available gridded precipitation datasets are not fine enough when applying to hydrologic models. Under conditions of global warming, an application of spatial interpolation methods is a crucial for the climate change impact studies to obtain the spatial continuous data. In recent research projects, although some methods can perform better than others do, no methods draw the best results for all cases. The objective of this paper therefore, is to investigate different spatial interpolation methods for daily precipitation over a small basin (approximately 400 km2) located in coastal region, Southern Vietnam and find out the most efficient interpolation method on this catchment. The five different interpolation methods consisting of cressman, ordinary kriging, regression kriging, dual kriging and inverse distance weighting have been applied to identify the best method for the area of study on the spatio-temporal scale (daily, 10 km x 10 km). A 30-year precipitation database was created and merged into available gridded datasets. Finally, observed changes in constructed precipitation were performed. The results demonstrate that the method of ordinary kriging interpolation is an effective approach to analyze the daily precipitation. The mixed trends of increasing and decreasing monthly, seasonal and annual precipitation have documented at significant levels.

Keywords: interpolation, precipitation, trend, vietnam

Procedia PDF Downloads 273

Authors: Shaojian Li

Abstract:

The traditional Chinese patterns, as an integral part of Chinese culture, possess unique values in history, culture, and art. However, with the passage of time and societal changes, many of these traditional patterns are at risk of being lost, damaged, or forgotten. To undertake the digital preservation and protection of these traditional patterns, this paper will collect and organize images of traditional Chinese patterns. It will provide exhaustive and comprehensive semantic annotations, creating a resource library of traditional Chinese pattern images. This will support the digital preservation and application of traditional Chinese patterns.

Keywords: digitization of cultural heritage, traditional Chinese patterns, digital humanities, database construction

Procedia PDF Downloads 55

Authors: Katalin Bodor, Zsolt Bodor, Robert Szep

Abstract:

The particulate matter (PM) smaller than 2.5 μm are less studied due to the limited availability of PM₂.₅, and less information is available on the health effects attributable to PM₁₀ in Central-Eastern Europe. The objective of the current study was to assess the human health risk and characterize the spatial and temporal variation of PM₂.₅ and PM₁₀ in eight Romanian regions between the 2009-2018 and. The PM concentrations showed high variability over time and spatial distribution. The highest concentration was detected in the Bucharest region in the winter period, and the lowest was detected in West. The relative risk caused by the PM₁₀ for all-cause mortality varied between 1.017 (B) and 1.025 (W), with an average 1.020. The results demonstrate a positive relative risk of cardiopulmonary and lung cancer disease due to exposure to PM₂.₅ on the national average 1.26 ( ± 0.023) and 1.42 ( ± 0.037), respectively.

Keywords: PM₂.₅, PM₁₀, relative risk, health effect

Procedia PDF Downloads 157

Authors: Rama Umesh Pandey, Jyoti Yadav

Abstract:

Flooding is one of the waterborne disasters that causes extensive destruction in urban areas. Developing countries are at a higher risk of such damage and more than half of the global flooding events take place in Asian countries including India. Urban flooding is more of a human-induced disaster rather than natural. This is highly influenced by the anthropogenic factors, besides metrological and hydrological causes. Unplanned urbanization and poor management of cities enhance the impact manifold and cause huge loss of life and property in urban areas. It is an irony that urban areas have been facing water scarcity in summers and flooding during monsoon. This paper is an attempt to highlight the factors responsible for flooding in a city especially from an urban planning perspective and to suggest mitigating measures through spatial planning interventions. Analysis has been done in two stages; first is to assess the impacts of previous flooding events and second to analyze the factors responsible for flooding at macro and micro level in cities. Bhopal, a city in Central India having nearly two million population, has been selected for the study. The city has been experiencing flooding during heavy rains in monsoon. The factors responsible for urban flooding were identified through literature review as well as various case studies from different cities across the world and India. The factors thus identified were analyzed for both macro and micro level influences. For macro level, the previous flooding events that have caused huge destructions were analyzed and the most affected areas in Bhopal city were identified. Since the identified area was falling within the catchment of a drain so the catchment area was delineated for the study. The factors analyzed were: rainfall pattern to calculate the return period using Weibull’s formula; imperviousness through mapping in ArcGIS; runoff discharge by using Rational method. The catchment was divided into micro watersheds and the micro watershed having maximum impervious surfaces was selected to analyze the coverage and effect of physical infrastructure such as: storm water management; sewerage system; solid waste management practices. The area was further analyzed to assess the extent of violation of ‘building byelaws’ and ‘development control regulations’ and encroachment over the natural water streams. Through analysis, the study has revealed that the main issues have been: lack of sewerage system; inadequate storm water drains; inefficient solid waste management in the study area; violation of building byelaws through extending building structures ether on to the drain or on the road; encroachments by slum dwellers along or on to the drain reducing the width and capacity of the drain. Other factors include faulty culvert’s design resulting in back water effect. Roads are at higher level than the plinth of houses which creates submersion of their ground floors. The study recommends spatial planning interventions for mitigating urban flooding and strategies for management of excess rain water during monsoon season. Recommendations have also been made for efficient land use management to mitigate water logging in areas vulnerable to flooding.

Keywords: mitigating strategies, spatial planning interventions, urban flooding, violation of development control regulations

Procedia PDF Downloads 324

Authors: Yaner Yan, Ning Li, Yajun Qiao, Shuqing An

Abstract:

Although most studies have focused on assessing and mapping terrestrial ecosystem services, there is still a knowledge gap on coastal ecosystem services and an urgent need to assess them. Lau (2013) clearly defined five types of costal ecosystem services: carbon sequestration, shoreline protection, fish nursery, biodiversity, and water quality. While high-resolution remote sensing can provide the more direct, spatially estimates of biophysical parameters, such as species distribution relating to biodiversity service, and Fluorescence information derived from remote sensing direct relate to photosynthesis, availing in estimation of carbon sequestration and the response to environmental changes in coastal wetland. Here, we review the capabilities of high-resolution and fluorescence remote sesing for describing biodiversity, vegetation condition, ecological processes and highlight how these prodicts may contribute to costal ecosystem service assessment. In so doing, we anticipate rapid progress to combine the high-resolution and fluorescence remote sesing to estimate the spatial pattern of costal ecosystem services.

Keywords: ecosystem services, high resolution, remote sensing, chlorophyll fluorescence

Procedia PDF Downloads 494

Authors: Bin Liu, Weijie Liu, Bin Sun, Yihui Luo

Abstract:

In order to solve the problem of lower spatial resolution and block effect in the fusion method based on separable wavelet transform in the resulting fusion image, a new sampling mode based on multi-resolution analysis of two-channel non separable wavelet transform, whose dilation matrix is [1,1;1,-1], is presented and a multispectral image fusion method based on this kind of sampling mode is proposed. Filter banks related to this kind of wavelet are constructed, and multiresolution decomposition of the intensity of the MS and panchromatic image are performed in the sampled mode using the constructed filter bank. The low- and high-frequency coefficients are fused by different fusion rules. The experiment results show that this method has good visual effect. The fusion performance has been noted to outperform the IHS fusion method, as well as, the fusion methods based on DWT, IHS-DWT, IHS-Contourlet transform, and IHS-Curvelet transform in preserving both spectral quality and high spatial resolution information. Furthermore, when compared with the fusion method based on nonsubsampled two-channel non separable wavelet, the proposed method has been observed to have higher spatial resolution and good global spectral information.

Keywords: image fusion, two-channel sampled nonseparable wavelets, multispectral image, panchromatic image

Procedia PDF Downloads 435

Authors: Maryam Ghavam Sadri, Kimia Moiniafshari

Abstract:

Objectives: The prevalence of Autism in the world has taken on a growing trend. Autism is a neuro-developmental disorder that is identified at the age of three. Studies have been shown that nutritional management can control nutritional deficiencies in Autism. This review study aimed to assess the role of nutritional management strategies for Autism in children has been made. Methods: This review study was accomplished by using the keywords related to the topic, 68 articles were found (2000-2015) and finally 15 articles with criteria such as including dietary pattern, nutritional deficiencies and Autism controlling were selected. Results: The studies showed that intake of vitamins D, E, and calcium because of restricted diet (casein and gluten free) in autistic children is less than typically developing children (TYP) (p value ≤ 0.001) and as a result of restrictions on the consumption of fresh fruits and vegetables, vitamin C and magnesium intake is less than TYP children (p value ≤ 0.001). Autistic children also get omega-3 less than TYP children. Studies have shown that food sources rich in omega-3 can improve behavioral indicators, especially in reducing hyperactivity (95% CI = -2.2 - 5.2). Zinc deficiency in these children leads to a high serum level of mercury, lead and cadmium. As a result of the repetitive dietary pattern, Sodium intake in autistic children is more than TYP children (p value < 0.001).Because of low food variety in autistic children, healthy eating index (HEI) is less than TYP children (p value = 0.008).Food selectivity in Autism due to repetitive and restricted dietary pattern and nutritional deficiencies. Conclusion: Because of restricted (casein and gluten free) and repetitive dietary pattern, the intake of some micronutrients are denied in autistic children. The nutritional strategy programs appear to help controlling of Autism.

Keywords: autism, food selectivity, nutrient intake, nutritional strategies

Procedia PDF Downloads 422

Authors: Sidra Naeem, Ayesha Naeem, Sahar Rahim, Nadia Nawaz Qadri

Abstract:

Citrus greening is a bacterial disease that causes considerable damage to citrus fruits worldwide. Efficient method for this disease detection must be carried out to minimize the production loss. This paper presents a pattern recognition system that comprises three stages for the detection of citrus greening from Orange leaves: segmentation, feature extraction and classification. Image segmentation is accomplished by adaptive thresholding. The feature extraction stage comprises of three visual descriptors i.e. shape, color and texture. From shape feature we have used asymmetry index, from color feature we have used histogram of Cb component from YCbCr domain and from texture feature we have used local binary pattern. Classification was done using support vector machines and k nearest neighbors. The best performances of the system is Accuracy = 88.02% and AUROC = 90.1% was achieved by automatic segmented images. Our experiments validate that: (1). Segmentation is an imperative preprocessing step for computer assisted diagnosis of citrus greening, and (2). The combination of shape, color and texture features form a complementary set towards the identification of citrus greening disease.

Keywords: citrus greening, pattern recognition, feature extraction, classification

Procedia PDF Downloads 176

Authors: Beate Englich, Linda Schlittenbauer, Christiane Pfeifer, Isabel Kratochvil, Michael Borte, Gabriele I. Stangl, Martin von Bergen, Thorsten Reemtsma, Irina Lehmann, Kristin M. Junge

Abstract:

The worldwide production of endocrine disrupting compounds (EDC) has risen dramatically over the last decades, as so has the prevalence for obesity. Many EDCs are believed to contribute to this obesity epidemic, by enhancing adipogenesis or disrupting relevant metabolism. This effect is most tremendous in the early prenatal period when priming effects find a highly vulnerable time window. Therefore, we investigate the impact of parabens on childhood overweight development and adipogenesis in general. Parabens are ester of 4-hydroxy-benzoic acid and part of many cosmetic products or food packing. Therefore, ubiquitous exposure can be found in the westernized world, with exposure already starting during the sensitive prenatal period. We assessed maternal cosmetic product consumption, prenatal paraben exposure and infant BMI z-scores in the prospective German LINA cohort. In detail, maternal urinary concentrations (34 weeks of gestation) of methyl paraben (MeP), ethyl paraben (EtP), n-propyl paraben (PrP) and n-butyl paraben (BuP) were quantified using UPLC-MS/MS. Body weight and height of their children was assessed during annual clinical visits. Further, we investigated the direct influence of those parabens on adipogenesis in-vitro using a human mesenchymal stem cell (MSC) differentiation assay to mimic a prenatal exposure scenario. MSC were exposed to 0.1 – 50 µM paraben during the entire differentiation period. Differentiation outcome was monitored by impedance spectrometry, real-time PCR and triglyceride staining. We found that maternal cosmetic product consumption was highly correlated with urinary paraben concentrations at pregnancy. Further, prenatal paraben exposure was linked to higher BMI Z-scores in children. Our in-vitro analysis revealed that especially the long chained paraben BuP stimulates adipogenesis by increasing the expression of adipocyte specific genes (PPARγ, ADIPOQ, LPL, etc.) and triglyceride storage. Moreover, we found that adiponectin secretion is increased whereas leptin secretion is reduced under BuP exposure in-vitro. Further mechanistic analysis for receptor binding and activation of PPARγ and other key players in adipogenesis are currently in process. We conclude that maternal cosmetic product consumption is linked to prenatal paraben exposure of children and contributes to the development of infant overweight development by triggering key pathways of adipogenesis.

Keywords: adipogenesis, endocrine disruptors, paraben, prenatal exposure

Procedia PDF Downloads 268

Authors: Rafia S. Al-lamki, Jun Wang, Simon Pacey, Jordan Pober, John R. Bradley

Abstract:

Tumor necrosis factor alpha (TNF), signaling through TNFR2, may act an autocrine growth factor for renal tubular epithelial cells. Clear cell renal carcinomas (ccRCC) contain cancer stem cells (CSCs) that give rise to progeny which form the bulk of the tumor. CSCs are rarely in cell cycle and, as non-proliferating cells, resist most chemotherapeutic agents. Thus, recurrence after chemotherapy may result from the survival of CSCs. Therapeutic targeting of both CSCs and the more differentiated bulk tumor populations may provide a more effective strategy for treatment of RCC. In this study, we hypothesized that TNFR2 signaling will induce CSCs in ccRCC to enter cell cycle so that treatment with ligands that engage TNFR2 will render CSCs susceptible to chemotherapy. To test this hypothesis, we have utilized wild-type TNF (wtTNF) or specific muteins selective for TNFR1 (R1TNF) or TNFR2 (R2TNF) to treat either short-term organ cultures of ccRCC and adjacent normal kidney (NK) tissue or cultures of CD133+ cells isolated from ccRCC and adjacent NK, hereafter referred to as stem cell-like cells (SCLCs). The effect of cyclophosphamide (CP), currently an effective anticancer agent, was tested on CD133+SCLCs from ccRCC and NK before and after R2TNF treatment. Responses to TNF were assessed by flow cytometry (FACS), immunofluorescence, and quantitative real-time PCR, TUNEL, and cell viability assays. Cytotoxic effect of CP was analyzed by Annexin V and propidium iodide staining with FACS. In addition, we assessed the effect of TNF on isolated SCLCs differentiation using a three-dimensional (3D) culture system. Clinical samples of ccRCC contain a greater number SCLCs compared to NK and the number of SCSC increases with higher tumor grade. Isolated SCLCs show expression of stemness markers (oct4, Nanog, Sox2, Lin28) but not differentiation markers (cytokeratin, CD31, CD45, and EpCAM). In ccRCC organ cultures, wtTNF and R2TNF increase CD133 and TNFR2 expression and promote cell cycle entry whereas wtTNF and R1TNF increase TNFR1 expression and promote cell death of SCLCs. Similar findings are observed in SCLCs isolated from NK but the effect was greater in SCLCs isolated from ccRCC. Application of CP distinctly triggered apoptotic and necrotic cell death in SLCSs pre-treatment with R2TNF as compared to CP treatment alone, with SCLCs from ccRCC more sensitive to CP compared to SLCS from NK. Furthermore, TNF promotes differentiation of SCLCs to an epithelial phenotype in 3D cultures, confirmed by cytokeratin expression and loss of stemness markers Nanog and Sox2. The differentiated cells show positive expression of TNF and TNFR2. These findings provide evidence that selective engagement of TNFR2 drive CSCs to cell proliferation/differentiation, and targeting of cycling cells with TNFR2 agonist in combination with anti-cancer agents may be a potential therapy for RCC.

Keywords: cancer stem cells, ccRCC, cell cycle, cell death, TNF, TNFR1, TNFR2, CD133

Procedia PDF Downloads 259

Authors: Mohammad Tahsin Karimi Nezhad, Zaynab Shadbahr, Ali Gholami

Abstract:

In recent years many attempts have been made to assess groundwater contamination by nitrates worldwide. The assessment of spatial and temporal variations of physico-chemical parameters of water is necessary to mange water quality. The objectives of the study were to evaluate spatial variability and temporal changes of hydrochemical factors by water sampling from 24 wells in the Shoush City suburb. The analysis was conducted for the whole area and for different land use and geological classes. In addition, nitrate concentration variability with descriptive parameters such as sampling depth, dissolved oxygen, and on ground nitrogen loadings was also investigated The results showed that nitrate concentrations did not exceed the standard limit (50 mg/l). EC of water samples, ranged from 900 to 1200 µs/cm, TDS from 775 to 830 mg/l and pH from 5.6 to 9.

Keywords: groundwater, GIS, water quality, Iran

Procedia PDF Downloads 426

Authors: Oladejo S. O, Tomori W. B, Adebayo A. O

Abstract:

The main objective of this research is to identify the geochemical and mineralogical characteristics potential of unexplored tailings around the gold deposit region using spatial statistics and map modeling. Some physicochemical parameters such as pH, redox potential, electrical conductivity, cation exchange capacity, total organic carbon, total organic matter, residual humidity, Cation exchange capacity, and particle size were determined from both the mine drains and tailing samples using standard methods. The physicochemical parameters of tailings ranges obtained were pH (6.0 – 7.3), Eh (−16 - 95 Mev), EC (49 - 156 µS/cm), RH (0.20-2.60%), CEC (3.64-6.45 cmol/kg), TOC (3.57-18.62%), TOM (6.15-22.93%). The geochemical oxide composition were identified using Proton Induced X-ray emission and the results indicated that SiO2>Al2O3>Fe2O3>TiO2>K2O>MgO>CaO>Na2O> P2O5>MnO>Cr2O3>SrO>K2O>P2O5. The major mineralogical components in the tailing samples were determined by quantitative X-ray diffraction techniques using the Rietveld method. Geostatistical relationships among the known points were determined using ArcGIS 10.2 software to interpolate mineral concentration with respect to the study area. The Rietveld method gave a general Quartz value of 73.73-92.76%, IImenite as 0.38-4.77%, Kaolinite group as 3.19-20.83%, Muscovite as 0.77-11.70% with a trace of other minerals. The high percentage of quartz is an indication of a sandy environment with a loose binding site.

Keywords: tailings, geochemical, mineralogy, spatial

Procedia PDF Downloads 61

Authors: Abdul Soofi, Katherine Wolf, Egon Ranghini, Gregory Dressler

Abstract:

Obesity and its associated complications, such as insulin resistance and non-alcoholic fatty liver disease, are reaching epidemic proportions. In mice, the TGF-β superfamily is implicated in the regulation of white and brown adipose tissues differentiation. The Kielin/Chordin-like Protein (KCP) is a secreted regulator of the TGF-β superfamily pathways that can inhibit both TGF-β and Activin signals while enhancing the Bone Morphogenetic protein (BMP) signaling. However, the effects of KCP on metabolism and obesity have not been studied in animal models. Thus, we examined the effects of KCP loss or gain of function in mice that were maintained on either a regular or a high fat diet. Loss of KCP sensitized mice to obesity and associated complications such as hepatic steatosis and glucose intolerance. In contrast, transgenic mice that expressed KCP in the kidney, liver and adipose tissues were resistant to developing high fat diet induced obesity and had significantly reduced white adipose tissue. KCP over-expression was able to shift the pattern of Smad signaling in vivo, to increase the levels of P-Smad1 and decrease P-Smad3, resulting in resistance to high fat diet induced hepatic steatosis and glucose intolerance. In aging mice, loss of KCP promoted liver pathology even when mice were fed a normal diet. The data demonstrate that shifting the TGF-β superfamily signaling with a secreted inhibitor or enhancer can alter the physiology of adipose tissue to reduce obesity and can inhibit the initiation and progression of hepatic steatosis to significantly reduce the effects of high fat diet induced metabolic disease.

Keywords: adipose tissue, KCP, obesity, TGF-β, BMP, hepatic steatosis, metabolic syndrome

Procedia PDF Downloads 348

Authors: Almudena Espin Perez, Tyler Risom, Carl Pelz, Isabel English, Robert M. Angelo, Rosalie Sears, Andrew J. Gentles

Abstract:

Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly malignancies. The role of the tumor microenvironment (TME) is gaining significant attention in cancer research. Despite ongoing efforts, the nature of the interactions between tumors, immune cells, and stromal cells remains poorly understood. The cell-intrinsic properties that govern cell lineage plasticity in PDAC and extrinsic influences of immune populations require technically challenging approaches due to the inherently heterogeneous nature of PDAC. Understanding the cell lineage plasticity of PDAC will improve the development of novel strategies that could be translated to the clinic. Members of the team have demonstrated that the acquisition of ductal to neuroendocrine lineage plasticity in PDAC confers therapeutic resistance and is a biomarker of poor outcomes in patients. Our approach combines computational methods for deconvolving bulk transcriptomic cancer data using CIBERSORTx and high-throughput single-cell imaging using Multiplexed Ion Beam Imaging (MIBI) to study lineage plasticity in PDAC and its relationship to the infiltrating immune system. The CIBERSORTx algorithm uses signature matrices from immune cells and stroma from sorted and single-cell data in order to 1) infer the fractions of different immune cell types and stromal cells in bulked gene expression data and 2) impute a representative transcriptome profile for each cell type. We studied a unique set of 300 genomically well-characterized primary PDAC samples with rich clinical annotation. We deconvolved the PDAC transcriptome profiles using CIBERSORTx, leveraging publicly available single-cell RNA-seq data from normal pancreatic tissue and PDAC to estimate cell type proportions in PDAC, and digitally reconstruct cell-specific transcriptional profiles from our study dataset. We built signature matrices and optimized by simulations and comparison to ground truth data. We identified cell-type-specific transcriptional programs that contribute to cancer cell lineage plasticity, especially in the ductal compartment. We also studied cell differentiation hierarchies using CytoTRACE and predict cell lineage trajectories for acinar and ductal cells that we believe are pinpointing relevant information on PDAC progression. Collaborators (Angelo lab, Stanford University) has led the development of the Multiplexed Ion Beam Imaging (MIBI) platform for spatial proteomics. We will use in the very near future MIBI from tissue microarray of 40 PDAC samples to understand the spatial relationship between cancer cell lineage plasticity and stromal cells focused on infiltrating immune cells, using the relevant markers of PDAC plasticity identified from the RNA-seq analysis.

Keywords: deconvolution, imaging, microenvironment, PDAC

Procedia PDF Downloads 119

Authors: Kamal, Adil Ahmad

Abstract:

Earthquakes are among the most versatile natural and dynamic processes, and hence a fractal model is considered to be the best representative of the same. We present a novel method to process and analyse information hidden in earthquake sequences using Fractal Dimensions and Iterative Function Systems (IFS). Spatial and temporal variations in the fractal dimensions of seismicity observed around the Indian peninsula in last 30 years are studied. This was used as a possible precursor before large earthquakes in the region. IFS images for observed seismicity in the Himalayan belt were also obtained. We scan the whole data set and coarse grain of a selected window to reduce it to four bins. A critical analysis of four-cornered chaos-game clearly shows that the spatial variation in earthquake occurrences in Himalayan range is not random. Two subzones of Himalaya have a tendency to follow each other in time.

Keywords: earthquakes, fractals, Himalaya, iterated function systems

Procedia PDF Downloads 296

Authors: Ali Rabiee, Hessam Ghasemnejad

Abstract:

Extensive experimental investigation on the effect of stitching pattern on tubular composite structures was conducted. The effect of stitching reinforcement through thickness on using glass flux yarn on energy absorption of fiber-reinforced polymer (FRP) was investigated under high speed loading conditions at axial loading. Keeping the mass of the structure at 125 grams and applying different pattern of stitching at various locations in theory enables better energy absorption, and also enables the control over the behaviour of force-crush distance curve. The study consists of simple non-stitch absorber comparison with single and multi-location stitching behaviour and its effect on energy absorption capabilities. The locations of reinforcements are 10 mm, 20 mm, 30 mm, 10-20 mm, 10-30 mm, 20-30 mm, 10-20-30 mm and 10-15-20-25-30-35 mm from the top of the specimen. The effect of through the thickness reinforcements has shown increase in energy absorption capabilities and crushing load. The significance of this is that as the stitching locations are closer, the crushing load increases and consequently energy absorption capabilities are also increased. The implementation of this idea would improve the mean force by applying stitching and controlling the behaviour of force-crush distance curve.

Keywords: through-thickness stitching, 3D enforcement​, energy absorption, tubular composite structures

Procedia PDF Downloads 259

Authors: Seyed Mohammad Ali Zahedi

Abstract:

This field experiment was conducted in Isfahan in 2011 in order to study the effect of plant density and planting pattern on growth, yield and quality of silage corn (SC 704) using a randomized complete block design with split plot layout and four replications. The main plot consisted of three planting patterns (60 and 75 cm single planting row and 75 cm double planting row referred to as 60S, 75S and 75T, respectively). The subplots consisted of four levels of plant densities (65000, 80000, 95000 and 110000 plants per hectare). Each subplot consisted of 7 rows, each with 10m length. Vegetative and reproductive characteristics of plants at silking and hard dough stages (when the plants were harvested for silage) were evaluated. Results of variance analysis showed that the effects of planting pattern and plant density were significant on leaf area per plant, leaf area index (at silking), plant height, stem diameter, dry weights of leaf, stem and ear in silking and harvest stages and on fresh and dry yield, dry matter percentage and crude protein percentage at harvest. There was no planting pattern × plant density interaction for these parameters. As row space increased from 60 cm with single planting to 75 cm with single planting, leaf area index and plant height increased, but leaf area per plant, stem diameter, dry weight of leaf, stem and ear, dry matter percentage, dry matter yield and crude protein percentage decreased. Dry matter yield reduced from 24.9 to 18.5 t/ha and crude protein percentage decreased from 6.11 to 5.60 percent. When the plant density increased from 65000 to 110000 plant per hectare, leaf area index, plant height, dry weight of leaf, stem and ear and dry matter yield increased from 19.2 to 23.3 t/ha, whereas leaf area per plant, stem diameter, dry matter percentage and crude protein percentage decreased from 6.30 to 5.25. The best results were obtained with 60 cm row distance with single planting and 110000 plants per hectare.

Keywords: silage corn, plant density, planting pattern, yield

Procedia PDF Downloads 332

Authors: Xudong Guan, Ainong Li, Gaohuan Liu, Chong Huang, Wei Zhao

Abstract:

Due to the low spatial resolution of MODIS data, the accuracy of small-area plaque extraction with a high degree of landscape fragmentation is greatly limited. To this end, the study combines Landsat data with higher spatial resolution and MODIS data with higher temporal resolution for decision-level fusion. Considering the importance of the land heterogeneity factor in the fusion process, it is superimposed with the weighting factor, which is to linearly weight the Landsat classification result and the MOIDS classification result. Three levels were used to complete the process of data fusion, that is the pixel of MODIS data, the pixel of Landsat data, and objects level that connect between these two levels. The multilevel decision fusion scheme was tested in two sites of the lower Mekong basin. We put forth a comparison test, and it was proved that the classification accuracy was improved compared with the single data source classification results in terms of the overall accuracy. The method was also compared with the two-level combination results and a weighted sum decision rule-based approach. The decision fusion scheme is extensible to other multi-resolution data decision fusion applications.

Keywords: image classification, decision fusion, multi-temporal, remote sensing

Procedia PDF Downloads 115

Authors: Arif Ali, Divya Raj Sapkota

Abstract:

In this paper, we explain gravitational attraction as the consequence of the dynamics of four-dimensional bodies and the consequent distortion of space. This approach provides an alternative direction to understand various physical phenomena based on the existence of the fourth spatial dimension. For this interpretation, we formulate the acceleration due to gravity and orbital velocity based on the accelerating expansion of three-dimensional symmetric bodies. It is also shown how distortion in space caused by the dynamics of four-dimensional bodies counterbalances the effect of expansion. We find that the motion of four-dimensional bodies through four-dimensional space leads to gravitational attraction, and the expansion of bodies leads to surface gravity. Thus, dynamics in the fourth spatial dimension provide an alternative explanation to gravity.

Keywords: dimensions, four, gravity, voluceleration

Procedia PDF Downloads 91

Authors: Ruan Yi-Chen, Li Wang-Ming, Fang Yuan

Abstract:

With the rapid growth of urbanization in China in recent years, public services are in short supply because of expanding population and limitation of financial support, which makes delicate configuration of public service facilities to become a trend in urban planning. Besides, the facility configuration standard implemented in China is equal to the whole the urban area without considering internal differences in it. Therefore, this article focuses on population Spatial disparities analysis in order to optimize facility configuration in communities of main city district. The used data, including population of 93 communities during 2010 to 2015, comes from GongShu district, Hangzhou city, PRC. Through the analysis of population data, especially the age structure of those communities, the communities finally divided into 3 types. Obviously, urban public service facilities allocation situation directly affect the quality of residents common lives, which turns out that deferent kinds of communities with deferent groups of citizens will have divergences in facility demanding. So in the end of the article, strategies of facility configuration will be proposed based on the population analysis in order to optimize the quantity and location of facilities with delicacy.

Keywords: delicacy, facility configuration, population spatial disparities, urban area

Procedia PDF Downloads 379

Authors: Sangeeta Dhamdhere, G. V. P. Rao

Abstract:

Adolescent students need more energy, proteins, vitamins, and minerals because they grow to maturity in this age. Balanced diet plays important role in their wellbeing and health. The study conducted showed 48% students are not normal in their height and weight. 26% students found underweight, 18% overweight and 4% students found obese. The annual income group of underweight students was below 7 Lac and more than 90% students were staying at their home. The researcher has analysed the eating pattern of these students and concluded that there is need of awareness among the parents and students about balance diet and nutrition. The present research will help students improve their dietary habits and health, increase the number of attendees, and achieve academic excellence.

Keywords: balanced diet, nutrition, malnutrition, obesity, health education

Procedia PDF Downloads 63

Authors: Bo Liu, Chi-Man Pun

Abstract:

A novel technique for digital forgery detection by signal noise inconsistency is proposed in this paper. The forged area spliced from the other picture contains some features which may be inconsistent with the rest part of the image. Noise pattern and the level is a possible factor to reveal such inconsistency. To detect such noise discrepancies, the test picture is initially segmented into small pieces. The noise pattern and level of each segment are then estimated by using various filters. The noise features constructed in this step are utilized in energy-based graph cut to expose forged area in the final step. Experimental results show that our method provides a good illustration of regions with noise inconsistency in various scenarios.

Keywords: forgery detection, splicing forgery, noise estimation, noise

Procedia PDF Downloads 453

Authors: Sebastian Töpfer, Marta Gilaberte Basset, Jorge Fuenzalida, Fabian Steinlechner, Juan P. Torres, Markus Gräfe

Abstract:

This work introduces a combination of digital phase-shifting holography with a non-linear interferometer using undetected photons. Non-linear interferometers can be used in combination with a measurement scheme called quantum imaging with undetected photons, which allows for the separation of the wavelengths used for sampling an object and detecting it in the imaging sensor. This method recently faced increasing attention, as it allows to use of exotic wavelengths (e.g., mid-infrared, ultraviolet) for object interaction while at the same time keeping the detection in spectral areas with highly developed, comparable low-cost imaging sensors. The object information, including its transmission and phase influence, is recorded in the form of an interferometric pattern. To collect these, this work combines the method of quantum imaging with undetected photons with digital phase-shifting holography with a minimal sampling of the interference. With this, the quantum imaging scheme gets extended in its measurement capabilities and brings it one step closer to application. Quantum imaging with undetected photons uses correlated photons generated by spontaneous parametric down-conversion in a non-linear interferometer to create indistinguishable photon pairs, which leads to an effect called induced coherence without induced emission. Placing an object inside changes the interferometric pattern depending on the object’s properties. Digital phase-shifting holography records multiple images of the interference with determined phase shifts to reconstruct the complete interference shape, which can afterward be used to analyze the changes introduced by the object and conclude its properties. An extensive characterization of this method was done using a proof-of-principle setup. The measured spatial resolution, phase accuracy, and transmission accuracy are compared for different combinations of camera exposure times and the number of interference sampling steps. The current limits of this method are shown to allow further improvements. To summarize, this work presents an alternative holographic measurement method using non-linear interferometers in combination with quantum imaging to enable new ways of measuring and motivating continuing research.

Keywords: digital holography, quantum imaging, quantum holography, quantum metrology

Procedia PDF Downloads 84

Authors: A. A. Vasin, N. V. Klassen, A. M. Likhter

Abstract:

Water suspensions of in-organic (metals and oxides) and organic nano-objects (chitozan and collagen) were subjected to the treatment of direct and alternative electrical fields. In addition to quasi-periodical spatial patterning resonance-like performance of spatial distributions of these suspensions has been found at low frequencies of alternating electrical field. These resonances are explained as the result of creation of equilibrium states of groups of charged nano-objects with opposite signs of charges at the interparticle distances where the forces of Coulomb attraction are compensated by the repulsion forces induced by relatively negative polarization of hydrated regions surrounding the nanoparticles with respect to pure water. The low frequencies of these resonances are explained by comparatively big distances between the particles and their big masses with t\respect to masses of atoms constituting molecules with high resonance frequencies. These new resonances open a new approach to detailed modeling and understanding of mechanisms of the influence of electrical fields on the functioning of internal organs of living organisms at the level of cells and neurons.

Keywords: bio-polymers, chitosan, collagen, nanoparticles, coulomb attraction, polarization repulsion, periodical patterning, electrical low frequency resonances, transformations

Procedia PDF Downloads 542

Authors: U. Thisara G. Perera, C. M. Kanchana N. K. Chandrasekara

Abstract:

Dengue is an epidemic which is spread by Aedes Egyptai and Aedes Albopictus mosquitoes. The cases of dengue show a dramatic growth rate of the epidemic in urban and semi urban areas spatially in tropical and sub-tropical regions of the world. Incidence of dengue has become a prominent reason for hospitalization and deaths in Asian countries, including Sri Lanka. During the last decade the dengue epidemic began to spread from urban to semi-urban and then to rural settings of the country. The highest number of dengue infected patients was recorded in Sri Lanka in the year 2016 and the highest number of patients was identified in Colombo district. Together with the commercial, industrial, and other supporting services, the district suffers from rapid urbanization and high population density. Thus, drainage and waste disposal patterns of the people in this area exert an additional pressure to the environment. The district is situated in the wet zone and thus low lying lands constitute the largest portion of the district. This situation additionally facilitates mosquito breeding sites. Therefore, the purpose of the present study was to assess the spatial and temporal distribution patterns of dengue epidemic in Kolonnawa MOH area (Medical Officer of Health) in the district of Colombo. The study was carried out using 615 recorded dengue cases in Kollonnawa MOH area during the south east monsoon season from May to September 2016. The Moran’s I and Kernel density estimation were used as analytical methods. The analysis of data was accomplished through the integrated use of ArcGIS 10.1 software packages along with Microsoft Excel analytical tool. Field observation was also carried out for verification purposes during the study period. Results of the Moran’s I index indicates that the spatial distribution of dengue cases showed a cluster distribution pattern across the area. Kernel density estimation emphasis that dengue cases are high where the population has gathered, especially in areas comprising housing schemes. Results of the Kernel Density estimation further discloses that hot spots of dengue epidemic are located in the western half of the Kolonnawa MOH area, which is close to the Colombo municipal boundary and there is a significant relationship with high population density and unplanned urban land use practices. Results of the field observation confirm that the drainage systems in these areas function poorly and careless waste disposal methods of the people further encourage mosquito breeding sites. This situation has evolved harmfully from a public health issue to a social problem, which ultimately impacts on the economy and social lives of the country.

Keywords: Dengue epidemic, health hazards, Kernel density, Moran’s I, Sri Lanka

Procedia PDF Downloads 297

Authors: Janneth González, George Barreto, Ludis Morales, Angélica Sabogal

Abstract:

Sea anemone neurotoxins are peptides that interact with Na+ and K+ channels, resulting in specific alterations on their functions. Some of these neurotoxins (1ROO, 1BGK, 2K9E, 1BEI) are important for the treatment of nearly eighty autoimmune disorders due to their specificity for Kv1.3 channel. The aim of this study was to identify the common residues among these neurotoxins by computational methods, and establish whether there is a pattern useful for the future generation of a treatment for autoimmune diseases. Our results showed eight new key common residues between the studied neurotoxins interacting with a histidine ring and the selectivity filter of the receptor, thus showing a possible pattern of interaction. This knowledge may serve as an input for the design of more promising drugs for autoimmune treatments.

Keywords: neurotoxins, potassium channel, Kv1.3, computational methods, autoimmune diseases

Procedia PDF Downloads 368

Authors: Camilla Simoncelli

Abstract:

The connection between language and cognition has been one of the main interests of linguistics from several years. According to the Sapir-Whorf Linguistic Relativity Theory, the way we perceive reality depends on the language we speak which in turn has a central role in the human cognition. This paper is in line with this research work with the aim of analyzing how language structures reflect on our cognitive abilities even in the description of space, which is generally considered as a human natural and universal domain. The main objective is to identify the differences in the encoding of spatial inclusion relationships in French and Italian speakers to make evidence that a significant variation exists at various levels even in two similar systems. Starting from the constitution a corpora, the first step of the study has been to establish the relevant complex prepositions marking an inclusion relation in French and Italian: au centre de, au cœur de, au milieu de, au sein de, à l'intérieur de and the opposition entre/parmi in French; al centro di, al cuore di, nel mezzo di, in seno a, all'interno di and the fra/tra contrast in Italian. These prepositions had been classified on the base of the type of Noun following them (e.g. mass nouns, concrete nouns, abstract nouns, body-parts noun, etc.) following the Collostructional Analysis of lexemes with the purpose of analyzing the preferred construction of each preposition comparing the relations construed. Comparing the Italian and the French results it has been possible to define the degree of representativeness of each target Noun for the chosen preposition studied. Lexicostatistics and Statistical Association Measures showed the values of attraction or repulsion between lexemes and a given preposition, highlighting which words are over-represented or under-represented in a specific context compared to the expected results. For instance, a Noun as Dibattiti has a negative value for the Italian Al cuore di (-1,91), but it has a strong positive representativeness for the corresponding French Au cœur de (+677,76). The value, positive or negative, is the result of a hypergeometric distribution law which displays the current use of some relevant nouns in relations of spatial inclusion by French and Italian speakers. Differences on the kind of location conceptualization denote syntactic and semantic constraints based on spatial features as well as on linguistic peculiarity, too. The aim of this paper is to demonstrate that the domain of spatial relations is basic to human experience and is linked to universally shared perceptual mechanisms which create mental representations depending on the language use. Therefore, linguistic coding strongly correlates with the way spatial distinctions are conceptualized for non-verbal tasks even in close language systems, like Italian and French.

Keywords: cognitive semantics, cross-linguistic variations, locational terms, non-verbal spatial representations

Procedia PDF Downloads 108

Authors: Erik Kuravsky

Abstract:

One of the problems with a post-structuralist account of agency is that it appears to reject the freedom of an acting subject, thus seeming to deny the very phenomenon of agency. However, this is only a problem if we think that human beings can be agents exclusively in terms of being subjects, that is, if we think agency subjectively. Indeed, we tend to understand traditional theories of human freedom (e.g., Plato’s or Kant’s) in terms of a peculiar ability of the subject. The paper suggests to de-subjectivize agency with the help of Heidegger’s later thought. To do it, ir argues that classical theories of agency may indeed be interpreted as subject-oriented (sometimes even by their authors), but do not have to be read as such. Namely, the claim is that what makes agency what it is, what is essential in agency, is not its belonginess to a subject, but its ontological configuration. We may say that agency “happens,” and that there is a very specific ontological characteristics to this happening. The argument of the paper is that we can find these characteristic in the classical accounts of agency and that these characteristics are sufficient to distinguish human freedom from other natural phenomena. In particular, it offers to think agency not as one of human characteristics, but as an ontological event in which human beings take part. Namely, agency is a (non-human) characteristic of the different modes in which the experienceable existence of beings is determined by Being. To be an agent then is to participate in such ontological determination. What enables this participation is the ways human beings non-thematically understand the ontological difference. For example, for Plato, one acts freely only if one is led by an idea of the good, while for Kant the imperative for free action is categorial. The agency of an agent is thus dependent on the differentiation between ideas/categories and beings met in experience – one is “free” from contingent sensibility in terms of what is different from it ontologically. In this light, modern dependence on subjectivity is evident in the fact that the ontological difference is thought as belonging to one’s thinking, consciousness etc. That is, it is taken subjectively. A non-subjective account of agency, on the other hand, requires thinking this difference as belonging to Being itself, and thinking human beings as a medium within which occurs the non-human force of ontological differentiation.

Keywords: Heidegger, freedom, agency, poststructuralism

Procedia PDF Downloads 192