The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X 2 distributions that can be obtained using permutation with scaled X 2 approximation. We analyzed a genome-wide copy number data from patients of non-small-cell lung cancer. With the Molecular Signatures Database MSigDB pathway database, the genome-wide copy number data can be classified into biological pathways or gene sets. We investigated associations of the copy number profile of the gene sets with pack-years of cigarette smoking.
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The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established.
With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X 2 distributions that can be obtained using permutation with scaled X 2 approximation.
We analyzed a genome-wide copy number data from patients of non-small-cell lung cancer. With the Molecular Signatures Database MSigDB pathway database, the genome-wide copy number data can be classified into biological pathways or gene sets.
We investigated associations of the copy number profile of the gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment number data, and causal mechanisms of the five pathways require further study. This tool can be applied to determine curve numbers and to calculate runoff or infiltration for a rainfall event in a watershed.
Implementation of GIS techniques such as dissolving, intersecting, and a curve- number reference table improve efficiency. Technical processing time may be reduced from days, if not weeks, to hours for producing spatially varied curve number and runoff maps. All rights reserved. The rainfall and runoff relationship becomes an intriguing issue as urbanization continues to evolve worldwide. In this paper, we developed a simulation model based on the soil conservation service curve number SCS- CN method to analyze the rainfall-runoff relationship in Guangzhou, a rapid growing metropolitan area in southern China.
Decreasing particle number concentrations in a warming atmosphere and implications. Directory of Open Access Journals Sweden. Full Text Available New particle formation contributes significantly to the number concentration of condensation nuclei CN as well as cloud CN CCN, a key factor determining aerosol indirect radiative forcing of the climate system.
Using a physics-based nucleation mechanism that is consistent with a range of field observations of aerosol formation, it is shown that projected increases in global temperatures could significantly inhibit new particle, and CCN, formation rates worldwide. The possible reasons for larger observed long-term CN reductions at remote sites are discussed.
The combined effects of rising temperatures on aerosol nucleation rates and other chemical and microphysical processes may imply substantial decreases in future tropospheric particle abundances associated with global warming, delineating a potentially significant feedback mechanism that increases Earth's climate sensitivity to greenhouse gas emissions.
Further research is needed to quantify the magnitude of such a feedback process. Full Text Available The rainfall and runoff relationship becomes an intriguing issue as urbanization continues to evolve worldwide. In this model, the curve number CN is a key variable which is usually obtained by the look-up table of TR Thus, this paper develops a method to calculate CN by using remote sensing variables, including vegetation, impervious surface, and soil V-I-S.
The specific objectives of this paper are: 1 To extract the V-I-S fraction images using Linear Spectral Mixture Analysis; 2 To obtain composite CN by incorporating vegetation types, soil types, and V-I-S fraction images; and 3 To simulate direct runoff under the scenarios with precipitation of 57mm occurred once every five years by average and 81mm occurred once every ten years. Our experiment shows that the proposed method is easy to use and can derive composite CN effectively.
Explaining global surface aerosol number concentrations in terms of primary emissions and particle formation. Full Text Available We synthesised observations of total particle number CN concentration from 36 sites around the world. Many sites exhibit pronounced seasonality with summer time concentrations a factor of 2—10 greater than wintertime concentrations. We used these CN observations to evaluate primary and secondary sources of particle number in a global aerosol microphysics model.
We ran a number of simulations where we included an empirical BL nucleation mechanism either using the activation-type mechanism nucleation rate, J , proportional to gas-phase sulfuric acid concentration to the power one or kinetic-type mechanism J proportional to sulfuric acid to the power two with a range of nucleation coefficients.
The nucleation constants that resulted in best overall match between model and observed CN concentrations were. Spracklen, D. We synthesised observations of total particle number CN concentration from 36 sites around the world. We found that annual mean CN concentrations are typically cm-3 in the marine boundary layer and free troposphere FT and cm-3 in the continental boundary layer BL.
Many sites exhibit pronounced seasonality with summer time concentrations a factor of greater than wintertime concentrations. We ran a number of simulations where we included an empirical BL nucleation mechanism either using the activation-type mechanism nucleation rate, J, proportional to gas-phase sulfuric acid concentration to the power one or kinetic-type mechanism J proportional to sulfuric acid to the power two with a range of nucleation coefficients.
The nucleation constants that resulted in best overall match between model and observed CN concentrations were consistent with values derived in previous studies from detailed case studies at individual sites. In our model, kinetic and activation. More field data from recent decades were leaning against the assumption of the initial abstraction coefficient ratio value proposed by SCS in Physiographic conditions were identified as vital influencing factors to be considered under this methodology while practitioners of this method are encouraged to validate and derive regional specific relationship and employ the method with caution.
Experimental measurement of biodiesel CN is rather laborious and expensive. However, the high proportionality of biodiesel fatty acid methyl esters FAMEs profile with its CN is very appealing to develop straightforward and inexpensive computerized tools for biodiesel CN estimation.
Unfortunately, correlating the chemical structure of biodiesel to its CN using conventional statistical and mathematical approaches is very difficult. In the proposed approach, ANN paradigm was used for modeling the inner relation between the input and the output PLS score vectors. In addition, the capability of the developed method in predicting the biodiesel CN was compared with the basal PLS method.
The accuracy of the developed approaches for computing the biodiesel CN was assessed using three statistical criteria, i. In order to facilitate the use of the proposed model, an easy-to-use computer program was also developed on the basis of ANN-adapted PLS. MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Quantitative analyses of next-generation sequencing NGS data, such as the detection of copy number variations CNVs , remain challenging.
Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate FDR , even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing.
In contrast to previous approaches, cn. MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn. MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn. MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively.
The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn. MOPS outperformed its five competitors in terms of precision 1-FDR and recall for both gains and losses in all benchmark data sets. The software cn. The Vaerrioe environmental measurement station is founded in The aim of the station is to obtain more information on air quality influenced by Kola industrial areas and effects of pollutants on photosynthesis in subarctic climate.
In the station air quality and meteorological quantities are measured together with photosynthesis, which makes it quite unique in comparison with other measurement stations located in northern Finland. The measurements also provide information of aerosol and trace gas concentrations in order to study the direct and indirect aerosol effects on climate. These measurements also increase the knowledge of atmospheric chemistry and deposition in subarctic conditions.
Ahonen, T. FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate. Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6. A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power.
For controlling the FDR, we propose a probabilistic latent variable model, ' cn. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data.
On HapMap data, cn. Raster-based derivation of a flood runoff susceptibility map using the revised runoff curve number CN for the Kuantan watershed, Malaysia. This study aims to develop a methodology for generating a flood runoff susceptibility FRS map using a revised curve number CN method. The study area is in the Kuantan watershed KW , Malaysia, which was seriously affected by floods in December and December A revised runoff CN map w A revised runoff CN map However, the spatial extent of a high-risk zone in the downstream end and lowland areas of the KW could be considered to be the main cause of flood damage in recent years.
From practical point of view Intercomparison of aerosol instruments: number concentration. These ratios were very stable during the week and there was little effect of particle size or material. Most other comparisons were equally stable.
However, a review of past work at EML and elsewhere led to the disturbing conclusion that these ratios may change from year to year, or from season to season. This study aims to explore the potential of low- concentration of rhamnolipid in efficient treatment of wastewater with poor biodegradability. The aim of this study was to investigate the phytotoxicity of thin-walled carbon nanotubes CNTs to rice Oryza sativa L.
The CNTs significantly inhibited rice growth by decreasing the concentrations of endogenous plant hormones. Interestingly, the increase in the C:N ratio in roots was largely because of decreased N content, indicating that the CNTs significantly decreased N assimilation. Analyses of the Fe and Co contents in plant tissues, transmission electron microscope TEM observations and energy dispersive X-ray spectroscopy EDS analysis proved that the CNTs could penetrate the cell wall and the cell membrane, and then enter the root cells.
According to the author's knowledge, this is the first time to study the relationship between carbon nanotubes and carbon nitrogen ratio and plant hormones.
Multisite study of particle number concentrations in urban air. Particle number concentration data are reported from a total of eight urban site locations in the United Kingdom. Of these, six are central urban background sites, while one is an urban street canyon Marylebone Road and another is influenced by both a motorway and a steelworks Port Talbot.
The concentrations are generally of a similar order to those reported in the literature, although higher than those in some of the other studies. Highest concentrations are at the Marylebone Road site and lowest are at the Port Talbot site. The central urban background locations lie somewhere between with concentrations typically around 20 cm A seasonal pattern affects all sites, with highest concentrations in the winter months and lowest concentrations in the summer.
Data from all sites show a diurnal variation with a morning rush hour peak typical of an anthropogenic pollutant.
Ion transport number
Differences in transport number arise from differences in electrical mobility. For example, in an aqueous solution of sodium chloride, less than half of the current is carried by the positively charged sodium ions cations and more than half is carried by the negatively charged chloride ions anions because the chloride ions are able to move faster, i. The sum of the transport numbers for all of the ions in solution always equals unity. The concept and measurement of transport number were introduced by Johann Wilhelm Hittorf in the year There are two experimental techniques for the determination of transport numbers.