31 research outputs found

    Additional file 1: Table S1. of A powerful score-based statistical test for group difference in weighted biological networks

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    The location and SNP number for five susceptibility genes belonging to the network associated with leprosy. Table S2. The location and probe sets number for genes belonging to the subnetwork from PI3K-AKT signaling pathway and Notch signaling pathway. Table S3. Type I error rates of four methods (40 vertices and 54 edges in the network). Table S4. Type I error rates of four methods given the deviation from the normal distribution. Figure S1. A network including 40 vertices and 54 edges. Figure S2. The statistical power of the four methods under three scenarios. (a) only vertices change, (b) only edges change, (c) both vertices and edges change. (PDF 140 kb

    From Interaction to Co-Association —A Fisher <i>r</i>-To-<i>z</i> Transformation-Based Simple Statistic for Real World Genome-Wide Association Study

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    <div><p>Currently, the genetic variants identified by genome wide association study (GWAS) generally only account for a small proportion of the total heritability for complex disease. One crucial reason is the underutilization of gene-gene joint effects commonly encountered in GWAS, which includes their main effects and co-association. However, gene-gene co-association is often customarily put into the framework of gene-gene interaction vaguely. From the causal graph perspective, we elucidate in detail the concept and rationality of gene-gene co-association as well as its relationship with traditional gene-gene interaction, and propose two Fisher <i>r-to-z</i> transformation-based simple statistics to detect it. Three series of simulations further highlight that gene-gene co-association refers to the extent to which the joint effects of two genes differs from the main effects, not only due to the traditional interaction under the nearly independent condition but the correlation between two genes. The proposed statistics are more powerful than logistic regression under various situations, cannot be affected by linkage disequilibrium and can have acceptable false positive rate as long as strictly following the reasonable GWAS data analysis roadmap. Furthermore, an application to gene pathway analysis associated with leprosy confirms in practice that our proposed gene-gene co-association concepts as well as the correspondingly proposed statistics are strongly in line with reality.</p></div

    Data_Sheet_1_Moderate increase of precipitation stimulates CO2 production by regulating soil organic carbon in a saltmarsh.docx

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    Saltmarsh is widely recognized as a blue carbon ecosystem with great carbon storage potential. Yet soil respiration with a major contributor of atmospheric CO2 can offset its carbon sink function. Up to date, mechanisms ruling CO2 emissions from saltmarsh soil remain unclear. In particular, the effect of precipitation on soil CO2 emissions is unclear in coastal wetlands, due the lack of outdoor data in real situations. We conducted a 7-year field manipulation experiment in a saltmarsh in the Yellow River Delta, China. Soil respiration in five treatments (−60%, −40%, +0%, +40%, and + 60% of precipitation) was measured in the field. Topsoils from the last 3 years (2019–2021) were analyzed for CO2 production potential by microcosm experiments. Furthermore, quality and quantity of soil organic carbon and microbial function were tested. Results show that only the moderate precipitation rise of +40% induced a 66.2% increase of CO2 production potential for the microcosm experiments, whereas other data showed a weak impact. Consistently, soil respiration was also found to be strongest at +40%. The CO2 production potential is positively correlated with soil organic carbon, including carbon quantity and quality. But microbial diversity did not show any positive response to precipitation sizes. r-/K-strategy seemed to be a plausible explanation for biological factors. Overall, our finding reveal that a moderate precipitation increase, not decrease or a robust increase, in a saltmarsh is likely to improve soil organic carbon quality and quantity, and bacterial oligotroph:copiotroph ratio, ultimately leading to an enhanced CO2 production.</p

    "There are many possibilities how to spend a spring night...": About City Cipher Games Phenomenon

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    The presented Diploma Thesis deals with the phenomenon of city cipher games. Research was performed by the researcher participation in four city cipher games in Prague, by semi- structured and informal interviews and by cipher games web sites analysis It considers cipher games postmodern enjoyment which is characteristic for emphasizing an experience. The thesis is focused on two task groups: game and city. It examines city cipher games attributes, asks how players take the game and tries to realize the motivation for their participation. It shows that players undergo physical and intellectual exhaustion, discomfort and little hazard. Very strong experience connected with own limits' overcoming is the reason why they join the game again. Other essential reason is the unusual connection between a type of summer camp game and the city world. City is a coulisse with atmosphere for the game. Players experience the city in an unusual way. They learn to know it differently. They are undergoing a type of psychogeographic method. So the game not only takes benefits from the city but also creates players' relationships to the city. Players learn to know the city. It is important to mention that city and game are paramount arenas for freedom exerting

    A causal graph framework for two SNPs affected the disease.

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    <p> and represents main effects, denotes the traditional interaction, the nondirectional arc between SNP1 and SNP2 (correlation <i>r</i>) indicated that the two variables are associated for reasons other than affecting one another.</p

    Simulations for clarifying the relationship between co-association and interaction.

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    <p>a for Type I co-association; b for Type II co-association; c for Type III co-association given fixed interaction effect 0.2 and different correlation; d for Type III co-association given fixed correlation 0.4 and different interaction effects. The case with no main effects (), one main effects (, ) and two main effects (, ) are shown by blue, red and black lines respectively.</p