The role of assumptions in causal discovery

The paper looks at the conditional independence search approach to causal discovery, proposed by Spirtes et al. and Pearl and Verma, from the point of view of the mechanism-based view of causality in econometrics, explicated by Simon. As demonstrated by Simon, the problem of determining the causal structure from data is severely underconstrained and the perceived causal structure depends on the a priori assumptions that one is willing to make. I discuss the assumptions made in the independence search-based causal discovery and their identifying strength

The level of occlusion of included bark affects the strength of bifurcations in hazel (Corylus avellana L.)

Bark-included junctions in trees are considered a defect as the bark weakens the union between the branches. To more accurately assess this weakening effect, 241 bifurcations from young specimens of hazel (Corylus avellana L.), of which 106 had bark inclusions, were harvested and subjected to rupture tests. Three-point bending of the smaller branches acted as a benchmark for the relative strength of the bifurcations. Bifurcations with included bark failed at higher displacements, and their modulus of rupture was 24% lower than normally formed bifurcations, while stepwise regression showed that the best predictors of strength in these bark-included bifurcations were the diameter ratio and width of the bark inclusion, which explained 16.6% and 8.1% of the variability, respectively. Cup-shaped, bark-included bifurcations where included bark was partially occluded by xylem were found, on average, to be 36% stronger than those, where included bark was situated at the bifurcation apex. These findings show that there are significant gradations in the strength of bark-included bifurcations in juvenile hazel trees that relate directly to the level of occlusion of the bark into the bifurcation. It therefore may be possible to assess the extent of the defect that a bark-included bifurcation represents in a tree by assessing the relative level of occlusion of the included bark

Single DNA conformations and biological function

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.Comment: 53 pages, 45 figures. Slightly revised version of a review article, that is going to appear in the J. Comput. Theoret. Nanoscience; some typos correcte

Gene silencing and large-scale domain structure of the E. coli genome

The H-NS chromosome-organizing protein in E. coli can stabilize genomic DNA loops, and form oligomeric structures connected to repression of gene expression. Motivated by the link between chromosome organization, protein binding and gene expression, we analyzed publicly available genomic data sets of various origins, from genome-wide protein binding profiles to evolutionary information, exploring the connections between chromosomal organization, genesilencing, pseudo-gene localization and horizontal gene transfer. We report the existence of transcriptionally silent contiguous areas corresponding to large regions of H-NS protein binding along the genome, their position indicates a possible relationship with the known large-scale features of chromosome organization

An Analysis of Environmental and Anthropogenic Controls on Indoor Radon Distribution in Grand Forks, North Dakota

Indoor radon may be a potential health threat in a significant number of homes in Grand Forks, North Dakota. Ninety-three percent of the homes tested in 1988 to 1993 contained indoor radon levels greater than the Environmental Protection Agency’s recommended action level of 4 picoCuries per liter. In addition, the average reading of indoor radon concentrations was 18.9 picoCuries per liter, well above the action level guidelines. Several variables were examined through the use of regression analysis and a Geographic Information System in an attempt to characterize the controls on indoor radon levels in Grand Forks. The results of the analysis indicated no significant relationship with any of the variables tested: soil permeability, distance to surface water bodies, and house age. Bedrock and surficial geology are mainly homogeneous in nature and contain primarily shale, limestone, and sandstone which have been found to have high uranium concentrations. Therefore the bedrock and surficial geology play an important role in influencing high indoor radon levels. The outcome of the study led to the formulation of several alternative hypotheses for future studies. Studies investigating meteorological factors as well as building materials may prove to have a positive relationship with indoor radon levels in viii Grand Forks