Permissible idealizations for the purpose of prediction

Every model leaves out or distorts some factors that are causally connected to its target phenomenon—the phenomenon that it seeks to predict or explain. If we want to make predictions, and we want to base decisions on those predictions, what is it safe to omit or to simplify, and what ought a causal model to describe fully and correctly? A schematic answer: the factors that matter are those that make a difference to the target phenomenon. There are several ways to understand differencemaking. This paper advances a view as to which is the most relevant to the forecaster and the decision-maker. It turns out that the right notion of differencemaking for thinking about idealization in prediction is also the right notion for thinking about idealization in explanation; this suggests a carefully circumscribed version of Hempel’s famous thesis that there is a symmetry between explanation and prediction.     

Escherichia coli swim on the right-hand side

The motion of peritrichously flagellated bacteria close to surfaces is relevant to understanding the early stages of biofilm formation and of pathogenic infection. This motion differs from the random-walk trajectories of cells in free solution. Individual Escherichia coli cells swim in clockwise, circular trajectories near planar glass surfaces. On a semi-solid agar substrate, cells differentiate into an elongated, hyperflagellated phenotype and migrate cooperatively over the surface, a phenomenon called swarming. We have developed a technique for observing isolated E. coli swarmer cells moving on an agar substrate and confined in shallow, oxidized poly(dimethylsiloxane) (PDMS) microchannels. Here we show that cells in these microchannels preferentially 'drive on the right', swimming preferentially along the right wall of the microchannel (viewed from behind the moving cell, with the agar on the bottom). We propose that when cells are confined between two interfaces--one an agar gel and the second PDMS--they swim closer to the agar surface than to the PDMS surface (and for much longer periods of time), leading to the preferential movement on the right of the microchannel. Thus, the choice of materials guides the motion of cells in microchannels.     

Common variation at 10p12.31 near MLLT10 influences meningioma risk

To identify susceptibility loci for meningioma, we conducted a genome-wide association study of 859 affected individuals (cases) and 704 controls with validation in two independent sample sets totaling 774 cases and 1,764 controls. We identified a new susceptibility locus for meningioma at 10p12.31 (MLLT10, rs11012732, odds ratio = 1.46, P(combined) = 1.88 × 10(-14)). This finding advances our understanding of the genetic basis of meningioma development.     

Predation of artificial Sage Grouse nests in treated and untreated sagebrush

We measured predation on 120 artificial Sage Grouse ( Centrarcus urophasianus ) nests in montane sagebrush grassland in northern Utah. We examined nests in areas that had been chained and seeded 25 years previously (treated areas) and in areas that were untreated. Predation rates of artificial nests were higher in areas of untreated sagebrush, even though these areas had greater sagebrush cover, taller shrubs, and greater horizontal plant cover. These results differ from those previously hypothesized for treated sagebrush habitat and may reflect a greater abundance of other potential prey species, especially lagomorphs, in untreated areas that attracted greater densities of predators. In addition, over 80% of nests were depredated by mammals, which hunt using olfaction and are less likely than avian predators to be affected by nest cover. We conclude that, after treated sagebrush has recovered to some degree, predation rates of Sage Grouse nests may be lower in treated sagebrush. Consequently, factors other than nest predation (e.g., winter food, thermal cover, insects, perennial forb abundance) may be more important reasons for preserving mature sagebrush stands for Sage Grouse.     

Platelets in defense against bacterial pathogens

Platelets interact with bacterial pathogens through a wide array of cellular and molecular mechanisms. The consequences of this interaction may significantly influence the balance between infection and immunity. On the one hand, recent data indicate that certain bacteria may be capable of exploiting these interactions to gain a virulence advantage. Indeed, certain bacterial pathogens appear to have evolved specific ways in which to subvert activated platelets. Hence, it is conceivable that some bacterial pathogens exploit platelet responses. On the other hand, platelets are now known to possess unambiguous structures and functions of host defense effector cells. Recent discoveries emphasize critical features enabling such functions, including expression of toll-like receptors that detect hallmark signals of bacterial infection, an array of microbicidal peptides, as well as other host defense molecules and functions. These concepts are consistent with increased risk and severity of bacterial infection as correlates of clinical abnormalities in platelet quantity and quality. In these respects, the molecular and cellular roles of platelets in host defense against bacterial pathogens are explored with attention on advances in platelet immunobiology.     

Interaction and interrelation of P2X7 and P2X4 receptor complexes in mouse lung epithelial cells

P2X4 and P2X7 receptors are ATP-gated ion channels that are co-expressed in alveolar epithelial type I cells. Both receptors are localized to the plasma membrane and partly associated with lipid rafts. Here we report on our study in an alveolar epithelial cell line of the molecular organization of P2X7R and P2X4R receptors and the effect of their knockdown. Native gel electrophoresis reveals three P2X7R complexes of ~430, ~580 and ~760 kDa. The latter two correspond exactly in size to signals of Cav-1, the structural protein of caveolae. Interestingly knockdown of P2rx7 affects protein levels, the intracellular distribution and the supramolecular organization of Cav-1 as well as of P2X4R, which is mainly detected in a complex of ~430 kDa. Our data suggest upregulation of P2X4R as a compensatory mechanism of P2X7R depletion.