Possibility spaces and the notion of novelty: from music to biology

International audienceWe provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology

A parallelized surface extraction algorithm for large binary image data sets based on an adaptive 3D delaunay subdivision strategy

In this paper, we describe a novel 3D subdivision strategy to extract the surface of binary image data. This iterative approach generates a series of surface meshes that capture different levels of detail of the underlying structure. At the highest level of detail, the resulting surface mesh generated by our approach uses only about 10 percent of the triangles In comparison to the Marching Cube (MC) algorithm, even In settings where almost no image noise Is present. Our approach also eliminates the so-called "staircase effect," which voxel-based algorithms like the MC are likely to show, particularly if nonuniformly sampled images are processed. Finally, we show how the presented algorithm can be parallelized by subdividing 3D image space into rectilinear blocks of subimages. As the algorithm scales very well with an Increasing number of processors In a multithreaded setting, this approach is suited to process large image data sets of several gigabytes. Although the presented work is still computationally more expensive than simple voxel-based algorithms, It produces fewer surface triangles while capturing the same level of detail, is more robust toward image noise, and eliminates the above-mentioned "staircase" effect in anisotropic settings. These properties make it particularly useful for biomedical applications, where these conditions are often encountered

Time-varying image data visualization framework for application in cardiac catheterization procedures

Visualization plays an important role in image guided surgery. This paper presents a real-time 3D motion visualization method where pre-computed meshes of the beating heart are synchronized with and overlaid onto live X-ray images. This provides the surgeon with a navigational aid in guiding catheters during cardiac catheterization. In order to generate time-varying meshes of the beating heart, we first acquire a time-series of images of the patient using Magnetic Resonance Imaging (MRI). The MRI heart images used for the cardiac catheterization procedures can either be contrast-enhanced by injecting a contrast agent prior to imaging or they can be unenhanced. The contrast-enhanced images can easily be segmented and binarized using a fixed grey-level threshold. In this case, we can use an adaptive Delaunay-based surface extraction algorithm for mesh generation, for which specifically developed for noisy binary image data sets. For unenhanced images, we have to choose a semi-automated segmentation approach, where a region of interest in the patient's heart is outlined manually in an intermediate slice in the 3-D MRI data set and then propagated to neighbouring slices. In a next step, the extracted snake contours are propagated in time from the first phase of the cardiac cycle to subsequent phases using multiple snake contours. In this scenario, the final mesh is generated using a serial section reconstruction algorithm. However, due to the nature of the underlyling MRI images which frequently contain areas of inhomogenous contrast caused by motion and blood flow, it is difficult to generate a smooth mesh directly from the result of the previously described semi-automatic segmentation procedure. Therefore, we also introduce a contour-based mesh smoothing algorithm using a 1D Gaussian filter in order to post-process the snake contours along the series of cross-sections before reconstruction

Vitamin C blocks inflammatory platelet-activating factor mimetics created by cigarette smoking.

Cigarette smoking within minutes induces leukocyte adhesion to the vascular wall and formation of intravascular leukocyte-platelet aggregates. We find this is inhibited by platelet-activating factor (PAF) receptor antagonists, and correlates with the accumulation of PAF-like mediators in the blood of cigarette smoke-exposed hamsters. These mediators were PAF-like lipids, formed by nonenzymatic oxidative modification of existing phospholipids, that were distinct from biosynthetic PAF. These PAF-like lipids induced isolated human monocytes and platelets to aggregate, which greatly increased their secretion of IL-8 and macrophage inflammatory protein-1alpha. Both events were blocked by a PAF receptor antagonist. Similarly, blocking the PAF receptor in vivo blocked smoke-induced leukocyte aggregation and pavementing along the vascular wall. Dietary supplementation with the antioxidant vitamin C prevented the accumulation of PAF-like lipids, and it prevented cigarette smoke-induced leukocyte adhesion to the vascular wall and formation of leukocyte-platelet aggregates. This is the first in vivo demonstration of inflammatory phospholipid oxidation products and it suggests a molecular mechanism coupling cigarette smoke with rapid inflammatory changes. Inhibition of PAF-like lipid formation and their intravascular sequela by vitamin C suggests a simple dietary means to reduce smoking-related cardiovascular disease