A Digital Framework to Build,Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.     

Do memory processes occur also in plants?

Plantlets of Bidens pilosus L. "remembered" a symmetry-breaking signal (the puncturing of one of the cotyledons), but expressed it only after being made permissive (by removing the apex). The mean value of the memorization index was 0.52. There was a labile short-term and a well-fixed long-term memory. The memorization process was dependent on the number of stimuli, and on the mineral status of the plant.     

The integrated orderline batching,batch scheduling,and picker routing problem with multiple pickers: the benefits of splitting customer orders

Flexible Services and Manufacturing Journal - Fast delivery is one of the most popular services in e-commerce retail. It consists in shipping the items ordered on-line in short times. Customer...     

Reversible Adaptive Trees

We describe reversible adaptive trees, a class of stochastic algorithms modified from the formerly described adaptive trees. They evolve in time a finite subset of an ambient Euclidean space of any dimension, starting from a seed point and, accreting points to the evolving set, they grow branches towards a target set which can depend on time. In contrast with plain adaptive trees, which were formerly proven to have strong convergence properties to a static target, the points of reversible adaptive trees are removed from the tree when they have not been used recently enough in a path from the root to an accreted point. This, together with a straightening process performed on the branches, permits the tree to follow some moving targets and still remain adapted to it. We then discuss in what way one can see such reversible trees as a model for a qualitative property of resilience, which leads us to discuss qualitative modeling.     

Efficient heuristics to minimize the total tardiness of chemotherapy drug production and delivery

Flexible Services and Manufacturing Journal - This study considers the production of chemotherapy drugs for cancer treatment. An important factor determining the quality of service of chemotherapy...     

Adaptive branching in evolution and epigenesis

We describe one of the simplest models that exhibit an adaptive branching behaviour. It is analysed both experimentally and formally, and its successive bifurcations provide a good model of what R. Thom called 'generalized catastrophes'. Two theorems on the stochastic adaptivity of the algorithm to very general shapes of target are given. The model further displays the phenomenon of abortive branching: each macroscopic branching appears after a burst of microscopic branchings that stop growing after a very short time. The mathematical analysis of the model explains why and how this behaviour occurs. Possible applications of these models to Evolution (natural and artificial) and Epigenesis are briefly mentioned, and a higher dimensional version is applied to growing a tree in a space of shapes in the context of a database of medical images.     

Memorization and delayed expression of regulatory messages in plants

Plantlets of Bidens pilosus L., considered to be basically symmetrical, can be lateralized (A/B) by being administered a symmetry-breaking signal such as puncturing one of the plant cotyledons. The induced asymmetry remains latent as long as the plants have not been made permissive, i.e. as long as the plant apex is left functioning. When the apex has been removed (plant decapitation), the latent asymmetry is expressed by one of the cotyledonary buds (a/b) statistically beginning to elongate before the other. The interval of time between delivering the symmetry-breaking signal and making the plant permissive is the memorization-time, t. Memorization can be quantified by using a precedence index, q, the values of which range from 0 (no detectable asymmetry with regard to bud growth) to ±1 (bud growth perfectly asymmetric in favour of either bud b or a). Even for memorization times, t, up to 14 d, q-values up to 0.4 (or even larger) are observed. Various experimental characteristics (e.g. light, temperature, presence or absence of the root system) but not the plant age can affect the q-values, at the moment when the treatments are performed, at least in the range of 6 to 25 d. Combining several puncturing treatments either increases or decreases the q-values, depending on the nature of these treatments and the time-intervals, t, between them. Symmetrically removing both cotyledons in the minutes following the puncturing of one of them does not significantly alter the results, which means that the symmetry-breaking message is rapidly transported and memorized within the plant. Non-traumatic asymmetrical treatments (droplets of saline solutions, light-gradients) can also act as symmetry-breaking signals and be memorized. Plants other than Bidens are likely to possess similar memorization ability, although the q-values observed up to now have not been very large.     

Matching a surface to a given sectional curve

We describe an algorithm to position a rigid surface so as to make its cross-section by a given plane match a given curve in that plane, a problem relevant to model-based medical imaging. After building an atlas of cross-sections of the surface and searching it for a best position to start from, each iteration of the algorithm (1) determines a vector field along the intersection curve that will improve its matching with the target curve, and (2) computes and applies a small displacement of the surface whose effect on the intersection will approximate best the required vector field. Computations use least-square techniques, an exponential formula for Lie groups of transformations, and generic properties of cross-sections. Experiments with an implementation are reported and theoretical tools for justifying and improving the algorithm, some of them based on Catastrophe Theory, are outlined.