3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA

The file attached is the Published/publisher’s pdf version of the article

Assessment of Three Mitochondrial Genes (16S, Cytb, CO1) for Identifying Species in the Praomyini Tribe (Rodentia: Muridae)

The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments

Sulfur-containing species (sulfate and methansulfonate) in coastal Antarctic aerosol and precipitation

The concentrations of sulfur-containing species (sulfate and methanesulfonate (MSA)) of aerosols collected at three coastal Antarctic sites (Neumayer, Dumont d'Urville, and Halley) have been studied in order to investigate the natural sulfur cycle at high southern latitudes. The multiple-year data sets indicate annual mean concentrations of MSA and non-sea-salt (nss) sulfate of 38 and 151 ng m(-3) at Neumayer (1983-1995) and 20 and 147 ng m(-3) at Dumont d'Urville (1991-1995). On the basis of the study of a more limited time period (1991 and 1992), the Halley data set indicates significantly lower MSA and nss sulfate concentrations, 15 and 50 ng m(-3), respectiveley. The concentrations of both species exhibit a consistent and strong seasonal cycle with maxima from December to March and minima from May to September (from 2 to 4 and from 17 to 50 ng m(-3), for MSA and nss sulfate, respectively). These data, together with radionuclide studies (Pb-210 and Be-10), indicate that the marine biogenic source dominates the sulfur budget of the boundary layer of these regions throughout the year. The contribution of other sources, such as the long-range transported sulfur from continents and to a lesser extent the stratospheric sulfate reservoir, remains weak when averaged over the year. Differences in the seasonal pattern of the two sulfur-containing species, as well as intersite differences in the summer concentrations, are compared to several factors, mainly the spatial and temporal variations of the chlorophyll content of the surface ocean water and the seasonality of the sea ice cover. This permits investigation of the respective influence of marine regions emitting dimethylsulfide located either near the Antarctic continent (south of 60 degrees S) or at more temperate latitudes. A strong correlation is found between the chlorophyll content of the Antarctic ocean and the level of total nss sulfur. Furthermore, nss sulfate and MSA deposition fluxes determined from firn and ice cores extracted at sites located at various distances from the ocean and various altitudes allow assessment of the spatial variation of the marine biogenic sulfur input in Antarctica

Fracture de la paroi mediale de l'orbite. A propos de 4 observations. [Fracture of the medial wall of the orbit. Apropos of 4 cases]

Fractures or the medial wall of the orbit are uncommon and clinical signs are often discreet. This report was focused on isolated fractures of the medial wall of the orbit. Blow-out trauma is usually the cause. In these cases the clinical signs ranged from simple ecchymosis to blindness by haematoma of the orbital cone. Computed tomography is a major tool for diagnosis and making therapeutic indications for these fractures. Treatment depends on the oculomotor involvements as measured by forced duction tests