Sparse regularization for fiber ODF reconstruction: from the suboptimality of ℓ2 and ℓ1 priors to ℓ0.

Diffusion MRI is a well established imaging modality providing a powerful way to probe the structure of the white matter non-invasively. Despite its potential, the intrinsic long scan times of these sequences have hampered their use in clinical practice. For this reason, a large variety of methods have been recently proposed to shorten the acquisition times. Among them, spherical deconvolution approaches have gained a lot of interest for their ability to reliably recover the intra-voxel fiber configuration with a relatively small number of data samples. To overcome the intrinsic instabilities of deconvolution, these methods use regularization schemes generally based on the assumption that the fiber orientation distribution (FOD) to be recovered in each voxel is sparse. The well known Constrained Spherical Deconvolution (CSD) approach resorts to Tikhonov regularization, based on an ℓ(2)-norm prior, which promotes a weak version of sparsity. Also, in the last few years compressed sensing has been advocated to further accelerate the acquisitions and ℓ(1)-norm minimization is generally employed as a means to promote sparsity in the recovered FODs. In this paper, we provide evidence that the use of an ℓ(1)-norm prior to regularize this class of problems is somewhat inconsistent with the fact that the fiber compartments all sum up to unity. To overcome this ℓ(1) inconsistency while simultaneously exploiting sparsity more optimally than through an ℓ(2) prior, we reformulate the reconstruction problem as a constrained formulation between a data term and a sparsity prior consisting in an explicit bound on the ℓ(0)norm of the FOD, i.e. on the number of fibers. The method has been tested both on synthetic and real data. Experimental results show that the proposed ℓ(0) formulation significantly reduces modeling errors compared to the state-of-the-art ℓ(2) and ℓ(1) regularization approaches.

Pore space analysis of beech wood: The vessel network

Water transport in wood is vital for the survival of trees. With synchrotron radiation X-ray tomographic microscopy (SRXTM), it has become possible to characterize and quantify the three-dimensional (3D) network formed by vessels that are responsible for longitudinal transport. In the present study, the spatial size dependence of vessels and the organization inside single growth rings in terms of vessel-induced porosity was studied by SRXTM. Network characteristics, such as connectivity, were deduced by digital image analysis from the processed tomographic data and related to known complex network topologies.

Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

PGC1alpha expression is controlled in skeletal muscles by PPARbeta, whose ablation results in fiber-type switching, obesity, and type 2 diabetes.

Mice in which peroxisome proliferator-activated receptor beta (PPARbeta) is selectively ablated in skeletal muscle myocytes were generated to elucidate the role played by PPARbeta signaling in these myocytes. These somatic mutant mice exhibited a muscle fiber-type switching toward lower oxidative capacity that preceded the development of obesity and diabetes, thus demonstrating that PPARbeta is instrumental in myocytes to the maintenance of oxidative fibers and that fiber-type switching is likely to be the cause and not the consequence of these metabolic disorders. We also show that PPARbeta stimulates in myocytes the expression of PGC1alpha, a coactivator of various transcription factors, known to play an important role in slow muscle fiber formation. Moreover, as the PGC1alpha promoter contains a PPAR response element, the effect of PPARbeta on the formation and/or maintenance of slow muscle fibers can be ascribed, at least in part, to a stimulation of PGC1alpha expression at the transcriptional level.

Experimental calcium oxalate crystal production and dissolution by selected wood rot fungi.

Twenty-six species of white-rotting Agaricomycotina fungi (Basidiomycota) were screened for their ability to produce calcium-oxalate (CaOx) crystals in vitro. Most were able to produce CaOx crystals in malt agar medium in the absence of additional calcium. In the same medium enriched with Ca2+, all the species produced CaOx crystals (weddellite or whewellite). Hyphae of four species (Ganoderma lucidum, Polyporus ciliatus, Pycnoporus cinnabarinus, and Trametes versicolor) were found coated with crystals (weddellite/whewellite). The production of CaOx crystals during the growth phase was confirmed by an investigation of the production kinetics for six of the species considered in the initial screening (Pleurotus citrinopileatus, Pleurotus eryngii, Pleurotus ostreatus, P. cinnabarinus, Trametes suaveolens, and T. versicolor). However, the crystals produced during the growth phase disappeared from the medium over time in four of the six species (P. citrinopileatus, P. eryngii, P. cinnabarinus, and T. suaveolens). For P. cinnabarinus, the disappearance of the crystals was correlated with a decrease in the total oxalate concentration measured in the medium from 0.65 μg mm−2 (at the maximum accumulation rate) to 0.30 μg mm−2. The decrease in the CaOx concentration was correlated with a change in mycelia morphology. The oxalate dissolution capability of all the species was also tested in a medium containing calcium oxalate as the sole source of carbon (modified Schlegel medium). Three species (Agaricus blazei, Pleurotus tuberregium, and P. ciliatus) presented a dissolution halo around the growth zone. This study shows that CaOx crystal production is a widespread phenomenon in white-rot fungi, and that an excess of Ca2+ can enhance CaOx crystal production. In addition, it shows that some white-rot fungal species are capable of dissolving CaOx crystals after growth has ceased. These results highlight a diversity of responses around the production or dissolution of calcium oxalate in white-rot fungi and reveal an unexpected potential importance of fungi on the oxalate cycle in the environment.

Response to comment on "the geometric structure of the brain fiber pathways".

In response to Catani et al., we show that corticospinal pathways adhere via sharp turns to two local grid orientations; that our studies have three times the diffusion resolution of those compared; and that the noted technical concerns, including crossing angles, do not challenge the evidence of mathematically specific geometric structure. Thus, the geometric thesis gives the best account of the available evidence.

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene.

The phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus.

Prophylaxis with resin in wood ants

Animals may use plant compounds to defend themselves against parasites. Wood ants, Formica paralugubris, incorporate pieces of solidified conifer resin into their nests. This behaviour inhibits the growth of bacteria and fungi in nest material and protects the ants against some detrimental microorganisms. Here, we studied the resin-collecting behaviour of ants under field and laboratory conditions. First, we focused on an important assumption of the self-medication hypothesis, which is that the animals deliberately choose the active plant material. In field cafeteria tests, the ants indeed showed a strong preference for resin over twigs and stones, which are building materials commonly encountered in their environment. We detected seasonal variation in the choice of ants: the preference for resin over twigs was more pronounced in spring than in summer, whereas in autumn the ants collected twigs and resin at equal rates. Second, we found almost similar seasonal patterns when comparing the collecting rates of pieces of wood that had been impregnated with turpentine (a distillate of oleoresin) and untreated pieces of wood, which reveals that the preference for resin is based on odour cues. Third, we tested whether the collection of resin is prophylactic or therapeutic. We found that the relative collection rate of resin versus stones did not depend on an experimental infection with the entomopathogenic fungus Metarhizium anisopliae in laboratory colonies. Together, these results show that the ants deliberately choose the resin and suggest that resin collection is prophylactic rather than therapeutic.

Molecular markers allow sibling species identification in red wood ants (Formica rufa group)

Red wood ants (Formica rufa group) constitute a group of species that are considered to be among the most promising bioindicators in forest ecosystems. However, because of their morphological similarity and intraspecific variability, morphological species identification can be difficult. Considerable expertise is necessary to discriminate between the sibling species F. lugubris and F. paralugubris, two species that often live in sympatry in the same Alpine forests. New taxonomic tools providing rapid and reliable species identification are needed. We present a simple and reliable molecular technique based on mtDNA (COI gene) and a restriction enzyme for discriminating between F. lugubris and F. paralugubris. We confirm the validity of this method with a Bayesian analysis based on microsatellites. This new molecular tool represents a clear breakthrough for discriminating between F. lugubris and F. paralugubris and is likely to be helpful in large-scale biomonitoring.

Molecular taxonomy of the Formica rufa group (red wood ants) (Hymenoptera: Formicidae): a new cryptic species in the Swiss Alps?

Because of their beneficial impact on forest ecosystems, European red wood ants (Formica rufa group) are protected by law in many European countries and are considered to be among the most reliable bioindicators of forest stability. However, their taxonomy has been much debated and, unfortunately, it is too often neglected. This happens mainly because the morphology-based method for species delimitation requires lots of time and experience. We therefore employed 9 microsatellite loci and mitochondrial DNA (COI gene) to verify the power of genetic markers for red wood ant species delimitation and to investigate the cryptic diversity of these ants within the Eastern Swiss Alps. We analyzed 83 nests belonging to all red wood ant species that occur in the Swiss National Park area. Genetic data indicated that these species represent different genetic pools. Moreover, results showed that Formica aquilonia YARROW, 1955 and F. paralugubris SEIFERT, 1996 often hybridize within the Park, confirming that these two species are genetically very close and could have diverged only recently. Nevertheless, microsatellites also revealed that one entire population, located in the Minger Valley and morphologically identified as F. lugubris ZETTERSTEDT, 1838, is genetically different to all other analyzed F. lugubris populations found within the same area and to other red wood ant species. These findings, confirmed by mitochondrial DNA analyses, suggest the existence of a new cryptic species within the Eastern Swiss Alps. This putative cryptic species has been provisionally named F. lugubris-A2. These results have a great importance for future conservation plans, monitoring and evolutionary studies on these protected ants.