Dynamic consolidation problems in saturated soils solved through u-w formulation in a LME meshfree framework

A meshfree numerical model, based on the principle of Local Maximum Entropy (LME), including a B-bar algorithm to avoid instabilities, is applied to solve axisymmetric consolidation problems in elastic saturated soils. This numerical scheme has been previously validated for purely elastic problems without water (mono phase), as well as for steady seepage in elastic porous media. Hereinafter, an implementation of the novel numerical method in the axisymmetric configuration is proposed, and the model is validated for well known theoretical problems of consolidation in saturated soils, under both static and dynamic conditions with available analytical solutions. The solutions obtained with the new methodology are compared with a finite element commercial software for a set of examples. After validated, solutions for dynamic radial consolidation and sinks, which have not been found elsewhere in the literature, are presented as a novelty. This new numerical approach is demonstrated to be feasible for this kind of problems in porous media, particularly for high frequency, dynamic problems, for which very few results have been found in the literature in spite of their high practical importance

Association between competition and facilitation processes and vegetation spatial patterns in alpha steppes

11 páginas, 5 figuras, 3 tablas.-- El PDF del artículo es la versión post-print.In semiarid ecosystems, the self-organized spatial patterns of plants associated with catastrophic shifts can emerge from a variety of processes. In this study, on moderate slopes where Stipa tenacissima cover was high, the self-organization of some of the typical species of semiarid Mediterranean matorral (Phlomis purpurea, Sideritis oxteosylla, Helianthemum almeriense, and Brachypodium retusum) was negatively correlated with Stipa cover. The extent of Stipa cover did not affect desert pioneer species, such as Artemisia herba-alba, Fagonia cretica, and Launaea lanifera. On pronounced slopes, the self-organizing structure of brushwood vegetation did not vary predictably with the amount of Stipa cover. We examined the competition/facilitation processes associated with self-organizing patterns in the dwarf shrub (Phl. purpurea) and the half shrub (H. almeriense). The developmental stability of H. almeriense was positively correlated with Stipa cover, which was expected because they are associated species in this seral thyme brushwood community. Indeed, facilitation processes were manifested by the developmental stability increases under the Stipa canopy, particularly on high slope areas, where Stipa is less competitive. In Phl. purpurea, negative feedback processes from competition with Stipa were manifested where Stipa cover was high and on low slopes (developmental instability increased). In general, competition with Stipa on low slopes tended to decrease plant self-organization.We gratefully acknowledge support from the Spanish CICYT (Project REN2002-04668/GLO, Efectos de la fragmentación y uso del suelo en la conservación y dinámica de las zonas esteparias Mediterráneas).Peer reviewe

Malignant pilomatricoma with multiple bone metastases in a dog: Histological and immunohistochemical study.

An eleven year-old mongrel dog was referred with a history of left forelimb lameness and an ulcerated mass on the neck. Histologically, the cutaneous neoplasm revealed cystic lobules composed of basaloid cells with abrupt transition to central keratotic material, containing pycnotic and shadow cells. Approximately 3 months after primary diagnosis, a lesion of the cortical bone on the left humerus was observed using X-ray. Samples obtained from the humerus were processed for histopathological examination and the neoplastic tissue was observed to be similar to the type identified in the neck. Based on these findings, the tumor was diagnosed as a malignant pilomatricoma (MP) with bone metastasis. MP is a rare skin tumor that originates from hair matrix cells. To date, only nine reports have been presented in dogs. In the present study, we discuss the cytological and histological patterns of MP, confirmed by immunohistochemistry using β catenin antibody

Unbiased taxonomic annotation of metagenomic samples

The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under thereceiver operating characteristic (ROC) curve andF-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample.Peer ReviewedPostprint (published version

Field theory for a reaction-diffusion model of quasispecies dynamics

RNA viruses are known to replicate with extremely high mutation rates. These rates are actually close to the so-called error threshold. This threshold is in fact a critical point beyond which genetic information is lost through a second-order phase transition, which has been dubbed the ``error catastrophe.'' Here we explore this phenomenon using a field theory approximation to the spatially extended Swetina-Schuster quasispecies model [J. Swetina and P. Schuster, Biophys. Chem. {\bf 16}, 329 (1982)], a single-sharp-peak landscape. In analogy with standard absorbing-state phase transitions, we develop a reaction-diffusion model whose discrete rules mimic the Swetina-Schuster model. The field theory representation of the reaction-diffusion system is constructed. The proposed field theory belongs to the same universality class than a conserved reaction-diffusion model previously proposed [F. van Wijland {\em et al.}, Physica A {\bf 251}, 179 (1998)]. From the field theory, we obtain the full set of exponents that characterize the critical behavior at the error threshold. Our results present the error catastrophe from a new point of view and suggest that spatial degrees of freedom can modify several mean field predictions previously considered, leading to the definition of characteristic exponents that could be experimentally measurable.Comment: 13 page

Fractal dimension analysis of grey matter in multiple sclerosis

The fractal dimension (FD) is a quantitative parameter that characterizes the morphometric variability of a complex object. Among other applications, FD has been used to identify abnormalities of the human brain in conventional magnetic resonance imaging (MRI), including white matter abnormalities in patients with Multiple Sclerosis (MS). Extensive grey matter (GM) pathology has been recently identified in MS and it appears to be a key factor in long-term disability. The aim of the present work was to assess whether FD measurement of GM in T1 MRI sequences can identify GM abnormalities in patients with MS in the early phase of the disease. A voxel-based morphometry approach optimized for MS was used to obtain the segmented brain, where we later calculated the three-dimensional FD of the GM in MS patients and healthy controls.We found that patients with MS had a significant increase in the FD of the GM compared to controls. Such differences were present even in patients with short disease durations, including patients with first attacks of MS. In addition, the FD of the GM correlated with T1 and T2 lesion load, but not with GM atrophy or disability. The FD abnormalities of the GM here detected differed from the previously published FD of the white matter in MS, suggesting that different pathological processes were taking place in each structure. These results indicate that GM morphology is abnormal in patients with MS and that this alteration appears early in the course of the disease

Magnetization reversal and exchange bias effects in hard/soft ferromagnetic bilayers with orthogonal anisotropies

The magnetization reversal processes are discussed for exchange-coupled ferromagnetic hard/soft bilayers made from Co[subscript 0.66]Cr[subscript 0.22]Pt[subscript 0.12] (10 and 20 nm)/Ni (from 0 to 40 nm) films with out-of-plane and in-plane magnetic easy axes respectively, based on room temperature hysteresis loops and first-order reversal curve analysis. On increasing the Ni layer thicknesses, the easy axis of the bilayer reorients from out-of-plane to in-plane. An exchange bias effect, consisting of a shift of the in-plane minor hysteresis loops along the field axis, was observed at room temperature after in-plane saturation. This effect was associated with specific ferromagnetic domain configurations experimentally determined by polarized neutron reflectivity. On the other hand, perpendicular exchange bias effect was revealed from the out-of-plane hysteresis loops and it was attributed to residual domains in the magnetically hard layer.National Science Foundation (U.S.)MIT-Spain/La Cambra de Barcelona Seed Fun

PARL deficiency in mouse causes Complex III defects, coenzyme Q depletion, and Leigh-like syndrome

The mitochondrial intramembrane rhomboid protease PARL has been implicated in diverse functions in vitro, but its physiological role in vivo remains unclear. Here we show that ablation in mouse causes a necrotizing encephalomyelopathy similar to Leigh syndrome, a mitochondrial disease characterized by disrupted energy production. Mice with conditional PARL deficiency in the nervous system, but not in muscle, develop a similar phenotype as germline KOs, demonstrating the vital role of PARL in neurological homeostasis. Genetic modification of two major PARL substrates, PINK1 and PGAM5, do not modify this severe neurological phenotype. brain mitochondria are affected by progressive ultrastructural changes and by defects in Complex III (CIII) activity, coenzyme Q (CoQ) biosynthesis, and mitochondrial calcium metabolism. PARL is necessary for the stable expression of TTC19, which is required for CIII activity, and of COQ4, which is essential in CoQ biosynthesis. Thus, PARL plays a previously overlooked constitutive role in the maintenance of the respiratory chain in the nervous system, and its deficiency causes progressive mitochondrial dysfunction and structural abnormalities leading to neuronal necrosis and Leigh-like syndrome

Signature inversion in semi-decoupled bands: Residual interaction between h9/2 protons and i13/2 neutrons

Semi-decoupled bands based on the πh9/2 ⊗ vi13/2 configuration are observed in 162Tm,164Tm and 174Ta. Spins assigned to these bands imply an inversion of the expected signature splitting, which is interpreted as being the result of a residual proton-neutron interactionComisión Interministerial de Ciencia y Tecnología PB95-0533US Dept. of Energy DE-FGOS- 92ER4069

Divergent abiotic spectral pathways unravel pathogen stress signals across species

Abstract: Plant pathogens pose increasing threats to global food security, causing yield losses that exceed 30% in food-deficit regions. Xylella fastidiosa (Xf) represents the major transboundary plant pest and one of the world’s most damaging pathogens in terms of socioeconomic impact. Spectral screening methods are critical to detect non-visual symptoms of early infection and prevent spread. However, the subtle pathogen-induced physiological alterations that are spectrally detectable are entangled with the dynamics of abiotic stresses. Here, using airborne spectroscopy and thermal scanning of areas covering more than one million trees of different species, infections and water stress levels, we reveal the existence of divergent pathogen- and host-specific spectral pathways that can disentangle biotic-induced symptoms. We demonstrate that uncoupling this biotic–abiotic spectral dynamics diminishes the uncertainty in the Xf detection to below 6% across different hosts. Assessing these deviating pathways against another harmful vascular pathogen that produces analogous symptoms, Verticillium dahliae, the divergent routes remained pathogen- and host-specific, revealing detection accuracies exceeding 92% across pathosystems. These urgently needed hyperspectral methods advance early detection of devastating pathogens to reduce the billions in crop losses worldwide