Asterias: a parallelized web-based suite for the analysis of expression and aCGH data

Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the user to obtain additional information for user-selected genes by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data; converting between different types of gene/clone and protein identifiers; filtering and imputation; finding differentially expressed genes related to patient class and survival data; searching for models of class prediction; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity; searching for molecular signatures and predictive genes with survival data; detecting regions of genomic DNA gain or loss. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.Comment: web based application; 3 figure

Alginate Hydrogels as Scaffolds and Delivery Systems to Repair the Damaged Spinal Cord

Alginate (ALG) is a lineal hydrophilic polysaccharide present in brown algae cell walls, which turns into a gel state when hydrated. Gelation readily produces a series of three dimensional (3D) architectures like fibers, capillaries, and microspheres, used as biosensors and bio‐actuators in a plethora of biomedical applications like drug delivery and wound healing. Hydrogels have made a great impact on regenerative medicine and tissue engineering because they are able to mimic the mechanical properties of natural tissues due to their high water content. Recent advances in neurosciences have led to promising strategies for repairing and/or regenerating the damaged nervous system. Spinal cord injury (SCI) is particularly challenging, owing to its devastating medical, human, and social consequences. Although effective therapies to repair the damaged spinal cord (SC) are still lacking, multiple pharmacological, genetic, and cell‐based therapies are currently under study. In this framework, ALG hydrogels constitute a source of potential tools for the development of implants capable of promoting axonal growth and/or delivering cells or drugs at specific damaged sites, which may result in therapeutic strategies for SCI. In this mini‐review, the current state of the art of ALG applications in neural tissues for repairing the damaged spinal cord is discussed

Music Boundary Detection using Convolutional Neural Networks: A comparative analysis of combined input features

The analysis of the structure of musical pieces is a task that remains a challenge for Artificial Intelligence, especially in the field of Deep Learning. It requires prior identification of structural boundaries of the music pieces. This structural boundary analysis has recently been studied with unsupervised methods and \textit{end-to-end} techniques such as Convolutional Neural Networks (CNN) using Mel-Scaled Log-magnitude Spectograms features (MLS), Self-Similarity Matrices (SSM) or Self-Similarity Lag Matrices (SSLM) as inputs and trained with human annotations. Several studies have been published divided into unsupervised and \textit{end-to-end} methods in which pre-processing is done in different ways, using different distance metrics and audio characteristics, so a generalized pre-processing method to compute model inputs is missing. The objective of this work is to establish a general method of pre-processing these inputs by comparing the inputs calculated from different pooling strategies, distance metrics and audio characteristics, also taking into account the computing time to obtain them. We also establish the most effective combination of inputs to be delivered to the CNN in order to establish the most efficient way to extract the limits of the structure of the music pieces. With an adequate combination of input matrices and pooling strategies we obtain a measurement accuracy $F_1$ of 0.411 that outperforms the current one obtained under the same conditions

In vivo investigation of the tissue response to commercial Teflon insulin infusion sets in large swine for 14 days: the effect of angle of insertion on tissue histology and insulin spread within the subcutaneous tissue.

Objective: This study investigated the effects of the inflammatory tissue response (ITR) to an insulin infusion set (IIS) on insulin bolus spread over wear time, as well as the effect of cannula insertion angle on the ITR, bolus shape, and pump tubing pressure. Research design and methods: Angled or straight IISs were inserted every other day for 14 days into the subcutaneous tissue of 11 swine and insulin was delivered continuously. Prior to euthanasia, a 70 µL bolus of insulin/X-ray contrast agent was infused while recording a pressure profile (peak tubing pressure, pmax; area under the pressure curve, AUC), followed by the excision of the tissue-catheter specimen. Bolus surface area (SA) and volume (V) were assessed via micro-CT. Tissue was stained to analyze total area of inflammation (TAI) and inflammatory layer thickness (ILT) surrounding the cannula. Results: A bolus delivered through an angled IIS had a larger mean SA than a bolus delivered through a straight cannula (314.0±84.2 mm2 vs 229.0±99.7 mm2, p\u3c0.001) and a larger volume (198.7±66.9 mm3 vs 145.0±65.9 mm3, p=0.001). Both decreased significantly over wear time, independent of angle. There was a significant difference in TAI (angled, 9.1±4.0 mm2 vs straight, 14.3±8.6 mm2, p\u3c0.001) and ILT (angled, 0.7±0.4 vs straight, 1.2±0.7 mm, p\u3c0.001). pmax (p=0.005) and AUC (p=0.014) were lower using angled IIS. As ILT increased, pmax increased, while SA and V decreased. Conclusions: The progression of the ITR directly affected bolus shape and tubing pressure. Although straight insertion is clinically preferred, our data suggest that an angled IIS elicits lower grades of ITR and delivers a bolus with lower tubing pressure and greater SA and V. The subcutaneous environment plays a crucial role in IIS longevity, and the insertion angle needs to be considered in future IIS designs and clinical trials

Effect of preparation conditions on the polymorphism and transport properties of lanthanum molybdates

In this work, La6MoO12-based compounds were investigated as part of a new family of materials very competitive as hydrogen separation membranes [1,2]. La5.4MoO11.1 was synthesized by the freeze-drying precursor method and the calcination conditions were optimized in order to obtain single phases. Several cooling rates were applied and different polymorphs were obtained: a simple cubic fluorite symmetry (Fm-3m) for the sample cooled by quenching, and two different rhombohedral (R-3) space groups for the samples cooled at 50 ºC•min-1 and 0.5 ºC•min-1 (see Figure below). For the quenched sample, the Rietveld refinement was satisfactory in a Fm-3m space group. For the other two compositions no structural model was available and were indexed in a R-3 space group, however some small reflections were not given any intensity by the model used. Transmission electron microscopy confirmed the presence of superstructures for those samples. All ceramic materials were obtained with relative densities close to 100% after sintering at 1500 ºC. Stability studies demonstrated that all three polymorphs were stable in oxidizing and reducing conditions at 800 ºC for 48 hours. The three samples present a significant proton contribution to the conductivity at temperatures lower than 800 ºC. These results were confirmed by thermogravimetric analysis. The highest conductivity values were observed for the samples prepared by quenching. The three polymorphs display a small p-type electronic contribution to the overall conductivity in oxidizing conditions and n-type electronic one in very reducing conditions, much more significant for the samples cooled by quenching and at 50 ºC•min-1.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Exploring Halo Substructure with Giant Stars: Spectroscopy of Stars in the Galactic Anticenter Stellar Structure

To determine the nature of the recently discovered, ring-like stellar structure at the Galactic anticenter, we have collected spectra of a set of presumed constituent M giants selected from the 2MASS point source catalog. Radial velocities have been obtained for stars spanning ~100 degrees, exhibiting a trend in velocity with Galactic longitude and an estimated dispersion of 20 +/- 4 km/sec. A mean metallicity [Fe/H] = -0.4 +/- 0.3 measured for these stars combines with previous evidence from the literature to suggest a population with a significant metallicity spread. In addition, a curious alignment of at least four globular clusters of lower mean metallicity is noted to be spatially and kinematically consistent with this stellar distribution. We interpret the M giant sample position and velocity variation with Galactic longitude as suggestive of a satellite galaxy currently undergoing tidal disruption in a non-circular, prograde orbit about the Milky Way.Comment: (1) University of Virginia, 4 pages, 3 figures, accepted for publication in The Astrophysical Journal Letter

Permutation Invariant Recurrent Neural Networks for Sound Source Tracking Applications

Many multi-source localization and tracking models based on neural networks use one or several recurrent layers at their final stages to track the movement of the sources. Conventional recurrent neural networks (RNNs), such as the long short-term memories (LSTMs) or the gated recurrent units (GRUs), take a vector as their input and use another vector to store their state. However, this approach results in the information from all the sources being contained in a single ordered vector, which is not optimal for permutation-invariant problems such as multi-source tracking. In this paper, we present a new recurrent architecture that uses unordered sets to represent both its input and its state and that is invariant to the permutations of the input set and equivariant to the permutations of the state set. Hence, the information of every sound source is represented in an individual embedding and the new estimates are assigned to the tracked trajectories regardless of their order.Comment: Accepted for publication at Forum Acusticum 202