Signal reconstruction in the EM end-cap calorimeter and check with cosmic data in the region 0< eta <3.2

In 2007, the electromagnetic end-cap calorimeter joined the ATLAS commissioning effort. Since then, calibration and cosmic muon runs are taken regularly, allowing to set-up, debug and test in situ the signal reconstruction. These are the first data in the 1.4500 MeV) have been used to perform a systematic and quantitative comparison between data and predicted physics pulse shapes in a coherent way over the entire calorimeter coverage, 0< eta <3.2. This represents the first attempt to unify barrel and end-cap in situ data in a common analysis. Results are similar in the barrel and the end-cap, only slightly worse for the latter as expected from its more complex geometry. This is the first proof of the quality of an ATLAS-like signal reconstruction in the end-caps, despite its challenging aspect, and gives confidence that the energy reconstruction is in good control over the complete electromagnetic calorimeter coverage 0< eta <3.2

Antifungal activity of Myrtus communis and Zygophyllum album extracts against human pathogenic fungi

Fungal infections have been increasing in recent years due to a growing number of high-risk patients, particularly immunocompromised hosts. Currently, medicinal plants are known for their properties due to their essential oils and phenolic compounds. They have been empirically used as antimicrobial agents. So the composition of the phenolic extracts and essential oils of Myrtus communis and Zygophyllum album and their antifungal activity on&nbsp;Candida albicans,&nbsp;Aspergillus fumigatus fungal strains were studied. In this fact, essential oils from the aerial parts of the plant were obtained by hydrodistillation and analyzed by GC and GC-MS, for the phenolic extracts, several extraction methods with a preliminary phytochemical study were applied.&nbsp;The oils showed high contents of α-pinene and cineol for M. communis and verbenone and caryophyllene for the Z. album. The MIC and minimal lethal concentration were used to evaluate the antifungal activity against Candida and Aspergillus strains. Results showed that M. communis and Z. album essential oil and phenolic extracts exhibited a significant activity against clinically relevant fungi, a significant antifungal activity of the two extracts studied (MCA and ZAM) was observed on C. albicans of these, two extracts, MCA was found to be most active with an MFC value of 25 mg/ml versus 100 mg/ml for ZAM. Nevertheless, the essential oils exhibited stronger antifungal activity than the phenolic extracts. The present study indicates that&nbsp;the two medicinal plants have considerable antifungal activity, deserving further investigation for clinical applications. DOI: http://dx.doi.org/10.5281/zenodo.375120

PhylomeDB: a database for genome-wide collections of gene phylogenies

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.e

A simple device for in-situ direct shear and sinkage tests

This work introduces a simple device designed to perform in-situ direct shear and sinkage tests on granular materials as sand, clays, or regolith. It consists of a box nested within a larger box. Both have open bottoms, allowing them to be lowered into the material. Afterwards, two rotating plates on opposite sides of the outer box will rotate outwards in order to clear regolith on either side, providing room for the inner box to move relative to the plates and perform a shear test without the resistance of the surrounding soil. From this test, Coulomb parameters, including cohesion and internal friction angle, as well as, Bekker parameters can be inferred. This device has been designed for a laboratory setting, but with few modifications, could be put on the underside of a rover for use in a remote location. The goal behind this work is to ultimately create a compact, but accurate measuring tool to put onto a rover or any kind of exploratory vehicle to test for regolith properties of celestial bodies

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416 093 trees and 165 840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic access. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana, but also alternative model species such as the human pathogen Candida albicans, or the pea aphid Acyrtosiphon pisum. Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights

Expanding the scope of density derived electrostatic and chemical charge partitioning to thousands of atoms

The density derived electrostatic and chemical (DDEC/c3) method is implemented into the onetep program to compute net atomic charges (NACs), as well as higher-order atomic multipole moments, of molecules, dense solids, nanoclusters, liquids, and biomolecules using linear-scaling density functional theory (DFT) in a distributed memory parallel computing environment. For a &gt;1000 atom model of the oxygenated myoglobin protein, the DDEC/c3 net charge of the adsorbed oxygen molecule is approximately -1e (in agreement with the Weiss model) using a dynamical mean field theory treatment of the iron atom, but much smaller in magnitude when using the generalized gradient approximation. For GaAs semiconducting nanorods, the system dipole moment using the DDEC/c3 NACs is about 5% higher in magnitude than the dipole computed directly from the quantum mechanical electron density distribution, and the DDEC/c3 NACs reproduce the electrostatic potential to within approximately 0.1 V on the nanorod’s solvent-accessible surface. As examples of conducting materials, we study (i) a 55-atom Pt cluster with an adsorbed CO molecule and (ii) the dense solids Mo2C and Pd3V. Our results for solid Mo2C and Pd3V confirm the necessity of a constraint enforcing exponentially decaying electron density in the tails of buried atoms

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized