Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Angular dependence of the bulk nucleation field Hc2 of aligned MgB2 crystallites

Studies on the new MgB2 superconductor, with a critical temperature Tc ~ 39 K, have evidenced its potential for applications although intense magnetic relaxation effects limit the critical current density, Jc, at high magnetic fields. This means that effective pinning centers must be added into the material microstructure, in order to halt dissipative flux movements. Concerning the basic microscopic mechanism to explain the superconductivity in MgB2, several experimental and theoretical works have pointed to the relevance of a phonon-mediated interaction, in the framework of the BCS theory. Questions have been raised about the relevant phonon modes, and the gap and Fermi surface anisotropies, in an effort to interpret spectroscopic and thermal data that give values between 2.4 and 4.5 for the gap energy ratio. Preliminary results on the anisotropy of Hc2 have shown a ratio, between the in-plane and perpendicular directions, around 1.7 for aligned MgB2 crystallites and 1.8 for epitaxial thin films. Here we show a study on the angular dependence of Hc2 pointing to a Fermi velocity anisotropy around 2.5. This anisotropy certainly implies the use of texturization techniques to optimize Jc in MgB2 wires and other polycrystalline components.Comment: 10 pages + 4 Figs.; Revised version accepted in Phys. Rev.

Superfield covariant analysis of the divergence structure of noncommutative supersymmetric QED4_4

Commutative supersymmetric Yang-Mills is known to be renormalizable for ${\cal N} = 1, 2$, while finite for ${\cal N} = 4$. However, in the noncommutative version of the model (NCSQED$_4$) the UV/IR mechanism gives rise to infrared divergences which may spoil the perturbative expansion. In this work we pursue the study of the consistency of NCSQED$_4$ by working systematically within the covariant superfield formulation. In the Landau gauge, it has already been shown for ${\cal N} = 1$ that the gauge field two-point function is free of harmful UV/IR infrared singularities, in the one-loop approximation. Here we show that this result holds without restrictions on the number of allowed supersymmetries and for any arbitrary covariant gauge. We also investigate the divergence structure of the gauge field three-point function in the one-loop approximation. It is first proved that the cancellation of the leading UV/IR infrared divergences is a gauge invariant statement. Surprisingly, we have also found that there exist subleading harmful UV/IR infrared singularities whose cancellation only takes place in a particular covariant gauge. Thus, we conclude that these last mentioned singularities are in the gauge sector and, therefore, do not jeopardize the perturbative expansion and/or the renormalization of the theory.Comment: 36 pages, 11 figures. Minor correction

Matching Spherical Dust Solutions to Construct Cosmological Models

Conditions for smooth cosmological models are set out and applied to inhomogeneous spherically symmetric models constructed by matching together different Lemaitre-Tolman-Bondi solutions to the Einstein field equations. As an illustration the methods are applied to a collapsing dust sphere in a curved background. This describes a region which expands and then collapses to form a black hole in an Einstein de Sitter background. We show that in all such models if there is no vacuum region then the singularity must go on accreting matter for an infinite LTB time.Comment: 13 pages, Revtex; to appear Gen. Rel. Gra

Electrode Polarization Effects in Broadband Dielectric Spectroscopy

In the present work, we provide broadband dielectric spectra showing strong electrode polarization effects for various materials, belonging to very different material classes. This includes both ionic and electronic conductors as, e.g., salt solutions, ionic liquids, human blood, and colossal-dielectric-constant materials. These data are intended to provide a broad data base enabling a critical test of the validity of phenomenological and microscopic models for electrode polarization. In the present work, the results are analyzed using a simple phenomenological equivalent-circuit description, involving a distributed parallel RC circuit element for the modeling of the weakly conducting regions close to the electrodes. Excellent fits of the experimental data are achieved in this way, demonstrating the universal applicability of this approach. In the investigated ionically conducting materials, we find the universal appearance of a second dispersion region due to electrode polarization, which is only revealed if measuring down to sufficiently low frequencies. This indicates the presence of a second charge-transport process in ionic conductors with blocking electrodes.Comment: 9 pages, 6 figures, experimental data are provided in electronic form (see "Data Conservancy"

Diet of non-native pikeperch Sander lucioperca (Linnaeus, 1758) in Portugal: a first perspective on Tejo basin dietary patterns

The introduction rate of new species is expanding worldwide, being a major driver of biodiversity loss and biotic homogenisation (Strayer & Dudgeon 2010). Such phenomenon is particularly serious in Mediterranean regions (Anastácio et al. 2019) with the modification of habitats (construction of dams and barriers) associated with the establishment of non-native fish (hereafter NNF) (Radinger et al. 2019). The spread of these species promotes a cascade effect disrupting the food webs and ecosystems (Baxter et al. 2004, Clavero et al. 2013). Iberia is a bio-invasion hotspot for freshwater fish introductions containing nearly 30% of NNF relative to total number of present fish species (Leprieur et al. 2008, Leunda 2010). For instance, Portuguese freshwaters contain 20 NNF of a total of 64 fish species, and nearly half of these non-natives have arrived in the last 2 decades (1 new NNF/2 years) (Anastácio et al. 2019). Some of recent NNF are top predators with potential high impact to fish communities and aquatic food webs (Ribeiro & Leunda 2012). The pikeperch (Sander lucioperca) arrived to mainland Portugal in 1997, being firstly reported in Ermal reservoir (Ave basin, NW Portugal) (Barros et al. 1998). In less than a decade, it was spread across mainland Portugal, reaching the Guadiana basin in 2005 (Ribeiro et al. 2009a, b). Only one study has addressed the pikeperch diet in Iberian freshwaters (Perez-Bote & Roso 2012), being important to evaluate its predation pressure in different habitats (lotic and lentic) within its invaded range. Here it is described the diet of pikeperch in Tejo basin and how the diet competition varies between different habitats.info:eu-repo/semantics/publishedVersio

Intercalibration of the barrel electromagnetic calorimeter of the CMS experiment at start-up

Calibration of the relative response of the individual channels of the barrel electromagnetic calorimeter of the CMS detector was accomplished, before installation, with cosmic ray muons and test beams. One fourth of the calorimeter was exposed to a beam of high energy electrons and the relative calibration of the channels, the intercalibration, was found to be reproducible to a precision of about 0.3%. Additionally, data were collected with cosmic rays for the entire ECAL barrel during the commissioning phase. By comparing the intercalibration constants obtained with the electron beam data with those from the cosmic ray data, it is demonstrated that the latter provide an intercalibration precision of 1.5% over most of the barrel ECAL. The best intercalibration precision is expected to come from the analysis of events collected in situ during the LHC operation. Using data collected with both electrons and pion beams, several aspects of the intercalibration procedures based on electrons or neutral pions were investigated

Search for black holes and other new phenomena in high-multiplicity final states in proton-proton collisions at root s=13 TeV

Peer reviewe

Search for high-mass diphoton resonances in proton-proton collisions at 13 TeV and combination with 8 TeV search

Peer reviewe