Linking de novo assembly results with long DNA reads by dnaasm-link application

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, a result of \textit{de novo} assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of appropriate long DNA read, which improves the consistency of the resulting DNA sequences. This feature is very important, in particular for complex DNA regions, as presented in the paper. Finally, our implementation outperforms other state-of-the-art tools in terms of speed and memory requirements, which may enable the usage of the presented application for organisms with a large genome, which is not possible in~existing applications. The presented application has many advantages as (i) significant memory optimization and reduction of computation time (ii) filling the gaps through the appropriate fragment of a specified long DNA read (iii) reducing number of spanned and unspanned gaps in the existing genome drafts. The application is freely available to all users under GNU Library or Lesser General Public License version 3.0 (LGPLv3). The demo application, docker image and source code are available at http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure

Characterizations of some free random variables by properties of conditional moments of third degree polynomials

We investigate Laha-Lukacs properties of noncommutative random variables (processes). We prove that some families of free Meixner distributions can be characterized by the conditional moments of polynomial functions of degree 3. We also show that this fact has consequences in describing some free Levy processes. The proof relies on a combinatorial identity. At the end of this paper we show that this result can be extended to a q-Gausian variable.Comment: Journal of Theoretical Probability, 201

You Say Intrastate, I Say Interstate: Why We Should Call the Whole Thing Off

As society evolves, so do criminals. In the early twentieth century, America embraced the automobile, passed the Volstead Act, and created a national highway program. These developments inadvertently paved the way for interstate criminal enterprise. Infamous gangsters such as Al Capone were able to operate large-scale racketeering syndicates without fear of being prosecuted for two primary reasons: (1) states lacked jurisdiction, resources, or both to go after such criminals, and (2) there was no federal criminal statute to fill the gap left by the states. But as criminals evolve, so does society. In 1961, Congress, at the urging of Attorney General Robert F. Kennedy, passed the Travel Act. This statute makes it a federal crime to use interstate facilities to promote certain offenses that would otherwise have amounted to only state-level crimes. The Travel Act enumerates several crimes falling within its scope, including, but not limited to, gambling, prostitution, arson, bribery, and extortion. While the statute’s legislative history makes it clear that the Act targeted gangsters like Capone who were using interstate facilities to conduct interstate crimes, the Ninth Circuit has held that the federal government can exercise its jurisdiction whenever a facility of interstate commerce is used, even when that facility is used to facilitate wholly intrastate conduct. Interstate facilities include automated teller machines (ATMs), banks, cars, and cellphones, making the enumerated crimes in the Travel Act nearly always chargeable by the federal government under this holding. Given the potential breadth of the Ninth Circuit’s holding, this Note considers whether the Travel Act’s jurisdictional interstate requirement can be satisfied by the intrastate use of interstate facilities. Ultimately, this Note concludes that while reading the Act’s scope to include wholly intrastate activity may initially appear disconcerting, such an expansive interpretation should be encouraged

Errata to the Stanisław Czernik’s Biography: 1949

The subject of this paper is the writing activity of Stanisław Czernik in 1949. Czernik was an esteemed writer but concurrently he worked as censor in The Ministry of Culture and Art. He reviewed novels of many writers in the same department of Ministry where his novels were reviewed too. This paper discusses a number reviews wrote by Czernik and some reviews of Czernik’ books wrote by another censors of The Ministry

New characterization of two-state normal distribution

In this article we give a purely noncommutative criterion for the characterization of two-state normal distribution. We prove that families of two-state normal distribution can be described by relations which is similar to the conditional expectation in free probability, but has no classical analogue. We also show a generalization of Bozejko, Leinert and Speicher's formula (relating moments and noncommutative cumulants).Comment: 19 pages, 2 figures, accepted for publication by Infinite Dimensional Analysis, Quantum Probability and Related Topic

Efficient coding of spectrotemporal binaural sounds leads to emergence of the auditory space representation

To date a number of studies have shown that receptive field shapes of early sensory neurons can be reproduced by optimizing coding efficiency of natural stimulus ensembles. A still unresolved question is whether the efficient coding hypothesis explains formation of neurons which explicitly represent environmental features of different functional importance. This paper proposes that the spatial selectivity of higher auditory neurons emerges as a direct consequence of learning efficient codes for natural binaural sounds. Firstly, it is demonstrated that a linear efficient coding transform - Independent Component Analysis (ICA) trained on spectrograms of naturalistic simulated binaural sounds extracts spatial information present in the signal. A simple hierarchical ICA extension allowing for decoding of sound position is proposed. Furthermore, it is shown that units revealing spatial selectivity can be learned from a binaural recording of a natural auditory scene. In both cases a relatively small subpopulation of learned spectrogram features suffices to perform accurate sound localization. Representation of the auditory space is therefore learned in a purely unsupervised way by maximizing the coding efficiency and without any task-specific constraints. This results imply that efficient coding is a useful strategy for learning structures which allow for making behaviorally vital inferences about the environment.Comment: 22 pages, 9 figure

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Forewor