Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments. In previous work, we presented a novel algorithm that allows the BWT of human genome scale data to be computed on very moderate hardware, thus enabling us to investigate the BWT as a tool for the compression of such datasets. Results We first used simulated reads to explore the relationship between the level of compression and the error rate, the length of the reads and the level of sampling of the underlying genome and compare choices of second-stage compression algorithm. We demonstrate that compression may be greatly improved by a particular reordering of the sequences in the collection and give a novel `implicit sorting' strategy that enables these benefits to be realised without the overhead of sorting the reads. With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming a small proportion of low-quality bases from the reads improves the compression still further). This is more than 4 times smaller than the size achieved by a standard BWT-based compressor (bzip2) on the untrimmed reads, but an important further advantage of our approach is that it facilitates the building of compressed full text indexes such as the FM-index on large-scale DNA sequence collections.Comment: Version here is as submitted to Bioinformatics and is same as the previously archived version. This submission registers the fact that the advanced access version is now available at http://bioinformatics.oxfordjournals.org/content/early/2012/05/02/bioinformatics.bts173.abstract . Bioinformatics should be considered as the original place of publication of this article, please cite accordingl

Towards Communication-Efficient Quantum Oblivious Key Distribution

Oblivious Transfer, a fundamental problem in the field of secure multi-party computation is defined as follows: A database DB of N bits held by Bob is queried by a user Alice who is interested in the bit DB_b in such a way that (1) Alice learns DB_b and only DB_b and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi et al. [Phys. Rev. A, 83(2), 022301, Feb 2011] proposed a protocol for Oblivious Transfer using well known QKD techniques to establish an Oblivious Key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like impossibility of perfectly distinguishing non-orthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of SARG04). However, their Quantum Oblivious Key Distribution (QOKD) protocol requires a communication complexity of O(N log N). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.Comment: 7 page

Weak and strong electronic correlations in Fe superconductors

In this chapter the strength of electronic correlations in the normal phase of Fe-superconductors is discussed. It will be shown that the agreement between a wealth of experiments and DFT+DMFT or similar approaches supports a scenario in which strongly-correlated and weakly-correlated electrons coexist in the conduction bands of these materials. I will then reverse-engineer the realistic calculations and justify this scenario in terms of simpler behaviors easily interpreted through model results. All pieces come together to show that Hund's coupling, besides being responsible for the electronic correlations even in absence of a strong Coulomb repulsion is also the origin of a subtle emergent behavior: orbital decoupling. Indeed Hund's exchange decouples the charge excitations in the different Iron orbitals involved in the conduction bands thus causing an independent tuning of the degree of electronic correlation in each one of them. The latter becomes sensitive almost only to the offset of the orbital population from half-filling, where a Mott insulating state is invariably realized at these interaction strengths. Depending on the difference in orbital population a different 'Mottness' affects each orbital, and thus reflects in the conduction bands and in the Fermi surfaces depending on the orbital content.Comment: Book Chapte

Orbital-selective Mott Transitions in a Doped Two-band Hubbard Model

We extend previous studies on orbital-selective Mott transitions in the paramagnetic state of the half-filled degenerate two-band Hubbard model to the general doped case, using a high-precision quantum Monte Carlo dynamical mean-field theory solver. For sufficiently strong interactions, orbital-selective Mott transitions as a function of total band filling are clearly visible in the band-specific fillings, quasiparticle weights, double occupancies, and spectra. The results are contrasted with those of single-band models for similar correlation strengths.Comment: 12 pages, 12 figure

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined

Genome variations: Effects on the robustness of neuroevolved control for swarm robotics systems

Manual design of self-organized behavioral control for swarms of robots is a complex task. Neuroevolution has proved a viable alternative given its capacity to automatically synthesize controllers. In this paper, we introduce the concept of Genome Variations (GV) in the neuroevolution of behavioral control for robotic swarms. In an evolutionary setup with GV, a slight mutation is applied to the evolving neural network parameters before they are copied to the robots in a swarm. The genome variation is individual to each robot, thereby generating a slightly heterogeneous swarm. GV represents a novel approach to the evolution of robust behaviors, expected to generate more stable and robust individual controllers, and bene t swarm behaviors that can deal with small heterogeneities in the behavior of other members in the swarm. We conduct experiments using an aggregation task, and compare the evolved solutions to solutions evolved under ideal, noise-free conditions, and to solutions evolved with traditional sensor noise.info:eu-repo/semantics/acceptedVersio

Variation of Absorption Angstrom Exponent in Aerosols From Different Emission Sources

The absorption Angstrom exponent (AAE) describes the spectral dependence of light absorption by aerosols. AAE is typically used to differentiate between different aerosol types for example., black carbon, brown carbon, and dust particles. In this study, the variation of AAE was investigated mainly in fresh aerosol emissions from different fuel and combustion types, including emissions from ships, buses, coal-fired power plants, and residential wood burning. The results were assembled to provide a compendium of AAE values from different emission sources. A dual-spot aethalometer (AE33) was used in all measurements to obtain the light absorption coefficients at seven wavelengths (370-950 nm). AAE(470/950) varied greatly between the different emission sources, ranging from -0.2 +/- 0.7 to 3.0 +/- 0.8. The correlation between the AAE(470/950) and AAE(370-950) results was good (R-2 = 0.95) and the mean bias error between these was 0.02. In the ship engine exhaust emissions, the highest AAE(470/950) values (up to 2.0 +/- 0.1) were observed when high sulfur content heavy fuel oil was used, whereas low sulfur content fuels had the lowest AAE(470/950) (0.9-1.1). In the diesel bus exhaust emissions, AAE(470/950) increased in the order of acceleration (0.8 +/- 0.1), deceleration (1.1 +/- 0.1), and steady driving (1.2 +/- 0.1). In the coal-fired power plant emissions, the variation of AAE(470/950) was substantial (from -0.1 +/- 2.1 to 0.9 +/- 1.6) due to the differences in the fuels and flue gas cleaning conditions. Fresh wood-burning derived aerosols had AAE(470/950) from 1.1 +/- 0.1 (modern masonry heater) to 1.4 +/- 0.1 (pellet boiler), lower than typically associated with wood burning, while the burn cycle phase affected AAE variation.Peer reviewe

First laser ions at the CERN-MEDICIS facility

The CERN-MEDICIS facility aims to produce emerging medical radionuclides for the theranostics approach in nuclear medicine with mass separation of ion beams. To enhance the radioisotope yield and purity of collected samples, the resonance ionization laser ion source MELISSA was constructed, and provided the first laser ions at the facility in 2019. Several operational tests were accomplished to investigate its performance in preparation for the upcoming production of terbium radioisotopes, which are of particular interest for medical applications. © 2020, The Author(s).KU LeuvenHorizon 2020: 642889 MEDICIS-PROMED05P12UMCIA, 05P15UMCIAOpen Access funding provided by Projekt DEAL. We would like to acknowledge the help and assistance from the whole MEDICIS collaboration; from CERN-ISOLDE Technical and Physical groups. This research project has been supported by a Marie Skłodowska-Curie Innovative Training Network Fellowship of the European Commission’s Horizon 2020 Programme under contract number 642889 MEDICIS-PROMED; by the German Federal Ministry of Education and Research under the consecutive projects 05P12UMCIA and 05P15UMCIA; by the Research Foundation Flanders FWO (Belgium) and by a KU Leuven START grant

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13