bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of sub-stoichiometric hydrogenated silicon oxide films for surface passivation of crystalline silicon solar cells
Authors: Einsele Florian , Beyer Wolfhard , Rau Uwe
Published: September 2012

Thermal stability of passivating layers in amorphous/crystalline silicon (a-Si/c-Si) heterojunction solar cells is crucial for industrial processing and long-term device stability. Hydrogenated amorphous silicon (a-Si:H) yields outstanding surface passivation as atomic hydrogen saturates silicon dangling bonds at the a-Si/c-Si interface. Yet, a-Si surface passivation typically starts to degrade already at annealing temperatures in the range of 200 to 250 °C depending on annealing time, and optical absorption in front layers of a-Si reduces the short circuit current density. We show that oxygen incorporation into a-Si:H films enhances the thermal stability of the passivation and reduces parasitic absorption. We further show that for good passivation of the a-Si/c-Si interface, a compact material structure of the a-Si:O:H films is required where atomic hydrogen is the dominating type of diffusing hydrogen species. For plasma deposited a-Si:O:H films, oxygen incorporation of up to 10 at. % leads to an increase of the optical band gap while the hydrogen concentration is almost constant at approximately 10 at. %. For oxygen concentrations below 3%, the films yield surface recombination velocities as low as 10 cm/s on p-type wafers, and the temperature stability improves by about 50 K compared to pure a-Si:H. For films with relatively low oxygen content, hydrogen effusion spectra and Fourier transform infrared spectroscopy (FTIR) indicate a compact microstructure where only atomic H diffuses. For oxygen concentrations above 3%, the passivation quality reduces and H effusion and FTIR suggest the formation of an open, void-rich material where molecular H2 diffuses. In this case, annealing above 400 °C results in improved interface passivation, presumably due to a densification of the material. Likely, this densification results in an increased density of atomic H, which saturates Si dangling bonds near the c-Si interface.
Analytical model for current distribution in large-area organic light emitting diodes with parallel metal grid lines
Authors: Barink Marco , Harkema Stephan
Published: September 2012

In this study, an analytical solution for the current distribution of a large-area organic light emitting diodes (OLEDs) with parallel equidistant gridlines is derived. In contrast to numerical methods, this analytical solution allows for a very quick scan of the OLED design space, even for very large OLEDs, providing insight how different model parameters affect each other. The assumptions within the analytical derivation are verified with finite element simulations of the same OLED. Furthermore, the analytically calculated light distribution was experimentally verified by measuring the light distribution on a large-area OLED.
Exact non-additive kinetic potentials in realistic chemical systems
Authors: de Silva Piotr , Wesolowski Tomasz A.
Published: September 2012

In methods based on frozen-density embedding theory or subsystem formulation of density functional theory, the non-additive kinetic potential (\documentclass[12pt]{minimal}\begin{document}$v_t^{nad}(\mathbf {r})$\end{document}vtnad(r)) needs to be approximated. Since \documentclass[12pt]{minimal}\begin{document}$v_t^{nad}(\mathbf {r})$\end{document}vtnad(r) is defined as a bifunctional, the common strategies rely on approximating \documentclass[12pt]{minimal}\begin{document}$v_t^{nad}[\rho _A,\rho _B](\mathbf {r})$\end{document}vtnad[ρA,ρB](r). In this work, the exact potentials (not bifunctionals) are constructed for chemically relevant pairs of electron densities (ρA and ρB) representing: dissociating molecules, two parts of a molecule linked by a covalent bond, or valence and core electrons. The method used is applicable only for particular case, where ρA is a one-electron or spin-compensated two-electron density, for which the analytic relation between the density and potential exists. The sum ρA + ρB is, however, not limited to such restrictions. Kohn-Sham molecular densities are used for this purpose. The constructed potentials are analyzed to identify the properties which must be taken into account when constructing approximations to the corresponding bifunctional. It is comprehensively shown that the full von Weizsäcker component is indispensable in order to approximate adequately the non-additive kinetic potential for such pairs of densities.
Real-space, real-time calculation of dynamic hyperpolarizabilities
Authors: Goncharov Vladimir A. , Varga Kalman
Published: September 2012

The finite-difference method to calculate hyperpolarizabilities is generalized for dynamical case. The calculation of the dynamical hyperpolarizabilities from non-perturbative, explicitly time-dependent single particle states obtained in the framework of the time-dependent density functional theory, is implemented in real space and real time. The optical response functions up to the third order are extracted in frequency domain. The present approach is free of deficiencies associated with atom centered basis sets and allows treatment of large molecules. The calculated results are in good agreement with experiments and with other theoretical calculations for various test cases.
The effect of interfaces on magnetic activation volumes in single crystal Co2FeSi Heusler alloy thin films
Authors: Sagar J. , Sukegawa H. , Lari L. , Lazarov V. K. , Mitani S. , O'Grady K. , Hirohata A.
Published: September 2012

Structural and magnetization reversal studies have been carried out on single crystal Co2FeSi thin films grown on MgO (001) substrates. The films are highly L21 ordered after annealing above 500 °C. Magnetization reversal has been investigated by measurements of the activation volumes (Vact) within the films. This volume represents the unit of reversal in a magnetic material. Vact (∼4 × 103 nm3) has been found to be independent of the physical structure. Vact is found to correspond to an array of periodic misfit dislocations at the Co2FeSi/MgO interface. Such a small Vact potentially prevents coherent magnetization reversal as required for giant magnetoresistance or tunnel magnetoresistance devices.
High resolution space quartz-flexure accelerometer based on capacitive sensing and electrostatic control technology
Authors: Tian W. , Wu S. C. , Zhou Z. B. , Qu S. B. , Bai Y. Z. , Luo J.
Published: September 2012

High precision accelerometer plays an important role in space scientific and technical applications. A quartz-flexure accelerometer operating in low frequency range, having a resolution of better than 1 ng/Hz1/2, has been designed based on advanced capacitive sensing and electrostatic control technologies. A high precision capacitance displacement transducer with a resolution of better than 2 × 10−6 pF/Hz1/2 above 0.1 Hz, is used to measure the motion of the proof mass, and the mechanical stiffness of the spring oscillator is compensated by adjusting the voltage between the proof mass and the electrodes to induce a proper negative electrostatic stiffness, which increases the mechanical sensitivity and also suppresses the position measurement noise down to 3 × 10−10 g/Hz1/2 at 0.1 Hz. A high resolution analog-to-digital converter is used to directly readout the feedback voltage applied on the electrodes in order to suppress the action noise to 4 × 10−10 g/Hz1/2 at 0.1 Hz. A prototype of the quartz-flexure accelerometer has been developed and tested, and the preliminary experimental result shows that its resolution comes to about 8 ng/Hz1/2 at 0.1 Hz, which is mainly limited by its mechanical thermal noise due to low quality factor.
Hardness, yield strength, and plastic flow in thin film metallic-glass
Authors: Ye J. C. , Chu J. P. , Chen Y. C. , Wang Q. , Yang Y.
Published: September 2012

Thin film metallic-glasses (TFMGs) are a promising structural material for fabricating the next generation of micro- and nano-devices; however, a comprehensive study is still lacking today for understanding their mechanical behaviors. In this article, we present a systematic study on the Zr53Cu29Al12Ni6 TFMGs with varying thicknesses. Other than the intrinsic factor of structural amorphousness, our study pinpoints other extrinsic variables that could affect the hardness and yield strength of the TFMGs. Furthermore, the experimental results from microcompression show that the plastic flow in the TFMG-based micropillars exhibit strong sample size-and-shape dependence, which manifests as a smooth plastic deformation transition from the inhomogeneous to homogeneous mode when the TFMG-based micropillars with a submicron-scale film thickness are deformed into the shape of a low aspect ratio.
A high-efficiency overmoded klystron-like relativistic backward wave oscillator with low guiding magnetic field
Authors: Xiao Renzhen , Tan Weibing , Li Xiaoze , Song Zhimin , Sun Jun , Chen Changhua
Published: September 2012

A klystron-like relativistic backward wave oscillator with a ratio of transverse dimension to free-space wavelength being about four is presented. In the beam-wave interaction region, the electron beam interacts with surface wave and volume wave simultaneously. The cathode holder plays an important role in the reflection of backward waves. A guard electrode, an electron collector ring, and a reflection ring are used to optimize the beam-wave interaction. The particle in cell simulation results reveal that microwaves with a power of 2 GW and a frequency of 12.3 GHz are generated with an efficiency of 42% when the diode voltage is 400 kV, the beam current 12 kA, and the magnetic field 0.48 T.
Undamped electrostatic plasma waves
Authors: Valentini F. , Perrone D. , Califano F. , Pegoraro F. , Veltri P. , Morrison P. J. , O'Neil T. M.
Published: September 2012

Electrostatic waves in a collision-free unmagnetized plasma of electrons with fixed ions are investigated for electron equilibrium velocity distribution functions that deviate slightly from Maxwellian. Of interest are undamped waves that are the small amplitude limit of nonlinear excitations, such as electron acoustic waves (EAWs). A deviation consisting of a small plateau, a region with zero velocity derivative over a width that is a very small fraction of the electron thermal speed, is shown to give rise to new undamped modes, which here are named corner modes. The presence of the plateau turns off Landau damping and allows oscillations with phase speeds within the plateau. These undamped waves are obtained in a wide region of the (k,ωR) plane (ωR being the real part of the wave frequency and k the wavenumber), away from the well-known “thumb curve” for Langmuir waves and EAWs based on the Maxwellian. Results of nonlinear Vlasov-Poisson simulations that corroborate the existence of these modes are described. It is also shown that deviations caused by fattening the tail of the distribution shift roots off of the thumb curve toward lower k-values and chopping the tail shifts them toward higher k-values. In addition, a rule of thumb is obtained for assessing how the existence of a plateau shifts roots off of the thumb curve. Suggestions are made for interpreting experimental observations of electrostatic waves, such as recent ones in nonneutral plasmas.
Anisotropic optical transmission of femtosecond laser induced periodic surface nanostructures on indium-tin-oxide films
Authors: Wang Chih , Wang Hsuan-I , Luo Chih-Wei , Leu Jihperng
Published: September 2012

Two types of periodic nanostructures, self-organized nanodots and nanolines, were fabricated on the surfaces of indium-tin-oxide (ITO) films using femtosecond laser pulse irradiation. Multiple periodicities (approximately 800 nm and 400 nm) were clearly observed on the ITO films with nanodot and nanoline structures and were identified using two-dimensional Fourier transformation patterns. Both nanostructures show the anisotropic transmission characteristics in the visible range, which are strongly correlated with the geometry and the metallic content of the laser-induced nanostructures.
Living Radical Polymerization by the RAFT Process – A Third Update
Authors: Moad Graeme , Rizzardo Ezio , Thang San H.
Published: September 2012

This paper provides a third update to the review of reversible deactivation radical polymerization (RDRP) achieved with thiocarbonylthio compounds (ZC(=S)SR) by a mechanism of reversible addition-fragmentation chain transfer (RAFT) that was published in June 2005 (Aust. J. Chem. 2005, 58, 379). The first update was published in November 2006 (Aust. J. Chem. 2006, 59, 669) and the second in December 2009 (Aust. J. Chem. 2009, 62, 1402). This review cites over 700 publications that appeared during the period mid 2009 to early 2012 covering various aspects of RAFT polymerization which include reagent synthesis and properties, kinetics and mechanism of polymerization, novel polymer syntheses, and a diverse range of applications. This period has witnessed further significant developments, particularly in the areas of novel RAFT agents, techniques for end-group transformation, the production of micro/nanoparticles and modified surfaces, and biopolymer conjugates both for therapeutic and diagnostic applications.
The immunodominant myeloperoxidase T-cell epitope induces local cell-mediated injury in antimyeloperoxidase glomerulonephritis
Authors: Ooi Joshua D. , Chang Janet , Hickey Michael J. , Borza Dorin-Bogdan , Fugger Lars , Holdsworth Stephen R. , Kitching A. Richard
Published: September 2012

Microscopic polyangiitis is an autoimmune small-vessel vasculitis that often manifests as focal and necrotizing glomerulonephritis and renal failure. Antineutrophil cytoplasmic Abs (ANCAs) specific for myeloperoxidase (MPO) play a role in this disease, but the role of autoreactive MPO-specific CD4+T cells is uncertain. By screening overlapping peptides of 20 amino acids spanning the MPO molecule, we identified an immunodominant MPO CD4+T-cell epitope (MPO409–428). Immunizing C57BL/6 mice with MPO409–428induced focal necrotizing glomerulonephritis similar to that seen after whole MPO immunization, when MPO was deposited in glomeruli. Transfer of an MPO409–428-specific CD4+T-cell clone toRag1−/−mice induced focal necrotizing glomerulonephritis when glomerular MPO deposition was induced either by passive transfer of MPO-ANCA and LPS or by planting MPO409–428conjugated to a murine antiglomerular basement membrane mAb. MPO409–428also induced biologically active anti-MPO Abs in mice. The MPO409–428epitope has a minimum immunogenic core region of 11 amino acids, MPO415–426, with several critical residues. ANCA-activated neutrophils not only induce injury but lodged the autoantigen MPO in glomeruli, allowing autoreactive anti-MPO CD4+cells to induce delayed type hypersensitivity-like necrotizing glomerular lesions. These studies identify an immunodominant MPO T-cell epitope and redefine how effector responses can induce injury in MPO-ANCA–associated microscopic polyangiitis.
Predictors of Hospital-Acquired Urinary Tract–Related Bloodstream Infection
Authors: Greene M. Todd , Chang Robert , Kuhn Latoya , Rogers Mary A. M. , Chenoweth Carol E. , Shuman Emily , Saint Sanjay
Published: September 2012

Objective.

Bloodstream infection (BSI) secondary to nosocomial urinary tract infection is associated with substantial morbidity, mortality, and additional financial costs. Our objective was to identify predictors of nosocomial urinary tract-related BSI.

Design.

Matched case-control study.

Setting.

Midwestern tertiary care hospital.

Patients.

Casesn= 298) were patients with a positive urine culture obtained more than 48 hours after admission and a blood culture obtained within 14 days of the urine culture that grew the same organism. Controls (n= 667), selected by incidence density sampling, included patients with a positive urine culture who were at risk for BSI but did not develop one.

Methods.

Conditional logistic regression and classification and regression tree analyses.

Results.

The most frequently isolated microorganisms that spread from the urinary tract to the bloodstream wereEnterococcusspecies. Independent risk factors included neutropenia (odds ratio [OR], 10.99; 95% confidence interval [CI], 5.78-20.88), renal disease (OR, 2.96; 95% CI, 1.98-4.41), and male sex (OR, 2.18; 95% CI, 1.52-3.12). The probability of developing a urinary tract-related BSI among neutropenic patients was 70%. Receipt of immunosuppressants (OR, 1.53; 95% CI, 1.04-2.25), insulin (OR, 4.82; 95% CI, 2.52-9.21), and antibacterials (OR, 0.66; 95% CI, 0.44-0.97) also significantly altered risk.

Conclusions.

The heightened risk of urinary tract-related BSI associated with several comorbid conditions suggests that the management of nosocomial bacteriuria may benefit from tailoring to certain patient subgroups. Consideration of time-dependent risk factors, such as medications, may also help guide clinical decisions in reducing BSI.

Infect Control Hosp Epidemiol2012;33(10):1001-1007
Laboratory-Confirmed Pandemic H1N1 Influenza in Hospitalized Adults: Findings from the Canadian Nosocomial Infections Surveillance Program, 2009-2010
Authors: Wilkinson Krista , Mitchell Robyn , Taylor Geoffrey , Amihod Barbara , Frenette Charles , Gravel Denise , McGeer Allison , Suh Kathryn N. , Wong Alice ,   Canadian Nosocomial Infection Surveillance Program
Published: September 2012

Surveillance for pandemic H1N1 influenza was conducted between June 1, 2009, and May 31, 2010, among adults at 40 participating hospitals in the Canadian Nosocomial Infection Surveillance Program. The first wave was characterized by a higher proportion of Aboriginals and pregnant women as well as severe outcomes, compared to the second wave.

Infect Control Hosp Epidemiol 2012;33(10):1043-1046
The Use of Live Attenuated Influenza Vaccine (LAIV) in Healthcare Personnel (HCP): Guidance from the Society for Healthcare Epidemiology of America (SHEA)
Authors: Talbot Thomas R. , Babcock Hilary , Cotton Deborah , Maragakis Lisa L. , Poland Gregory A. , Septimus Edward J. , Tapper Michael L. , Weber David J. ,   SHEA Task Force on Healthcare Personnel Influenza Vaccination
Published: September 2012

Because of the live viral backbone of live attenuated influenza vaccine (LAIV), questions have arisen regarding infection control precautions and restrictions surrounding its use in healthcare personnel (HCP). This document provides guidance from the Society for Healthcare Epidemiology of America regarding use of LAIV in HCP and the infection control precautions that are recommended with its use in this population.

Infect Control Hosp Epidemiol 2012;33(10):981-983
Investigation of fast ion transport in TORPEX
Authors: Bovet A. , Furno I. , Fasoli A. , Gustafson K. , Ricci P.
Published: September 2012

Basic aspects of fast ion transport in ideal interchange-mode unstable plasmas are investigated in the simple toroidal plasma device TORPEX. Fast ions are generated by a miniaturized lithium 6+ ion source with energies up to 1 keV, and are detected using a double-gridded energy analyser mounted on a two-dimensional movable system in the poloidal cross-section. The signal-to-noise ratio is enhanced by applying a modulated biasing voltage to the fast ion source and using a synchronous detection scheme. An analogue lock-in amplifier has been developed, which allows removing the capacitive noise associated with the voltage modulation. We characterize vertical and radial transport of the fast ions, which is associated with the plasma turbulence. Initial experimental results show good agreement with numerical simulations of the fast ion transport in a global fluid simulation of the TORPEX plasma.
Mammalian SEPT9 isoforms direct microtubule-dependent arrangements of septin core heteromers
Authors: Sellin Mikael E. , Stenmark Sonja , Gullberg Martin
Published: September 2012

Septin-family proteins assemble into rod-shaped heteromeric complexes that form higher-order arrangements at the cell cortex, where they serve apparently conserved functions as diffusion barriers and molecular scaffolds. There are 13 confirmed septin paralogues in mammals, which may be ubiquitous or tissue specific. Septin hetero-oligomerization appears homology subgroup directed, which in turn determines the subunit arrangement of six- to eight-subunit core heteromers. Here we address functional properties of human SEPT9, which, due to variable mRNA splicing, exists as multiple isoforms that differ between tissues. Myeloid K562 cells express three SEPT9 isoforms, all of which have an equal propensity to hetero-oligomerize with SEPT7-containing hexamers to generate octameric heteromers. However, due to limiting amounts of SEPT9, K562 cells contain both hexameric and octameric heteromers. To generate cell lines with controllable hexamer-to-octamer ratios and that express single SEPT9 isoforms, we developed a gene product replacement strategy. By this means we identified SEPT9 isoform–specific properties that either facilitate septin heteromer polymerization along microtubules or modulate the size range of submembranous septin disks—a prevalent septin structure in nonadhered cells. Our findings show that the SEPT9 expression level directs the hexamer-to-octamer ratio, and that the isoform composition and expression level together determine higher-order arrangements of septins.
Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
Authors: Pfeifer Nico , Lengauer Thomas
Published: September 2012

Motivation: Due to the high mutation rate of human immunodeficiency virus (HIV), drug-resistant-variants emerge frequently. Therefore, researchers are constantly searching for new ways to attack the virus. One new class of anti-HIV drugs is the class of coreceptor antagonists that block cell entry by occupying a coreceptor on CD4 cells. This type of drug just has an effect on the subset of HIVs that use the inhibited coreceptor. A good prediction of whether the viral population inside a patient is susceptible to the treatment is hence very important for therapy decisions and pre-requisite to administering the respective drug. The first prediction models were based on data from Sanger sequencing of the V3 loop of HIV. Recently, a method based on next-generation sequencing (NGS) data was introduced that predicts labels for each read separately and decides on the patient label through a percentage threshold for the resistant viral minority.

Results: We model the prediction problem on the patient level taking the information of all reads from NGS data jointly into account. This enables us to improve prediction performance for NGS data, but we can also use the trained model to improve predictions based on Sanger sequencing data. Therefore, also laboratories without NGS capabilities can benefit from the improvements. Furthermore, we show which amino acids at which position are important for prediction success, giving clues on how the interaction mechanism between the V3 loop and the particular coreceptors might be influenced.

Availability: A webserver is available at http://coreceptor.bioinf.mpi-inf.mpg.de.

Contact:  nico.pfeifer@mpi-inf.mpg.de
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Authors: Rausch Tobias , Zichner Thomas , Schlattl Andreas , Stütz Adrian M. , Benes Vladimir , Korbel Jan O.
Published: September 2012

Motivation: The discovery of genomic structural variants (SVs) at high sensitivity and specificity is an essential requirement for characterizing naturally occurring variation and for understanding pathological somatic rearrangements in personal genome sequencing data. Of particular interest are integrated methods that accurately identify simple and complex rearrangements in heterogeneous sequencing datasets at single-nucleotide resolution, as an optimal basis for investigating the formation mechanisms and functional consequences of SVs.

Results: We have developed an SV discovery method, called DELLY, that integrates short insert paired-ends, long-range mate-pairs and split-read alignments to accurately delineate genomic rearrangements at single-nucleotide resolution. DELLY is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations. DELLY, thus, enables to ascertain the full spectrum of genomic rearrangements, including complex events. On simulated data, DELLY compares favorably to other SV prediction methods across a wide range of sequencing parameters. On real data, DELLY reliably uncovers SVs from the 1000 Genomes Project and cancer genomes, and validation experiments of randomly selected deletion loci show a high specificity.

Availability: DELLY is available at www.korbel.embl.de/software.html

Contact:  tobias.rausch@embl.de
LocTree2 predicts localization for all domains of life
Authors: Goldberg Tatyana , Hamp Tobias , Rost Burkhard
Published: September 2012

Motivation: Subcellular localization is one aspect of protein function. Despite advances in high-throughput imaging, localization maps remain incomplete. Several methods accurately predict localization, but many challenges remain to be tackled.

Results: In this study, we introduced a framework to predict localization in life's three domains, including globular and membrane proteins (3 classes for archaea; 6 for bacteria and 18 for eukaryota). The resulting method, LocTree2, works well even for protein fragments. It uses a hierarchical system of support vector machines that imitates the cascading mechanism of cellular sorting. The method reaches high levels of sustained performance (eukaryota: Q18=65%, bacteria: Q6=84%). LocTree2 also accurately distinguishes membrane and non-membrane proteins. In our hands, it compared favorably with top methods when tested on new data.

Availability: Online through PredictProtein (predictprotein.org); as standalone version at http://www.rostlab.org/services/loctree2.

Contact:  localization@rostlab.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings
Authors: Iacucci Ernesto , Tranchevent Léon-Charles , Popovic Dusan , Pavlopoulos Georgios A. , De Moor Bart , Schneider Reinhard , Moreau Yves
Published: September 2012

Motivation: The prediction of receptor—ligand pairings is an important area of research as intercellular communications are mediated by the successful interaction of these key proteins. As the exhaustive assaying of receptor—ligand pairs is impractical, a computational approach to predict pairings is necessary. We propose a workflow to carry out this interaction prediction task, using a text mining approach in conjunction with a state of the art prediction method, as well as a widely accessible and comprehensive dataset.

Among several modern classifiers, random forests have been found to be the best at this prediction task. The training of this classifier was carried out using an experimentally validated dataset of Database of Ligand-Receptor Partners (DLRP) receptor—ligand pairs. New examples, co-cited with the training receptors and ligands, are then classified using the trained classifier. After applying our method, we find that we are able to successfully predict receptor—ligand pairs within the GPCR family with a balanced accuracy of 0.96. Upon further inspection, we find several supported interactions that were not present in the Database of Interacting Proteins (DIPdatabase).

We have measured the balanced accuracy of our method resulting in high quality predictions stored in the available database ReLiance.

Availability:  http://homes.esat.kuleuven.be/~bioiuser/ReLianceDB/index.php

Contact:  yves.moreau@esat.kuleuven.be; ernesto.iacucci@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fractionation, rearrangement and subgenome dominance
Authors: Sankoff David , Zheng Chunfang
Published: September 2012

Motivation: Fractionation is arguably the greatest cause of gene order disruption following whole genome duplication, causing severe biases in chromosome rearrangement-based estimates of evolutionary divergence.

Results: We show how to correct for this bias almost entirely by means of a ‘consolidation’ algorithm for detecting and suitably transforming identifiable regions of fractionation. We characterize the process of fractionation and the performance of the algorithm through realistic simulations. We apply our method to a number of core eudicot genomes, we and by studying the fractionation regions detected, are able to address topical issues in polyploid evolution.

Availability and implementation: Code for the consolidation algorithm, and sample data, is available at: http://137.122.149.195/Software/Fractionation/fractionation.html

Contact:  sankoff@uottawa.ca
An accurate paired sample test for count data
Authors: Pham Thang V. , Jimenez Connie R.
Published: September 2012

Motivation: Recent technology platforms in proteomics and genomics produce count data for quantitative analysis. Previous works on statistical significance analysis for count data have mainly focused on the independent sample setting, which does not cover the case where pairs of measurements are taken from individual patients before and after treatment. This experimental setting requires paired sample testing such as the paired t-test often used for continuous measurements. A state-of-the-art method uses a negative binomial distribution in a generalized linear model framework for paired sample testing. A paired sample design assumes that the relative change within each pair is constant across biological samples. This model can be used as an approximation to the true model in cases of heterogeneity of response in complex biological systems. We aim to specify the variation in response explicitly in combination with the inherent technical variation.

Results: We formulate the problem of paired sample test for count data in a framework of statistical combination of multiple contingency tables. In particular, we specify explicitly a random distribution for the effect with an inverted beta model. The technical variation can be modeled by either a standard Poisson distribution or an exponentiated Poisson distribution, depending on the reproducibility of the acquisition workflow. The new statistical test is evaluated on both proteomics and genomics datasets, showing a comparable performance to the state-of-the-art method in general, and in several cases where the two methods differ, the proposed test returns more reasonable p-values.

Availability: Available for download at http://www.oncoproteomics.nl/.

Contact:  t.pham@vumc.nl
Telescoper: de novo assembly of highly repetitive regions
Authors: Bresler Ma'ayan , Sheehan Sara , Chan Andrew H. , Song Yun S.
Published: September 2012

Motivation: With advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.

Results: In this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.

Availability: Telescoper is publicly available for download at sourceforge.net/p/telescoper.

Contact:  yss@eecs.berkeley.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Accurate estimation of short read mapping quality for next-generation genome sequencing
Authors: Ruffalo Matthew , Koyutürk Mehmet , Ray Soumya , LaFramboise Thomas
Published: September 2012

Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants.

Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality.

Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms.

Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/.

Contact:  matthew.ruffalo@case.edu.
Drug target prediction using adverse event report systems: a pharmacogenomic approach
Authors: Takarabe Masataka , Kotera Masaaki , Nishimura Yosuke , Goto Susumu , Yamanishi Yoshihiro
Published: September 2012

Motivation: Unexpected drug activities derived from off-targets are usually undesired and harmful; however, they can occasionally be beneficial for different therapeutic indications. There are many uncharacterized drugs whose target proteins (including the primary target and off-targets) remain unknown. The identification of all potential drug targets has become an important issue in drug repositioning to reuse known drugs for new therapeutic indications.

Results: We defined pharmacological similarity for all possible drugs using the US Food and Drug Administration's (FDA's) adverse event reporting system (AERS) and developed a new method to predict unknown drug–target interactions on a large scale from the integration of pharmacological similarity of drugs and genomic sequence similarity of target proteins in the framework of a pharmacogenomic approach. The proposed method was applicable to a large number of drugs and it was useful especially for predicting unknown drug–target interactions that could not be expected from drug chemical structures. We made a comprehensive prediction for potential off-targets of 1874 drugs with known targets and potential target profiles of 2519 drugs without known targets, which suggests many potential drug–target interactions that were not predicted by previous chemogenomic or pharmacogenomic approaches.

Availability: Softwares are available upon request.

Contact:  yamanishi@bioreg.kyushu-u.ac.jp

Supplementary Information: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/aers/.
MaConDa: a publicly accessible mass spectrometry contaminants database
Authors: Weber Ralf J. M. , Li Eva , Bruty Jonathan , He Shan , Viant Mark R.
Published: September 2012

Mass spectrometry is widely used in bioanalysis, including the fields of metabolomics and proteomics, to simultaneously measure large numbers of molecules in complex biological samples. Contaminants routinely occur within these samples, for example, originating from the solvents or plasticware. Identification of these contaminants is crucial to enable their removal before data analysis, in particular to maintain the validity of conclusions drawn from uni- and multivariate statistical analyses. Although efforts have been made to report contaminants within mass spectra, this information is fragmented and its accessibility is relatively limited. In response to the needs of the bioanalytical community, here we report the creation of an extensive manually well-annotated database of currently known small molecule contaminants.

Availability: The Mass spectrometry Contaminants Database (MaConDa) is freely available and accessible through all major browsers or by using the MaConDa web service http://www.maconda.bham.ac.uk.

Contact:  m.viant@bham.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text
Authors: French Leon , Lane Suzanne , Xu Lydia , Siu Celia , Kwok Cathy , Chen Yiqi , Krebs Claudia , Pavlidis Paul
Published: September 2012

Motivation: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features.

Results: Co-occurrence based methods provided high recall with weak precision. The shallow linguistic kernel recalled 70.1% of the sentence-level connectivity statements at 50.3% precision. Owing to its speed and simplicity, we applied the shallow linguistic kernel to a large set of new abstracts. To evaluate the results, we compared 2688 extracted connections with the Brain Architecture Management System (an existing database of rat connectivity). The extracted connections were connected in the Brain Architecture Management System at a rate of 63.5%, compared with 51.1% for co-occurring brain region pairs. We found that precision increases with the recency and frequency of the extracted relationships.

Availability and implementation: The source code, evaluations, documentation and other supplementary materials are available at http://www.chibi.ubc.ca/WhiteText.

Contact:  paul@chibi.ubc.ca

Supplementary information:  Supplementary data are available at Bioinformatics Online.
Effect of Temperature, Wetness Duration, and Planting Density on Olive Anthracnose Caused by Colletotrichum spp.
Authors: Moral Juan , Jurado-Bello José , Sánchez M. Isabel , de Oliveira Rodrígues , Trapero Antonio
Published: September 2012

The influence of temperature, wetness duration, and planting density on infection of olive fruit by Colletotrichum acutatum and C. simmondsii was examined in laboratory and field experiments. Detached olive fruit of ‘Arbequina’, ‘Hojiblanca’, and ‘Picual’ were inoculated with conidia of several isolates of the pathogen and kept at constant temperatures of 5 to 35°C in humid chambers. Similarly, potted plants and stem cuttings with fruit were inoculated and subjected to wetness periods of 0 to 48 h. Infection occurred at 10 to 25°C, and disease severity was greater and the mean latent period was shorter at 17 to 20°C. Overall, C. acutatum was more virulent than C. simmondsii at temperatures <25°C. When temperature was not a limiting factor, disease severity increased with the wetness period from 0 to 48 h. Disease severity was modeled as a function of temperature and wetness duration; two critical fruit incidence thresholds were defined as 5 and 20%, with wetness durations of 1.0 and 12.2 h at the optimum temperature. In the field, anthracnose epidemics progressed faster in a super-high-density planting (1,904 olive trees/ha) than in the high-density plantings (204 to 816 olive trees/ha) and caused severe epidemics in the super-high-density planting even with the moderately resistant Arbequina. Data in this study will be useful for the development of a forecasting system for olive anthracnose epidemics.
Classical to quantum in large-number limit
Authors: Modi Kavan , Fazio Rosario , Pascazio Saverio , Vedral Vlatko , Yuasa Kazuya
Published: September 2012

We construct a quantumness witness following the work of Alicki & van Ryn (AvR). We reformulate the AvR test by defining it for quantum states rather than for observables. This allows us to identify the necessary quantities and resources to detect quantumness for any given system. The first quantity turns out to be the purity of the system. When applying the witness to a system with even moderate mixedness, the protocol is unable to reveal any quantumness. We then show that having many copies of the system leads the witness to reveal quantumness. This seems contrary to the Bohr correspondence, which asserts that, in the large-number limit, quantum systems become classical, whereas the witness shows quantumness when several non-quantum systems, as determined by the witness, are considered together. However, the resources required to detect the quantumness increase dramatically with the number of systems. We apply the quantumness witness for systems that are highly mixed but in the large-number limit that resembles nuclear magnetic resonance (NMR) systems. We make several conclusions about detecting quantumness in NMR-like systems.
Discovery of a novel Torque teno sus virus species: genetic characterization, epidemiological assessment and disease association
Authors: Cornelissen-Keijsers Vivian , Jiménez-Melsió Alexandra , Sonnemans Denny , Cortey Martí , Segalés Joaquim , van den Born Erwin , Kekarainen Tuija
Published: September 2012

The study describes a novel Torque teno sus virus (TTSuV) species, provisionally named Torque teno sus virus k2b (TTSuVk2b), originally found in commercial pig sera by applying the rolling-circle amplification technique. Full-length sequences of TTSuVk2b were obtained, annotated and used in the phylogenetic analyses, which revealed that TTSuVk2b is a novel Anellovirus species within the genus Kappatorquevirus of the family Anelloviridae. Quantitative PCR techniques were developed to determine total TTSuV DNA quantities as well as the prevalence and viral DNA quantities of TTSuV1, TTSuVk2a and TTSuVk2b. The mean total TTSuV load in seven commercial sera was determined at 6.3 log10 DNA copies ml−1 of serum, with TTSuVk2b loads being the lowest at 4.5 log10 DNA copies ml−1 of serum. Subsequently, prevalence and loads of TTSuVs were determined in pig sera from 17 countries. TTSuVk2b prevalence ranged from 0 to 100 % with viral loads from 3.3 to 4.6 log10 copies ml−1 of sera. TTSuVk2a, so far the only species in the genus Kappatorquevirus, has been linked to an economically important swine disease, namely post-weaning multisystemic wasting syndrome (PMWS). Considering the grouping of TTSuVk2b in the same genus as TTSuVk2a, TTSuVk2b prevalence and viral DNA load were determined in PMWS-affected animals and healthy counterparts. This revealed that TTSuVk2a and TTSuVk2b are not only genetically related, but also that their viral loads in serum are elevated in PMWS animals compared with those of healthy pen mates. In summary, the present work describes a novel TTSuV species including its genetic characterization, epidemiological assessment and potential disease association.
Environmental and demographic risk factors for egg allergy in a population‐based study of infants
Authors: Koplin J. J. , Dharmage S. C. , Ponsonby A.‐L. , Tang M. L. K. , Lowe A. J. , Gurrin L. C. , Osborne N. J. , Martin P. E. , Robinson M. N. , Wake M. , Hill D. J. , Allen K. J.
Published: September 2012

Background

Although egg allergy is the most common food allergy in infants and young children, risk factors for egg allergy remain largely unknown. This study examined the relationship between environmental and demographic factors and egg allergy in a population‐based infant cohort.

Methods

In a study of 5276 infants (HealthNuts), infants underwent skin prick testing (SPT) to egg white at 12 months of age. Questionnaire data on relevant exposures were obtained. 699/873 (80%) infants eligible for oral food challenge (detectable wheal on SPT) attended for formal assessment of egg allergy status; 453 had confirmed egg allergy (positive challenge and SPT ≥ 2 mm). Associations between environmental and demographic factors and egg allergy were investigated using multivariable logistic regression.

Results

Children with older siblings and those with a pet dog at home were less likely to develop egg allergy by 1 year of age (adjusted OR [aOR], 0.72; 95% CI, 0.62, 0.83 per sibling; and aOR, 0.72; 95% CI, 0.52, 0.99, respectively). Caesarean section delivery, antibiotic use in infancy, childcare attendance and maternal age were not associated with egg allergy. History of allergic disease in an immediate family member and having parents born in East Asia were strong risk factors for infantile egg allergy (aOR, 1.82; 95% CI, 1.40, 2.36; and aOR, 3.30; 95% CI, 2.45, 4.45, respectively).

Conclusions

Exposure in the first year of life to siblings and dogs may decrease the risk of subsequent egg allergy. Infants with a family history of allergy and those with parents born in East Asia are at increased risk of egg allergy.
Magnetic resonance angiography‐defined intracranial vasculopathy is associated with silent cerebral infarcts and glucose‐6‐phosphate dehydrogenase mutation in children with sickle cell anaemia
Authors: Thangarajh Mathula , Yang Genyan , Fuchs Dana , Ponisio Maria R. , McKinstry Robert C. , Jaju Alok , Noetzel Michael J. , Casella James F. , Barron‐Casella Emily , Hooper W. Craig , Boulet Sheree L. , Bean Christopher J. , Pyle Meredith E. , Payne Amanda B. , Driggers Jennifer , Trau Heidi A. , Vendt Bruce A. , Rodeghier Mark , DeBaun Michael R.
Published: September 2012

Silent cerebral infarct (SCI) is the most commonly recognized cause of neurological injury in sickle cell anaemia (SCA). We tested the hypothesis that magnetic resonance angiography (MRA)‐defined vasculopathy is associated with SCI. Furthermore, we examined genetic variations in glucose‐6‐phosphate dehydrogenase (G6PD) and HBA (α‐globin) genes to determine their association with intracranial vasculopathy in children with SCA. Magnetic resonance imaging (MRI) of the brain and MRA of the cerebral vasculature were available in 516 paediatric patients with SCA, enrolled in the Silent Infarct Transfusion (SIT) Trial. All patients were screened for G6PD mutations and HBA deletions. SCI were present in 41·5% (214 of 516) of SIT Trial children. The frequency of intracranial vasculopathy with and without SCI was 15·9% and 6·3%, respectively (P < 0·001). Using a multivariable logistic regression model, only the presence of a SCI was associated with increased odds of vasculopathy (P = 0·0007, odds ratio (OR) 2·84; 95% Confidence Interval (CI) = 1·55–5·21). Among male children with SCA, G6PD status was associated with vasculopathy (P = 0·04, OR 2·78; 95% CI = 1·04–7·42), while no significant association was noted for HBA deletions. Intracranial vasculopathy was observed in a minority of children with SCA, and when present, was associated with G6PD status in males and SCI.