bluuebunny/crossref_metadata_2025 huggingface dataset:
A Hamiltonian approach to wave-current interactions in two-layer fluids
Authors: Constantin A. , Ivanov R. I.
Published: August 2015

We provide a Hamiltonian formulation for the governing equations describing the two-dimensional nonlinear interaction between coupled surface waves, internal waves, and an underlying current with piecewise constant vorticity, in a two-layered fluid overlying a flat bed. This Hamiltonian structure is a starting point for the derivation of simpler models, which can be obtained systematically by expanding the Hamiltonian in dimensionless parameters. These enable an in-depth study of the coupling between the surface and internal waves, and how both these wave systems interact with the background current.
Gamma and x-ray irradiation effects on different Ge and Ge/F doped optical fibers
Authors: Alessi A. , Girard S. , Reghioua I. , Fanetti M. , Di Francesca D. , Agnello S. , Cannas M. , Marcandella C. , Martin-Samos L. , Richard N. , Boukenter A. , Ouerdane Y.
Published: August 2015

We performed electron paramagnetic resonance (EPR) measurements on γ and X ray irradiated Ge doped and Ge/F co-doped optical fibers. We considered three different drawing conditions (speed and tension), and for each type of drawing, we studied Ge and Ge/F doped samples having Ge doping level above 4% by weight. The EPR data recorded for the γ ray irradiated fibers confirm that all the samples exhibit a very close radiation response regardless of the drawing conditions corresponding to values used for the production of specialty fibers. Furthermore, as for the X irradiated materials, in the γ ray irradiated F co-doped fibers, we observed that the Ge(1) and the Ge(2) defects generation is unchanged, whereas it was enhanced for the E'Ge. In the various fibers, the comparison of the γ and X-ray induced concentrations of these kinds of Ge related defects indicates that the two irradiations induce similar effects regardless of the different employed dose rates and sources. Confocal microscopy luminescence results show that the starting content of the Germanium Lone Pair Center (GLPC) is neither strongly affected by the Ge content nor by the drawing conditions, and we consider the similarity of the GLPC content as key factor in determining many of the above reported similarities.
Correlation between dynamic slowing down and local icosahedral ordering in undercooled liquid Al80Ni20 alloy
Authors: Jakse N. , Pasturel A.
Published: August 2015

We use ab initio molecular dynamics simulations to study the correlation between the local ordering and the dynamic properties of liquid Al80Ni20 alloy upon cooling. Our results evidence a huge increase of local icosahedral ordering (ISRO) in the undercooled regime which is more developed around Ni than Al atoms. We show that ISRO has a strong impact on self-diffusion coefficients of both species and is at the origin of their crossover from Arrhenius to non-Arrhenius behavior around a crossover temperature TX = 1000 K, located in the undercooled region. We also clearly identify that this temperature corresponds to the development of dynamic heterogeneities and to the breakdown of the Stokes-Einstein relation. At temperatures below this crossover, we find that the behavior of the diffusion and relaxation dynamics is mostly incompatible with predictions of the mode-coupling theory. Finally, an analysis of the van Hove function indicates that the crossover temperature TX marks the onset of a change in the diffusion mechanism from a normal flow to an activated process with hopping. From these results, the glass-forming ability of the alloy is discussed.
Study of morphology effects on magnetic interactions and band gap variations for 3d late transition metal bi-doped ZnO nanostructures by hybrid DFT calculations
Authors: Datta Soumendu , Kaphle Gopi Chandra , Baral Sayan , Mookerjee Abhijit
Published: August 2015

Using density functional theory (DFT) based electronic structure calculations, the effects of morphology of semiconducting nanostructures on the magnetic interaction between two magnetic dopant atoms as well as a possibility of tuning band gaps have been studied in the case of the bi-doped (ZnO)24 nanostructures with the impurity dopant atoms of the 3d late transition metals—Mn, Fe, Co, Ni, and Cu. To explore the morphology effect, three different structures of the host (ZnO)24 nano-system, having different degrees of spatial confinement, have been considered: a two dimensional nanosheet, a one dimensional nanotube, and a finite cage-shaped nanocluster. The present study employs hybrid density functional theory to accurately describe the electronic structure of all the systems. It is shown here that the magnetic coupling between the two dopant atoms remains mostly anti-ferromagnetic in the course of changing the morphology from the sheet geometry to the cage-shaped geometry of the host systems, except for the case of energetically most stable bi-Mn doping, which shows a transition from ferromagnetic to anti-ferromagnetic coupling with decreasing aspect ratio of the host system. The effect of the shape change, however, has a significant effect on the overall band gap variations of both the pristine as well as all the bi-doped systems, irrespective of the nature of the dopant atoms and provides a means for easy tunability of their optoelectronic properties.
Nanosecond Nd-YAG laser induced plasma emission characteristics in low pressure CO2 ambient gas for spectrochemical application on Mars
Authors: Lie Zener Sukra , Pardede Marincan , Tjia May On , Kurniawan Koo Hendrik , Kagawa Kiichiro
Published: August 2015

An experimental study is conducted on the possibility and viability of performing spectrochemical analysis of carbon and other elements in trace amount in Mars, in particular, the clean detection of C, which is indispensible for tracking the sign of life in Mars. For this study, a nanosecond Nd-YAG laser is employed to generate plasma emission from a pure copper target in CO2 ambient gas of reduced pressure simulating the atmospheric condition of Mars. It is shown that the same shock wave excitation mechanism also works this case while exhibiting remarkably long cooling stage. The highest Cu emission intensities induced by 4 mJ laser ablation energy is attained in 600 Pa CO2 ambient gas. Meanwhile the considerably weaker carbon emission from the CO2 gas appears relatively featureless over the entire range of pressure variation, posing a serious problem for sensitive trace analysis of C contained in a solid sample. Our time resolved intensity measurement nevertheless reveals earlier appearance of C emission from the CO2 gas with a limited duration from 50 ns to 400 ns after the laser irradiation, well before the initial appearance of the long lasting C emission from the solid target at about 1 μs, due to the different C-releasing processes from their different host materials. The unwanted C emission from the ambient gas can thus be eliminated from the detected spectrum by a proper time gated detection window. The excellent spectra of carbon, aluminum, calcium, sodium, hydrogen, and oxygen obtained from an agate sample are presented to further demonstrate and verify merit of this special time gated LIBS using CO2 ambient gas and suggesting its viability for broad ranging in-situ applications in Mars.
Effect of temperature and micro-morphology on the Ag Raman peak in nanocrystalline CuO thin films
Authors: Ravi Shrividya , Kaiser Alan B. , Bumby Chris W.
Published: August 2015

Raman spectra obtained from a nanocrystalline CuO thin film are observed to exhibit significant variation in the peak position and peak line-shape as a function of spatial position within the film. We attribute this effect to variation in the degree of local heating beneath the focused spot of the Raman probe laser. To understand this, we have undertaken a detailed study of the temperature-dependence of the CuO Ag Raman peak. We observe a linear relationship between line-width and peak position, which persists over a wide temperature range, and is characteristic of a Raman process in which the temperature-dependence is dominated by anharmonic 3-phonon decay. We provide an analytical description of the Raman line-shape as a function of temperature and use this model to interpret the degree of laser heating observed within our sample. Using this relationship, we identify that the local micro-morphology of the CuO sample under study can dramatically affect the temperature achieved due to laser heating. We find that spectra collected from the surface of “micro-bubbles” within the CuO film studied can reach temperatures of >1000 K beneath the focused spot of our low power (5 mW) probe laser.
Nonlinear stability of the Boltzmann equation in a periodic box
Authors: Wu Kung-Chien
Published: August 2015

We study the nonlinear stability of the Boltzmann equation in the 3-dimensional periodic box with size 1/ε of each side, where 0 < ε ≪ 1 is the Knudsen number. The initial perturbation is not necessary smooth. The convergence rate is algebraic for small time region and exponential for large time region. Moreover, the algebraic rate is optimal and the exponential rate depends on the size of the domain (Knudsen number).
Self-duality for the two-component asymmetric simple exclusion process
Authors: Belitsky V. , Schütz G. M.
Published: August 2015

We study a two-component asymmetric simple exclusion process (ASEP) that is equivalent to the ASEP with second-class particles. We prove self-duality with respect to a family of duality functions which are shown to arise from the reversible measures of the process and the symmetry of the generator under the quantum algebra Uq[𝔤𝔩3]. We construct all invariant measures in explicit form and discuss some of their properties. We also prove a sum rule for the duality functions.
Generation of radially polarized high energy mid-infrared optical vortex by use of a passive axially symmetric ZnSe waveplate
Authors: Wakayama Toshitaka , Oikawa Hiroki , Sasanuma Atsushi , Arai Goki , Fujii Yusuke , Dinh Thanh-Hung , Higashiguchi Takeshi , Sakaue Kazuyuki , Washio Masakazu , Miura Taisuke , Takahashi Akihiko , Nakamura Daisuke , Okada Tatsuo , Yonemura Motoki , Otani Yukitoshi
Published: August 2015

We demonstrated the generation of the intense radially polarized mid-infrared optical vortex at a wavelength of 10.6 μm by use of a passive axially symmetric zinc selenide (ZnSe) waveplate with high energy pulse throughput. The phase of the radially polarized optical vortex with the degree of polarization of 0.95 was spirally distributed in regard to the angle. The converted laser beam energy of about 2.6 mJ per pulse was obtained at the input pulse energy of 4.9 mJ, corresponding to the energy conversion efficiency of 56%.
Effects of configurational changes on molecular dynamics in polyvinylidene fluoride and poly(vinylidene fluoride-trifluoroethylene) ferroelectric polymers
Authors: Jalarvo N. , Pramanick A. , Do C. , Diallo S. O.
Published: August 2015

We present a comparative study of proton dynamics in unpoled non-ferroelectric polymer polyvinylidene fluoride (PVDF) and in its trifluoroethylene containing ferroelectric copolymer (with 70/30 molar proportion), using quasi-elastic neutron scattering. The neutron data reveal the existence of two distinct types of molecular motions in the temperature range investigated. The slower motion, which is characterized in details here, is ascribed to protons jump diffusion along the polymeric carbon chains, while the faster motion could be attributed to localized rotational motion of methylene groups. At temperatures below the Curie point (Tc ∼ 385 K) of the composite polymer, the slower diffusive mode experiences longer relaxation times in the ferroelectric blend than in the bare PVDF, although the net corresponding diffusion coefficient remains comparatively the same in both polymers with characteristic activation energy of EA ≈ 27–33 kJ/mol. This arises because of a temperature dependent jump length r0, which we observe to be effectively longer in the copolymer, possibly due to the formation of ordered ferroelectric domains below Tc. Above Tc, there is no appreciable difference in r0 between the two systems. This observation directly relates the known dependence of Tc on molar ratio to changes in r0, providing fundamental insight into the ferroelectric properties of PVDF-based copolymers.
Degenerate mobilities in phase field models are insufficient to capture surface diffusion
Authors: Lee Alpha A. , Münch Andreas , Süli Endre
Published: August 2015

Phase field models frequently provide insight into phase transitions and are robust numerical tools to solve free boundary problems corresponding to the motion of interfaces. A body of prior literature suggests that interface motion via surface diffusion is the long-time, sharp interface limit of microscopic phase field models such as the Cahn-Hilliard equation with a degenerate mobility function. Contrary to this conventional wisdom, we show that the long-time behaviour of degenerate Cahn-Hilliard equation with a polynomial free energy undergoes coarsening, reflecting the presence of bulk diffusion, rather than pure surface diffusion. This reveals an important limitation of phase field models that are frequently used to model surface diffusion.
Experimental study of a building-integrated dual-function solar collector system
Authors: Luo Chenglong , Ji Jie , Xiong Jihai , Fan Min , Sun Liyuan , Liao Mengyin
Published: August 2015

As a novel building-integrated solar thermal system, a building-integrated dual-function solar collector system are designed with two operating modes: passive space heating mode in cold winter and water heating mode in warmer seasons. Based on a long-term experimental test, the paper investigates the performance of the system operating under these two modes. Experimental results indicated that the characteristic thermal efficiency of the system working at the water-heating mode with natural circulation was calculated to be 40.5% and at the space-heating mode the functional relationship between the temperature difference of the indoor air and the solar radiation on the absorber plate of the solar collector can be expressed as two linear equations.
Growth of antiphase-domain-free GaP on Si substrates by metalorganic chemical vapor deposition using an in situ AsH3 surface preparation
Authors: Warren Emily L. , Kibbler Alan E. , France Ryan M. , Norman Andrew G. , Stradins Paul , McMahon William E.
Published: August 2015

Antiphase-domain (APD) free GaP films were grown on Si(100) substrates prepared by annealing under dilute AsH3 in situ in an MOCVD reactor. LEED and AES surface analysis of Si(100) surfaces prepared by this treatment show that AsH3 etching quickly removes O and C contaminants at a relatively low temperature (690–740 °C), and creates a single-domain “A-type” As/Si surface reconstruction. The resulting GaP epilayers grown at the same temperature are APD-free, and could thereby serve as templates for direct growth of III-V semiconductors on Si. This single chamber process has a low thermal budget, and can enable heteroepitaxial integration of III-Vs and Si at an industrial scale.
Writing a skyrmion on multiferroic materials
Authors: Mochizuki Masahito , Watanabe Yoshio
Published: August 2015

This paper reports on a theoretical proposal for electrical creation of magnetic skyrmions on a thin-film specimen of a multiferroic chiral magnet by local application of an electric field, instead of an electric current, via an electrode tip. This method can be traced back to the mutual coupling between skyrmion spins and the electric polarizations in multiferroics and represents a unique technique for use in potential skyrmion-based memory devices without Joule-heating losses.
Nonlinear terahertz response of HgTe/CdTe quantum wells
Authors: Chen Qinjun , Sanderson Matthew , Zhang Chao
Published: August 2015

Without breaking the topological order, HgTe/CdTe quantum wells can have two types of bulk band structure: direct gap type (type I) and indirect gap type (type II). We report that the strong nonlinear optical responses exist in both types of bulk states under a moderate electric field in the terahertz regime. Interestingly, for the type II band structure, the third order conductivity changes sign when chemical potentials lies below 10 meV due to the significant response of the hole excitation close to the bottom of conduction band. Negative nonlinear conductivities suggest that HgTe/CdTe quantum wells can find application in the gain medium of a laser for terahertz radiation. The thermal influences on nonlinear optical responses of HgTe/CdTe quantum wells are also studied.
A multigene phylogenetic analysis results in a redefinition of the genus Notonomus Chaudoir (Coleoptera, Carabidae) and descriptions of new species of the subgenus Leiradira Castelnau
Authors: Will Kipling
Published: August 2015

Bayesian analysis of four partial gene sequences (28S rDNA, wg, CAD and COI mtDNA) from exemplars of all genera and 12 of 17 informal groups of the Notonomus-series of pterostichine carabids strongly supports a clade requiring redefinition of Notonomus Chaudoir, 1862. Notonomus is redefined to include all species currently placed in Notonomus by Lorenz (2005a) plus two Sarticus Motschulsky, 1865 species (S. blackburni (Sloane, 1895) and S. impar (Sloane, 1893)), all species of Leiradira Castelnau, 1867, Conchitella Moore, 1962 Loxodactylus Chaudoir, 1865 and Acanthoferonia Moore, 1965. Analysis of combined data places Sarticus sister to Notonomus with low support. Individual gene analyses indicated wg is in conflict with other loci and analyses exclusive of wg place Parhypates Motschulsky, 1866 sister to Notonomus with very high support. Leiradira species form a clade within Notonomus including Notonomus dimorphicus Darlington, 1961 and N. flos Darlington, 1961. Six new species of the subgenus Leiradira from Queensland are described; Notonomus (Leiradira) thynnefiliarum, N. (L.) vadosus, N. (L.) viridis, N. (L.) spectabilis, N. (L.) iridescens and N. (L.) barrae. Two additional species of Notonomus s.l. are described; Notonomus hephaestus from the Lamb Range, Queensland, which is part of a mimicry complex with Notonomus (Leiradira) aurifer (Darlington, 1961); and Notonomus nocturnocappellus, from New South Wales, which represents a unique combination of characteristics for the genus. Descriptions of all species of Notonomus (Leiradira) with a wide gula, a grouping equivalent to Darlington’s concept of Leiradira, are given. An identification key to species of Notonomus (Leiradira), the two newly described Notonomus s.l. species and all recognised subgenera of Notonomus is provided.
Using the features of translated language to investigate translation expertise
Authors: Redelinghuys Karien , Kruger Haidee
Published: August 2015

The study reported on in this article set out to test the hypothesis that linguistic operationalisations of the features of translated language will demonstrate significant differences in the work of experienced and inexperienced translators. A custom-built comparable English corpus was used, comprising three subcorpora: translations produced by experienced translators, translations by inexperienced translators, and non-translated texts. A number of linguistic operationalisations were selected for three of the features of translated language: explicitation, simplification and normalisation. The differences in these linguistic features in the three subcorpora were analysed, using parametric or non-parametric ANOVA, and T-tests or Mann-Whitney U-tests as post-hoc tests where applicable. The findings of the study indicate substantial (though not unqualified) support for the hypothesis. It is argued that experience-related variation in register sensitivity, language competence, awareness of written language conventions and sensitivity to translation norms are the main factors contributing to expertise.
Shell-nounhood in academic discourse
Authors: Benitez-Castro Miguel-Angel , Thompson Paul
Published: August 2015

Numerous studies to date have investigated the cohesive, evaluative and formal features of semantically unspecific abstract nouns such as objective or assumption. These nouns share the property of ‘shell-nounhood’, associated with their ability to package and characterise complex discourse segments. One broad genre where this ability is widely exploited is academic discourse, which favours a markedly nominal cohesive style. Despite the extensive use of academic corpora in the study of shell-nounhood, the research focus has been primarily on specific sub-genres, formal patterns and rhetorical functions. This paper critically reviews the available evidence on this genre, using the corpora from which such evidence was obtained as its basic organising principle. In so doing, it uncovers some of the gaps to be addressed by future research, thereby setting the stage for more comprehensive descriptions that may usher in new pedagogies for the teaching of this crucial aspect of lexical cohesion in academic discourse.
Pourquoi le présent n’est-il pas si simple d’un point de vue psycholinguistique ?
Authors: Granget Cyrille
Published: August 2015

This study is concerned with the emergence of morphological means to express present time. The analysis of narratives produced by English speakers learning French as a second language shows that the present tense is only used by two learners among those who are mostly exposed to French. Most of the learners use a variable verbal form without any morphological marking. But the use of an analytic verbal form with imperfective meaning indicates that there is an intermediate stage in the process of morphological development. Its use suggests an influence of morphological procedures on the order and rhythm of morphological development. Acquiring the present tense is difficult for two reasons, the lack of functional motivation to do so and irregular inflection. This is confirmed by the breadth of the lexical repertoire at different stages.
Spiritual institutional entrepreneurs: an introduction and examination
Authors: Porter Tracy H. , Mitchell Matthew C.
Published: August 2015

The business environment has undergone dramatic changes over the past decades that have brought about new expectations within the work environment. Entrepreneurship is one of many areas that has been affected by this shift. In fact, the definition of entrepreneur has evolved beyond
the traditional external focus to include an internal organizational perspective known as institutional entrepreneur (IE). IEs initiate structural change within their organizations that transforms the way business is conducted. Current research has demonstrated the importance of workplace
spirituality as an element in developing an inclusive organizational culture. In this paper, we draw from the institutional entrepreneurship literature to examine the rise of IEs who champion the development of spiritual workplaces. We call these individuals spiritual institutional entrepreneurs
(SIEs). We also present a conceptual model for analyzing the role of SIEs and offer notable executive exemplars who reimagined their organizations through the lens of workplace spirituality.
Research Verification of Production Practices Using Intensive Aeration at a Hybrid Catfish Operation
Authors: Bott Lisa B , Roy Luke A , Hanson Terrill R , Chappell Jesse , Whitis Gregory N
Published: August 2015

Aquaculture research verification programs are designed to demonstrate and test research-based practices recommended by extension services on commercial-scale operations. From 2010 to 2013, in western Alabama, three management protocols were followed over three crop cycles on a farm producing hybrid catfish (female Channel Catfish Ictalurus punctatus × male Blue Catfish I. furcatus) using high levels of aeration. The protocols were an owner-defined, multiple-batch treatment and single-batch and multiple-batch treatments defined by the Alabama Cooperative Extension System (ACES). Results from nine production cycles were analyzed to calculate yields, feed conversion ratios (FCRs), cost of production, and net returns. Over three production cycles the owner-defined, multiple-batch treatment outperformed the two ACES-recommended treatments in terms of yield, survival, FCR, and net returns. The owner-defined treatment could vary, and the producer chose to feed above the recommended daily maximum and observed no low dissolved oxygen levels. High losses owing to disease in the ACES multiple-batch treatment led to poor results. The owner-defined multiple-batch system completed three crops in 2.8 years compared with 3.6–3.7 years for the other two treatments. Thus, this study highlights the importance of research-based recommendations being verified under commercial catfish production conditions and the value of research verification programs.
Searching for a counterexample to Kurepa’s conjecture
Authors: Andrejić Vladica , Tatarevic Milos
Published: August 2015

Kurepa’s conjecture states that there is no odd prime

p
p

that divides

!
p
=
0
!
+
1
!
+
⋯
+
(
p
−
1
)
!

!p=0!+1!+\cdots +(p-1)!

. We search for a counterexample to this conjecture for all

p
>

2

34

p>2^{34}

. We introduce new optimization techniques and perform the computation using graphics processing units. Additionally, we consider the generalized Kurepa’s left factorial given by
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="factorial Superscript k Baseline n equals left-parenthesis 0 factorial right-parenthesis Superscript k Baseline plus left-parenthesis 1 factorial right-parenthesis Superscript k Baseline plus midline-horizontal-ellipsis plus left-parenthesis left-parenthesis n minus 1 right-parenthesis factorial right-parenthesis Superscript k">

!

k

n
=
(
0
!

)
k

+
(
1
!

)
k

+
⋯
+
(
(
n
−
1
)
!

)

k

!^{k}n=(0!)^k +(1!)^k +\cdots +((n-1)!)^{k}

, and show that for all integers

1
>
k
>
100

1>k>100

there exists an odd prime

p
p

such that

p
∣

!
k

p

p\mid !^k p

.
Identification of hierarchical chromatin domains
Authors: Weinreb Caleb , Raphael Benjamin J.
Published: August 2015

Motivation: The three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy.

Results: We introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart have a greater enrichment of contacts than positions that are close together. We find that the increase in contact enrichment with distance is stronger for the inner TAD than for the outer TAD in a TAD/sub-TAD pair. Using this model, we develop the TADtree algorithm for detecting hierarchies of nested TADs. TADtree compares favorably with previous methods, finding TADs with a greater enrichment of chromatin marks such as CTCF at their boundaries.

Availability and implementation: A python implementation of TADtree is available at http://compbio.cs.brown.edu/software/

Contact:  braphael@cs.brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
EPGA2: memory-efficient de novo assembler
Authors: Luo Junwei , Wang Jianxin , Li Weilong , Zhang Zhen , Wu Fang-Xiang , Li Min , Pan Yi
Published: August 2015

Motivation: In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.

Results: In this article, we present an update algorithm called EPGA2, which applies some new modules and can bring about improved assembly results in small memory. For reducing peak memory in genome assembly, EPGA2 adopts memory-efficient DSK to count K-mers and revised BCALM to construct De Bruijn Graph. Moreover, EPGA2 parallels the step of Contigs Merging and adds Errors Correction in its pipeline. Our experiments demonstrate that all these changes in EPGA2 are more useful for genome assembly.

Availability and implementation: EPGA2 is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA2.

Contact:  jxwang@csu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
HiXCorr: a portable high-speed XCorr engine for high-resolution tandem mass spectrometry
Authors: Kim Hyunwoo , Jo Hosung , Park Heejin , Paek Eunok
Published: August 2015

Summary: Peptide identification is an important problem in proteomics. One of the most popular scoring schemes for peptide identification is XCorr (cross-correlation). Since calculating XCorr is computationally intensive, a lot of efforts have been made to develop fast XCorr engines. However, the existing XCorr engines are not suitable for high-resolution MS/MS spectrometry because they are either slow or require a specific type of CPU. We present a portable high-speed XCorr engine for high-resolution tandem mass spectrometry by developing a novel algorithm for calculating XCorr. The algorithm enables XCorr calculation 1.25–49 times faster than previous algorithms for 0.01 Da fragment tolerance. Furthermore, our engine is easily portable to any machine with different types of CPU because it is developed in C language. Hence, our XCorr engine will expedite peptide identification by high-resolution tandem mass spectrometry.

Availability and implementation: Available at http://isa.hanyang.ac.kr/HiXCorr/HiXCorr.html.

Contact:  hjpark@hanyang.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations
Authors: Pybus Marc , Luisi Pierre , Dall'Olio Giovanni Marco , Uzkudun Manu , Laayouni Hafid , Bertranpetit Jaume , Engelken Johannes
Published: August 2015

Motivation: Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations. Furthermore, few methods address the challenge of classifying selective events according to specific features such as age, intensity or state (completeness).

Results: We have developed a machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Our method also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios. We calibrated and applied the method to three reference human populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves detection of selective sweep by overcoming the classical selection versus no-selection classification strategy, and offers an explanation to the lack of consistency observed among selection tests when applied to real data. Very few signals were observed in the African population studied, while our method presents higher sensitivity in this population demography.

Availability and implementation: The genome-wide results for three human populations from The 1000 Genomes Project and an R-package implementing the ‘Hierarchical Boosting’ framework are available at http://hsb.upf.edu/.

Contact:  jaume.bertranpetit@upf.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
msa: an R package for multiple sequence alignment
Authors: Bodenhofer Ulrich , Bonatesta Enrico , Horejš-Kainrath Christoph , Hochreiter Sepp
Published: August 2015

Summary: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.

Availability and implementation: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.

Contact:  bodenhofer@bioinf.jku.at or msa@bioinf.jku.at
Magnetar activity via the density–shear instability in Hall-MHD
Authors: Gourgouliatos Konstantinos N. , Kondić Todor , Lyutikov Maxim , Hollerbach Rainer
Published: August 2015

We investigate the density–shear instability in Hall-magnetohydrodynamics (Hall-MHD) via numerical simulation of the full non-linear problem in the context of magnetar activity. We confirm the development of the instability of a plane-parallel magnetic field with an appropriate intensity and electron density profile, in accordance with analytic theory. We find that the instability also appears for a monotonically decreasing electron number density and magnetic field, a plane-parallel analogue of an azimuthal or meridional magnetic field in the crust of a magnetar. The growth rate of the instability depends on the Hall properties of the field (magnetic field intensity, electron number density and the corresponding scaleheights), while being insensitive to weak resistivity. Since the Hall effect is the driving process for the evolution of the crustal magnetic field of magnetars, we argue that this instability is critical for systems containing strong meridional or azimuthal fields. We find that this process mediates the formation of localized structures with much stronger magnetic field than the average, which can lead to magnetar activity and accelerate the dissipation of the field and consequently the production of Ohmic heating. Assuming a 5 × 1014 G magnetic field at the base of crust, we anticipate that magnetic field as strong as 1015 G will easily develop in regions of typical size of a few hundred metres, containing magnetic energy of 1043 erg, sufficient to power magnetar bursts. These active regions are more likely to appear in the magnetic equator where the tangential magnetic field is stronger.
Mass ratio of the 2 pc binary brown dwarf LUH 16 and limits on planetary companions from astrometry
Authors: Sahlmann J. , Lazorenko P. F.
Published: August 2015

We analyse FORS2/VLT I-band imaging data to monitor the motions of both components in the nearest known binary brown dwarf WISE J104915.57-531906.1AB (LUH 16) over one year. The astrometry is dominated by parallax and proper motion, but with a precision of ∼0.2 mas per epoch we accurately measure the relative position change caused by the orbital motion of the pair. This allows us to directly measure a mass ratio of q = 0.78 ± 0.10 for this system. We also search for the signature of a planetary-mass companion around either of the A and B component and exclude at 3σ the presence of planets with masses larger than 2 MJ and orbital periods of 20–300 d. We update the parallax of LUH 16 to 500.51 ± 0.11 mas, i.e. just within 2 pc. This study yields the first direct constraint on the mass ratio of LUH 16 and shows that the system does not harbour any close-in giant planets.
Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates
Authors: Jumas-Bilak Estelle , Bouvet Philippe , Allen-Vercoe Emma , Aujoulat Fabien , Lawson Paul A. , Jean-Pierre Hélène , Marchandin Hélène
Published: August 2015

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the generaPyramidobacter,Jonquetella, andDethiosulfovibrio; the type strain ofPyramidobacter piscolenswas the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0and C16 : 0, each of which could be used to differentiate the strains fromP. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus,Rarimicrobiumgen. nov., is proposed with one novel species,Rarimicrobium hominissp. nov., named after the exclusive and rare finding of the taxon in human samples.Rarimicrobiumis the fifth genus of the 14 currently characterized in the phylumSynergistetesand the third one in subdivision B that includes human isolates. The type strain ofRarimicrobium hominisis ADV70T( = LMG 28163T = CCUG 65426T).
Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells
Authors: Váraljai Renáta , Islam Abul B.M.M.K. , Beshiri Michael L. , Rehman Jalees , Lopez-Bigas Nuria , Benevolenskaya Elizaveta V.
Published: August 2015

The retinoblastoma tumor suppressor protein pRb restricts cell growth through inhibition of cell cycle progression. Increasing evidence suggests that pRb also promotes differentiation, but the mechanisms are poorly understood, and the key question remains as to how differentiation in tumor cells can be enhanced in order to diminish their aggressive potential. Previously, we identified the histone demethylase KDM5A (lysine [K]-specific demethylase 5A), which demethylates histone H3 on Lys4 (H3K4), as a pRB-interacting protein counteracting pRB's role in promoting differentiation. Here we show that loss ofKdm5arestores differentiation through increasing mitochondrial respiration. This metabolic effect is both necessary and sufficient to induce the expression of a network of cell type-specific signaling and structural genes. Importantly, the regulatory functions of pRB in the cell cycle and differentiation are distinct because although restoring differentiation requires intact mitochondrial function, it does not necessitate cell cycle exit. Cells lackingRb1exhibit defective mitochondria and decreased oxygen consumption. Kdm5a is a direct repressor of metabolic regulatory genes, thus explaining the compensatory role ofKdm5adeletion in restoring mitochondrial function and differentiation. Significantly, activation of mitochondrial function by the mitochondrial biogenesis regulator Pgc-1α (peroxisome proliferator-activated receptor γ-coactivator 1α; also called PPARGC1A) a coactivator of the Kdm5a target genes, is sufficient to override the differentiation block. Overexpression of Pgc-1α, likeKDM5Adeletion, inhibits cell growth inRB-negative human cancer cell lines. The rescue of differentiation by loss of KDM5A or by activation of mitochondrial biogenesis reveals the switch to oxidative phosphorylation as an essential step in restoring differentiation and a less aggressive cancer phenotype.
Proteomic analysis of pRb loss highlights a signature of decreased mitochondrial oxidative phosphorylation
Authors: Nicolay Brandon N. , Danielian Paul S. , Kottakis Filippos , Lapek John D. , Sanidas Ioannis , Miles Wayne O. , Dehnad Mantre , Tschöp Katrin , Gierut Jessica J. , Manning Amity L. , Morris Robert , Haigis Kevin , Bardeesy Nabeel , Lees Jacqueline A. , Haas Wilhelm , Dyson Nicholas J.
Published: August 2015

The retinoblastoma tumor suppressor (pRb) protein associates with chromatin and regulates gene expression. Numerous studies have identified Rb-dependent RNA signatures, but the proteomic effects of Rb loss are largely unexplored. We acutely ablated Rb in adult mice and conducted a quantitative analysis of RNA and proteomic changes in the colon and lungs, where RbKO was sufficient or insufficient to induce ectopic proliferation, respectively. As expected, RbKO caused similar increases in classic pRb/E2F-regulated transcripts in both tissues, but, unexpectedly, their protein products increased only in the colon, consistent with its increased proliferative index. Thus, these protein changes induced by Rb loss are coupled with proliferation but uncoupled from transcription. The proteomic changes in common between RbKO tissues showed a striking decrease in proteins with mitochondrial functions. Accordingly, RB1 inactivation in human cells decreased both mitochondrial mass and oxidative phosphorylation (OXPHOS) function. RBKO cells showed decreased mitochondrial respiratory capacity and the accumulation of hypopolarized mitochondria. Additionally, RB/Rb loss altered mitochondrial pyruvate oxidation from 13C-glucose through the TCA cycle in mouse tissues and cultured cells. Consequently, RBKO cells have an enhanced sensitivity to mitochondrial stress conditions. In summary, proteomic analyses provide a new perspective on Rb/RB1 mutation, highlighting the importance of pRb for mitochondrial function and suggesting vulnerabilities for treatment.
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
Authors: Schep Alicia N. , Buenrostro Jason D. , Denny Sarah K. , Schwartz Katja , Sherlock Gavin , Greenleaf William J.
Published: August 2015

Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal “fingerprint” as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.
Diffraction analysis of strongly inhomogeneous residual stress depth distributions by modification of the stress scanning method. I. Theoretical concept
Authors: Meixner M. , Fuss T. , Klaus M. , Genzel Ch.
Published: August 2015

Exploiting the advantages of energy-dispersive synchrotron diffraction, a method for the determination of strongly inhomogeneous residual stress depth gradients is developed, which is an enhancement of the stress scanning technique. For this purpose, simulations on the basis of a very steep residual stress depth profile are performed, and it is shown that conventional real space evaluation approaches fail, because they do not take into account the variation of the residual stresses within the gauge volume. Therefore, a concept facilitating the deconvolution of the diffraction signal by considering the effect of the gauge volume geometry as well as the influence of the material absorption on the average information depth is proposed. It is demonstrated that data evaluation requires a three-dimensional least-squares fit procedure in this case. Furthermore, possible aberrations and their impact on the analysis of the residual stresses by applying the `modified stress scanning' method are treated theoretically.
Reliably distinguishing protein nanocrystals from amorphous precipitate by means of depolarized dynamic light scattering
Authors: Schubert Robin , Meyer Arne , Dierks Karsten , Kapis Svetlana , Reimer Rudolph , Einspahr Howard , Perbandt Markus , Betzel Christian
Published: August 2015

Crystallization of biological macromolecules such as proteins implies several prerequisites, for example, the presence of one or more initial nuclei, sufficient amounts of the crystallizing substance and the chemical potential to provide the free energy needed to force the process. The initiation of a crystallization process itself is a stochastic event, forming symmetrically assembled nuclei over kinetically preferred protein-dense liquid clusters. The presence of a spatial repetitive orientation of macromolecules in the early stages of the crystallization process has so far proved undetectable. However, early identification of the occurrences of unit cells is the key to nanocrystal detection. The optical properties of a crystal lattice offer a potential signal with which to detect whether a transition from disordered to ordered particles occurs, one that has so far not been tested in nanocrystalline applications. The ability of a lattice to depolarize laser light depends on the different refractive indices along different crystal axes. In this study a unique experimental setup is used to detect nanocrystal formation by application of depolarized scattered light. The results demonstrate the successful detection of nano-sized protein crystals at early stages of crystal growth, allowing an effective differentiation between protein-dense liquid cluster formation and ordered nanocrystals. The results are further verified by complementary methods like X-ray powder diffraction, second harmonic generation, ultraviolet two-photon excited fluorescence and scanning electron microscopy.
Empirical correction for resolution- and temperature-dependent errors caused by factors such as thermal diffuse scattering
Authors: Niepötter Benedikt , Herbst-Irmer Regine , Stalke Dietmar
Published: August 2015

Charge density investigations of the compounds [Mg{(pz*)3C}2] (1) (pz* = 3,5-dimethylpyrazolyl) and (Ph2P=S)C14H9(2) show two disturbing features in each case. First, the models derived from high-resolution data sets at different temperatures differ significantly. Additionally, residual density appears close to or even at the atomic positions, especially for data sets measured at 100 K. This indicates significant errors that could be caused by thermal diffuse scattering (TDS). A reduction of the integration box size leads to a substantial improvement in the model quality and removes the differences in the models. At the same time it indicates TDS to be the reason for these errors. However, this method is very time consuming and an alternative is needed. In endeavouring to improve the method, it was noticed that the refinement of resolution-dependent scale factors can be employed as a validation tool to detect such errors. In a nested interval approach, a correction factor {α =a[sin(θ)/λ]2+b[sin(θ)/λ]3} is determined that minimizes these errors and improves the model quality. This model is now based on refinement of only a single scale factor.