bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and implementation of an electromagnetic levitation system for active magnetic bearing wheels
Authors: Park Yonmook
Published: November 2013

In this study, an electromagnetic levitation system is developed as a prototype for developing active magnetic bearing wheels. The main mechanical parts of the electromagnetic levitation system consists of a rotor, a shaft, a cover and a base. A meaningful electromagnetic force, which is the minimal norm solution to an equation associated with the force and torques of the electromagnetic levitation system, is derived by using the singular value decomposition. A control system using the proportional‐integral‐derivative controller is developed to levitate the rotor at a target position against the force of gravity and regulate the two gimbal angles of the rotor. The numerical simulation and experimental results on the control of the electromagnetic levitation system are given to demonstrate the validity of the control design presented in this study.
Quasi‐finite‐rank approximation of compression operators on L∞ [0, h) with application to stability analysis of time‐delay systems
Authors: Kim Jung Hoon , Hagiwara Tomomichi
Published: November 2013

This study discusses a new method for approximating compression operators, which play important roles in the operator‐theoretic approach to sampled‐data systems and time‐delay systems. Stimulated by the success in the application of quasi‐finite‐rank approximation of compression operators defined on the Hilbert space L2 [0, h), the authors study a parallel problem for compression operators defined on the Banach space L∞ [0, h). In spite of similarity between these problems, they are led to applying a completely different approach because of essential differences in the underlying spaces. More precisely, they apply the idea of the conventional fast‐sample/fast‐hold (FSFH) approximation technique, and show that the approximation problem can be transformed into such a linear programming problem that asymptotically leads to optimal approximation as the FSFH approximation parameter M tends to infinity. Finally, they demonstrate the effectiveness of the L∞ [0, h)‐based approximation technique through numerical examples, with particular application to stability analysis of time‐delay systems.
Robust regional eigenvalue‐clustering analysis for grey discrete‐time systems with/without state delay
Authors: Chen Shinn‐Horng , Chou Jyh‐Horng , Zheng Liang‐An
Published: November 2013

The regional eigenvalue‐clustering robustness problem of grey discrete‐time systems with/without state delay is considered. Based on both spectral radius approach and matrix measure approach, three new sufficient conditions are proposed to preserve the regional eigenvalue‐clustering property of grey discrete‐time systems with/without state delay. If all eigenvalues are only required to be located within the unit circle, the proposed criteria become stability criteria. The proposed sufficient conditions are mathematically proven to be less conservative than those reported in the literature. Three examples are given to demonstrate that the proposed sufficient conditions are applicable and obtain less conservative results compared with those reported recently in the literature.
X-ray absorption spectroscopy and magnetic circular dichroism studies of L1-Mn-Ga thin films
Authors: Glas M. , Sterwerf C. , Schmalhorst J. M. , Ebke D. , Jenkins C. , Arenholz E. , Reiss G.
Published: November 2013

Tetragonally distorted Mn3−xGax thin films with 0.1<x<2 show a strong perpendicular magnetic anisotropy and low magnetization and thus have the potential to serve as electrodes in spin transfer torque magnetic random access memory. Because a direct capping of these films with MgO is problematic due to oxide formation, we examined the influence of a CoFeB interlayer and of two different deposition methods for the MgO barrier on the formation of interfacial Mn-O for Mn62Ga38 by element specific X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (XMCD). A highly textured L10 crystal structure of the Mn-Ga films was verified by X-ray diffraction measurements. For samples with e-beam evaporated MgO barrier no evidence for Mn-O was found whereas in samples with magnetron sputtered MgO, Mn-O was detected, even for the thickest interlayer thickness. Both XAS and XMCD measurements showed an increasing interfacial Mn-O amount with decreasing CoFeB interlayer thickness. Additional element specific full hysteresis loops determined an out-of-plane magnetization axis for the Mn and Co, respectively.
Study of cross-shaped ultrasonic array sensor applied to partial discharge location in transformer oil
Authors: Li Jisheng , Xin Xiaohu , Luo Yongfen , Ji Haiying , Li Yanming , Deng Junbo
Published: November 2013

A conformal combined sensor is designed and it is used in Partial Discharge (PD) location experiments in transformer oil. The sensor includes a cross-shaped ultrasonic phased array of 13 elements and an ultra-high-frequency (UHF) electromagnetic rectangle array of 2 × 2 elements. Virtual expansion with high order cumulants, the ultrasonic array can achieve the effect of array with 61 elements. This greatly improves the aperture and direction sharpness of original array and reduces the cost of follow-up hardware. With the cross-shaped ultrasonic array, the results of PD location experiments are precise and the maximum error of the direction of arrival (DOA) is less than 5°.
Electron scattering mechanisms in fluorine-doped SnO2 thin films
Authors: Rey G. , Ternon C. , Modreanu M. , Mescot X. , Consonni V. , Bellet D.
Published: November 2013

Polycrystalline fluorine-doped SnO2 (FTO) thin films have been grown by ultrasonic spray pyrolysis on glass substrate. By varying growth conditions, several FTO specimens have been deposited and the study of their structural, electrical, and optical properties has been carried out. By systematically investigating the mobility as a function of carrier density, grain size, and crystallite size, the contribution of each physical mechanism involved in the electron scattering has been derived. A thorough comparison of experimental data and calculations allows to disentangle these different mechanisms and to deduce their relative importance. In particular, the roles of extended structural defects such as grain or twin boundaries as revealed by electron microscopy or x-ray diffraction along with ionized impurities are discussed. As a consequence, based on the quantitative analysis presented here, an experimental methodology leading to the improvement of the electro-optical properties of FTO thin films is reported. FTO thin films assuming an electrical resistivity as low as 3.7 · 10−4 Ω cm (square sheet resistance of 8 Ω/◻) while retaining good transmittance up to 86% (including substrate effect) in the visible range have been obtained.
Electron energy distribution function by using probe method in electron cyclotron resonance multicharged ion source
Authors: Kumakura Sho , Kurisu Yosuke , Kimura Daiju , Yano Keisuke , Imai Youta , Sato Fuminobu , Kato Yushi , Iida Toshiyuki
Published: November 2013

We are constructing a tandem type electron cyclotron resonance (ECR) ion source (ECRIS). High-energy electrons in ECRIS plasma affect electron energy distribution and generate multicharged ion. In this study, we measure electron energy distribution function (EEDF) of low energy region (≦100 eV) in ECRIS plasma at extremely low pressures (10−3–10−5 Pa) by using cylindrical Langmuir probe. From the result, it is found that the EEDF correlates with the electron density and the temperature from the conventional probe analysis. In addition, we confirm that the tail of EEDF spreads to high energy region as the pressure rises and that there are electrons with high energy in ECR multicharged ion source plasma. The effective temperature estimated from the experimentally obtained EEDF is larger than the electron temperature obtained from the conventional method.
The critical compressibility factor of fluids from the global isomorphism approach
Authors: Kulinskii V. L.
Published: November 2013

The relation between the critical compressibility factors Zc of the Lennard-Jones fluid and the Lattice Gas (Ising model) is derived within the global isomorphism approach. On this basis, we obtain the alternative form for the value of the critical compressibility factor which is different from widely used phenomenological Timmermans relation. The estimates for the critical pressure Pc and Zc of the Lennard-Jones fluid are obtained in case of two and three dimensions. The extension of the formalism is proposed to include the Pitzer's acentric factor into consideration.
Effect of Mg diffusion on photoluminescence spectra of MgZnO/ZnO bi-layers annealed at different temperatures
Authors: Das Amit K. , Misra P. , Ajimsha R. S. , Bose A. , Joshi S. C. , Porwal S. , Sharma T. K. , Oak S. M. , Kukreja L. M.
Published: November 2013

MgZnO/ZnO bilayers (Mg concentration of ∼30%) have been grown and subsequently annealed at different temperatures in the range of 600–900 °C with the specific interest of studying the effect of inter-diffusion of Mg on the photoluminescence (PL) properties of the bilayers. The influence of Mg diffusion and material homogenization is evaluated through absorption, PL, and secondary ion mass spectrometry (SIMS) measurements. No appreciable change in the spectral positions is seen either in PL or absorption up to an annealing temperature of 700 °C, which is also supported by SIMS. However at higher annealing temperatures, diffusion of Mg into the ZnO layer is clearly evident in SIMS profile, which results in the red-shift (blue-shift) of spectral positions of MgZnO (ZnO) layer, respectively. Finally, for the sample annealed at 900 °C, the two layers are completely merged providing a single peak at ∼3.60 eV in PL/absorption corresponding to a completely homogenized MgZnO layer. Spectroscopic results are corroborated by the numerical simulations based on a simple theoretical model, which correlates the observed PL spectra of the heterostructures with the experimental Mg diffusion profiles across the heterointerface, as measured by SIMS.
Dielectric function of sol-gel prepared nano-granular zinc oxide by spectroscopic ellipsometry
Authors: Gilliot Mickaël , Eypert Céline , Hadjadj Aomar
Published: November 2013

ZnO thin films have been prepared by sol gel and deposited by spin coating. The dielectric function has been determined by spectroscopic ellipsometry. Ellipsometric spectra are inverted by a direct numerical method without using the standard fitting procedures. The obtained dielectric function presents a broad excitonic effect. The dielectric function is studied using Elliot excitonic theory including exciton plus band-to-band Coulomb interactions with standard Lorentzian broadening. A modification of this model dielectric function with independent bound and unbound exciton contributions is empirically proposed to improve modelling of the band gap excitonic peak.
Microstructural coarsening effects on redox instability and mechanical damage in solid oxide fuel cell anodes
Authors: Abdeljawad F. , Haataja M.
Published: November 2013

In state-of-the-art high temperature solid oxide fuel cells (SOFCs), a porous composite of nickel and yttria stabilized zirconia (Ni/YSZ) is employed as the anode. The rapid oxidation of Ni into NiO is regarded as the main cause of the so-called reduction-oxidation (redox) instability in Ni/YSZ anodes, due to the presence of extensive bulk volume changes associated with this reaction. As a consequence, the development of internal stresses can lead to performance degradation and/or structural failure. In this study, we employ a recently developed continuum formalism to quantify the mechanical deformation behavior and evolution of internal stresses in Ni/YSZ porous anodes due to re-oxidation. In our approach, a local failure criterion is coupled to the continuum framework in order to account for the heterogeneous damage accumulation in the YSZ phase. The hallmark of our approach is the ability to track the spatial evolution of mechanical damage and capture the interaction of YSZ damaged regions with the local microstructure. Simulation results highlight the importance of the microstructure characterized by Ni to YSZ particle size ratio on the redox behavior and damage accumulation in as-synthesized SOFC anode systems. Moreover, a redox-strain-to-failure criterion is developed to quantify the degree by which coarsened anode microstructures become more susceptible to mechanical damage during re-oxidation.
Design of a new broadband monopole optical nano-antenna
Authors: Zhou Rongguo , Ding Jun , Arigong Bayaner , Lin Yuankun , Zhang Hualiang
Published: November 2013

In this paper, we propose a novel design of broadband monopole optical nano-antennas. It is consisted of a corrugated half elliptical patch inside an elliptical aperture. By adjusting the dimensions of the elliptical patch and the elliptical aperture, the overall performance of the proposed monopole nano-antenna can be made remarkable broadband. Full wave electromagnetic simulations have been used to investigate the effects of different parameters on the nano-antenna performance. Moreover, the proposed broadband nano-antenna can support light waves with different polarizations. It is expected that the new optical antenna will pave the way towards the development of high performance optical antennas and optical systems.
Vacancy-type defects in InxGa1−xN grown on GaN templates probed using monoenergetic positron beams
Authors: Uedono Akira , Watanabe Tomohito , Kimura Shogo , Zhang Yang , Lozac'h Mickael , Sang Liwen , Ishibashi Shoji , Oshima Nagayasu , Suzuki Ryoichi , Sumiya Masatomo
Published: November 2013

Native defects in InxGa1−xN layers grown by metalorganic chemical vapor deposition were studied using monoenergetic positron beams. Measurements of Doppler broadening spectra of the annihilation radiation and lifetime spectra of positrons for a 200-nm-thick In0.13Ga0.87N layer showed that vacancy-type defects were introduced by InN alloying, and the major species of such defects was identified as complexes between a cation vacancy and nitrogen vacancies. The presence of the defects correlated with lattice relaxation of the In0.13Ga0.87N layer and the increase in photon emissions from donor-acceptor-pair recombination. The species of native defects in In0.06Ga0.94N layers was the same but its concentration was decreased by decreasing the InN composition. With the layer thickness increased from 120 nm to 360 nm, a defect-rich region was introduced in the subsurface region (<160 nm), which can be associated with layer growth with the relaxation of compressive stress.
Segregation and mixture profiles in dense, inclined flows of two types of spheres
Authors: Larcher Michele , Jenkins James T.
Published: November 2013

We study dry flows of two types of spheres down an inclined, rigid, bumpy bed in the absence of sidewalls. The flow is assumed to be steady and uniform in all but the direction normal to the free surface, collisions between particles are dissipative, and the sizes and masses of the particles are not too different. We restrict our analysis to dense flows and use an extension of kinetic theory to predict the concentration of the mixture and the profile of mixture velocity. A kinetic theory for a binary mixture of nearly elastic spheres that do not differ by much in their size or mass is employed to predict profiles of the concentration fraction of one type of sphere. We also determine the ratio of the radii and of the masses of the two species for which there is no segregation. We compare the predictions of the theory to the results of numerical simulations.
Controlled growth of vertically aligned MoO3 nanoflakes by plasma assisted paste sublimation process
Authors: Sharma Rabindar K. , Reddy G. B.
Published: November 2013

In this work, we have successfully developed plasma assisted paste sublimation route to deposit vertically aligned MoO3 nanoflakes (NFs) on nickel coated glass substrate in oxygen plasma ambience with the assistant of Ni thin layer as a catalyst. In our case, sublimation source (Mo strip surface) is resistively heated by flowing current across it. The structural, morphological, and optical properties of NFs have been investigated systematically using x-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) with selected area electron diffraction (SAED), High resolution transmission electron microscopy (HRTEM), micro-Raman spectroscopy, and Photoluminescence (PL) spectroscopy. Studies reveal that the presence of oxygen plasma and the nickel thin layer are very essential for the growth of vertically aligned NFs. The observed results divulge that α-MoO3 NFs are deposited uniformly on large scale with very high aspect (height/thickness) ratio more than 30 and well aligned along [0 k 0] crystallographic direction where k is even (2, 4, 6). Raman spectrum shows a significant size effect on the vibrational property of MoO3 nanoflakes. The PL spectrum of MoO3 NFs was recorded at room temperature and four prominent peaks at 365 nm, 395 nm, 452 nm, and 465 nm corresponding to UV-visible region were observed. In this paper, a three step growth strategy for the formation of MoO3 NFs has been proposed in detail.
Extended investigation of intermartensitic transitions in Ni-Mn-Ga magnetic shape memory alloys: A detailed phase diagram determination
Authors: Çakιr Aslι , Righi Lara , Albertini Franca , Acet Mehmet , Farle Michael , Aktürk Selçuk
Published: November 2013

Martensitic transitions in shape memory Ni-Mn-Ga Heusler alloys take place between a high temperature austenite and a low temperature martensite phase. However, intermartensitic transformations have also been encountered that occur from one martensite phase to another. To examine intermartensitic transitions in magnetic shape memory alloys in detail, we carried out temperature dependent magnetization, resistivity, and x-ray diffraction measurements to investigate the intermartensitic transition in Ni50Mn50–xGax in the composition range 12≤x≤25 at. %. Rietveld refined x-ray diffraction results are found to be consistent with magnetization and resistivity data. Depending on composition, we observe that intermartensitic transitions occur in the sequences 7M→L10, 5M→7M, and 5M→7M→L10 with decreasing temperature. The L10 non-modulated structure is most stable at low temperature.
Reversible magnetism switching in graphene-based systems via the decoration of photochromic molecules
Authors: Nurbawono Argo , Zhang Chun
Published: November 2013

By first principles calculations, we demonstrate that when decorated with photochromic molecules, it is possible to use light to reversibly control the magnetic properties of a nanoscale magnetic system. The combination of a graphene-based magnetic system and a photochromic azobenzene molecule is chosen as a model system. The trans and cis isomers of the azobenzene molecule that can be converted between each other by means of photoexcitations are found to have drastically different effects on the magnetic properties of the system. The results may pave the way for the future design of light controllable molecular-scale spintronic devices.
Surface-enhanced Raman scattering from graphene covered gold nanocap arrays
Authors: Long Kailin , Luo Xiaoguang , Nan Haiyan , Du Deyang , Zhao Weiwei , Ni Zhenhua , Qiu Teng
Published: November 2013

This work reports an efficient method to fabricate large-area flexible substrates for surface enhanced Raman scattering (SERS) application. Our technique is based on a single-step direct imprint process via porous anodic alumina stamps. Periodic hexagonal arrangements of porous anodic alumina stamps are transferred to the polyethylene terephthalate substrates by mechanically printing process. Printed nanocaps will turn into “hot spots” for electromagnetic enhancement with a deposited gold film by high vacuum evaporation. The gaps between the nanocaps are controllable with a tight correspondence to the thickness of the deposited gold, which dramatically influence the enhancement factor. After covered with a single-layer graphene sheet, the gold nanocap substrate can be further optimized with an extra enhancement of Raman signals, and it is available for the trace detection of probe molecules. This convenient, simple, and low-cost method of making flexible SERS-active substrates potentially opens a way towards biochemical analysis and disease detection.
Assessment of agricultural electric vehicles based on photovoltaics in China
Authors: Xue Jinlin
Published: November 2013

Solar-powered agricultural vehicles facilitate the reduction in the use of fossil fuel, decreasing the emissions of air pollutants and greenhouse gases. This paper assessed the agricultural electric vehicle (AEV) based on photovoltaics in China, taking into consideration three aspects, i.e., power supply mode for AEV, power of AEV, and economy analysis. The power supply mode, whether on-board photovoltaic (PV) system or off-board PV system, is subjected to the size and the power of the designed AEV, but the AEV's power depends on the area of PV panels which affects the initial investment cost of the PV system and the AEV. Three analysis indicators including payback period, net present value, and benefit-cost ratio were taken into consideration when comparing the projects of 10 kW and 30 kW AEVs based on PV system and the respective conventional tractors. Results show that the off-board PV system is more applicable to the AEV, the PV-based AEV with low power is a wise, economical investment, and this type of system is particularly appropriate for rural and remote areas in China, although the initial investment cost is huge for the most of the Chinese farmers.
Coherent microscopy at resolution beyond diffraction limit using post-experimental data extrapolation
Authors: Latychevskaia Tatiana , Fink Hans-Werner
Published: November 2013

Conventional microscopic records represent intensity distributions whereby local sample information is mapped onto local information at the detector. In coherent microscopy, the superposition principle of waves holds; field amplitudes are added, not intensities. This non-local representation is spread out in space and interference information combined with wave continuity allows extrapolation beyond the actual detected data. Established resolution criteria are thus circumvented and hidden object details can retrospectively be recovered from just a fraction of an interference pattern.
Pathogen selection drives nonoverlapping associations between HLA loci
Authors: Penman Bridget S. , Ashby Ben , Buckee Caroline O. , Gupta Sunetra
Published: November 2013

Significance

Human leukocyte antigens (HLA), first identified in tissue-matching for transplantation, play a critical role in immunity. HLAs are extraordinarily diverse, but certain sets of HLA genes are more likely to be found together than others. Here, we show that associations between HLA genes can arise through their coevolutionary interaction with pathogens. Technological advances are making it easier to determine HLA types, but DNA sequence alone cannot fully predict an HLA’s functional properties. Our work offers a new evolutionary approach to tackling this problem.
Dative and genitive variability in Late Modern English
Authors: Wolk Christoph , Bresnan Joan , Rosenbach Anette , Szmrecsanyi Benedikt
Published: November 2013

We present a cross-constructional approach to the history of the genitive alternation and the dative alternation in Late Modern English (AD 1650 to AD 1999), drawing on richly annotated datasets and modern statistical modeling techniques. We identify cross-constructional similarities in the development of the genitive and the dative alternation over time (mainly with regard to the loosening of the animacy constraint), a development which parallels distributional changes in animacy categories in the corpus material. Theoretically, we transfer the notion of ‘probabilistic grammar’ to historical data and claim that the corpus models presented reflect past speakers’ knowledge about the distribution of genitive and dative variants. The historical data also helps to determine what is constant (and timeless) in the effect of selected factors such as animacy or length, and what is variant.
Effects of tubulin acetylation and tubulin acetyltransferase binding on microtubule structure
Authors: Howes Stuart C. , Alushin Gregory M. , Shida Toshinobu , Nachury Maxence V. , Nogales Eva
Published: November 2013

Tubulin undergoes posttranslational modifications proposed to specify microtubule subpopulations for particular functions. Most of these modifications occur on the C-termini of tubulin and may directly affect the binding of microtubule-associated proteins (MAPs) or motors. Acetylation of Lys-40 on α-tubulin is unique in that it is located on the luminal surface of microtubules, away from the interaction sites of most MAPs and motors. We investigate whether acetylation alters the architecture of microtubules or the conformation of tubulin, using cryo–electron microscopy (cryo-EM). No significant changes are observed based on protofilament distributions or microtubule helical lattice parameters. Furthermore, no clear differences in tubulin structure are detected between cryo-EM reconstructions of maximally deacetylated or acetylated microtubules. Our results indicate that the effect of acetylation must be highly localized and affect interaction with proteins that bind directly to the lumen of the microtubule. We also investigate the interaction of the tubulin acetyltransferase, αTAT1, with microtubules and find that αTAT1 is able to interact with the outside of the microtubule, at least partly through the tubulin C-termini. Binding to the outside surface of the microtubule could facilitate access of αTAT1 to its luminal site of action if microtubules undergo lateral opening between protofilaments.
Centrosome-dependent asymmetric inheritance of the midbody ring inDrosophilagermline stem cell division
Authors: Salzmann Viktoria , Chen Cuie , Chiang C.-Y. Ason , Tiyaboonchai Amita , Mayer Michael , Yamashita Yukiko M.
Published: November 2013

Many stem cells, including Drosophila germline stem cells (GSCs), divide asymmetrically, producing one stem cell and one differentiating daughter. Cytokinesis is often asymmetric, in that only one daughter cell inherits the midbody ring (MR) upon completion of abscission even in apparently symmetrically dividing cells. However, whether the asymmetry in cytokinesis correlates with cell fate or has functional relevance has been poorly explored. Here we show that the MR is asymmetrically segregated during GSC divisions in a centrosome age–dependent manner: male GSCs, which inherit the mother centrosome, exclude the MR, whereas female GSCs, which we here show inherit the daughter centrosome, inherit the MR. We further show that stem cell identity correlates with the mode of MR inheritance. Together our data suggest that the MR does not inherently dictate stem cell identity, although its stereotypical inheritance is under the control of stemness and potentially provides a platform for asymmetric segregation of certain factors.
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
Authors: Raney Brian J. , Dreszer Timothy R. , Barber Galt P. , Clawson Hiram , Fujita Pauline A. , Wang Ting , Nguyen Ngan , Paten Benedict , Zweig Ann S. , Karolchik Donna , Kent W. James
Published: November 2013

Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror.

Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.

Contact:  donnak@soe.ucsc.edu
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Authors: Lienhard Matthias , Grimm Christina , Morkel Markus , Herwig Ralf , Chavez Lukas
Published: November 2013

Motivation: DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA.

Results: Here, we present a major update of the R/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor’s annotation databases to facilitate annotation of specific genomic regions.

Availability and implementation: The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http://www.bioconductor.org.

Contact:  lienhard@molgen.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Recommendations for best practice in deep-sea habitat classification: Bullimore et al. as a case study
Authors: Henry Lea-Anne , Roberts J. Murray
Published: November 2013

We assert that the reef framework-forming coral, Solenosmilia variabilis Duncan, 1873, is sometimes incorrectly recorded as another coral, Lophelia pertusa (Linnaeus, 1758) in surveys of deep-sea habitat (e.g. Bullimore, R., Foster, N., and Howell, K. 2013. Coral-characterized benthic assemblages of the deep Northeast Atlantic: defining “Coral Gardens” to support future habitat mapping efforts. ICES Journal of Marine Science, 70: 511–522). Accurate species lists are critical for developing robust deep-sea habitat classification schemes that allow us to map the distribution of different vulnerable marine ecosystems (VMEs) and predict their occurrences under future climate change scenarios, both of which help prioritize areas for marine protected areas. We recommend that the survey reported by Bullimore et al. (2013), as well as analogous surveys, consider the likelihood of Solenosmilia having been misidentified, and revise their data if necessary. We also make two further recommendations for best practice in deep-sea habitat classification using Bullimore et al. (2013) as a case study. Preferably, physical specimens should be obtained during deep-sea surveys. However, in the absence of identifications confirmed with specimens, image-based analyses of deep-sea communities can be achieved with high confidence when (i) independent validation is provided by senior taxonomic specialists in taxa that are indicators of VMEs, such as cold-water coral reefs, coral gardens, sponge grounds, cold seeps and xenophyophore fields; and (ii) stronger consideration is given to methods in classical taxonomy, the chemical oceanographic setting and community ecology.
Estimates of acoustic target strength for giant jellyfish Nemopilema nomurai Kishinouye in the coastal Northwest Pacific
Authors: Kang Donhyug , Park Jusam , Jung Seom-Kyu , Cho Sungho
Published: November 2013

Acoustic target strength (TS) measurements were made of ex situ giant jellyfish Nemopilema nomurai Kishinouye at 38 and 120 kHz. These TS data may be useful for developing acoustic scattering models, and surveying giant jellyfish distributions and biomasses. Each jellyfish was tethered in seawater using a monofilament line that vertically penetrated its bell's centre. During the acoustic measurements, an underwater video camera was used to continuously monitor the jellyfish's behaviour. Acoustic measurements were made using split-beam transducers. TS measurements were made of 27 individual jellyfish, but data were analysed for 23 specimens (bell diameter in air, Dair = 21–65 cm) at 38 kHz, and 19 specimens (Dair = 21–46 cm) at 120 kHz, respectively. Least-squares regression fits of TS vs. log(Dair) were TS38kHz = 20•log10Dair–82.7 (r = 0.76) and TS120kHz = 20•log10Dair–86.7 (r = 0.79). The mean TS values at 38 and 120 kHz, using the average Dair = 40.3 cm and 35.5 cm, respectively, were −50.6 and −55.7 dB. The reduced TS, a function of the ratio of Dair to wavelength (λ), was RTS(Dair/λ) = −6.1•log10(Dair/λ) –36.1 (r = 0.51). These RTS values decreased with increasing Dair/λ. Symbiotic medusa shrimp (Latreutes anoplonyx Kemp) contributed negligible bias to our TS measurements of giant jellyfish. These ex situ TS measurements may be used in acoustic surveys to estimate the distributions and biomasses of N. nomurai.
Radiative levitation of silicon in the atmospheres of two Hyades DA white dwarfs
Authors: Chayer P.
Published: November 2013

The presence of silicon at the surface of the two Hyades DA white dwarfs WD 0421+162 and WD 0431+126 requires mechanisms that counteract the effects of the downward diffusion. Radiative levitation calculations indicate that the silicon abundance observed in WD 0431+126 corresponds to the abundance supported by radiative levitation. Detailed time-dependent diffusion calculations that take into account radiative levitation and accretion indicate that accretion with rates of $\dot{M}_{\rm {Si}} \lesssim 10^4$ g s−1 could also be present without disrupting the abundance supported by radiative levitation. In the case of WD 0421+162, accretion with a rate of $\dot{M}_{\rm {Si}} = 10^{5.1}$ g s−1 must be invoked, because its observed silicon abundance is larger than the abundance supported by radiative levitation. This accretion rate is lower than the accretion rate given by the accretion–diffusion model, because the radiative levitation slows down the downward diffusion of silicon. The silicon abundances observed in the two Hyades white dwarfs cannot be interpreted solely in terms of accretion. The interpretation of the silicon abundances must take into account the interplay between radiative levitation and accretion.
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
Authors: Colloms Sean D. , Merrick Christine A. , Olorunniji Femi J. , Stark W. Marshall , Smith Margaret C. M. , Osbourn Anne , Keasling Jay D. , Rosser Susan J.
Published: November 2013

Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
“Last-Place Aversion”: Evidence and Redistributive Implications *
Authors: Kuziemko Ilyana , Buell Ryan W. , Reich Taly , Norton Michael I.
Published: November 2013

We present evidence from laboratory experiments showing that individuals are “last-place averse.” Participants choose gambles with the potential to move them out of last place that they reject when randomly placed in other parts of the distribution. In modified dictator games, participants randomly placed in second-to-last place are the most likely to give money to the person one rank above them instead of the person one rank below. Last-place aversion suggests that low-income individuals might oppose redistribution because it could differentially help the group just beneath them. Using survey data, we show that individuals making just above the minimum wage are the most likely to oppose its increase. Similarly, in the General Social Survey, those above poverty but below median income support redistribution significantly less than their background characteristics would predict.
Higher Protein Intake Improves Length, Not Weight, z Scores in Preterm Infants
Authors: Olsen Irene E. , Harris Cheryl L. , Lawson M. Louise , Berseth Carol L.
Published: November 2013

Objective:

The aim of the study was to evaluate the relation between nutritional intake (kilocalories, protein) and weight and length growth in preterm infants, and to describe their metabolic tolerance with a focus on those with high protein intake (≥4.6 g · kg−1 · day−1).

Methods:

Secondary analysis of data from appropriate‐for‐gestational age preterm infants in a 28‐day randomized clinical trial that evaluated growth, tolerance, and safety of a new ultraconcentrated liquid human milk fortifier (original study n = 150). This subset of 56 infants had complete growth and nutrition data and met criteria for the original study's “efficacy analysis” (eg, >80% of kilocalorie intake from study diet). Nutritional intake was estimated, not actual. Regressions were used to test cumulative kilocalories and protein as the predictors of 28‐day change in weight and length z scores (growth status), and to evaluate protein tolerance.

Results:

Average intake was 118 ± 8 kcal · kg−1 · day−1 and 4.3 ± 0.4 g protein · kg−1 · day−1, with 16 ± 3 g · kg−1 · day−1 and 1.1 ± 0.2 cm/week growth for 28 days. Cumulative total kilocalories and protein were significant predictors of improved length z score (P = 0.0054, 0.0005) but not weight z score change. Regression models indicated that protein not kilocalories explained the improvement in length z score, with protein explaining 19% of the variability. The high protein group averaged 4.6 to 5.5 g · kg−1 · day−1 (n = 16). Protein tolerance was adequate for all of the study infants based on metabolic measures (blood urea nitrogen, serum carbon dioxide, pH).

Conclusions:

Higher cumulative protein intake was tolerated and overall lessened the commonly occurring decline in the length but not weight growth status in a 28‐day study of preterm infants.
ESPGHAN Revised Porto Criteria for the Diagnosis of Inflammatory Bowel Disease in Children and Adolescents
Authors: Levine Arie , Koletzko Sibylle , Turner Dan , Escher Johanna C. , Cucchiara Salvatore , de Ridder Lissy , Kolho Kaija‐Leena , Veres Gabor , Russell Richard K. , Paerregaard Anders , Buderus Stephan , Greer Mary‐Louise C. , Dias Jorge A. , Veereman‐Wauters Gigi , Lionetti Paolo , Sladek Malgorzata , Martin de Carpi Javier , Staiano Annamaria , Ruemmele Frank M. , Wilson David C.
Published: November 2013

Background:

The diagnosis of pediatric‐onset inflammatory bowel disease (PIBD) can be challenging in choosing the most informative diagnostic tests and correctly classifying PIBD into its different subtypes. Recent advances in our understanding of the natural history and phenotype of PIBD, increasing availability of serological and fecal biomarkers, and the emergence of novel endoscopic and imaging technologies taken together have made the previous Porto criteria for the diagnosis of PIBD obsolete.

Methods:

We aimed to revise the original Porto criteria using an evidence‐based approach and consensus process to yield specific practice recommendations for the diagnosis of PIBD. These revised criteria are based on the Paris classification of PIBD and the original Porto criteria while incorporating novel data, such as for serum and fecal biomarkers. A consensus of at least 80% of participants was achieved for all recommendations and the summary algorithm.

Results:

The revised criteria depart from existing criteria by defining 2 categories of ulcerative colitis (UC, typical and atypical); atypical phenotypes of UC should be treated as UC. A novel approach based on multiple criteria for diagnosing IBD‐unclassified (IBD‐U) is proposed. Specifically, these revised criteria recommend upper gastrointestinal endoscopy and ileocolonscopy for all suspected patients with PIBD, with small bowel imaging (unless typical UC after endoscopy and histology) by magnetic resonance enterography or wireless capsule endoscopy.

Conclusions:

These revised Porto criteria for the diagnosis of PIBD have been developed to meet present challenges and developments in PIBD and provide up‐to‐date guidelines for the definition and diagnosis of the IBD spectrum.
Long‐Term Outcome of Home Parenteral Nutrition in Patients With Ultra‐Short Bowel Syndrome
Authors: Diamanti Antonella , Conforti Andrea , Panetta Fabio , Torre Giuliano , Candusso Manila , Bagolan Pietro , Papa Raffaele Edo , Grimaldi Chiara , Fusaro Fabio , Capriati Teresa , Elia Domenica , de Goyet Jean De Ville
Published: November 2013

Objective:

The patients with ultra‐short bowel syndrome (U‐SBS) have been considered potential candidates for a preemptive/rehabilitative intestinal transplantation owing to the high risk of death from the underlying disease. We hypothesized that children with U‐SBS, in the absence of intestinal failure‐associated liver disease (IFALD), could also have a good rate of survival on home parenteral nutrition (HPN).

Methods:

A prospective database from the “Bambino Gesù” Artificial Nutrition and Intestinal Failure Program was used to evaluate outcomes and morbidities of consecutive patients with ≤10 cm of small bowel enrolled since 2000.

Results:

Eleven patients were identified with a median bowel length of 7.5 (3–9) cm. Eight patients developed IFALD, which reversed in 7 of them; the IFALD progressively worsened in 1 patient until death. One patient underwent isolated intestinal transplantation and 1 patient is no longer receiving parenteral nutrition (PN) and both are fully enterally fed. The other patients remained at least partially dependent on HPN. The number of days of inpatient care decreased in all of the patients except for the 1 who had repeated episodes of central line infections.

Conclusions:

The survival of patients with U‐SBS receiving HPN was good. Although IFALD was frequent, it had been manageable in most of the patients, but in a single complex case, it led to death. The multidisciplinary management warranted to these patients to approach the school age, to grow, and to maintain the oral intake. Patients with U‐SBS are rare, and to better understand their long‐term survival, further studies, including more large patient populations, are required.
Why is timing of bird migration advancing when individuals are not?
Authors: Gill Jennifer A. , Alves José A. , Sutherland William J. , Appleton Graham F. , Potts Peter M. , Gunnarsson Tómas G.
Published: November 2013

Recent advances in spring arrival dates have been reported in many migratory species but the mechanism driving these advances is unknown. As population declines are most widely reported in species that are not advancing migration, there is an urgent need to identify the mechanisms facilitating and constraining these advances. Individual plasticity in timing of migration in response to changing climatic conditions is commonly proposed to drive these advances but plasticity in individual migratory timings is rarely observed. For a shorebird population that has significantly advanced migration in recent decades, we show that individual arrival dates are highly consistent between years, but that the arrival dates of new recruits to the population are significantly earlier now than in previous years. Several mechanisms could drive advances in recruit arrival, none of which require individual plasticity or rapid evolution of migration timings. In particular, advances in nest-laying dates could result in advanced recruit arrival, if benefits of early hatching facilitate early subsequent spring migration. This mechanism could also explain why arrival dates of short-distance migrants, which generally return to breeding sites earlier and have greater scope for advance laying, are advancing more rapidly than long-distance migrants.
Diagnosis of neuroschistosomiasis by antibody specificity index and semi-quantitative real-time PCR from cerebrospinal fluid and serum
Authors: Härter Georg , Frickmann Hagen , Zenk Sebastian , Wichmann Dominic , Ammann Bettina , Kern Peter , Fleischer Bernhard , Tannich Egbert , Poppert Sven
Published: November 2013

We describe the case of a 16-year-old German male expatriate from Ghana who presented with obstipation, dysuria, dysaesthesia of the gluteal region and the lower limbs, bilateral plantar hypaesthesia and paraesthesia without pareses. A serum–cerebrospinal fluid (CSF) Schistosoma spp. specific antibody specificity index of 3.1 was considered highly suggestive of intrathecal synthesis of anti-Schistosoma spp. specific antibodies, although standardization of this procedure has not previously been described. Diagnosis was confirmed by detection of Schistosoma DNA in CSF by semi-quantitative real-time PCR at 100-fold concentration compared with serum. Accordingly the two diagnostic procedures, which have not previously been applied for routine diagnosis, appear to be useful for the diagnosis of neuroschistosomiasis. Clinical symptoms resolved following anthelmintic and anti-inflammatory therapy.