bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic state controllable critical temperature in epitaxial Ho/Nb bilayers
Authors: Gu Yuanzhou , Robinson J. W. A. , Bianchetti M. , Stelmashenko N. A. , Astill D. , Grosche F. M. , MacManus-Driscoll J. L. , Blamire M. G.
Published: April 2014

We study the magnetic properties of Ho thin films with different crystallinity (either epitaxial or non-epitaxial) and investigate their proximity effects with Nb thin films. Magnetic measurements show that epitaxial Ho has large anisotropy in two different crystal directions in contrast to non-epitaxial Ho. Transport measurements show that the superconducting transition temperature (Tc) of Nb thin films can be significantly suppressed at zero field by epitaxial Ho compared with non-epitaxial Ho. We also demonstrate a direct control over Tc by changing the magnetic states of the epitaxial Ho layer, and attribute the strong proximity effects to exchange interaction.
Continuous size-based separation of microparticles in a microchannel with symmetric sharp corner structures
Authors: Fan Liang-Liang , He Xu-Kun , Han Yu , Du Li , Zhao Liang , Zhe Jiang
Published: April 2014

A new microchannel with a series of symmetric sharp corner structures is reported for passive size-dependent particle separation. Micro particles of different sizes can be completely separated based on the combination of the inertial lift force and the centrifugal force induced by the sharp corner structures in the microchannel. At appropriate flow rate and Reynolds number, the centrifugal force effect on large particles, induced by the sharp corner structures, is stronger than that on small particles; hence after passing a series of symmetric sharp corner structures, large particles are focused to the center of the microchannel, while small particles are focused at two particle streams near the two side walls of the microchannel. Particles of different sizes can then be completely separated. Particle separation with this device was demonstrated using 7.32 μm and 15.5 μm micro particles. Experiments show that in comparison with the prior multi-orifice flow fractionation microchannel and multistage-multiorifice flow fractionation microchannel, this device can completely separate two-size particles with narrower particle stream band and larger separation distance between particle streams. In addition, it requires no sheath flow and complex multi-stage separation structures, avoiding the dilution of analyte sample and complex operations. The device has potentials to be used for continuous, complete particle separation in a variety of lab-on-a-chip and biomedical applications.
Structural and magnetic characterization of as-prepared and annealed FeCoCu nanowire arrays in ordered anodic aluminum oxide templates
Authors: Rodríguez-González B. , Bran C. , Warnatz T. , Rivas J. , Vazquez M.
Published: April 2014

Herein, we report on the preparation, structure, and magnetic characterization of FeCoCu nanowire arrays grown by DC electrodeposition inside self-assembled ordered nanopores of anodic aluminum oxide templates. A systematic study of their structure has been performed both in as-prepared samples and after annealing in the temperature range up to 800 °C, although particular attention has been paid to annealing at 700 °C after which maximum magnetic hardening is achieved. The obtained nanowires have a diameter of 40 nm and their Fe0.28Co0.67Cu0.05 composition was confirmed by energy dispersive X-ray spectroscopy (EDS). Focused ion-beam lamellas of two samples (as-prepared and annealed at 700 °C) were prepared for their imaging in the high-resolution transmission electron microscopy (HRTEM) perpendicularly to the electron beam, where the obtained EDS compositional mappings show a homogeneous distribution of the elements. X-ray diffraction analysis, and selected area electron diffraction (SAED) patterns confirm that nanowires exhibit a bcc cubic structure (space group Im-3m). In addition, bright-dark field images show that the nanowires have a polycrystalline structure that remains essentially the same after annealing, but some modifications were observed: (i) an overall increase and sharpening of recrystallized grains, and (ii) an apparent shrinkage of the nanowires diameter. Obtained SAED patterns also show strong textured components with determined ⟨111⟩ and ⟨112⟩ crystalline directions parallel to the wires growth direction. The presence of both directions was also confirmed in the HRTEM images doing Fourier transform analyses. Magnetic measurements show strong magnetic anisotropy with magnetization easy axis parallel to the nanowires in as-prepared and annealed samples. The magnetic properties are tuned by suitable thermal treatments so that, maximum enhanced coercivity (∼2.7 kOe) and normalized remanence (∼0.91 Ms) values are achieved after annealing at temperature of 700 °C. The contribution of the changes in the crystalline structure, induced by the heat treatment, to the magnetic hardening of the FeCoCu nanowires is discussed.
Single-step in-situ synthesis and optical properties of ZnSe nanostructured dielectric nanocomposites
Authors: Dey Chirantan , Rahaman Molla Atiar , Tarafder Anal , Kr Mishra Manish , De Goutam , Goswami Madhumita , Kothiyal G. P. , Karmakar Basudeb
Published: April 2014

This work provides the evidence of visible red photoluminescent light emission from ZnSe nanocrystals (NCs) grown within a dielectric (borosilicate glass) matrix synthesized by a single step in-situ technique for the first time and the NC sizes were controlled by varying only the concentration of ZnSe in glass matrix. The ZnSe NCs were investigated by UV-Vis optical absorption spectroscopy, Raman spectroscopy, and transmission electron microscopy (TEM). The sizes of the ZnSe NCs estimated from the TEM images are found to alter in the range of 2–53 nm. Their smaller sizes of the NCs were also calculated by using the optical absorption spectra and the effective mass approximation model. The band gap enlargements both for carrier and exciton confinements were evaluated and found to be changed in the range of 0–1.0 eV. The Raman spectroscopic studies showed blue shifted Raman peaks of ZnSe at 295 and 315 cm−1 indicating phonon confinement effect as well as compressive stress effect on the surface atoms of the NCs. Red photoluminescence in ZnSe-glass nanocomposite reveals a broad multiple-peak structure due to overlapping of emission from NC size related electron-hole recombination (∼707 nm) and emissions from defects to traps, which were formed due to Se and Zn vacancies signifying potential application in photonics.
Periodic and chaotic oscillations in a tumor and immune system interaction model with three delays
Authors: Bi Ping , Ruan Shigui , Zhang Xinan
Published: April 2014

In this paper, a tumor and immune system interaction model consisted of two differential equations with three time delays is considered in which the delays describe the proliferation of tumor cells, the process of effector cells growth stimulated by tumor cells, and the differentiation of immune effector cells, respectively. Conditions for the asymptotic stability of equilibria and existence of Hopf bifurcations are obtained by analyzing the roots of a second degree exponential polynomial characteristic equation with delay dependent coefficients. It is shown that the positive equilibrium is asymptotically stable if all three delays are less than their corresponding critical values and Hopf bifurcations occur if any one of these delays passes through its critical value. Numerical simulations are carried out to illustrate the rich dynamical behavior of the model with different delay values including the existence of regular and irregular long periodic oscillations.
Three-dimensional simulations of discharge plasma evolution on a dielectric barrier discharge plasma actuator
Authors: Nishida Hiroyuki , Nonomura Taku , Abe Takashi
Published: April 2014

To develop simulation techniques for reconstructing microdischarges in a dielectric barrier discharge (DBD) plasma actuator and analyze spanwise non-uniformity in a body force field, three-dimensional discharge plasma simulations of a DBD plasma actuator were conducted assuming step-like positive and negative applied voltages. Our study showed that to break the spanwise uniformity, some disturbances were required in the computational conditions to reconstruct the three-dimensional microdischarges, and the attachment of some minute bumps (several tens of micrometers in size) on the electrode edge allowed for the successful reconstruction of glow-type microdischarges and streamer-type filamentary discharges in the negative and positive applied voltage cases, respectively. The tentative body force field has strong spanwise non-uniformity corresponding to the plasma structure, and in addition, a spanwise directional body force also exists, especially in the streamer discharge. However, the spanwise averaged body force has the same spatial-distribution and time-evolution characteristics obtained with the two-dimensional simulation.
Anisotropy in the hole mobility measured along the [110] and [1¯10] orientations in a strained Ge quantum well
Authors: Hassan A. H. A. , Morris R. J. H. , Mironov O. A. , Beanland R. , Walker D. , Huband S. , Dobbie A. , Myronov M. , Leadley D. R.
Published: April 2014

In this paper, we report on anisotropic transport properties of strained germanium (sGe) quantum wells grown on Si (001) substrates with p-type doping beneath the sGe channel. Mobility measurements were made along orthogonal [110] directions. The level of measured resistivity anisotropy in the [110] and [1¯10] orientations was found to vary between 2 and 9 for different samples. This corresponds to an actual mobility anisotropy ratio of between 1.3 and 2, values that are significantly higher than previously found for sGe. From modeling of the low temperature (12 K) mobility, using the relaxation time approach, the anisotropy in mobility was accounted for by a difference in interface roughness scattering between the two orientations. For the [110] orientation, a step height of Δ = 0.28 nm and interface roughness periodicity of λ = 7 nm were found while for the [1¯10] orientation, λ reduced to 4 nm and Δ increased to 0.42 nm. High-resolution X-ray diffraction and transmission electron microscopy confirmed a 1° off-cut in the wafer towards the [1¯10] direction.
Site-controlled fabrication of Ga nanodroplets by focused ion beam
Authors: Xu Xingliang , Wu Jiang , Wang Xiaodong , Li Handong , Zhou Zhihua , Wang Zhiming M.
Published: April 2014

Ga droplets are created by focused ion beam irradiation of GaAs surface. We report that ordered Ga droplets can be formed on the GaAs surface without any implantation damage. The droplets are characterized with bigger sizes than those droplets formed on damaged area. These aligned Ga droplets are formed via the migration of Ga atoms from ion irradiation area to the edge of undamaged GaAs surface and further nucleation into droplets. The morphological evolution and size distribution of these nanodroplets are investigated systematically with different beam irradiation time and incident angles. Based on this method, well positioned Ga nanodroplets, such as chains, are achieved by using focus ion beam patterning. The controllable assembly of droplets on undamaged semiconductor surface can be used to fabricate templates, to fabricate quantum structures and quantum devices by droplet epitaxy technique.
Position of fermi level on Al0.2Ga0.8N surface and distribution of electric field in Al0.2Ga0.8N/GaN heterostructures without and with AlN layer
Authors: Gladysiewicz M. , Janicki L. , Kudrawiec R. , Misiewicz J. , Wosko M. , Paszkiewicz R. , Paszkiewicz B. , Tłaczała M.
Published: April 2014

Position of Fermi level on Al0.2Ga0.8N surface and distribution of electric field in Al0.2Ga0.8N/GaN transistor heterostructures without and with AlN layer were studied experimentally using contactless electroreflectance and theoretically solving Schrodinger-Poisson equation with various surface boundary conditions. It has been observed that the thin AlN layer changes very strongly the distribution of electric field in this heterostructure but the Fermi level position on Al0.2Ga0.8N surface does not change significantly. Its position is the same within experimental uncertainly (i.e., ∼0.5 eV below conduction band) for both bulk Al0.2Ga0.8N and Al0.2Ga0.8N/GaN heterostructures.
Defect generation in amorphous-indium-gallium-zinc-oxide thin-film transistors by positive bias stress at elevated temperature
Authors: Um Jae Gwang , Mativenga Mallory , Migliorato Piero , Jang Jin
Published: April 2014

We report on the generation and characterization of a hump in the transfer characteristics of amorphous indium gallium zinc-oxide thin-film transistors by positive bias temperature stress. The hump depends strongly on the gate bias stress at 100 °C. Due to the hump, the positive shift of the transfer characteristic in deep depletion is always smaller that in accumulation. Since, the latter shift is twice the former, with very good correlation, we conclude that the effect is due to creation of a double acceptor, likely to be a cation vacancy. Our results indicate that these defects are located near the gate insulator/active layer interface, rather than in the bulk. Migration of donor defects from the interface towards the bulk may also occur under PBST at 100 °C.
Upconversion and pump saturation mechanisms in Er3+/Yb3+ co-doped Y2Ti2O7 nanocrystals
Authors: Wang Fengxiao , Song Feng , Zhang Gong , Han Yingdong , Li Qiong , Ming Chengguo , Tian Jianguo
Published: April 2014

The Er3+/Yb3+ co-doped Y2Ti2O7 nanocrystals were synthesized by the sol–gel method. X-ray diffraction, transmission electronic microscopy, and photoluminescence spectra were measured to verify the Y2Ti2O7 nanocrystalline produced in the sample annealed at 800 °C. The anomalous slopes of the fitted line in the log-log plots for upconversion emissions and the pump-saturation effect of near-infrared emission were observed in the nanocrystalline samples. A theoretical model of practical Er3+/Yb3+ co-doped system based on the rate equations were put forward and explained the experimental phenomena well.
Low temperature dependent ferroelectric resistive switching in epitaxial BiFeO3 films
Authors: Yan F. , Xing G. Z. , Li L.
Published: April 2014

The ferroelectric switchable diode induced resistive switching behavior at low temperature has been investigated in the epitaxial BiFeO3 (BFO) thin films. The switchable diode can be tuned using a higher voltage at low temperatures. The diode barrier is determined to be ∼0.55 eV at the interface between BFO and electrode. The resistive switchable barrier with respect to the ferroelectric domain switching has been systematically characterized at various low temperatures. The temperature dependent conduction and leakage mechanisms have also been identified. These results can advance our understanding of resistive switching based on ferroelectric switchable diode at low working temperatures and potentially extend the applications of memristor to a larger temperature scale.
Role of an interlayer at a TiN/Ge contact to alleviate the intrinsic Fermi-level pinning position toward the conduction band edge
Authors: Yamamoto Keisuke , Mitsuhara Masatoshi , Hiidome Keisuke , Noguchi Ryutaro , Nishida Minoru , Wang Dong , Nakashima Hiroshi
Published: April 2014

TiN/Ge contacts, prepared by direct sputter deposition from a TiN target, can alleviate the intrinsic Fermi-level pinning (FLP) position toward the conduction band edge. This work focuses on studying the origin of the FLP alleviation. Investigations on both the electrical properties and interfacial structures of TiN/Ge contacts showed that an amorphous interlayer (IL) containing nitrogen played an important role in the alleviation. For comparison, the properties of Ti/Ge contacts were also studied. Based on these results, the IL structure that induced the FLP alleviation was clearly shown and a model was proposed to explain the FLP alleviation.
Stacking-dependent electronic structure of bilayer silicene
Authors: Fu Huixia , Zhang Jin , Ding Zijing , Li Hui , Meng Sheng
Published: April 2014

Bilayer silicene (BLS) is a class of material that possibly holds both topological and superconducting properties; however, its structure is not fully understood. By scanning stacking modes and lattice constants using first principles calculations, several meta-stable configurations are identified, including a slightly faulted-AA packing structure, named slide-2AA. Different from the metallic properties of conventional AA and AB stacking forms, band structure of slide-2AA bilayer presents a sizeable indirect energy gap of ∼1.16 eV. A metal-semiconductor phase transition along the sliding pathway with a small energy barrier is also observed, indicating its electronic properties can be easily tuned by applying small shear force along the BLS surface plane. Such unique quantitative relationship of structure and electronic properties has profound implications in nanoelectronics and electromechanical devices.
Nanoindentation and thermal characterization of poly (vinylidenefluoride)/MWCNT nanocomposites
Authors: Eggedi Obulapathi , Valiyaneerilakkal Uvais , Darla M. R. , Varghese Soney
Published: April 2014

We report the preparation, thermal and micro/nanomechanical behavior of poly (vinylidine diflouride) (PVDF)/multiwalled carbon nanotube (MWCNT) nanocomposites. It has been found that the addition of MWCNT considerably enhances the β-phase formation, thermal and mechanical properties of PVDF. Atomic force microscope (AFM) studies have been performed on the composites under stress conditions to measure the mechanical properties. The nanoscale mechanical properties of the composites like Young's modulus and hardness of the nanocomposites were investigated by nanoindentation technique. Morphological studies of the nanocomposites were also studied, observations show a uniform distribution of MWCNT in the matrix and interfacial adhesion between PVDF and MWCNT was achieved, which was responsible for enhancement in the hardness and Young's modulus. Differential scanning calorimetry (DSC) studies indicate that the melting temperature of the composites have been slightly increased while the heat of fusion markedly decreased with increasing MWCNT content.
Principles and guidelines for managing cattle grazing in the grazing lands of northern Australia: stocking rates, pasture resting, prescribed fire, paddock size and water points – a review
Authors: Hunt L. P. , McIvor J. G. , Grice A. C. , Bray S. G.
Published: April 2014

Beef cattle grazing is the dominant land use in the extensive tropical and sub-tropical rangelands of northern Australia. Despite the considerable knowledge on land and herd management gained from both research and practical experience, the adoption of improved management is limited by an inability to predict how changes in practices and combinations of practices will affect cattle production, economic returns and resource condition. To address these issues, past Australian and international research relating to four management factors that affect productivity and resource condition was reviewed in order to identify key management principles. The four management factors considered were stocking rates, pasture resting, prescribed fire, and fencing and water point development for managing grazing distribution. Four management principles for sound grazing management in northern Australia were formulated as follows: (1) manage stocking rates to meet goals for livestock production and land condition; (2) rest pastures to maintain them in good condition or to restore them from poor condition to increase pasture productivity; (3) devise and apply fire regimes that enhance the condition of grazing land and livestock productivity while minimising undesirable impacts; and (4) use fencing and water points to manipulate grazing distribution. Each principle is supported by several more specific guidelines. These principles and guidelines, and the supporting research on which they are based, are presented.
Assessing the impact of seasonal precipitation and temperature on vegetation in a grass-dominated rangeland
Authors: Chen Fang , Weber Keith T.
Published: April 2014

Changes in vegetation are affected by many climatic factors and have been successfully monitored through satellite remote sensing over the past 20 years. In this study, the Normalised Difference Vegetation Index (NDVI), derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Terra satellite, was selected as an indicator of change in vegetation. Monthly MODIS composite NDVI at a 1-km resolution was acquired throughout the 2004–09 growing seasons (i.e. April–September). Data describing daily precipitation and temperature, primary factors affecting vegetation growth in the semiarid rangelands of Idaho, were derived from the Surface Observation Gridding System and local weather station datasets. Inter-annual and seasonal fluctuations of precipitation and temperature were analysed and temporal relationships between monthly NDVI, precipitation and temperature were examined. Results indicated NDVI values observed in June and July were strongly correlated with accumulated precipitation (R2 >0.75), while NDVI values observed early in the growing season (May) as well as late in the growing season (August and September) were only moderately related with accumulated precipitation (R2 ≥0.45). The role of ambient temperature was also apparent, especially early in the growing season. Specifically, early growing-season temperatures appeared to significantly affect plant phenology and, consequently, correlations between NDVI and accumulated precipitation. It is concluded that precipitation during the growing season is a better predictor of NDVI than temperature but is interrelated with influences of temperature in parts of the growing season.
Future fire danger climatology for Tasmania, Australia, using a dynamically downscaled regional climate model
Authors: Fox-Hughes Paul , Harris Rebecca , Lee Greg , Grose Michael , Bindoff Nathan
Published: April 2014

Daily values of McArthur Forest Fire Danger Index were generated at ~10-km resolution over Tasmania, Australia, from six dynamically downscaled CMIP3 climate models for 1961–2100, using a high (A2) emissions scenario. Multi-model mean fire danger validated well against observations for 2002–2012, with 99th percentile fire dangers having the same distribution and largely similar values to those observed over the same time. Model projections showed a broad increase in fire danger across Tasmania, but with substantial regional variation – the increase was smaller in western Tasmania (district mean cumulative fire danger increasing at 1.07 per year) compared with parts of the east (1.79 per year), for example. There was also noticeable seasonal variation, with little change occurring in autumn, but a steady increase in area subject to springtime 99th percentile fire danger from 6% in 1961–1980 to 21% by 2081–2100, again consistent with observations. In general, annually accumulated fire danger behaved similarly. Regional mean sea level pressure patterns resembled observed patterns often associated with days of dangerous fire weather. Days of elevated fire danger displaying these patterns increased in frequency during the simulated twenty-first century: in south-east Tasmania, for example, the number of such events detected rose from 101 (across all models) in 1961–1980 to 169 by 2081–2100. Correspondence of model output with observations and the regional detail available suggest that these dynamically downscaled model data are useful projections of future fire danger for landscape managers and the community.
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis
Authors: Lee Eunjee , de Ridder Jeroen , Kool Jaap , Wessels Lodewyk F. A. , Bussemaker Harmen J.
Published: April 2014

Significance

Each individual tumor harbors a unique combination of genetic lesions, which together are responsible for the aberrant behavior of its cells. Cancer-causing viruses have been used in mice to systematically sample this genetic diversity. Corresponding changes in global gene expression can be monitored using high-throughput technology. In this study, we present a computational strategy that integrates information at the genetic and molecular level to construct a genome-wide signature that captures the effect of an individual genetic lesion on the gene regulatory network of the cell. We show how these signatures can be exploited to gain insight into the processes and regulatory pathways perturbed by each lesion and suggest drugs that can counteract its effect.
Yeast DJ-1 superfamily members are required for diauxic-shift reprogramming and cell survival in stationary phase
Authors: Miller-Fleming Leonor , Antas Pedro , Pais Teresa Faria , Smalley Joshua L. , Giorgini Flaviano , Outeiro Tiago Fleming
Published: April 2014

Significance

To our knowledge, we show for the first time that the yeast DJ-1 homologs are required for diauxic-shift, an important metabolic reprogramming stage that is triggered by glucose deprivation. Deletion of the
HSP31-34
genes results in reduced lifespan and alterations in several hallmarks of stationary-phase, including impairment of autophagy induction through deregulation of target of rapamycin complex 1 (TORC1). As both autophagy and TORC1 are associated with human disorders, our work has broad relevance toward the understanding of these processes in health and disease.
Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin
Authors: Rognoni Lorenz , Möst Tobias , Žoldák Gabriel , Rief Matthias
Published: April 2014

Significance

Biological processes in the cell are highly dynamic and complex, and their correct interplay is ensured by a multitude of regulatory mechanisms. Among these, proline isomerization acts as a molecular switch that toggles two protein conformations, and thus functions, over time. In mechanosensing, mechanical stress is transduced into chemical signals. The molecular mechanisms underlying this regulation are crucial for understanding cell behavior and development. However, only a few experimental techniques are capable of studying force at the molecular level. In this paper, we use single-molecule mechanical experiments to investigate how the force-sensing region of the cytoskeletal cross-linker filamin is modulated by a proline switch.
Spatial characterization of the focus produced by an EUV Schwarzschild objective
Authors: Ewald Johannes , Wieland Marek , Nisius Thomas , Henning Lars , Feigl Torsten , Drescher Markus , Wilhein Thomas
Published: April 2014

Schwarzschild objectives are used in the EUV spectral range because of their large aperture, high mechanical stability and excellent achromaticity. The large aperture results in a small, theoretically diffraction limited focus diameter with ideal values of below 200 nm with the current configuration. We employed a zone plate with matched numerical aperture (0.19) to image the focus onto an X-ray CCD camera. Emission from high harmonic generation and a liquid-jet laser-plasma were used as light sources. Images at magnifications of about 150-fold were acquired and focus diameters of 300 nm (FWHM) were observed.
Cohomology of arithmetic families of (𝜑,Γ)-modules
Authors: Kedlaya Kiran , Pottharst Jonathan , Xiao Liang
Published: April 2014

We prove the finiteness and compatibility with base change of the

(
φ
,
Γ
)

(\varphi , \Gamma )

-cohomology and the Iwasawa cohomology of arithmetic families of

(
φ
,
Γ
)

(\varphi , \Gamma )

-modules. Using this finiteness theorem, we show that a family of Galois representations that is densely pointwise refined in the sense of Mazur is actually trianguline as a family over a large subspace. In the case of the Coleman-Mazur eigencurve, we determine the behavior at all points.
The Ca2+-activated Cl−channel ANO1/TMEM16A regulates primary ciliogenesis
Authors: Ruppersburg Chelsey Chandler , Hartzell H. Criss
Published: April 2014

Many cells possess a single, nonmotile, primary cilium highly enriched in receptors and sensory transduction machinery that plays crucial roles in cellular morphogenesis. Although sensory transduction requires ion channels, relatively little is known about ion channels in the primary cilium (with the exception of TRPP2). Here we show that the Ca2+-activated Cl−channel anoctamin-1 (ANO1/TMEM16A) is located in the primary cilium and that blocking its channel function pharmacologically or knocking it down with short hairpin RNA interferes with ciliogenesis. Before ciliogenesis, the channel becomes organized into a torus-shaped structure (“the nimbus”) enriched in proteins required for ciliogenesis, including the small GTPases Cdc42 and Arl13b and the exocyst complex component Sec6. The nimbus excludes F-actin and coincides with a ring of acetylated microtubules. The nimbus appears to form before, or independent of, apical docking of the mother centriole. Our data support a model in which the nimbus provides a scaffold for staging of ciliary components for assembly very early in ciliogenesis and chloride transport by ANO1/TMEM16A is required for the genesis or maintenance of primary cilia.
Trimmomatic: a flexible trimmer for Illumina sequence data
Authors: Bolger Anthony M. , Lohse Marc , Usadel Bjoern
Published: April 2014

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data.

Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.

Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic

Contact:  usadel@bio1.rwth-aachen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
Authors: Li Yi , Xie Xiaohui
Published: April 2014

Motivation: Next-generation sequencing (NGS) has revolutionized the study of cancer genomes. However, the reads obtained from NGS of tumor samples often consist of a mixture of normal and tumor cells, which themselves can be of multiple clonal types. A prominent problem in the analysis of cancer genome sequencing data is deconvolving the mixture to identify the reads associated with tumor cells or a particular subclone of tumor cells. Solving the problem is, however, challenging because of the so-called ‘identifiability problem’, where different combinations of tumor purity and ploidy often explain the sequencing data equally well.

Results: We propose a new model to resolve the identifiability problem by integrating two types of sequencing information—somatic copy number alterations and loss of heterozygosity—within a unified probabilistic framework. We derive algorithms to solve our model, and implement them in a software package called PyLOH. We benchmark the performance of PyLOH using both simulated data and 12 breast cancer sequencing datasets and show that PyLOH outperforms existing methods in disambiguating the identifiability problem and estimating tumor purity.

Availability and implementation: The PyLOH package is written in Python and is publicly available at https://github.com/uci-cbcl/PyLOH .

Contact:  xhx@ics.uci.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Heparin-Binding Protein: A Diagnostic Biomarker of Urinary Tract Infection in Adults
Authors: Kjölvmark Charlott , Påhlman Lisa I. , Åkesson Per , Linder Adam
Published: April 2014

Background.  Urinary tract infections (UTIs) are associated with significant morbidity and high frequency of antibiotic prescription. Diagnosing UTI is often difficult, particularly in the critically ill patient and in patients with unspecific and mild symptoms. The standard rapid tests have limited value, and there is a need for more reliable diagnostic tools. Heparin-binding protein (HBP) is released from neutrophils and has previously been studied as a diagnostic and predictive biomarker in different bacterial infections.

Methods.  This prospective survey enrolled adult patients at 2 primary care units and 2 hospital emergency departments, to investigate in urine HBP as a biomarker of UTI. In addition, urine levels of interleukin-6, white blood cells, and nitrite were analyzed and compared with HBP. Based on symptoms of UTI and microbiological findings, patients were classified into different groups, UTI (cystitis and pyelonephritis) and no UTI.

Results.  Three hundred ninety patients were evaluated. The prevalence of UTI in the study group was 45.4%. The sensitivity and specificity for HBP in urine as a marker for UTI were 89.2% and 89.8%, respectively. The positive and negative predictive values were 90.2% and 88.8%, respectively. Heparin-binding protein was the best diagnostic marker for UTI, with an area-under-curve value of 0.94 (95% confidence interval, 0.93–0.96). Heparin-binding protein was significantly better in distinguishing cystitis from pyelonephritis, compared with the other markers.

Conclusions.  An elevated level of HBP in the urine is associated with UTI and may be a useful diagnostic marker in adult patients with a suspected UTI.
New Onset of Kaposi Sarcoma in a Human Immunodeficiency Virus-1-Infected Homosexual Man, Despite Early Antiretroviral Treatment, Sustained Viral Suppression, and Immune Restoration
Authors: von Braun Amrei , Braun Dominique L. , Kamarachev Jivko , Günthard Huldrych F.
Published: April 2014

This is a rare case of new onset Kaposi sarcoma in a man infected with human immunodeficiency virus (HIV) and receiving antiretroviral treatment since primary HIV infection, with normal CD4+ cell count and suppressed viral load. The presentation questions the general understanding of Kaposi sarcoma as an acquired immune deficiency syndrome-defining disease occurring predominantly in severely immunocompromised patients infected with HIV.
Empiric Vancomycin Use in Febrile Neutropenic Oncology Patients
Authors: Libuit Jessica , Whitman Andrew , Wolfe Rebecca , Washington Casey S.
Published: April 2014

Vancomycin is commonly added as empiric therapy for febrile neutropenia. A retrospective chart review was conducted at a large community teaching institution to evaluate vancomycin use in oncology patients. The results revealed that a majority of empiric vancomycin therapy was inappropriate, raising concern for antibiotic resistance and prompting opportunities for improvement.
ID Learning Unit: Understanding and Interpreting Testing for Clostridium difficile
Authors: Solomon Daniel A. , Milner Danny A.
Published: April 2014

Understanding and interpreting the molecular tests for Clostridium difficile is challenging because there are several different types of assays and most laboratories combine multiple tests in order to assess for presence of disease. This learning unit demonstrates the basic principles of each test along with its strengths and weaknesses, and illustrates how the tests are used in clinical practice.
Sex-biased expression of microRNAs inDrosophila melanogaster
Authors: Marco Antonio
Published: April 2014

Most animals have separate sexes. The differential expression of gene products, in particular that of gene regulators, is underlying sexual dimorphism. Analyses of sex-biased expression have focused mostly on protein-coding genes. Several lines of evidence indicate that microRNAs, a class of major gene regulators, are likely to have a significant role in sexual dimorphism. This role has not been systematically explored so far. Here, I study the sex-biased expression pattern of microRNAs in the model speciesDrosophila melanogaster. As with protein-coding genes, sex-biased microRNAs are associated with the reproductive function. Strikingly, contrary to protein-coding genes, male-biased microRNAs are enriched in the X chromosome, whereas female microRNAs are mostly autosomal. I propose that the chromosomal distribution is a consequence of high rates of de novo emergence, and a preference for new microRNAs to be expressed in the testis. I also suggest that demasculinization of the X chromosome may not affect microRNAs. Interestingly, female-biased microRNAs are often encoded within protein-coding genes that are also expressed in females. MicroRNAs with sex-biased expression do not preferentially target sex-biased gene transcripts. These results strongly suggest that the sex-biased expression of microRNAs is mainly a consequence of high rates of microRNA emergence in the X chromosome (male bias) or hitchhiked expression by host genes (female bias).
Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans
Authors: Liu Qian-Qian , Wang Ying , Li Juan , Du Zong-Jun , Chen Guan-Jun
Published: April 2014

A Gram-stain-negative, facultatively anaerobic, gliding, yellow-pigmented bacterium, designated SS12T, was isolated from shark gill homogenate and characterized using a polyphasic approach. The strain was catalase-positive and oxidase-negative. Optimal growth occurred at 28–30 °C, pH 7.0–7.5 and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The strain contained MK-7 as the prevailing menaquinone; iso-C15 : 0 and anteiso-C15 : 0 as the major cellular fatty acids; and phosphatidylethanolamine and an unknown lipid as the predominant polar lipids. Comparative analysis of 16S rRNA gene sequences demonstrated that the novel isolate showed the highest sequence similarity (94.68 %) to

Saccharicrinis fermentans

DSM 9555T and the sequence similarities among the type strains of all other species studied were less than 92 %. A phylogenetic tree, based on 16S rRNA gene sequences, showed that strain SS12T and

Saccharicrinis fermentans

DSM 9555T formed a distinct cluster within the family

Marinilabiliaceae

. On the basis of its phylogenetic position and phenotypic traits, strain SS12T represents a novel species of genus

Saccharicrinis

, for which the name Saccharicrinis
carchari sp. nov. is proposed. The type strain is SS12T ( = CICC 10590T = DSM 27040T). Emended descriptions of the genus

Saccharicrinis

and

Saccharicrinis fermentans

are also provided.
Lysobacter panacisoli sp. nov., isolated from ginseng soil
Authors: Choi Jung-Hye , Seok Ji-Hye , Cha Ju-Hee , Cha Chang-Jun
Published: April 2014

A novel bacterial strain, designated CJ29T, was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29T were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29T grew optimally at 28–30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29T was shown to belong to the genus

Lysobacter

within the class

Gammaproteobacteria

and was related most closely to

Lysobacter soli

DCY21T (98.5 % similarity) and

Lysobacter niastensis

GH41-7T (98.2 %). DNA–DNA relatedness between strain CJ29T and its closest relatives was below 55.6 %. The predominant cellular fatty acids of strain CJ29T were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29T from related species of the genus

Lysobacter

. On the basis of data from this polyphasic taxonomic study, strain CJ29T is considered to represent a novel species of the genus

Lysobacter

, for which the name

Lysobacter

panacisoli sp. nov. is proposed. The type strain is CJ29T ( = KACC 17502T = JCM 19212T).
Streptococcus suis serotyping by a new multiplex PCR
Authors: Kerdsin Anusak , Akeda Yukihiro , Hatrongjit Rujirat , Detchawna Unchaya , Sekizaki Tsutomu , Hamada Shigeyuki , Gottschalk Marcelo , Oishi Kazunori
Published: April 2014

A multiplex PCR was developed to detect all true serotypes of Streptococcus suis. This multiplex PCR was composed of four reaction sets. The first set identified nine serotypes (serotypes 1/2, 1, 2, 3, 7, 9, 11, 14 and 16), the second set identified eight serotypes (serotypes 4, 5, 8, 12, 18, 19, 24 and 25), the third set identified seven serotypes (serotypes 6, 10, 13, 15, 17, 23 and 31), and the last set identified five serotypes (serotypes 21, 27, 28, 29 and 30). This assay correctly detected serotypes 2, 5, 14 and 24 in human isolates, and serotypes 1, 2, 1/2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 19, 24, 28 and 31 in pig isolates from Thailand. No cross-reaction was observed with other bacterial species. Our multiplex PCR was able to simultaneously amplify a DNA mixture of reference Streptococcus suis serotypes. This assay should be useful for serotype surveillance of human and pig isolates of Streptococcus suis.
The changes of PCR ribotype and antimicrobial resistance of Clostridium difficile in a tertiary care hospital over 10 years
Authors: Lee Jong-Han , Lee Yangsoon , Lee Kyungwon , Riley Thomas V. , Kim Heejung
Published: April 2014

The aims of this study were to investigate any change in PCR ribotypes and to determine the antimicrobial resistance of common PCR ribotypes over a 10-year period in a tertiary care hospital. We conducted PCR ribotyping, antimicrobial susceptibility testing and DNA gyrase sequencing to identify changes in 1407 Clostridium difficile non-duplicated isolates obtained between 2000 and 2009. A total of 74 different ribotypes were found. The most prevalent ribotype was ribotype 001 (26.1 %). The prevalence of ribotype 017 was 17 % and that of ribotype 014/020 was 9.6 %. Ribotyping showed that the prevalence of ribotype 001 decreased and the prevalence of ribotypes 017, 014/020 and 018 increased over the 10 years. Antimicrobial resistance rates in prevalent ribotypes were: clindamycin, 81 %; cefotetan, 19 %; moxifloxacin, 42 %; imipenem, 8 %; ciprofloxacin, 100 % and erythromycin, 80 %. Ribotype 018 showed greater antimicrobial resistance than other ribotypes. All ribotype 018 strains showing moxifloxacin resistance had a substitution of a gyrA coding amino acid (Thr82 to Ile). This study will help the understanding of PCR ribotype trends and antimicrobial resistance of C. difficile in Korea.
Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma
Authors: Lertpiriyapong Kvin , Handt Laurence , Feng Yan , Mitchell Thomas W. , Lodge Kenneth E. , Shen Zeli , Dewhirst Floyd E. , Muthupalani Sureshkumar , Fox James G.
Published: April 2014

Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter species (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26–35 years) had IAC. Of the 36 rhesus, 35 (97 %) were positive for EHS using PCR or bacterial isolation from faeces, colonic or tumour tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were from three Helicobacter taxa: Helicobacter macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507, and Helicobacter sp. rhesus monkey taxon 4, related to Helicobacter fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13, 54 %), EHS rhesus monkey taxon 4 (4/13, 31 %) or a mixture of the two EHS (2/13, 15 %). These results indicate that EHS are prevalent among aged rhesus macaques with IAC. Using Helicobacter genus-specific florescent in situ hybridization, EHS were detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL-8, IL-6, TNF-α and iNOS, while downregulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6 and NLRC4 in the human colonic T84 cell line (P<0.0001). These results suggest that EHS may represent an aetiological agent mediating diarrhoea, chronic inflammation, and possibly intestinal cancer in non-human primates, and may play a role in similar disease syndromes in humans. Downregulation of inflammasome function may represent an EHS strategy for long-term persistence in the host and play a role in inducing pathological changes in the host’s lower bowel.
Physiological roles of small RNA molecules
Authors: Michaux Charlotte , Verneuil Nicolas , Hartke Axel , Giard Jean-Christophe
Published: April 2014

Unlike proteins, RNA molecules have emerged lately as key players in regulation in bacteria. Most reviews hitherto focused on the experimental and/orin silicomethods used to identify genes encoding small RNAs (sRNAs) or on the diverse mechanisms of these RNA regulators to modulate expression of their targets. However, less is known about their biological functions and their implications in various physiological responses. This review aims to compile what is known presently about the diverse roles of sRNA transcripts in the regulation of metabolic processes, in different growth conditions, in adaptation to stress and in microbial pathogenesis. Several recent studies revealed that sRNA molecules are implicated in carbon metabolism and transport, amino acid metabolism or metal sensing. Moreover, regulatory RNAs participate in cellular adaptation to environmental changes, e.g. through quorum sensing systems or development of biofilms, and analyses of several sRNAs under various physiological stresses and culture conditions have already been performed. In addition, recent experiments performed with Gram-positive and Gram-negative pathogens showed that regulatory RNAs play important roles in microbial virulence and during infection. The combined results show the diversity of regulation mechanisms and physiological processes in which sRNA molecules are key actors.