bluuebunny/crossref_metadata_2025 huggingface dataset:
Epitaxial refractory-metal buffer layers with a chemical gradient for adjustable lattice parameter and controlled chemical interface
Authors: Fruchart O. , Rousseau A. , Schmaus D. , L’Hoir A. , Haettel R. , Ortega L.
Published: April 2011

We have developed and characterized the structure and composition of nanometers-thick solid-solution epitaxial layers of (V,Nb) on sapphire (112¯0), displaying a continuous lateral gradient of composition from one to another pure element. Further covered with an ultrathin pseudomorphic layer of W, these provide a template for the fast combinatorial investigation of growth or physical properties depending of strain.
Influence of hydrodynamic coupling on the electric linear dichroism of DNA fragments
Authors: Umazano Juan P. , Bertolotto Jorge A.
Published: April 2011

In the present work, we study the effect of translational–rotational hydrodynamic coupling on the stationary electric linear dichroism of DNA fragments. The theoretical resolution of the problem has, so far, been dealt with analytic methods valid only in the limit of low electric fields. In this work, we apply numerical methods that allow us to study the problem and also consider electric fields of arbitrary strength. We use the bent rod molecules model to describe DNA fragments with physical properties characterized by their electric charge, electric polarizability tensor, rotational diffusion tensor, and translation–rotation coupling diffusion tensor. The necessary orientational distribution function to calculate electric dichroism is obtained by solving the Fokker–Planck equation through the finite difference method. We analyze the different contributions due to electric polarizability and translational–rotational coupling to the electric dichroism.
A microfluidic platform for on-demand formation and merging of microdroplets using electric control
Authors: Gu Hao , Murade Chandrashekhar U. , Duits Michael H. G. , Mugele Frieder
Published: April 2011

We discuss a microfluidic system in which (programmable) local electric fields originating from embedded and protected electrodes are used to control the formation and merging of droplets in a microchannel. The creation of droplets-on-demand (DOD) is implemented using the principle of electrowetting. Combined with hydrodynamic control, the droplet size and formation frequency can be varied independently. Using two synchronized DOD injectors, merging-on-demand (MOD) is achieved via electrocoalescence. The efficiency of MOD is 98% based on hundreds of observations. These two functionalities can be activated independently.
Introduction to Focus Issue: Mesoscales in Complex Networks
Authors: Almendral Juan A. , Criado Regino , Leyva Inmaculada , Buldú Javier M. , Sendiña-Nadal Irene
Published: April 2011

Although the functioning of real complex networks is greatly determined by modularity, the majority of articles have focused, until recently, on either their local scale structure or their macroscopical properties. However, neither of these descriptions can adequately describe the important features that complex networks exhibit due to their organization in modules. This Focus Issue precisely presents the state of the art on the study of complex networks at that intermediate level. The reader will find out why this mesoscale level has become an important topic of research through the latest advances carried out to improve our understanding of the dynamical behavior of modular networks. The contributions presented here have been chosen to cover, from different viewpoints, the many open questions in the field as different aspects of community definition and detection algorithms, moduli overlapping, dynamics on modular networks, interplay between scales, and applications to biological, social, and technological fields.
A novel power amplification scheme for nuclear magnetic resonance/nuclear quadrupole resonance systems
Authors: Zhang Xinwang , Schemm Nathan , Balkır Sina
Published: April 2011

Nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR)-based chemical analysis systems have been widely utilized in various areas such as medicine, security, and academic research. In these applications, the power amplifier stage plays a key role in generating the required oscillating magnetic fields within a radio frequency coil that serves as the probe. However, the bulky size and relatively low efficiency of the traditional power amplification schemes employed present a bottleneck for the realization of compact sized and portable NMR and NQR systems. To address this problem, this work presents a class D voltage-switching power amplification scheme with novel fast-start and fast-stop functions that are suitable for generating ideal NMR and NQR excitation signals. Compared to the traditional analog power amplifiers (PAs), the proposed switched-mode PA can achieve significant improvement on the power efficiency as well as the physical volume. A PA circuit for portable NQR-based explosive detection systems has been designed and built using the proposed scheme with 1 kW possible maximum output power and 10 MHz maximum operating frequency. Test results show that the presented PA achieves more than 60% measured efficiency within a highly compact volume while sustaining fast start and stop of excitation signals in the order of microseconds.
Broad gain bandwidth injectorless quantum-cascade lasers with a step well design
Authors: Li H. , Katz Simeon , Boehm Gerhard , Amann Markus-Christian
Published: April 2011

The authors present a broad gain bandwidth injectorless quantum-cascade laser (QCL) with a “short period superlattice” design which provides an equivalent GaInAlAs alloy quantum step well in each active module. Devices employing the proposed step well design demonstrate an ultrabroadband gain spectrum of 480 cm−1 (∼4 μm) around the threshold at room temperature in pulsed mode. The fabricated 30 μm wide and 4 mm long laser shows the lowest room temperature threshold current density of 1.1 kA/cm2 among the broad gain QCLs emitting at similar wavelengths and a high slope efficiency of 1.6 W/A at room temperature in pulsed mode.
Lasing in metal-coated GaN nanostripe at room temperature
Authors: Wang Yow-Gwo , Chen Cheng-Chang , Chiu Ching-Hsueh , Kuo Ming-Yen , Shih M. H. , Kuo Hao-Chung
Published: April 2011

This study demonstrated a metal-coated GaN nanostripe laser operable at room temperature. The ultraviolet lasing mode was observed at a wavelength of approximately 370 nm with a low threshold power density of 0.042 kW/cm2. The lasing mode of the metal-coated nanostripe was characterized using finite-element method simulation. The results showed the significance of metal coatings in this nanocavity structure for lasing at room temperature.
Phase-locked cantilever magnetometry
Authors: Jang Joonho , Budakian Raffi , Maeno Yoshiteru
Published: April 2011

We describe a feedback-based dynamic cantilever magnetometry technique capable of achieving thermal limited magnetic moment sensitivity with low applied fields. Using this technique, we have observed periodic entry of vortices into mesoscopic Sr2RuO4 rings. The quantized jump in the magnetic moment of the particle produced by individual vortices was measured with a resolution of 7×10−16 emu with an applied field of 1 Oe.
Selective two-photon excitation of a vibronic state by correlated photons
Authors: Oka Hisaki
Published: April 2011

We theoretically investigate the two-photon excitation of a molecular vibronic state by correlated photons with energy anticorrelation. A Morse oscillator having three sets of vibronic states is used, as an example, to evaluate the selectivity and efficiency of two-photon excitation. We show that a vibrational mode can be selectively excited with high efficiency by the correlated photons, without phase manipulation or pulse-shaping techniques. This can be achieved by controlling the quantum correlation so that the photon pair concurrently has two pulse widths, namely, a temporally narrow width and a spectrally narrow width. Though this concurrence is seemingly contradictory, we can create such a photon pair by tailoring the quantum correlation between two photons.
The tunneling of heat
Authors: Mahan G. D.
Published: April 2011

Heat can tunnel across a vacuum gap due to near-field electromagnetic effects. The effect is a result of image potential theory, and heat transfer falls off roughly as the inverse of the gap distance. This effect is in addition to the transfer of heat by photons. This phenomena has been observed previously in scanning tunneling microscopy.
Encapsulated carbon nanotube-oxide-silicon solar cells with stable 10% efficiency
Authors: Jia Yi , Li Peixu , Gui Xuchun , Wei Jinquan , Wang Kunlin , Zhu Hongwei , Wu Dehai , Zhang Luhui , Cao Anyuan , Xu Ying
Published: April 2011

We report a metal-insulator-semiconductor heterojunction solar cell by depositing a carbon nanotube film onto silicon substrate, followed by acid oxidation of the Si surface to form a thin oxide layer at the junction interface. The nanotube-oxide-Si solar cells with polymer encapsulation show stable efficiencies of above 10%, owing to enhanced photon absorption, inhibited charge recombination, and reduced internal resistance. Parallel and series connections without sacrificing cell efficiencies were demonstrated.
Transport imaging for contact-free measurements of minority carrier diffusion in GaN, GaN/AlGaN, and GaN/InGaN core-shell nanowires
Authors: Baird Lee , Ong C. P. , Cole R. Adam , Haegel N. M. , Talin A. Alec , Li Qiming , Wang George T.
Published: April 2011

Minority carrier diffusion lengths (Ld) are measured for GaN, GaN/AlGaN, and GaN/InGaN core-shell nanowires using a technique based on imaging of recombination luminescence. The effect of shell material on transport properties is measured. An AlGaN shell produces Ld values in excess of 1 μm and a relative insensitivity to wire diameter. An InGaN shell reduces effective diffusion length, while a dependence of Ld on diameter is observed for uncoated nanowires.
Direct measurements of field-induced adiabatic temperature changes near compound phase transitions in Ni–Mn–In based Heusler alloys
Authors: Kazakov A. P. , Prudnikov V. N. , Granovsky A. B. , Zhukov A. P. , Gonzalez J. , Dubenko I. , Pathak A. K. , Stadler S. , Ali N.
Published: April 2011

The adiabatic temperature changes (ΔTad) in the vicinity of the Curie and martensitic transition temperatures of Ni50Mn35In15 and Ni50Mn35In14Z (Z=Al and Ge) Heusler alloys have been studied using an adiabatic magnetocalorimeter of 250–350 K temperature interval for applied magnetic field changes up to ΔH=1.8 T. The largest measured changes were ΔTad=−2 and 2 K near the martensitic (first-order) and ferromagnetic (second-order) transitions for ΔH=1.8 T, respectively. It was observed that |ΔTad|≈1 K for relatively small field changes (ΔH=1 T) for both types of transitions. The results indicate that these materials should be further explored as potential working materials in magnetic refrigeration applications.
Temperature-insensitive laser frequency locking near absorption lines
Authors: Kostinski Natalie , Olsen Ben A. , Marsland Robert , McGuyer Bart H. , Happer William
Published: April 2011

Combined magnetically induced circular dichroism and Faraday rotation of an atomic vapor are used to develop a variant of the dichroic atomic vapor laser lock that eliminates lock sensitivity to temperature fluctuations of the cell. Operating conditions that eliminate first-order sensitivity to temperature fluctuations can be determined by low-frequency temperature modulation. This temperature-insensitive gyrotropic laser lock can be accurately understood with a simple model, that is in excellent agreement with observations in potassium vapor at laser frequencies in a 2 GHz range about the 770.1 nm absorption line. The methods can be readily adapted for other absorption lines.
Ge/SiGe multiple quantum well photodiode with 30 GHz bandwidth
Authors: Chaisakul Papichaya , Marris-Morini Delphine , Isella Giovanni , Chrastina Daniel , Le Roux Xavier , Edmond Samson , Cassan Eric , Coudevylle Jean-René , Vivien Laurent
Published: April 2011

We demonstrate high speed Ge/SiGe multiple quantum wells photodiodes using a surface-illuminated vertical p-i-n structure. The device, with a mesa diameter of 12 μm, exhibits a low dark current of 231 nA at −1 V bias. An optical bandwidth of 10 and 26 GHz is measured at −1 and −4 V reverse bias, respectively, and reaches over 30 GHz at a reverse bias of −7 V. These results prove the suitability of Ge/SiGe multiple quantum well structures for high performance optoelectronic devices required for optical interconnection applications.
Solar-blind photodiodes composed of a Au Schottky contact and a β-Ga2O3 single crystal with a high resistivity cap layer
Authors: Suzuki Rikiya , Nakagomi Shinji , Kokubun Yoshihiro
Published: April 2011

We fabricated Ga2O3 photodiodes composed of a Au Schottky contact and a β-Ga2O3 single-crystal substrate with a sol–gel prepared high resistivity cap layer. The photodiodes with the cap layer showed solar-blind photosensitivity under both forward and reverse biases in contrast to conventional Schottky photodiodes. Finally, we proposed energy band diagram of the i-n junction to determine the photodetection mechanism of our photodiodes. The photoconductive device model explained the high responsivity of over 1 A/W at forward bias. In this model, the cap layer behaves like a photoconductor, and the substrate behaves like an electrode that replenishes electrons.
Research Designs for Evaluating the Impact of Community-Based Management on Natural Resource Conservation
Authors: Thomas Craig W. , Koontz Tomas M.
Published: April 2011

Community-based management has increasingly replaced centralized planning and regulation as an alternative means for conserving natural resources. But there is little empirical evidence to suggest whether community-based management has a positive or negative impact on the actual condition of natural resources. If, as is commonly argued, conservation success depends largely on local context, then we must think carefully about the entire causal chain of community-based management activities, from the inputs supporting decision-making processes to management outputs and environmental outcomes. We accordingly discuss appropriate methodologies for demonstrating the causal impacts of community-based management on natural resource conservation.
Geographic Expression of Social Values in Bioregional Planning: A Case Study of the Palouse
Authors: Donovan Shannon , Wulfhorst J.D. , Jennings Michael
Published: April 2011

Support for landscape-level planning across the Palouse comes from non-profit organizations working with local policymakers to develop regional conservation ordinances. However, developing landscape-level conservation plans is limited by the lack of consensus on the region's boundaries. To address this issue, we conducted archival research and qualitative interviews with ninety stakeholders to determine their definitions of the Palouse. In this study, we reveal the range of reasons participants have for defining the Palouse and its boundaries. Most study participants perceived that geographic boundaries extend beyond political borders, suggesting a need for a bioregional planning approach.
PPPC 4 DM ID: a poor particle physicist cookbook for dark matter indirect detection
Authors: Marco Cirelli  , Gennaro Corcella  , Andi Hektor  , Gert Hütsi  , Mario Kadastik  , Paolo Panci  , Martti Raidal  , Filippo Sala  , Alessandro Strumia
Published: April 2011

We provide ingredients and recipes for computing signals of TeV-scale Dark Matter annihilations and decays in the Galaxy and beyond. For each DM channel, we present the energy spectra ofat production, computed by high-statistics simulations. We estimate the Monte Carlo uncertainty by comparing the results yielded by the Pythia and Herwig event generators. We then provide the propagation functions for charged particles in the Galaxy, for several DM distribution profiles and sets of propagation parameters. Propagation ofe±is performed with an improved semi-analytic method that takes into account position-dependent energy losses in the Milky Way. Using such propagation functions, we compute the energy spectra ofe±,p̄ and d̄ at the location of the Earth. We then present the gamma ray fluxes, both from prompt emission and from Inverse Compton scattering in the galactic halo. Finally, we provide the spectra of extragalactic gamma rays. All results areavailable in numerical formand ready to be consumed.
The impact of 𝜁(𝑠) complex zeros on 𝜋(𝑥) for 𝑥<10^{10¹³}
Authors: Stoll Douglas , Demichel Patrick
Published: April 2011

An analysis of the local variations of the prime counting function

π
(
x
)

\pi (x)

due to the impact of the non-trivial, complex zeros

ϱ
k

\varrho _k

of

ζ
(
s
)

\zeta (s)

is provided for

x
>

10

10

13

x>10^{10^{13}}

using up to 200 billion

ζ
(
s
)

\zeta (s)

complex zeros. A new bound for
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|

l
i

(
x
)
−
π
(
x
)

|

>

x

1

/

2

(

l
o
g

l
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l
o
g

x
+
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+
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)

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e

l
o
g

x

|\mathrm {li}(x)-\pi (x)|>x^{1/2}(\mathrm {log}\,\mathrm {log}\,\mathrm {log}\,x+e+1)/e\, \mathrm {log}\,x

is proposed consistent with the error growth rate in Littlewood’s proof that

l
i

(
x
)
−
π
(
x
)

\mathrm {li}(x)-\pi (x)

changes sign infinitely often. This bound is also consistent with all presently known cases where

π
(
x
)
>

l
i

(
x
)

\pi (x)>\mathrm {li}(x)

including many new examples listed. This implies that Littlewood’s constant

K

=
1

/

e

\mathrm {K}=1/e

, the lower bound for Skewes’ number is

3.17
×

10

114

3.17\times 10^{114}

and the positive constant

c
c

in the Riemann Hypothesis equivalent
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|

l
i

(
x
)
−
π
(
x
)

|

>
c

l
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g

(
x
)

x

1

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|\mathrm {li}(x)-\pi (x)|>c\,\mathrm {log}(x)x^{1/2}

is less than

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×

10

−
27

3\times 10^{-27}

.
The Rhetoric of Restraint: The Struggle for Legitimacy of the Dutch Temporary Work Agency Industry, 1961–1996
Authors: Koene Bas , Driel Hugo van
Published: April 2011

In many countries governments and labor unions have contested the post-war rise of temporary agency work, arguing that this innovation infringed on workers' rights and security. We investigate the rhetorical strategies used by Dutch temporary work agencies (TWAs) to gain legitimacy for their business between 1961 and 1996. Our conclusion is that the TWAs' trade association ABU developed a sophisticated rhetoric of “self-restraint” to legitimize the deployment of a non-standard labor arrangement. The core message was that – if applied properly - agency work did not threaten permanent employment. The complexity of the inclusive nature of this rhetorical approach, aiming to acknowledge the concerns of multiple stakeholders, was reflected in ABU's difficulty in aligning its claims of socially responsible behavior with an effective defense of the sector's economic interests. Still, the consistent focus on restraint lent credibility to the claimed function of “allocating” workers to their jobs that eventually gained the TWA industry fundamental acceptance as a responsible labor market actor.
Roles of RpoS and PsrA in cyst formation and alkylresorcinol synthesis in Azotobacter vinelandii
Authors: Cocotl-Yañez Miguel , Sampieri Arístides , Moreno Soledad , Núñez Cinthia , Castañeda Miguel , Segura Daniel , Espín Guadalupe
Published: April 2011

Azotobacter vinelandii is a soil bacterium that undergoes differentiation to form cysts that are resistant to desiccation. Upon induction of cyst formation, the bacterium synthesizes alkylresorcinols that are present in cysts but not in vegetative cells. Alternative sigma factors play important roles in differentiation. In A. vinelandii, AlgU (sigma E) is involved in controlling the loss of flagella upon induction of encystment. We investigated the involvement of the sigma factor RpoS in cyst formation in A. vinelandii. We analysed the transcriptional regulation of the rpoS gene by PsrA, the main regulator of rpoS in Pseudomonas species, which are closely related to A. vinelandii. Inactivation of rpoS resulted in the inability to form cysts resistant to desiccation and to produce cyst-specific alkylresorcinols, whereas inactivation of psrA reduced by 50 % both production of alkylresorcinols and formation of cysts resistant to desiccation. Electrophoretic mobility shift assays revealed specific binding of PsrA to the rpoS promoter region and that inactivation of psrA reduced rpoS transcription by 60 %. These results indicate that RpoS and PsrA are involved in regulation of encystment and alkylresorcinol synthesis in A. vinelandii.
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes
Authors: Fasolo Joseph , Sboner Andrea , Sun Mark G.F. , Yu Haiyuan , Chen Rui , Sharon Donald , Kim Philip M. , Gerstein Mark , Snyder Michael
Published: April 2011

Protein kinases are key regulators of cellular processes. In spite of considerable effort, a full understanding of the pathways they participate in remains elusive. We globally investigated the proteins that interact with the majority of yeast protein kinases using protein microarrays. Eighty-five kinases were purified and used to probe yeast proteome microarrays. One-thousand-twenty-three interactions were identified, and the vast majority were novel. Coimmunoprecipitation experiments indicate that many of these interactions occurred in vivo. Many novel links of kinases to previously distinct cellular pathways were discovered. For example, the well-studied Kss1 filamentous pathway was found to bind components of diverse cellular pathways, such as those of the stress response pathway and the Ccr4–Not transcriptional/translational regulatory complex; genetic tests revealed that these different components operate in the filamentation pathway in vivo. Overall, our results indicate that kinases operate in a highly interconnected network that coordinates many activities of the proteome. Our results further demonstrate that protein microarrays uncover a diverse set of interactions not observed previously.
Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition
Authors: Chen Jing , Melton Collin , Suh Nayoung , Oh Jeong Su , Horner Kathleen , Xie Fang , Sette Claudio , Blelloch Robert , Conti Marco
Published: April 2011

Oocyte maturation, fertilization, and early embryonic development occur in the absence of gene transcription. Therefore, it is critical to understand at a global level the post-transcriptional events that are driving these transitions. Here we used a systems approach by combining polysome mRNA profiling and bioinformatics to identify RNA-binding motifs in mRNAs that either enter or exit the polysome pool during mouse oocyte maturation. Association of mRNA with the polysomes correlates with active translation. Using this strategy, we identified highly specific patterns of mRNA recruitment to the polysomes that are synchronized with the cell cycle. A large number of the mRNAs recovered with translating ribosomes contain motifs for the RNA-binding proteins DAZL (deleted in azoospermia-like) and CPEB (cytoplasmic polyadenylation element-binding protein). Although a Dazl role in early germ cell development is well established, no function has been described during oocyte-to-embryo transition. We demonstrate that CPEB1 regulates Dazl post-transcriptionally, and that DAZL is essential for meiotic maturation and embryonic cleavage. In the absence of DAZL synthesis, the meiotic spindle fails to form due to disorganization of meiotic microtubules. Therefore, Cpeb1 and Dazl function in a progressive, self-reinforcing pathway to promote oocyte maturation and early embryonic development.
Preparation of Rat Serum for Culturing Mouse Embryos: Figure 1.
Authors: Garcia Monica D. , Udan Ryan S. , Hadjantonakis Anna-Katerina , Dickinson Mary E.
Published: April 2011

INTRODUCTION

The most important component of proper mammalian embryo culture is high-quality rat serum. Some commercial sources exist, but control over anesthetization methods and serum extractions means that preparations consistently give superior results. To obtain ∼100 mL of rat serum, 30 adult male Sprague Dawley rats must be used. Depending on the number of cultures performed per week, this amount of rat serum can last for several months. This protocol requires two people to collect blood from the rat.
Magnetic Twisting Cytometry
Authors: Kasza Karen E. , Vader David , Köster Sarah , Wang Ning , Weitz David A.
Published: April 2011

INTRODUCTION

This protocol provides the general steps for magnetic twisting cytometry (MTC). MTC is an active microrheology method well-suited to measuring the mechanical properties of the individual adherent cells. Specialized equipment is required for producing the magnetic fields used in this technique. Specific cells, reagents, and experimental times and temperatures will depend on the objectives of the investigator.
Megaselia abdita: Culturing and Egg Collection
Authors: Rafiqi Ab. Matteen , Lemke Steffen , Schmidt-Ott Urs
Published: April 2011

INTRODUCTION

This protocol describes methods for maintaining the scuttle fly Megaselia abdita as a lab culture. It comprises procedures for fly husbandry and egg collection. The completion of the M. abdita life cycle requires ∼18–20 d at 25°C. Embryogenesis lasts ∼24 h, larval development, 4 d, and the pupal stage ∼10 d.
Growing and Harvesting TAP-Tagged Yeast Cells
Authors: Link Andrew J. , Weaver Connie , Farley Adam
Published: April 2011

INTRODUCTION

One approach to identifying protein–protein interactions is the biochemical purification of a target protein from cells or tissues under nondenaturing conditions followed by the mass spectrometric identification of the components of the purified protein complex. This combination of highly specific protein purification strategies and mass spectrometry has proven to be a very successful approach for identifying protein–protein interactions. The tandem affinity purification (TAP) affinity tag and purification method allows efficient recovery of proteins present at low cellular concentrations under native conditions. Expressing the target protein at its natural levels avoids the assembly of overexpressed proteins into nonphysiological complexes. This protocol describes the preparation of TAP-tagged yeast cells.
Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform
Authors: Clark Randy T. , MacCurdy Robert B. , Jung Janelle K. , Shaff Jon E. , McCouch Susan R. , Aneshansley Daniel J. , Kochian Leon V.
Published: April 2011

A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform’s capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P < 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture.
Incoherent neutron scattering from multi-element materials
Authors: Glinka Charles J.
Published: April 2011

In a neutron diffraction measurement, including small-angle scattering, there is generally a featureless (i.e.Q-independent) component due to incoherent scattering. This scattering contains no information about the atomic structure or structure on any scale. There may also be featureless scattering that arises from atomic disorder in multi-element materials. This scattering is sometimes referred to as compositional or mixture incoherent scattering. However, this designation is misleading. A much better designation is diffuse coherent scattering. Here the differences and distinguishing characteristics of incoherent scatteringvis-à-visdiffuse coherent scattering due to atomic disorder are delineated and demonstrated experimentally.
Application of high‐throughput genome sequencing to intrapathovar variation in Pseudomonas syringae
Authors: STUDHOLME DAVID J.
Published: April 2011

One reason for the success of Pseudomonas syringae as a model pathogen has been the availability of three complete genome sequences since 2005. Now, at the beginning of 2011, more than 25 strains of P. syringae have been sequenced and many more will soon be released. To date, published analyses of P. syringae have been largely descriptive, focusing on catalogues of genetic differences among strains and between species. Numerous powerful statistical tools are now available that have yet to be applied to P. syringae genomic data for robust and quantitative reconstruction of evolutionary events. The aim of this review is to provide a snapshot of the current status of P. syringae genome sequence data resources, including very recent and unpublished studies, and thereby demonstrate the richness of resources available for this species. Furthermore, certain specific opportunities and challenges in making the best use of these data resources are highlighted.
A chromatographic survey of methods for extracting long‐chain grass fructans
Authors: Kagan I. A. , Kirch B. H. , Strickland J. R.
Published: April 2011

To optimize yields of long‐chain fructans extracted from herbage, fructan concentrations and chromatographic profiles were compared in four cool‐season grasses extracted by different methods. In a preliminary study, extraction temperatures, pH prior to extract concentration, numbers of extractions, and tissue coarseness were varied to evaluate their effects on chromatographic profiles and quantities of total long‐chain fructan (degree of polymerization (DP) of ∼7 or higher). Fructans were separated by anion‐exchange high‐performance liquid chromatography (HPLC) with pulsed amperometric detection (PAD). The identity of the putative fructan peaks was confirmed by acid hydrolysis of fructans to fructose. Tall fescue and bluegrass fructans were below the detection limits used in this study. Pooled timothy and cocksfoot data indicated that two or three extractions at the same temperature yielded similar amounts of fructans and that adjusting pH from 6 to 7 did not affect recovery. Replicated extractions of cocksfoot by four methods chosen from the preliminary study demonstrated that the least fructan was extracted from chopped cocksfoot at ambient temperature (P = 0·019). One C18 solid‐phase extraction cleanup step sufficed for analysis. The extraction method recommended is two boiling water extractions of either chopped or ground material. However, ground material extracted at ambient temperature is comparable in total fructan concentration and maximum DP.
Improved functional ability and independence in activities of daily living for older adults at high risk of hospital readmission: a randomized controlled trial
Authors: Courtney Mary D. , Edwards Helen E. , Chang Anne M. , Parker Anthony W. , Finlayson Kathleen , Bradbury Carolyn , Nielsen Zoë
Published: April 2011

Objective  During hospitalization older people often experience functional decline which impacts on their future independence. The objective of this study was to evaluate a multifaceted transitional care intervention including home‐based exercise strategies for at‐risk older people on functional status, independence in activities of daily living (ADLs) and walking ability.

Methods  A randomized controlled trial was undertaken in a metropolitan hospital in Australia with 128 patients (64 intervention, 64 control) aged over 65 years with an acute medical admission and at least one risk factor for hospital readmission. The intervention group received an individually tailored programme for exercise and follow‐up care which was commenced in hospital and included regular visits in hospital by a physiotherapist and a registered nurse, a home visit following discharge and regular telephone follow‐up for 24 weeks following discharge. The programme was designed to improve health‐promoting behaviours, strength, stability, endurance and mobility. Data were collected at baseline, then 4, 12 and 24 weeks following discharge using the Index of ADL, Instrumental Activities of Daily Living (IADL) and the Walking Impairment Questionnaire (WIQ; modified).

Results  Significant improvements were found in the intervention group in IADL scores (P < 0.001), ADL scores (P < 0.001) and WIQ scale scores (P < 0.001) in comparison to the control group. The greatest improvements were found in the first 4 weeks following discharge.

Conclusions  Early introduction of a transitional model of care incorporating a tailored exercise programme and regular telephone follow‐up for hospitalized at‐risk older adults can improve independence and functional ability.
A Bnr‐like formin links actin to the spindle pole body during sporulation in the filamentous fungus Ashbya gossypii
Authors: Kemper Michael , Mohlzahn Lars , Lickfeld Manuela , Lang Claudia , Wählisch Sabrina , Schmitz Hans‐Peter
Published: April 2011

Formin proteins are nucleators of actin filaments and regulators of the microtubule cytoskeleton. As such, they play important roles in the development of yeast and other fungi. We show here that AgBnr2, a homologue of the ScBnr1 formin from the filamentous fungus Ashbya gossypii, localizes to the spindle pole body (SPB), the fungal analogue of the centrosome of metazoans. This protein plays an important role in the development of the typical needle‐shaped spores of A. gossypii, as suggested by several findings. First, downregulation of AgBNR2 causes defects in sporangium formation and a decrease in the total spore number. Second, a fusion of AgBNR2 to GFP that is driven by the native AgBNR2 promoter is only visible in sporangia. Third, AgBnr2 interacts with a AgSpo21, a sporulation‐specific component of the SPB. Furthermore, we provide evidence that AgBnr2 might nucleate actin cables, which are connected to SPBs during sporulation. Our findings add to our understanding of fungal sporulation, particularly the formation of spores with a complex, elongated morphology, and provide novel insights into formin function.
Transcription of integron‐harboured gene cassette impacts integration efficiency in class 1 integron
Authors: Wei Quhao , Jiang Xiaofei , Li Min , Chen Xiaoyun , Li Gang , Li Ru , Lu Yuan
Published: April 2011

Class 1 integrons play important roles in the dissemination of antibiotic resistance genes among bacteria. Generally, class 1 integron consists of an integrase gene (intI1), a recombination site (attI1) and a promoter (Pc) that drives the transcription of the downstreamed gene cassettes. Occasionally, there is a second promoter P2 downstream of the Pc promoter. Several Pc variants and Pc–P2 combinations have been defined and they display different transcription strengths, but the influence of the transcription of integron‐harboured gene cassette on the integration efficiency has never been comprehensively studied. In this study, the integration frequencies of gene cassettes into the attI1 sites that downstream of four different Pc variants as well as their combinations with P2 promoter were measured. The results showed that there was an inverse correlation between the strength of Pc promoter and the integration efficiency and, with the same Pc promoter, the integration efficiency was significantly decreased when a P2 promoter preceded the attI1 site. Our findings indicate there is a relationship between the transcription of integron‐harboured gene cassette and the integration of exogenous gene cassettes. The interrelationship between these two relatively independent processes may throw a light on our understanding the regulation system of class 1 integron.
The Vibrio cholerae quorum sensing response is mediated by Hfq‐dependent sRNA/mRNA base pairing interactions
Authors: Bardill J. Patrick , Zhao Xiaonan , Hammer Brian K.
Published: April 2011

Vibrio cholerae quorum sensing controls expression of four redundant sRNAs, Qrr1‐4. The Qrr sRNAs are predicted to alter the translation of several mRNAs, including, hapR, which encodes a transcription factor that controls genes for virulence factors, biofilm formation, protease production and DNA uptake. Each Qrr contains a 21 nucleotide region absolutely conserved among pathogenic Vibrios, and predicted to base pair with mRNA targets, like hapR, aided by the RNA chaperone Hfq. This molecular mechanism was not experimentally tested previously, and we provide here both in vivo and in vitro evidence to validate this model. In Escherichia coli, Qrr expression repressed a HapR‐GFP translational fusion, and a specific nucleotide substitution in the 21 nucleotide region eliminated HapR control, while a compensatory mutation in hapR restored it. In V. cholerae, the identical mutations also deregulated HapR‐dependent gene expression and corresponding QS phenotypes by altering HapR protein levels. We calculated in vitro binding affinities of a Qrr/hapR complex and show that Hfq stabilizes complex formation. Finally, the Qrr mutation with in vivo defects also prevented Qrr/hapR binding, while the compensatory hapR mutation restored binding. These results demonstrate that the V. cholerae QS response is mediated by base pairing interactions between Qrr sRNAs and hapR mRNA.
Micro‐collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)
Authors: Yu Qingyi , Guyot Romain , de Kochko Alexandre , Byers Anne , Navajas‐Pérez Rafael , Langston Brennick J. , Dubreuil‐Tranchant Christine , Paterson Andrew H. , Poncet Valérie , Nagai Chifumi , Ming Ray
Published: April 2011

Arabica coffee (Coffea arabica L.) is a self‐compatible perennial allotetraploid species (2n = 4x = 44), whereas Robusta coffee (C. canephora L.) is a self‐incompatible perennial diploid species (2n = 2x = 22). C. arabica (CaCaEaEa) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between Ea and Ca) to 94.6% (between Ca and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the Ca sub‐genome compared to its diploid relative. In particular, we showed that insertion of a Ty1‐copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub‐genomes of C. arabica, Ca and Ea, showed sufficient sequence differences, and a whole‐genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.
Fairness in service choice: an important yet underdeveloped path to universal coverage
Authors: Baltussen R. , Norheim O. F. , Johri M.
Published: April 2011

Editorial: L’équité dans le choix de services: un chemin important mais sous‐développé vers la couverture universelle

Les efforts pour aboutir à une couverture universelle des services de santé ont mis l’accent sur la façon d’atteindre une plus grande partie de la population et sur la protection contre les conséquences financières de la mauvaise santé, par le biais de prépaiement et de mise en commun des ressources. Mais, les facteurs liés à la couverture des services tels que: ‘quels services sont couverts’ et ‘pour quels services la couverture devraient être améliorée’, devraient également jouer un rôle essentiel.
Genetic diversity of the newly invasive weed Flaveria bidentis (Asteraceae) reveals consequences of its rapid range expansion in northern China
Authors: MA J W , GENG S L , WANG S B , ZHANG G L , FU W D , SHU B
Published: April 2011

Ma JW, Geng SL, Wang SB, Zhang GL, Fu WD & Shu B (2011). Genetic diversity of the newly invasive weed Flaveria bidentis (Asteraceae) reveals consequences of its rapid range expansion in northern China. Weed Research51, 363–372.

The South American weed Flaveria bidentis has spread rapidly across northern China since its introduction to the Tianjin area in 2001. To explore its introduction dynamics and mechanism of rapid range expansion in northern China, we examined genetic diversity in 26 populations across the invaded range, using inter‐simple sequence repeat markers. We found relatively high intraspecies genetic diversity (He = 0.279; I = 0.415) and wide‐ranging genetic variation within populations (He = 0.095–0.263; I = 0.160–0.383), with relatively high genetic diversity in both older established populations and some newly established populations. Approximately 78% of genetic variation resides within populations, according to analysis of molecular variance. The unweighted pair group method with arithmetic mean clustered populations into two groups, composed of most populations distributed along the G106 or G107 National Roads. Moreover, a Mantel test showed no significant correlation between geographical and genetic distances. The findings indicate that during F. bidentis invasion, sexual reproduction and multiple introductions have maintained high genetic diversity, while secondary introductions or admixtures of populations have mitigated losses of genetic variation caused by founder events and promoted local adaptation and colonisation. In addition, human‐mediated long‐distance seed dispersal, via National Roads, may have contributed to its weak geographical genetic structure and rapid range expansion in northern China. To prevent further introductions, imports should be monitored at Tianjin (the likely first arrival point). To control established populations, efforts should focus on populations with high genetic diversity, populations along the G106 and G107 National Roads and regions that are climatically similar to its native range.
Fabry disease in children and response to enzyme replacement therapy: results from the Fabry Outcome Survey
Authors: Ramaswami U , Parini R , Pintos‐Morell G , Kalkum G , Kampmann C , Beck M ,   on behalf of the FOS Investigators
Published: April 2011

Ramaswami U, Parini R, Pintos‐Morell G, Kalkum G, Kampmann C, Beck M, on behalf of the FOS Investigators. Fabry disease in children and response to enzyme replacement therapy: results from the Fabry Outcome Survey.

The Fabry Outcome Survey (FOS) was established to extend the knowledge of the natural history of Fabry disease and to assess the effects of enzyme replacement therapy (ERT) with agalsidase alfa. As of March 2009, 64 boys and 34 girls with Fabry disease had enrolled in the FOS and been treated with agalsidase alfa for at least 6 months. The prevalence of symptoms tended to be reduced after 12 and 24 months of ERT in patients who experienced symptoms at baseline. In the entire population, non‐significant decreases in the prevalence of gastrointestinal problems in boys and pain crises in girls were observed after 12–24 months. Kidney function and left ventricular mass indexed to height remained stable. Fifty‐eight treatment‐related adverse events were reported in 23 patients (21 boys and 2 girls), including 55 infusion reactions. Anti‐agalsidase alfa IgG antibodies were found in two boys. No IgE antibodies were reported. This study represents the largest observational study of paediatric Fabry disease patients treated with ERT and indicates continued safety of long‐term ERT in children. Continued long‐term follow‐up is recommended to determine early initiation of ERT, which could potentially slow or prevent the progression of serious morbidities of Fabry disease.
Nutritional status of vegetarians on maintenance haemodialysis
Authors: WU TAI‐TE , CHANG CHIEH‐YING , HSU WEI‐MIN , WANG I‐KWAN , HSU CHIH‐HAO , CHENG SHU‐HWA , LIANG CHIH‐CHIA , CHANG CHIZ‐TZUNG , HUANG CHIU‐CHING
Published: April 2011

Aim:  Vegetarian diets have long been thought of as beneficial to health. However, vegetarian diets are often low in protein, which is contradictory to the high protein diet guideline for uraemia patients. The purpose of the study was to investigate the impact of a vegetarian diet on the nutritional status of haemodialysis (HD) patients.

Methods:  Patients on chronic HD for over 6 months were included in the study. The normalized protein catabolic rate (nPCR) was used to reflect daily protein intake. Biochemical markers of nutrition, anthropometric parameters, subjective global assessment (SGA) and functional activity of daily living were assessed to evaluate the nutritional status of vegetarians on chronic HD.

Results:  Nineteen out of 318 HD patients were vegetarians. The nPCR was lower in the vegetarian group (1.20 ± 0.24 vs 1.10 ± 0.29 g/kg per day, non‐Veg vs Veg, P < 0.05). The serum albumin and prealbumin were similar in vegetarian and non‐vegetarian HD patients. The body mass index (BMI) and mid‐arm muscular circumference (MAMC) were lower in vegetarian patients (P < 0.05). The haematocrit of vegetarians can be maintained at a level similar to that of non‐vegetarian patients but erythropoietin doses needed were higher in vegetarian patients (P < 0.05). The muscle strength evaluated by the hand‐grip test, SGA and activities of daily living were similar in vegetarians and non‐vegetarians.

Conclusion:  The present study revealed that HD patients on vegetarian diets might have a smaller BMI, but SGA and function of daily activities were similar to those of the non‐vegetarians. The haematocrit of vegetarians can be maintained with a higher erythropoietin dose.