bluuebunny/crossref_metadata_2025 huggingface dataset:
Two photon absorption laser induced fluorescence measurements of neutral density in a helicon plasma
Authors: Galante M. E. , Magee R. M. , Scime E. E.
Published: May 2014

We have developed a new diagnostic based on two-photon absorption laser induced fluorescence (TALIF). We use a high intensity (5 MW/cm2), narrow bandwidth (0.1 cm−1) laser to probe the ground state of neutral hydrogen, deuterium and krypton with spatial resolution better than 0.2 cm, a time resolution of 10 ns, and a measurement cadence of 20 Hz. Here, we describe proof-of-principle measurements in a helicon plasma source that demonstrate the TALIF diagnostic is capable of measuring neutral densities spanning four orders of magnitude; comparable to the edge neutral gradients predicted in the DIII-D tokamak pedestal. The measurements are performed in hydrogen and deuterium plasmas and absolute calibration is accomplished through TALIF measurements in neutral krypton. The optical configuration employed is confocal, i.e., both light injection and collection are accomplished with a single lens through a single optical port in the vacuum vessel. The wavelength resolution of the diagnostic is sufficient to separate hydrogen and deuterium spectra and we present measurements from mixed hydrogen and deuterium plasmas that demonstrate isotopic abundance measurements are feasible. Time resolved measurements also allow us to explore the evolution of the neutral hydrogen density and temperature and effects of wall recycling. We find that the atomic neutral density grows rapidly at the initiation of the discharge, reaching the steady-state value within 1 ms. Additionally, we find that neutral hydrogen atoms are born with 0.08 eV temperatures, not 2 eV as is typically assumed.
Plasma generation for controlled microwave-reflecting surfaces in plasma antennas
Authors: Bliokh Yury P. , Felsteiner Joshua , Slutsker Yakov Z.
Published: May 2014

The idea of replacing metal antenna elements with equivalent plasma objects has long been of interest because of the possibility of switching the antenna on and off. In general, two kinds of designs have so far been reported: (a) Separate plasma “wires” which are thin glass tubes filled with gas, where plasma appears due to discharge inside. (b) Reflecting surfaces, consisting of tightly held plasma wires or specially designed large discharge devices with magnetic confinement. The main disadvantages of these antennas are either large weight and size or too irregular surfaces for proper reflection. To design a microwave plasma antenna in the most common radar wavelength range of 1–3 cm with a typical gain of 30 dB, a smooth plasma mirror having a 10–30 cm diameter and a proper curvature is required. The plasma density must be 1012–1014 cm−3 in order to exceed the critical density for the frequency of the electromagnetic wave. To achieve this we have used a ferromagnetic inductively coupled plasma (FICP) source, where a thin magnetic core of a large diameter is fully immersed in the plasma. In the present paper, we show a way to adapt the FICP source for creating a flat switchable microwave plasma mirror with an effective diameter of 30 cm. This mirror was tested as a microwave reflector and there was found no significant difference when compared with a copper plate having the same diameter.
Combined UHV/high-pressure catalysis setup for depth-resolved near-surface spectroscopic characterization and catalytic testing of model catalysts
Authors: Mayr Lukas , Rameshan Raffael , Klötzer Bernhard , Penner Simon , Rameshan Christoph
Published: May 2014

An ultra-high vacuum (UHV) setup for “real” and “inverse” model catalyst preparation, depth-resolved near-surface spectroscopic characterization, and quantification of catalytic activity and selectivity under technologically relevant conditions is described. Due to the all-quartz reactor attached directly to the UHV-chamber, transfer of the catalyst for in situ testing without intermediate contact to the ambient is possible. The design of the UHV-compatible re-circulating batch reactor setup allows the study of reaction kinetics under close to technically relevant catalytic conditions up to 1273 K without contact to metallic surfaces except those of the catalyst itself. With the attached differentially pumped exchangeable evaporators and the quartz-microbalance thickness monitoring equipment, a reproducible, versatile, and standardised sample preparation is possible. For three-dimensional near-surface sample characterization, the system is equipped with a hemispherical analyser for X-ray photoelectron spectroscopy (XPS), electron-beam or X-ray-excited Auger-electron spectroscopy, and low-energy ion scattering measurements. Due the dedicated geometry of the X-ray gun (54.7°, “magic angle”) and the rotatable sample holder, depth analysis by angle-resolved XPS measurements can be performed. Thus, by the combination of characterisation methods with different information depths, a detailed three-dimensional picture of the electronic and geometric structure of the model catalyst can be obtained. To demonstrate the capability of the described system, comparative results for depth-resolved sample characterization and catalytic testing in methanol steam reforming on PdGa and PdZn near-surface intermetallic phases are shown.
Physical model of the contact resistivity of metal-graphene junctions
Authors: Chaves Ferney A. , Jiménez David , Cummings Aron W. , Roche Stephan
Published: May 2014

While graphene-based technology shows great promise for a variety of electronic applications, including radio-frequency devices, the resistance of the metal-graphene contact is a technological bottleneck for the realization of viable graphene electronics. One of the most important factors in determining the resistance of a metal-graphene junction is the contact resistivity. Despite the large number of experimental works that exist in the literature measuring the contact resistivity, a simple model of it is still lacking. In this paper, we present a comprehensive physical model for the contact resistivity of these junctions, based on the Bardeen Transfer Hamiltonian method. This model unveils the role played by different electrical and physical parameters in determining the specific contact resistivity, such as the chemical potential of interaction, the work metal-graphene function difference, and the insulator thickness between the metal and graphene. In addition, our model reveals that the contact resistivity is strongly dependent on the bias voltage across the metal-graphene junction. This model is applicable to a wide variety of graphene-based electronic devices and thus is useful for understanding how to optimize the contact resistance in these systems.
Magnetically induced enhancement of reversibly responding conductometric sensors
Authors: Baker Caitlin , Laminack William , Tune Travis , Gole James
Published: May 2014

Small magnetic fields are found to greatly enhance the reversible room temperature conductometric responses of n and p- type porous silicon (PS) interfaces, treated with nanostructured island sites containing paramagnetic Co(II) and Fe(II). At concentrations sufficiently low so as to avoid cross talk between the nanostructured island sites, the response to NO concentrations demonstrates the significant effect which the Co(II) and Fe(II) have on the decorated extrinsic semiconductor majority charge carriers as they direct a dominant electron transduction process for reversible electron transduction and chemical sensing (Inverse Hard and Soft acid/base principle) in the absence of significant chemical bond formation. Co(II) and Fe(II) oxide sites enhance response and provide a means for small magnetic fields to interact with and enhance the sensor interface response. For p-type systems, the interaction is with small virtually constant thermal electron populations lying above the Fermi energy at 0 K. The electron removal rate increases with magnetic field strength. At the highest magnetic fields and NO analyte concentrations the available electron population is depleted, and the response to the analyte decreases at higher concentrations. At lower magnetic fields (<1000 G), the response faithfully follows concentration. For n-type systems, the magnetic field interaction increases resistance. This increase in response may be attributed to the interaction with donor levels ∼0.025 eV below the conduction band. A substantial enhancement of sensor response relative to that for the Co(II) and Fe(II) treated PS interfaces is observed, with the introduction of a small magnetic field greatly increasing an already enhanced conductometric response.
Spin relaxation time dependence on optical pumping intensity in GaAs:Mn
Authors: Burobina V. , Binek Ch.
Published: May 2014

We analyze the dependence of electron spin relaxation time on optical pumping intensity in a partially compensated acceptor semiconductor GaAs:Mn using analytic solutions for the kinetic equations of the charge carrier concentrations. Our results are applied to previous experimental data of spin-relaxation time vs. excitation power for magnetic concentrations of approximately 1017 cm−3. The agreement of our analytic solutions with the experimental data supports the mechanism of the earlier-reported atypically long electron-spin relaxation time in the magnetic semiconductor.
Temperature dependence of the indirect bandgap in thallium bromide from cathodoluminescence spectroscopy
Authors: Ray A. , Smith Holland M. , Haegel N. M.
Published: May 2014

The temperature dependence of the indirect bandgap in thallium bromide has been determined using variable temperature (5 K to 300 K) cathodoluminescence. The spectra include transitions associated with both the indirect (2.66 eV at 5 K) and the direct (3.0 eV at 5 K) bandgaps. Least-squares analysis has been used to obtain fitting parameters for three analytical models commonly applied to describe the dependence of the bandgap on temperature for the lowest energy indirect transition. The indirect bandgap emission shifts to an energy of 2.86 eV at 300 K. We find a significant difference in the behavior of the luminescence associated with the direct bandgap, which does not appear to shift to the extent predicted by earlier measurements of the exciton absorption edge.
Measurements of continuous mix evolution in a high energy density shear flow
Authors: Loomis E. , Doss F. , Flippo K. , Fincke J.
Published: May 2014

We report on the novel integration of streaked radiography into a counter-flowing High Energy Density (HED) shear environment that continually measures a growing mix layer of Al separating two low-density CH foams. Measurements of the mix width allow us to validate compressible turbulence models and with streaked imaging, make this possible with a minimal number of experiments on large laser facilities. In this paper, we describe how the HED counter-flowing shear layer is created and diagnosed with streaked radiography. We then compare the streaked data to previous two-dimensional, single frame radiography and radiation hydrodynamic simulations of the experiment with inline compressible turbulent mix models.
Evolution of ion-induced nanoparticle arrays on GaAs surfaces
Authors: Kang M. , Beskin I. , Al-Heji A. A. , Shende O. , Huang S. , Jeon S. , Goldman R. S.
Published: May 2014

We have examined the evolution of irradiation-induced Ga nanoparticle (NP) arrays on GaAs surfaces. Focused-ion-beam irradiation of pre-patterned GaAs surfaces induces monotonic increases in the NP volume and aspect ratio up to a saturation ion dose, independent of NP location within the array. Beyond the saturation ion dose, the NP volume continues to increase monotonically while the NP aspect ratio decreases monotonically. In addition, the NP volumes (aspect ratios) are highest (lowest) for the corner NPs. We discuss the relative influences of bulk and surface diffusion on the evolution of Ga NP arrays.
Enhanced optical limiting effects of graphene materials in polyimide
Authors: Gan Yao , Feng Miao , Zhan Hongbing
Published: May 2014

Three different graphene nanostructure suspensions of graphene oxide nanosheets (GONSs), graphene oxide nanoribbons (GONRs), and graphene oxide quantum dots (GOQDs) are prepared and characterized. Using a typical two-step method, the GONSs, GONRs, and GOQDs are incorporated into a polyimide (PI) matrix to synthesize graphene/PI composite films, whose nonlinear optical (NLO) and optical limiting (OL) properties are investigated at 532 nm in the nanosecond regime. The GONR suspension exhibits superior NLO and OL effects compared with those of GONSs and GOQDs because of its stronger nonlinear scattering and excited-state absorption. The graphene/PI composite films exhibit NLO and OL performance superior to that of their corresponding suspensions, which is attributed primarily to a combination of nonlinear mechanisms, charge transfer between graphene materials and PI, and the matrix effect.
Influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures and lattice defects accumulation
Authors: Sedao Xxx , Maurice Claire , Garrelie Florence , Colombier Jean-Philippe , Reynaud Stéphanie , Quey Romain , Pigeon Florent
Published: May 2014

The influence of crystal orientation on the formation of femtosecond laser-induced periodic surface structures (LIPSS) has been investigated on a polycrystalline nickel sample. Electron Backscatter Diffraction characterization has been exploited to provide structural information within the laser spot on irradiated samples to determine the dependence of LIPSS formation and lattice defects (stacking faults, twins, dislocations) upon the crystal orientation. Significant differences are observed at low-to-medium number of laser pulses, outstandingly for (111)-oriented surface which favors lattice defects formation rather than LIPSS formation.
Visual measurement of the pulse laser ablation process on liquid surface by using digital holography
Authors: Wang J. , Zhao J. L. , Di J. L. , Rauf A. , Yang W. Z. , Wang X. L.
Published: May 2014

We present a visual method to dynamically and quantitatively measure the ablation process on liquid surface induced by pulse laser based on digital holography. Taking deionized water as a liquid example, the quantitative data of the evolution of cavity, jet, and pressure in ablation process are experimentally obtained. According to Abel inversion, the refractive index and the thickness contained in the phase information of the axisymmetric jet are decoupled. The temporal resolution, temporal stability, and measurement accuracy of this method are analyzed based on digital holographic theory. In addition, a numerical simulation is performed to calculate the maximum cavity depth, and the results are in good agreement with the experimental data.
Carrier dynamics in Beryllium doped low-temperature-grown InGaAs/InAlAs
Authors: Globisch B. , Dietz R. J. B. , Stanze D. , Göbel T. , Schell M.
Published: May 2014

The electron and hole dynamics in low-temperature-grown InGaAs/InAlAs multiple quantum well structures are studied by optical pump-probe transmission measurements for Beryllium (Be) doping levels between 3 × 1017 cm−3 and 4 × 1018 cm−3. We investigate electron dynamics in the limit cases of unsaturated and completely saturated electron trapping. By expanding a rate equation model in these limits, the details of carrier dynamics are revealed. Electrons are trapped by ionized arsenic antisites, whereas recombination occurs between trapped electrons and holes trapped by negatively charged Be dopants.
Probing the domain structure of BiFeO3 epitaxial films with three-dimensional reciprocal space mapping
Authors: Luo Z. L. , Huang H. , Zhou H. , Chen Z. H. , Yang Y. , Wu L. , Zhu C. , Wang H. , Yang M. , Hu S. , Wen H. , Zhang X. , Zhang Z. , Chen L. , Fong D. D. , Gao C.
Published: May 2014

High-resolution 3-Dimensional Reciprocal Space Mapping (3D-RSM) has been performed on mixed-phase BiFeO3 (BFO) epitaxial films on (001)-oriented LaAlO3 substrates. Our results demonstrate that 3D-RSM is an effective way to present a structural overview of the different BFO polymorphs, domain variants, and even the interfacial regions between coexisting triclinic phases. The dislocation-free boundaries between the triclinic phases revealed by these 3D-RSMs are believed to be responsible for the large electromechanical response found in mixed-phase BFO films. This study demonstrates the unique merits of the 3D-RSM technique for the structural characterization of ferroic films with complicated domain structures.
Polarization measurement detects primordial gravitational waves
Authors: Chodos Alan
Published: May 2014

Cosmic inflation is bolstered, but some inconsistencies await resolution.
Unusual defect physics underlies perovskite solar cells’ exceptional performance
Authors: Miller Johanna L.
Published: May 2014

First-principles calculations provide insight into one of the newest and most promising classes of materials for photovoltaic devices.
R&D ekes out an increase in FY 2015 budget request
Authors: Kramer David
Published: May 2014

With spending caps in place, President Obama proposes an off-budget fund to support additional R&D. NASA would ground a flying observatory, and DOE would sharply curtail its nonproliferation programs.
Topological physics with light
Authors: Hafezi Mohammad , Taylor Jacob M.
Published: May 2014

Electrons in a so-called topological insulator circulate around the material’s boundary without ever straying into the bulk. Uncharged photons can be induced to carry out similar behavior.
Identification of the 11-
cis-
specific retinyl-ester synthase in retinal Müller cells as multifunctional
O-
acyltransferase (MFAT)
Authors: Kaylor Joanna J. , Cook Jeremy D. , Makshanoff Jacob , Bischoff Nicholas , Yong Jennifer , Travis Gabriel H.
Published: May 2014

Significance

The noncanonical visual cycle permits sustained vision in daylight by providing chromophore precursor (11-
cis-
retinol) to cone photoreceptors at high rates. The isomerase of this pathway catalyzes equilibrium isomerization of retinol. At equilibrium, all-
trans-
retinol and 13-
cis-
retinol are strongly favored over 11-
cis-
retinol. A mechanism of mass action is hence required to drive production of 11-
cis-
retinol. Homogenates of cone-dominant retinas convert all-
trans-
retinol to 11-
cis-
retinyl esters, suggesting that secondary esterification of 11-
cis-
retinol drives production of 11-
cis-
retinoids for synthesis of chromophore. Here, we identified an enzyme, multifunctional
O-
acyltransferase (MFAT), that specifically esterifies 11-
cis-
retinol. MFAT acts cooperatively with isomerase-2 in Müller cells to drive production of 11-
cis-
retinoids. Thus, the energy of retinoid isomerization comes from hydrolysis of the thioester in an activated fatty acid by MFAT.
Frizzled3
is required for the development of multiple axon tracts in the mouse central nervous system
Authors: Hua Zhong L. , Jeon Sangmin , Caterina Michael J. , Nathans Jeremy
Published: May 2014

Significance

Axons within the mammalian central nervous system must navigate with high accuracy over long distances. Tissue polarity (also called planar cell polarity) signaling is emerging as a major axon guidance system.
Frizzled3
(
Fz3
), a core polarity gene, is shown here to be essential for a wide variety of axon guidance decisions in the mouse brain and spinal cord beginning with the earliest axon trajectories in the day 12 embryo. In particular, this work shows that axon guidance defects in
Fz3
mutant embryos involve erroneous directions of growth rather than axon elongation per se. In adult mice in which the spinal cord is missing Fz3, anatomic and behavioral analyses show that sensory information from the limbs does not reach the brain.
Metabolic regulator Fnip1 is crucial for iNKT lymphocyte development
Authors: Park Heon , Tsang Mark , Iritani Brian M. , Bevan Michael J.
Published: May 2014

Significance

Identifying factors that regulate the development of cytokine-producing immunoregulatory invariant natural killer T (iNKT) cells is critical for understanding how to modulate these cells to promote cell-mediated immunity to cancer and infectious organisms or suppress excessive inflammation in autoimmune disease. Here, we identified an essential role for the metabolic regulator Folliculin-interacting protein 1 (Fnip1) in iNKT cell development and survival. Fnip1 physically interacts with AMPK, an energy-sensing enzyme that stimulates mitochondria and ATP production in response to energy deficit, while inhibiting mammalian target of rapamycin (mTOR)-mediated cell growth. Fnip1-deficient iNKT cells contain reduced mitochondrial number and hyperactive mTOR, which resulted in decreased ATP levels and increased sensitivity to apoptosis. Our findings indicate that Fnip1 is vital for maintaining metabolic balance during iNKT cell development.
Intrinsic circle domains
Authors: Crane Edward
Published: May 2014

Using quasiconformal mappings, we prove that any Riemann surface of finite connectivity and finite genus is conformally equivalent to an intrinsic circle domain

Ω
\Omega

in a compact Riemann surface

S
S

. This means that each connected component

B
B

of

S
∖
Ω

S\setminus \Omega

is either a point or a closed geometric disc with respect to the complete constant curvature conformal metric of the Riemann surface

(
Ω
∪
B
)

(\Omega \cup B)

. Moreover, the pair

(
Ω
,
S
)

(\Omega , S)

is unique up to conformal isomorphisms. We give a generalization to countably infinite connectivity. Finally, we show how one can compute numerical approximations to intrinsic circle domains using circle packings and conformal welding.
The ubiquitin ligase deltex-3l regulates endosomal sorting of the G protein–coupled receptor CXCR4
Authors: Holleman Justine , Marchese Adriano
Published: May 2014

G protein–coupled receptor (GPCR) sorting into the degradative pathway is important for limiting the duration and magnitude of signaling. Agonist activation of the GPCR CXCR4 induces its rapid ubiquitination and sorting to lysosomes via the endosomal sorting complex required for transport (ESCRT) pathway. We recently reported that ESCRT-0 ubiquitination is linked to the efficiency with which CXCR4 is sorted for lysosomal degradation; however mechanistic insight is lacking. Here we define a novel role for the really interesting new gene–domain E3 ubiquitin ligase deltex-3-like (DTX3L) in regulating CXCR4 sorting from endosomes to lysosomes. We show that DTX3L localizes to early endosomes upon CXCR4 activation and interacts directly with and inhibits the activity of the E3 ubiquitin ligase atrophin-1 interacting protein 4. This serves to limit the extent to which ESCRT-0 is ubiquitinated and is able to sort CXCR4 for lysosomal degradation. Therefore we define a novel role for DTX3L in GPCR endosomal sorting and reveal an unprecedented link between two distinct E3 ubiquitin ligases to control the activity of the ESCRT machinery.
Airway management
Authors: Ross-Anderson Davina , Patel Anil , Fell Abigail , Frerk Chris
Published: May 2014

The ability to manage confidently the difficult airway, both anticipated and unanticipated, is an essential skill for any anaesthetist; these cases describe successful strategies that have been deployed in the management of difficult airways and the rationale underpinning them. Case 1.1 discusses the management of a suspected difficult airway while case 1.2 deals with an unanticipated scenario. Planning, communication and team working are essential for success, alongside familiarity with the specialised equipment and techniques available (such as videolaryngoscopes, percutaneous airways and fibre-optic intubation). Understanding the limitations of clinical airway assessment, regular practice of failed intubation drills (such as the Difficult Airway Society Guidelines) and an appreciation of the priority of oxygenation over intubation increase the safety of anaesthetic practice. Extubation requires planning when airway problems have been encountered and patients should be informed when difficulties have been encountered with their airways intraoperatively. Almost all anaesthetists will encounter difficult airways in their practice; no single strategy will be suitable for all scenarios.
Paediatric anaesthesia
Authors: Dibb-Fuller Erica , Wellesley Hugo , Homer Rachel , Wilkinson Kathy
Published: May 2014

Paediatric anaesthesia brings many challenges; this chapter explores the issues of anaesthetising a neonate for MRI (case 6.1) and provides a detailed approach to anaesthesia for tonsillectomy (case 6.2). Neonates present a challenging and high risk group to anaesthetise. Practical issues relating to intravenous access, airway management, temperature and fluid management are coupled with a need for understanding the physiological responses of the neonate and an ability to discuss the potential risks of anaesthesia with the parents. Prematurity and anaesthesia in remote locations (such as the MRI scanner) add to the challenges. Tonsillectomy may be performed for recurrent tonsillitis or obstructive sleep apnoea (OSA). Children with OSA require especially detailed pre-assessment to identify those at high risk of complications to allow appropriate management planning. Airway management requires a collaborative approach by surgeon and anaesthetist. Post-tonsillectomy bleeding requires a calm, careful team approach to ensure safety and avoid further distress to an already frightened child.
Destruction of wide binary stars in low-mass elliptical galaxies: implications for initial mass function estimates
Authors: Maccarone Thomas J.
Published: May 2014

We discuss the effects of destruction of wide binaries in the nuclei of the lower mass giant elliptical galaxies. We show that the numbers of barium stars and extrinsic S stars should be dramatically reduced in these galaxies compared to what is seen in the largest elliptical galaxies. Given that the extrinsic S stars show strong Wing–Ford band and Na i D absorption, we argue that the recent claims of different initial mass functions from the most massive elliptical galaxies versus lower mass ellipticals may be the result of extrinsic S stars, rather than bottom-heavy initial mass function.
Liberibacter
crescens gen. nov., sp. nov., the first cultured member of the genus Liberibacter
Authors: Fagen Jennie R. , Leonard Michael T. , Coyle Janelle F. , McCullough Connor M. , Davis-Richardson Austin G. , Davis Michael J. , Triplett Eric W.
Published: May 2014

The Gram-stain-negative, rod-shaped bacterial isolate BT-1T is the closest relative to the genus ‘Candidatus

Liberibacter
’ cultured to date. BT-1T was recovered from the phloem sap of a defoliating mountain papaya in Puerto Rico. The BT-1T 16S rRNA gene sequence showed that strain BT-1T is most closely related to members of the genus ‘Ca.

Liberibacter
’ sharing 94.7 % 16S rRNA gene sequence similarity with ‘Ca.

Liberibacter americanus
’ and ‘Ca.

Liberibacter asiaticus
’. Additionally, average nucleotide identity, 16S rRNA gene sequences and conserved protein sequences supported inclusion of the previously described species of the genus ‘Ca.

Liberibacter
’ in a genus with BT-1T. The prominent fatty acids of isolate BT-1T were C18 : 1ω7c (77.2 %), C16 : 0 OH (4.8 %), C18 : 0 (4.4 %) and C16 : 0 (3.5 %). Both physiological and genomic characteristics support the creation of the genus

Liberibacter

, as well as the novel species Liberibacter crescens gen. nov., sp. nov. with type strain BT-1T ( = ATCC BAA-2481T = DSM 26877T).
Inhibition of co-colonizing cystic fibrosis-associated pathogens by Pseudomonas aeruginosa and Burkholderia multivorans
Authors: Costello Anne , Reen F. Jerry , O’Gara Fergal , Callaghan Máire , McClean Siobhán
Published: May 2014

Cystic fibrosis (CF) is a recessive genetic disease characterized by chronic respiratory infections and inflammation causing permanent lung damage. Recurrent infections are caused by Gram-negative antibiotic-resistant bacterial pathogens such as Pseudomonas aeruginosa, Burkholderia cepacia complex (Bcc) and the emerging pathogen genus Pandoraea. In this study, the interactions between co-colonizing CF pathogens were investigated. Both Pandoraea and Bcc elicited potent pro-inflammatory responses that were significantly greater than Ps. aeruginosa. The original aim was to examine whether combinations of pro-inflammatory pathogens would further exacerbate inflammation. In contrast, when these pathogens were colonized in the presence of Ps. aeruginosa the pro-inflammatory response was significantly decreased. Real-time PCR quantification of bacterial DNA from mixed cultures indicated that Ps. aeruginosa significantly inhibited the growth of Burkholderia multivorans, Burkholderia cenocepacia, Pandoraea
pulmonicola and Pandoraea
apista, which may be a factor in its dominance as a colonizer of CF patients. Ps. aeruginosa cell-free supernatant also suppressed growth of these pathogens, indicating that inhibition was innate rather than a response to the presence of a competitor. Screening of a Ps. aeruginosa mutant library highlighted a role for quorum sensing and pyoverdine biosynthesis genes in the inhibition of B. cenocepacia. Pyoverdine was confirmed to contribute to the inhibition of B. cenocepacia strain J2315. B. multivorans was the only species that could significantly inhibit Ps. aeruginosa growth. B. multivorans also inhibited B. cenocepacia and Pa. apista. In conclusion, both Ps. aeruginosa and B. multivorans are capable of suppressing growth and virulence of co-colonizing CF pathogens.
The function of the transmembrane and cytoplasmic domains of pneumococcal penicillin-binding proteins 2x and 2b extends beyond that of simple anchoring devices
Authors: Berg Kari Helene , Straume Daniel , Håvarstein Leiv Sigve
Published: May 2014

The biosynthesis of cell-wall peptidoglycan is a complex process that involves six different penicillin-binding proteins (PBPs) inStreptococcus pneumoniae. Two of these, PBP2x and PBP2b, are monofunctional transpeptidases that catalyse the formation of peptide cross-links between adjacent glycan strands. Both of them are bitopic membrane proteins with a small cytoplasmic and a large extracellular domain. PBP2x and PBP2b are essential for septal and peripheral peptidoglycan synthesis, respectively. Although several studies have investigated the properties of their extracellular catalytic domains, it is not known whether the role of their N-terminal non-catalytic domains extends beyond that of being simple anchoring devices. We therefore decided to use reciprocal domain swapping and mutational analysis to gain more information about the biological function of the membrane anchors and cytoplasmic tails of PBP2x and PBP2b. In the case of PBP2x both domains are essential, but neither the membrane anchor nor the cytoplasmic domain of PBP2x appear to serve as major localization signals. Instead, our results suggest that they are involved in interactions with other components of the divisome. Mutations of conserved amino acids in the cytoplasmic domain of PBP2x resulted in loss of function, underlining the importance of this region. The cytoplasmic domain of PBP2b could be swapped with the corresponding domain from PBP2x, whereas replacement of the PBP2b transmembrane domain with the corresponding PBP2x domain gave rise to slow-growing cells with grossly abnormal morphology. When both domains were exchanged simultaneously the cells were no longer viable.
Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast
Authors: Chen Miao , Gartenberg Marc R.
Published: May 2014

tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC–tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs.
Dual views of SRF: a genomic exposure
Authors: Clark Kathleen A. , Graves Barbara J.
Published: May 2014

Esnault and colleagues (pp. 943–958) take a genomics approach to investigate the role of SRF (serum response factor) in the serum response of fibroblasts. The well-established dual role of SRF with alternative cofactors and responsiveness to two signaling pathways is illustrated at the genome-wide level, yet new insight comes from this global picture.
LINking microRNAs, kidney development, and Wilms tumors
Authors: Hohenstein Peter , Hastie Nicholas D.
Published: May 2014

In this issue of Genes & Development, Urbach and colleagues (pp. 971–982) provide compelling data suggesting a role for LIN28 in the pathogenesis of a significant percentage of Wilms tumors. These data extend our insights in the genetics underlying Wilms tumor development and emphasize the importance of stemness and microRNA-mediated processes in the origins of these tumors.
Exploring Oscillations in a Point Model of the Intracellular Ca2+ Concentration
Authors: Thul Rüdiger
Published: May 2014

Intracellular calcium (Ca2+) oscillations are a key signaling mechanism in most cell types. A prominent approach to modeling intracellular Ca2+ oscillations is the use of ordinary differential equations (ODEs), which treat the intracellular Ca2+ concentration as spatially homogenous. Although ODEs cannot account for the interaction of Ca2+ microdomains to form cell-wide Ca2+ patterns, modelers still choose ODEs because (a) the study of ODEs is computationally cheap, and a large body of techniques is available to investigate ODEs in great detail, or (b) sufficient experimental data are not available to develop a spatially extended model. Irrespective of the reason, analyzing ODEs is a key instrument in the toolbox of modelers. In this protocol, we look at a well-known model for Ca2+ oscillations, the De Young–Keizer model, along with the Li–Rinzel approximation of the De Young–Keizer model. The main emphasis of this protocol is the use of the open source software package XPPAUT to numerically study ODEs. The knowledge gained here can be directly transferred to other ODE systems and therefore may serve as a template for future studies.
Time to Blip—Stochastic Simulation of Single Channel Opening
Authors: Thul Rüdiger
Published: May 2014

The stochastic dynamics of the inositol-1,4,5-trisphosphate (IP3) receptor (IP3R) is key to understanding a wide range of observed calcium (Ca2+) signals. The stochastic nature results from the constant binding and unbinding of Ca2+ and IP3 to and from their respective binding sites and is especially important in the initiation of a Ca2+ puff (i.e., the release of Ca2+ through a cluster of IP3Rs). Once the first IP3R opens, the Ca2+ concentration rises significantly around the ion channel, increasing the open probability for neighboring IP3Rs. This opening may trigger the activation of further receptors, giving rise to a Ca2+ puff. In this protocol, we determine the time that it takes for a single IP3R to open from rest. We explicitly take into account the tetrameric structure of the IP3R and the fact that multiple subunits must be active before the channel opens. We develop code for a stochastic simulation of the IP3R and simulate it using the software package MATLAB. This protocol shows the basic form of a stochastic simulation algorithm and may serve as a starting point to investigate more complex gating dynamics.
Mouse Tissue Fixation
Authors: Cardiff Robert D. , Miller Claramae H. , Munn Robert J.
Published: May 2014

One of the primary goals of fixation is to stop postmortem changes that degrade the tissue and allow optimal preservation of morphologic and cytological detail as well as nucleic acid integrity. Following death, tissues soon undergo autolysis, and if organisms from the gastrointestinal, urinary, or respiratory tracts are present, their colonization can soon cause putrefaction. Time is of the essence because warmer temperatures accelerate both types of degradation. Placing the tissue into a fixative stops the postmortem changes. Fixatives have their effect on tissue by cross-linking, coagulation, or a combination of both. This article outlines the basic tissue fixation procedure and offers guidance on choosing an appropriate fixative, the timing and duration of fixation, sample storage, and quality issues.
Translating Intracellular Calcium Signaling into Models
Authors: Thul Rüdiger
Published: May 2014

The rich experimental data on intracellular calcium has put theoreticians in an ideal position to derive models of intracellular calcium signaling. Over the last 25 years, a large number of modeling frameworks have been suggested. Here, I will review some of the milestones of intracellular calcium modeling with a special emphasis on calcium-induced calcium release (CICR) through inositol-1,4,5-trisphosphate and ryanodine receptors. I will highlight key features of CICR and how they are represented in models as well as the challenges that theoreticians face when translating our current understanding of calcium signals into equations. The selected examples demonstrate that a successful model provides mechanistic insights into the molecular machinery of the Ca2+ signaling toolbox and determines the contribution of local Ca2+ release to global Ca2+ patterns, which at the moment cannot be resolved experimentally.
Analysis of Apoptosis in Caenorhabditis elegans
Authors: Lant Benjamin , Derry W. Brent
Published: May 2014

The nematode worm Caenorhabditis elegans has provided researchers with a wealth of information on the molecular mechanisms controlling programmed cell death (apoptosis). Its genetic tractability, optical clarity, and relatively short lifespan are key advantages for rapid assessment of apoptosis in vivo. The use of forward and reverse genetics methodology, coupled with in vivo imaging, has provided deep insights into how a multicellular organism orchestrates the self-destruction of specific cells during development and in response to exogenous stresses. Strains of C. elegans carrying mutations in the core elements of the apoptotic pathway, or in tissue-specific regulators of apoptosis, can be used for genetic analyses to reveal conserved mechanisms by which apoptosis is regulated in the somatic and reproductive (germline) tissue. Here we present an introduction to the study of apoptosis in C. elegans, including current techniques for visualization, analysis, and screening.
Coherent Raman Tissue Imaging in the Brain
Authors: Saar Brian G. , Freudiger Christian W. , Xu Xiaoyin , Huttner Anita , Kesari Santosh , Young Geoffrey , Xie X. Sunney
Published: May 2014

Imaging in neuroscience has been dramatically impacted by the advent of multiphoton microscopy. Multiphoton-excited fluorescence (MPF) in combination with endogenous fluorophores or labeling by fluorescent molecules has proven to be particularly powerful. However, endogenous fluorescence is limited to relatively few molecular species, and practical labeling schemes do not exist for many classes of molecules. Coherent Raman scattering (CRS) techniques, including coherent anti-Stokes Raman scattering and stimulated Raman scattering, allow imaging without the need for staining or fluorescent labeling. Such label-free imaging is desirable in biomedical research, because labeling often perturbs the function of small metabolite and drug molecules and may be too toxic to use in vivo. CRS techniques have similar imaging parameters to MPF, making use of pulsed near-infrared lasers to deliver high-sensitivity, high spatial resolution in three dimensions and rapid image acquisition. In this introduction, we will discuss the basic principles of CRS imaging, present the instrumentation requirements for high-speed CRS imaging, and show an example of imaging brain tumors and healthy tissue based on their intrinsic vibrational signatures. This discussion is intended to introduce the benefits and tradeoffs associated with different CRS techniques and show one example of the powerful capabilities of label-free chemical imaging.
Multicultural ethics and diversity discourse
Authors: M.L. Wallace Heather , F. Hoover Kristine , B. Pepper Molly
Published: May 2014

Purpose

– Responses to diversity management have resulted in disappointment to many organizations (Cox, 2001). Previous work has situated rational for diversity in deontological ethics by equality scholars, while the business case for diversity has commonly rested on utilitarian ethics (van Dijket al., 2012). The purpose of this paper is to examine a possible shift in rational for diversity – to explore if and how the ethic of care has been utilized in the diversity statements of companies earning recognition as one of the “100 Best Companies to Work For” in 2012.

Design/methodology/approach

– This study utilized visual rhetoric analysis and was designed to examine multiple elements of these diversity statements as published in the company web sites, including presence of the ethic of care, visual communication, and logistics.

Findings

– Of note are the results of the presence of the ethic of care as a primary or secondary rationale in 70 percent of the statements studied. Statistically significant results were found in the number of images of people from diverse backgrounds, as well as levels pleasantness and activation of the tone of the ethics statements.

Originality/value

– This study contributes to a better understanding of identifiable characteristics of these diversity statements at organizations which have been identified by their employees and the Great Place to Work Institute.
Achieving alliance ambidexterity through managing paradoxes of cooperation
Authors: Sun Biao , Lo Yi-Ju
Published: May 2014

Purpose

– The purpose of this paper is to define co-exploitation, co-exploration, and alliance ambidexterity from the perspective of organizational learning; to analyze how knowledge bases, structural arrangements, and control mechanisms of R&D alliances influence co-exploitation and co-exploration; and to discuss how to achieve alliance ambidexterity by managing paradoxes around knowledge bases, structural arrangements, and control mechanisms.

Design/methodology/approach

– This is a conceptual paper focussing on how to balance exploitation and exploration at the alliance level through managing three paradoxes of cooperation: similarity vs complementarity, integration vs modularity, and contracts vs trust.

Findings

– While technological similarity, structural integration, and contracts are more likely to promote co-exploitation, technological complementarity, structural modularity, and trust are more likely to facilitate co-exploration. Alliance ambidexterity, which is beneficial for alliance performance, derives from either the combination of technological complementarity, structural integration, and contracts, or the combination of technological similarity, structural modularity, and trust temporally.

Research limitations/implications

– Researchers should analyze the possibility of building alliance ambidexterity in other types of interorganizational relationships, and find other possible antecedents of interorganizational learning.

Practical implications

– Managers should not simply treat R&D alliances as one of exploratory interorganizational relationships, but pay equal attention to co-exploitation and co-exploration. To achieve this balance, practitioners should combine technological complementarity with structural integration and contracts, or integrate technological similarity with structural modularity and trust.

Originality/value

– This paper is one of the first contributions that analyze how an R&D alliance could gain its ambidexterity through the management of nested cooperation paradoxes.
The place of communities of practice in knowledge management studies: a critical review
Authors: Bolisani Ettore , Scarso Enrico
Published: May 2014

Purpose

– Since its introduction, the notion of Communities of Practice (CoPs) has gained immediate popularity, especially among Knowledge Management scholars. The paper aims at reviewing the past and discussing what has been done. In particular the purposes are: to assess the importance of CoPs in the KM literature; to trace how this notion is defined and used, both in practical and theoretical terms; to classify the approaches used by KM research on CoPs; to discuss the results that research and practice in CoPs have led so far, the open issues, and the potential role of this notion in a future KM research agenda.

Design/methodology/approach

– The paper illustrates and discusses the findings of a systematic literature review on CoPs focusing on papers published in the most influential Knowledge Management and Intellectual Capital Journals.

Findings

– The study analyses 82 articles published in 12 different KM and IC leading journals from 1997 to 2012. Each article was examined to determine the following information: type of study; domain of application; research methodology applied and addressed topic. Emerging trends, open questions and further research needs are identified and discussed. In particular, an issue for researchers is the necessity to formulate an agreed definition of CoPs under the KM umbrella, which can also help to implement comparable empirical studies and to build theories that provide understanding of how CoPs can be managed.

Practical implications

– The outcomes of the review is particularly important for KM scholars dealing with CoPs, who can find suggestions for their future research. It can also provide food for thought to practitioners, by illustrating the state-of-the-art and prospects of this important organisational form. In addition, the paper highlights that, despite the huge amount of studies on this topic, the notion of CoP is still used in different ways and the specific experience of each company is difficult to generalise and transfer to other cases.

Originality/value

– This is the most up-to-date analysis of research on CoPs in its elective field of application that is Knowledge Management.
Regulation of Epstein–Barr virus reactivation from latency
Authors: Murata Takayuki
Published: May 2014

The Epstein–Barr virus (EBV) is a human gamma‐herpesvirus that is implicated in various types of proliferative diseases. Upon infection, it predominantly establishes latency in B cells and cannot ever be eradicated; it persists for the host's lifetime. Reactivation of the virus from latency depends on expression of the viral immediate‐early gene, BamHI Z fragment leftward open reading frame 1 (BZLF1). The BZLF1 promoter normally exhibits only low basal activity but is activated in response to chemical or biological inducers, such as 12‐O‐tetradecanoylphorbol‐13‐acetate, calcium ionophore, histone deacetylase inhibitor, or anti‐Ig. Transcription from the BZLF1 promoter is activated by myocyte enhancer factor 2, specificity protein 1, b‐Zip type transcription factors and mediating epigenetic modifications of the promoter, such as histone acetylation and H3K4me3. In contrast, repression of the promoter is mediated by transcriptional suppressors, such as ZEB, ZIIR‐BP, and jun dimerization protein 2, causing suppressive histone modifications like histone H3K27me3, H3K9me2/3 and H4K20me3. Interestingly, there is little CpG DNA methylation of the promoter, indicating that DNA methylation is not crucial for suppression of BZLF1. This review will focus on the molecular mechanisms by which the EBV lytic switch is controlled and discuss the physiological significance of this switching for its survival and oncogenesis.