bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytical device model for graphene bilayer field-effect transistors using weak nonlocality approximation
Authors: Ryzhii V. , Ryzhii M. , Satou A. , Otsuji T. , Mitin V.
Published: March 2011

We develop an analytical device model for graphene bilayer field-effect transistors (GBL-FETs) with the back and top gates. The model is based on the Boltzmann equation for the electron transport and the Poisson equation in the weak nonlocality approximation for the potential in the GBL-FET channel. The potential distributions in the GBL-FET channel are found analytically. The source-drain current in GBL-FETs and their transconductance are expressed in terms of the geometrical parameters and applied voltages by analytical formulas in the most important limiting cases. These formulas explicitly account for the short-gate effect and the effect of drain-induced barrier lowering. The parameters characterizing the strength of these effects are derived. It is shown that the GBL-FET transconductance exhibits a pronounced maximum as a function of the top-gate voltage swing. The interplay of the short-gate effect and the electron collisions results in a nonmonotonic dependence of the transconductance on the top-gate length.
InP/InAlGaAs light-emitting transistors and transistor lasers with a carbon-doped base layer
Authors: Huang Yong , Ryou Jae-Hyun , Dupuis Russell D. , Dixon Forest , Feng Milton , Holonyak Nick
Published: March 2011

Characteristics of InP/InAlGaAs light-emitting transistors (LETs) and transistor lasers (TLs) using carbon (C) for p-type doping of the base region were investigated. The N-InP/p-In0.52(Al0.4Ga0.6)0.48As/N-In0.52Al0.48As LETs show a current gain of 0.22 and light emission at wavelength of λ ∼ 1610 nm. The low current gain is attributed to the short minority carrier lifetime in the C-doped base with a quantum well. The TL demonstrates continuous-wave operation at −190 °C with a threshold current of IB = 35 mA. By comparing the optical output characteristics of the TL and a laser diode with similar structure, it is suggested that the low differential quantum efficiency and the high threshold current density in the TL is related to the strong inter-valence band absorption in the heavily doped base layer.
Optically-induced charge separation and terahertz emission in unbiased dielectrics
Authors: Fisher W. M. , Rand S. C.
Published: March 2011

Charge separation mediated by linearly-polarized light in transparent insulators is analyzed numerically by integrating the equations of motion of a bound charge. It is shown that large static and transient dipole moments can be induced by the magnetic component of light at nonrelativistic intensities regardless of whether the pumplight is coherent or incoherent. Quantitative estimates show that efficient conversion of optical beams to electrical power is possible in lossless dielectric media and that THz radiation can be generated in unbiased materials through the use of transverse optical magnetism.
Localized surface plasmon resonance biosensing by electro-optic modulation with sensitivity and resolution tunability
Authors: Wang Tzyy-Jiann , Ho Po-Ching
Published: March 2011

The authors demonstrate a localized surface plasmon resonance (LSPR) biosensing technique based on electro-optically modulated attenuated total reflection. Electro-optic effect is utilized to modulate the wavevector of the light for exciting LSPR with the initial wavevector specified by setting the incident angle. The power variation of the attenuated-total-reflected light with the voltage is analyte-dependent and used as indicator to determine analyte concentration. Increasing the voltage has the effects of enlarging the power variation and enhancing the detection resolution. Detection sensitivity depends on the initial light wavevector and can be tuned under various sensing environments for optimal operation. The presented LSPR biosensing possesses the unique features of convenient sensitivity and resolution tunability.
Effect of particle size and annealing on spin and phonon behavior in TbMnO3
Authors: Das Raja , Jaiswal Adhish , Adyanthaya Suguna , Poddar Pankaj
Published: March 2011

Interest has grown to study TbMnO3 as it was recently reported to show a gigantic magnetoelectric effect. Here, we report the synthesis and detailed magnetic and Raman spectroscopy study on TbMnO3 particles of size ∼25 nm and 2–3 μm, respectively. The incommensurate–commensurate (lock-in) transition, usually observed at 27 K for bulk phase of TbMnO3 was not observed in susceptibility versus T curve but was seen at 30 K in the coercivity versus T curve in ∼25 nm particles. This transition, which is due to the spin modulation length scale, gets weakened in nanosize due to the increased intrinsic lattice strain observed in 2–3 μm particles, due to the effect of increased particle size. The increased value of magnetization in the 2–3 μm sample was attributed to double exchange interactions between Mn+3 and Mn+4 spins. The role of annealing related effects on the fate of the Néel temperature for TbMnO3 was investigated. Raman spectroscopy indicated a decrease in the lattice distortion for ∼25 nm particles.
Ammonia adsorption on iron phthalocyanine on Au(111): Influence on adsorbate–substrate coupling and molecular spin
Authors: Isvoranu Cristina , Wang Bin , Ataman Evren , Schulte Karina , Knudsen Jan , Andersen Jesper N. , Bocquet Marie-Laure , Schnadt Joachim
Published: March 2011

The adsorption of ammonia on Au(111)-supported monolayers of iron phthalocyanine has been investigated by x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory calculations. The ammonia-induced changes of the x-ray photoemission lines show that a dative bond is formed between ammonia and the iron center of the phthalocyanine molecules, and that the local spin on the iron atom is quenched. This is confirmed by density functional theory, which also shows that the bond between the iron center of the metalorganic complex and the Au(111) substrate is weakened upon adsorption of ammonia. The experimental results further show that additional adsorption sites exist for ammonia on the iron phthalocyanine monolayer.
Wireless communication capability of a reconfigurable plasma antenna
Authors: Kumar Rajneesh , Bora Dhiraj
Published: March 2011

A 30 cm long plasma column is excited by a surface wave, which acts as a plasma antenna. Using plasma properties (pattern formation/striations in plasmas) single plasma antenna can be transformed into array, helical, and spiral plasma antenna. Experiments are carried out to study the power patterns, directivity, and half power beam width of such different plasma antennas. Moreover, field properties of plasma and copper antenna are studied. Further, wireless communication and jamming capability of plasma antenna are tested. Findings of this study suggest that directivity and communication range can be increased by converting single plasma antenna in to array/helical/spiral plasma antenna. Field frequencies of plasma antenna determine the communication and jamming of radio frequency waves. Therefore, this study invokes applications of pattern formation or striations of plasmas in plasma antenna technology.
Stabilization of positive charge on polytetrafluoroethylene electret films treated with titanium-tetrachloride vapor
Authors: Rychkov Dmitry , Gerhard Reimund
Published: March 2011

The surface of polytetrafluoroethylene films was treated with titanium-tetrachloride vapor. The treatment was carried out in a flow reactor by means of molecular-layer deposition, a method from the arsenal of chemical nanotechnology. X-ray photoelectron spectroscopy reveals that such a treatment results in considerable changes in the chemical composition at and near the surface of the fluoropolymer film. Both, defluorination and oxidation of the surface were observed. At the same time, samples treated with titanium tetrachloride show a significant enhancement in the thermal stability of the positive homocharge. The thermally stimulated surface-potential-decay curves were observed to shift to higher temperatures by more than 100 °C
Structural stability and electronic properties of SiC nanocones: First-principles calculations and symmetry considerations
Authors: Alfieri G. , Kimoto T.
Published: March 2011

The structural and electronic properties of SiC nanocones (SiCNCs), as a function of the disclination angle and electric field intensity and orientation, are investigated by means of ab initio calculations. Phonon analysis revealed that SiCNCs with only three disclination angles are allowed and, among these, the band gap of only one SiCNC is affected by a transverse electric field. An interpretation of these findings, from a group theoretical point of view, is also given.
Anomalous on-current and subthreshold swing improvement in low-temperature polycrystalline-silicon thin-film transistors under Gate bias stress
Authors: Lin Chia-Sheng , Chen Ying-Chung , Chang Ting-Chang , Jian Fu-Yen , Li Hung-Wei , Chen Yi-Chuan , Chen Te-Chih , Tai Ya-Hsiang
Published: March 2011

This work investigates an improvement in anomalous on-current and subthreshold swing (SS) in Low-temperature polycrystalline-silicon thin-film transistors after positive gate bias stress. The experimental results reveal that the improved electric properties are due to the hole trapping at SiO2 above the lightly doped drain regions, which causes a strong electric field at the gate corners. The effect of the hole trapping is to reduce the effective channel length and the SS. Besides, the stress-related electric field was also simulated by TCAD software to verify the mechanism above.
Children’s lexical skills and task demands affect gestural behavior in mothers of late-talking children and children with typical language development
Authors: Grimminger Angela , Rohlfing Katharina J. , Stenneken Prisca
Published: March 2011

To evaluate the influence of lexical development and task demands on maternal gestural behavior, we observed 17 German-speaking mothers and their children with typically language development (TD) and 9 mothers with their late talkers (LT) aged 22–25 months in task-oriented dialogues. Mothers instructed their children to put two objects together; canonical and — as more difficult tasks — noncanonical spatial relationships were requested. Deictic gestures were dominant in both groups and were used to reinforce speech. However, LT’s mothers gestured more than TD’s mothers and tended to hold their gestures throughout a complete utterance. Regarding the task demands, all mothers gestured more in noncanonical settings and this trend was more pronounced in LT’s mothers. Thus, certain aspects of gestural motherese (frequency and duration of gestures but not redundancy) seem to ‘operate’ on a scale between task difficulty and children’s language skills, suggesting that maternal communicative behavior is fine-tuned to children’s learning process.
The type of shared activity shapes caregiver and infant communication
Authors: Puccini Daniel , Hassemer Mireille , Salomo Dorothé , Liszkowski Ulf
Published: March 2011

For the beginning language learner, communicative input is not based on linguistic codes alone. This study investigated two extralinguistic factors which are important for infants’ language development: the type of ongoing shared activity and non-verbal, deictic gestures. The natural interactions of 39 caregivers and their 12-month-old infants were recorded in two semi-natural contexts: a free play situation based on action and manipulation of objects, and a situation based on regard of objects, broadly analogous to an exhibit. Results show that the type of shared activity structures both caregivers’ language usage and caregivers’ and infants’ gesture usage. Further, there is a specific pattern with regard to how caregivers integrate speech with particular deictic gesture types. The findings demonstrate a pervasive influence of shared activities on human communication, even before language has emerged. The type of shared activity and caregivers’ systematic integration of specific forms of deictic gestures with language provide infants with a multimodal scaffold for a usage-based acquisition of language.
Mathematical learning and gesture
Authors: Gerofsky Susan
Published: March 2011

This paper reports on a research project in mathematics education involving the use of gesture, movement and vocal sound to highlight mathematically salient features of the graphs of polynomial functions. Empirical observations of students’ spontaneous gesture types when enacting elicited gestures of these graphs reveal a number of useful binaries (proximal/distal, being the graph/seeing the graph, within sight/within reach). These binaries inform an analysis of videotaped gestural and interview data and appear to predict teachers’ assessments of student mathematical engagement and understanding with great accuracy. Reframing this data in terms of C-VPT and O-VPT adds a further layer of sophistication to the analysis and connects it with deeper findings in cognitive and neuroscience and gesture studies.
A grammatical formalism based on patterns of Part of Speech tags
Authors: Gamallo Otero Pablo , González López Isaac
Published: March 2011

In this paper, we describe a grammatical formalism, called DepPattern, to write dependency grammars using patterns of Part of Speech (PoS) tags augmented with lexical and morphological information. The formalism inherits ideas from Sinclair’s work and Pattern Grammar. To properly analyze semi-fixed idiomatic expressions, DepPattern distinguishes between open-choice and idiomatic rules. A grammar is defined as a set of lexical-syntactic rules at different levels of abstraction. In addition, a compiler was implemented so as to generate deterministic and robust parsers from DepPattern grammars. These parsers identify dependencies which can be used to improve corpus-based applications such as information extraction. At the end of this article, we describe an experiment which evaluates the efficiency of a dependency parser generated from a simple DepPattern grammar. In particular, we evaluated the precision of a semantic extraction method making use of a DepPattern-based parser.
A vertebrate N-end rule degron reveals that Orc6 is required in mitosis for daughter cell abscission
Authors: Bernal Juan A. , Venkitaraman Ashok R.
Published: March 2011

Orc6, an evolutionarily conserved component of the origin recognition complex, is essential for deoxyribonucleic acid (DNA) replication initiation from yeast to humans. Whether vertebrate Orc6 has a mitotic function remains unresolved. In vertebrates, but not yeast, its depletion causes centrosome amplification and multinucleate division, but replication stress indirectly causes similar abnormalities. In this paper, we exploit Varshavsky’s N-end rule to create a temperature-sensitive degron form of avian Orc6. Orc6 depletion during the S phase triggers centrosome amplification suppressed by G2 checkpoint inhibition, reflecting an indirect consequence of aberrant DNA replication. However, Orc6 depletion during mitosis suffices to cause asymmetric division and failure in cytokinesis, with a delay in daughter cell abscission revealed by a fluorescence-bleaching assay. A mutant lacking the C-terminal 25 residues cannot rescue these defects. Thus, vertebrate Orc6 is necessary during mitosis for the abscission stage of cytokinesis. Our findings exemplify N-end rule degrons as tools to unravel functions of a single protein during different phases of the vertebrate cell cycle.
The yeast lipin orthologue Pah1p is important for biogenesis of lipid droplets
Authors: Adeyo Oludotun , Horn Patrick J. , Lee SungKyung , Binns Derk D. , Chandrahas Anita , Chapman Kent D. , Goodman Joel M.
Published: March 2011

Lipins are phosphatidate phosphatases that generate diacylglycerol (DAG). In this study, we report that yeast lipin, Pah1p, controls the formation of cytosolic lipid droplets. Disruption of PAH1 resulted in a 63% decrease in droplet number, although total neutral lipid levels did not change. This was accompanied by an accumulation of neutral lipids in the endoplasmic reticulum (ER). The droplet biogenesis defect was not a result of alterations in neutral lipid ratios. No droplets were visible in the absence of both PAH1 and steryl acyltransferases when grown in glucose medium, even though the strain produces as much triacylglycerol as wild type. The requirement of PAH1 for normal droplet formation can be bypassed by a knockout of DGK1. Nem1p, the activator of Pah1p, localizes to a single punctum per cell on the ER that is usually next to a droplet, suggesting that it is a site of droplet assembly. Overall, this study provides strong evidence that DAG generated by Pah1p is important for droplet biogenesis.
MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis
Authors: Williams Corey L. , Li Chunmei , Kida Katarzyna , Inglis Peter N. , Mohan Swetha , Semenec Lucie , Bialas Nathan J. , Stupay Rachel M. , Chen Nansheng , Blacque Oliver E. , Yoder Bradley K. , Leroux Michel R.
Published: March 2011

Meckel-Gruber syndrome (MKS), nephronophthisis (NPHP), and related ciliopathies present with overlapping phenotypes and display considerable allelism between at least twelve different genes of largely unexplained function. We demonstrate that the conserved C. elegans B9 domain (MKS-1, MKSR-1, and MKSR-2), MKS-3/TMEM67, MKS-5/RPGRIP1L, MKS-6/CC2D2A, NPHP-1, and NPHP-4 proteins exhibit essential, collective functions at the transition zone (TZ), an underappreciated region at the base of all cilia characterized by Y-shaped assemblages that link axoneme microtubules to surrounding membrane. These TZ proteins functionally interact as members of two distinct modules, which together contribute to an early ciliogenic event. Specifically, MKS/MKSR/NPHP proteins establish basal body/TZ membrane attachments before or coinciding with intraflagellar transport–dependent axoneme extension and subsequently restrict accumulation of nonciliary components within the ciliary compartment. Together, our findings uncover a unified role for eight TZ-localized proteins in basal body anchoring and establishing a ciliary gate during ciliogenesis, and suggest that disrupting ciliary gate function contributes to phenotypic features of the MKS/NPHP disease spectrum.
Casting a wide net: the Journal Impact Factor numerator
Authors: HUBBARD Stephen C. , McVEIGH Marie E.
Published: March 2011

All metrics published in the Journal Citation Reports™ are dependent on the complete and correct aggregation of citations to each journal title. Here, we explain how unique cited titles are created for Thomson Reuters indexing, and how variations and ambiguities in titles are collected in order to create the Journal Impact Factor numerator.
Selling to the BRIC — Russia: scholarly e‐products and the Russian market
Authors: KUZNETSOV Alexander , RAZUMOVA Irina
Published: March 2011

We present the history, a present‐day analysis and perspectives of the market for scholarly e‐resources (e‐journals, e‐books, etc) in Russia. Our study is based on 10 years' experience of the Russian national library consortium NEICON, which is one of the major players in the market. Indicators and trends of the economics, human resources, and scientific output of Russian science are presented. The NEICON consortium activities are described. The perspectives, peculiarities, and practicalities of entering the Russian market are outlined, as well as what a new publisher entrant might expect to achieve.
Book Reviews
Authors: FULLER Louise
Published: March 2011

The craft of scientific communication Joseph E. Harmon and Alan G. Gross Chicago and London, University of Chicago Press, 2010, 240pp. ISBN‐13: 978‐0‐2263‐166‐11 (hbk), 978‐0‐2263‐166‐28 (pbk), $20.00
An equilibrium model for tungsten fuzz in an eroding plasma environment
Authors: Doerner R.P. , Baldwin M.J. , Stangeby P.C.
Published: March 2011

A model equating the growth rate of tungsten fuzz on a plasma-exposed surface to the erosion rate of the fuzzy surface is developed to predict the likelihood of tungsten fuzz formation in the steady-state environment of toroidal confinement devices. To date this question has not been answered because the operational conditions in existing magnetic confinement machines do not necessarily replicate those expected in future fusion reactors (i.e. high-fluence operation, high temperature plasma-facing materials and edge plasma relatively free of condensable impurities). The model developed is validated by performing plasma exposure experiments at different incident ion energies (thereby varying the erosion rate) and measuring the resultant fuzz layer thickness. The results indicate that if the conditions exist for fuzz development in a steady-state plasma (surface temperature and energetic helium flux), then the erosion rate will determine the equilibrium thickness of the surface fuzz layer.
Real-time feedback control of the plasma density profile on ASDEX Upgrade
Authors: Mlynek A. , Reich M. , Giannone L. , Treutterer W. , Behler K. , Blank H. , Buhler A. , Cole R. , Eixenberger H. , Fischer R. , Lohs A. , Lüddecke K. , Merkel R. , Neu G. , Ryter F. , Zasche D.
Published: March 2011

The spatial distribution of density in a fusion experiment is of significant importance as it enters in numerous analyses and contributes to the fusion performance. The reconstruction of the density profile is therefore commonly done in offline data analysis. In this paper, we present an algorithm which allows for density profile reconstruction from the data of the submillimetre interferometer and the magnetic equilibrium in real-time. We compare the obtained results to the profiles yielded by a numerically more complex offline algorithm. Furthermore, we present recent ASDEX Upgrade experiments in which we used the real-time density profile for active feedback control of the shape of the density profile.
Runaway electron drift orbits in magnetostatic perturbed fields
Authors: Papp G. , Drevlak M. , Fülöp T. , Helander P.
Published: March 2011

Disruptions in large tokamaks can lead to the generation of a relativistic runaway electron beam that may cause serious damage to the first wall. To mitigate the disruption and suppress the runaway beam the application of resonant magnetic perturbations has been suggested. In this work we investigate the effect of resonant magnetic perturbations on the confinement of runaway electrons by simulating their drift orbits in magnetostatic perturbed fields and calculating the orbit losses for various initial energies and magnetic perturbation magnitudes. In the simulations we use a TEXTOR-like configuration and solve the relativistic, gyro-averaged drift equations for the runaway electrons including synchrotron radiation and collisions. The results indicate that runaway electrons are well confined in the core of the device, but the onset time of runaway losses closer to the edge is dependent on the magnetic perturbation level and thereby can affect the maximum runaway current. However, the runaway current damping rate is not sensitive to the magnetic perturbation level, in agreement with experimental observations.
Spinor sheaves on singular quadrics
Authors: Addington Nicolas
Published: March 2011

We define, using matrix factorizations of the equation of

Q
Q

, reflexive sheaves on a singular quadric

Q
Q

that generalize the spinor bundles on smooth quadrics. We study the first properties of these spinor sheaves, give a Horrocks-type criterion, and show that they are semi-stable, and indeed stable in some cases.
SplamiR—prediction of spliced miRNAs in plants
Authors: Thieme Christoph J. , Gramzow Lydia , Lobbes Dajana , Theißen Günter
Published: March 2011

Motivation: MicroRNAs (miRNAs) are important regulators of biological processes in plants and animals. Recently, miRNA genes have been discovered, whose primary transcripts are spliced and which cannot be predicted directly from genomic sequence. Hence, more sophisticated programs for the detection of spliced miRNAs are required.

Results: Here, we present the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem–loop structures. Next, in silico splice variants of database sequences with complementarity to an mRNA of interest are classified as to whether they could represent miRNAs targeting this mRNA. Our method identifies all known cases of spliced miRNAs in rice, and a previously undiscovered miRNA in maize which is supported by an expressed sequence tag (EST). SplamiR permits identification of spliced miRNAs for a given target mRNA in many plant genomes.

Availability: The program is freely available at http://www.uni-jena.de/SplamiR.html.

Contact:  guenter.theissen@uni-jena.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns
Authors: Yang Xinan , Li Jianrong , Lee Younghee , Lussier Yves A.
Published: March 2011

Summary:  GO-Module is a web-accessible synthesis and visualization tool developed for end-user biologists to greatly simplify the interpretation of prioritized Gene Ontology (GO) terms. GO-Module radically reduces the complexity of raw GO results into compact biomodules in two distinct ways, by (i) constructing biomodules from significant GO terms based on hierarchical knowledge, and (ii) refining the GO terms in each biomodule to contain only true positive results. Altogether, the features (biomodules) of GO-Module outputs are better organized and on average four times smaller than the input GO terms list (P = 0.0005, n = 16).

Availability:  http://lussierlab.org/GO-Module

Contact:  ylussier@bsd.uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition
Authors: Bécavin Christophe , Tchitchek Nicolas , Mintsa-Eya Colette , Lesne Annick , Benecke Arndt
Published: March 2011

Motivation: Multidimensional scaling (MDS) is a well-known multivariate statistical analysis method used for dimensionality reduction and visualization of similarities and dissimilarities in multidimensional data. The advantage of MDS with respect to singular value decomposition (SVD) based methods such as principal component analysis is its superior fidelity in representing the distance between different instances specially for high-dimensional geometric objects. Here, we investigate the importance of the choice of initial conditions for MDS, and show that SVD is the best choice to initiate MDS. Furthermore, we demonstrate that the use of the first principal components of SVD to initiate the MDS algorithm is more efficient than an iteration through all the principal components. Adding stochasticity to the molecular dynamics simulations typically used for MDS of large datasets, contrary to previous suggestions, likewise does not increase accuracy. Finally, we introduce a k nearest neighbor method to analyze the local structure of the geometric objects and use it to control the quality of the dimensionality reduction.

Results: We demonstrate here the, to our knowledge, most efficient and accurate initialization strategy for MDS algorithms, reducing considerably computational load. SVD-based initialization renders MDS methodology much more useful in the analysis of high-dimensional data such as functional genomics datasets.

Contact:  arndt@ihes.fr
Development and evaluation of a cpue-based harvest control rule for the southern and eastern scalefish and shark fishery of Australia
Authors: Little L. Richard , Wayte Sally E. , Tuck Geoffrey N. , Smith Anthony D. M. , Klaer Neil , Haddon Malcolm , Punt André E. , Thomson Robin , Day Jemery , Fuller Mike
Published: March 2011

Little, L. R., Wayte, S. E., Tuck, G. N., Smith, A. D. M., Klaer, N., Haddon, M., Punt, A. E., Thomson, R., Day, J., and Fuller, M. 2011. Development and evaluation of a cpue-based harvest control rule for the southern and eastern scalefish and shark fishery of Australia. – ICES Journal of Marine Science, 68: 1699–1705. Many fishery management agencies are adopting harvest control rules (HCRs) to achieve harvest policies and management objectives. HCRs, however, often require data-intensive stock assessments to facilitate the harvest prescription. An HCR based on catch and catch per unit effort (cpue) was developed for the southern and eastern scalefish and shark fishery of Australia, for stocks that lack the data needed to conduct a full statistical catch-at-age assessment. The HCR produces a recommended biological catch and is characterized by two parameters, target cpue and target catch, both derived from historical data. Simulation tests showed that the HCR could guide the stock to the desired state from different initial levels of depletion. However, the selection of parameter values for the HCR was critical. Achieving fishery objectives was difficult when the target catch was a function of recent catch, rather than data from a predefined historical reference period. Problems may also arise when specifying the reference period on which the HCR parameters are determined. The cpue-based HCR is a valuable tool for managing fisheries where monitoring and assessment activities are relatively expensive, or in general, where data are scarce.
Bronchiolitis
Authors: Quinn Thomas
Published: March 2011

Bronchiolitis is the most common lower respiratory tract infection in infants, the leading cause of hospital admission in young children and the most frequent cause of respiratory failure in children admitted to paediatric intensive care units in the UK. Due to the seasonal pattern of this illness, GPs are likely to see many infants presenting with bronchiolitis during the winter. GPs need to be aware of how to assess and manage infants with bronchiolitis and know when to refer them to the paediatrician.
Ultrasonography of the Adult Thoracic and Lumbar Spine for Central Neuraxial Blockade
Authors: Chin Ki Jinn , Karmakar Manoj Kumar , Peng Philip , Warner David S.
Published: March 2011

The role of ultrasound in central neuraxial blockade has been underappreciated, partly because of the relative efficacy of the landmark-guided technique and partly because of the perceived difficulty in imaging through the narrow acoustic windows produced by the bony framework of the spine. However, this also is the basis for the utility of ultrasound: an interlaminar window that permits passage of sound waves into the vertebral canal also will permit passage of a needle. In addition, ultrasound aids in identification of intervertebral levels, estimation of the depth to epidural and intrathecal spaces, and location of important landmarks, including the midline and interlaminar spaces. This can facilitate neuraxial blockade, particularly in patients with difficult surface anatomic landmarks. In this review article, the authors summarize the current literature, describe the key ultrasonographic views, and propose a systematic approach to ultrasound imaging for the performance of spinal and epidural anesthesia in the adult patient.
Myocardial Blood Flow during General Anesthesia with Xenon in Humans
Authors: Schaefer Wolfgang , Meyer Philipp T. , Rossaint Rolf , Baumert Jan H. , Coburn Mark , Fries Michael , Rex Steffen
Published: March 2011

Background

Xenon has only minimal hemodynamic side effects and induces pharmacologic preconditioning. Thus, the use of xenon could be an interesting option in patients at risk for perioperative myocardial ischemia. However, little is known about the effects of xenon anesthesia on myocardial blood flow (MBF) and coronary vascular resistance in humans.

Methods

Myocardial blood flow was noninvasively quantified by H₂¹⁵O positron emission tomography in six healthy volunteers (age: 38 ± 8 yr). MBF was measured at baseline and during general anesthesia induced with propofol and maintained with xenon, 59 ± 0%. Absolute quantification of MBF was started after the calculated plasma concentration of propofol had decreased to less than 1.5 μg · ml⁻¹.

Results

Compared with baseline (MBFbaseline, 1.03 ± 0.09 ml · min⁻¹ · g⁻¹; mean ± SD), MBF was decreased insignificantly by xenon (MBFxenon, 0.80 ± 0.22 ml · min⁻¹ · g⁻¹; -21%, P = 0.11). Xenon decreased the rate-pressure product (RPP; heart rate × systolic arterial pressure), an indicator of cardiac work and myocardial oxygen consumption (-15%, P < 0.04). When correcting for the RPP, the decrease in MBF observed during xenon anesthesia was reduced to -9% (MBFcorr-xenon, 1.42 ± 0.28 ml · g⁻¹ · mmHg⁻¹ vs. MBFcorr-baseline, 1.60 ± 0.28 ml · g⁻¹ · mmHg⁻¹, P = 0.32). Xenon did not affect the dependency of MBF on the RPP. Coronary vascular resistance did not significantly change (+15 ± 23%, P = 0.18) during xenon anesthesia.

Conclusions

In healthy subjects, xenon has only minimal effects on coronary flow dynamics. These effects are probably of indirect nature, reflecting the decrease in myocardial oxygen consumption induced by the effects of xenon anesthesia on cardiac work.
Effects of Volatile and Intravenous Anesthesia on the Alveolar and Systemic Inflammatory Response in Thoracic Surgical Patients
Authors: Schilling Thomas , Kozian Alf , Senturk Mert , Huth Christof , Reinhold Annegret , Hedenstierna Göran , Hachenberg Thomas
Published: March 2011

Background

One-lung ventilation (OLV) results in alveolar proinflammatory effects, whereas their extent may depend on administration of anesthetic drugs. The current study evaluates the effects of different volatile anesthetics compared with an intravenous anesthetic and the relationship between pulmonary and systemic inflammation in patients undergoing open thoracic surgery.

Methods

Sixty-three patients scheduled for elective open thoracic surgery were randomized to receive anesthesia with 4 mg · kg⁻¹ · h⁻¹ propofol (n = 21), 1 minimum alveolar concentration desflurane (n = 21), or 1 minimum alveolar concentration sevoflurane (n = 21). Analgesia was provided by remifentanil (0.25 μg · kg⁻¹ · min⁻¹). After intubation, all patients received pressure-controlled mechanical ventilation with a tidal volume of approximately 7 ml · kg ideal body weight, a peak airway pressure lower than 30 cm H₂O, a respiratory rate adjusted to a Paco2 of 40 mmHg, and a fraction of inspired oxygen lower than 0.8 during OLV. Fiberoptic bronchoalveolar lavage of the ventilated lung was performed immediately after intubation and after surgery. The expression of inflammatory cytokines was determined in the lavage fluids and serum samples by multiplexed bead-based immunoassays.

Results

Proinflammatory cytokines increased in the ventilated lung after OLV. Mediator release was more enhanced during propofol anesthesia compared with desflurane or sevoflurane administration. For tumor necrosis factor-α, the values were as follows: propofol, 5.7 (8.6); desflurane, 1.6 (0.6); and sevoflurane, 1.6 (0.7). For interleukin-8, the values were as follows: propofol, 924 (1680); desflurane, 390 (813); and sevoflurane, 412 (410). (Values are given as median [interquartile range] pg · ml⁻¹). Interleukin-1β was similarly reduced during volatile anesthesia. The postoperative serum interleukin-6 concentration was increased in all patients, whereas the systemic proinflammatory response was negligible.

Conclusions

OLV increases the alveolar concentrations of proinflammatory mediators in the ventilated lung. Both desflurane and sevoflurane suppress the local alveolar, but not the systemic, inflammatory responses to OLV and thoracic surgery.
Steady-state invariant genetics: probing the role of morphogen gradient dynamics in developmental patterning
Authors: Nahmad Marcos
Published: March 2011

Morphogen-mediated patterning is the predominant mechanism by which positional information is established during animal development. In the classical view, the interpretation of positional signals depends on the equilibrium distribution of a morphogen, regardless of the dynamics of gradient formation. The problem of whether or not morphogen dynamics contribute to developmental patterning has not been explored in detail, partly because genetic experiments, which selectively affect signalling dynamics while maintaining unchanged the steady-state morphogen profile, are difficult to design and interpret. Here, I present a modelling-based approach to identify genetic mutations in developmental patterning that may affect the transient, but leave invariant the steady-state signalling gradient. As a case study, this approach is used to explore the dynamic properties of Hedgehog (Hh) signalling in the developing wing of the fruitfly,Drosophila melanogaster. This analysis provides insights into how different properties of the Hh gradient dynamics, such as the duration of exposure to the signal or the maximum width of the transient gradient, can be genetically perturbed without affecting the steady-state distribution of the Hh concentration profile. I propose that this method can be used as an experimental design tool to investigate the role of transient morphogen gradients in developmental patterning and discuss the generality of these ideas in other problems.
Atomistic and electronic structure of (X
2
O
3
)

n

nanoclusters;
n
=1–5, X=B, Al, Ga, In and Tl
Authors: Woodley Scott M.
Published: March 2011

The stable and metastable, as measured using an all-electron density functional theory approach, stoichiometric clusters of boron, aluminium, gallium, indium and thallium oxide are reported. Initial candidate structures were found using an evolutionary algorithm to search the energy landscape, defined using classical interatomic potentials, for alumina and india followed by data mining or rescaling. Characterization of the refined structures was performed by electronic structure techniques at the hybrid density functional and many-body GW levels of theory. We make accurate predictions of the spectroscopic properties represented by mean ionization potentials of 11.4, 9.9, 9.8, 8.8 and 8.4 eV and electron affinities of 0.05, 1.1, 1.6, 1.9 and 2.5 eV for boria, alumina, gallia, india and thallia, respectively. The changes in the global minima, atomistic and electronic properties with respect to the cluster and cation size are discussed.
Lactobacillus gigeriorum sp. nov., isolated from chicken crop
Authors: Cousin Sylvie , Gulat-Okalla Marie-Laure , Motreff Laurence , Gouyette Catherine , Bouchier Christiane , Clermont Dominique , Bizet Chantal
Published: March 2011

In the early 1980s, a facultatively anaerobic, non-motile, short rod, designated 202T, was isolated from a chicken crop and identified as a homofermentative lactic acid bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was affiliated with the genus Lactobacillus, clustering within the Lactobacillus acidophilus–delbrueckii group. In this analysis, strain 202T appeared to be most closely related to the type strains of Lactobacillus intestinalis and Lactobacillus amylolyticus, with gene sequence similarities of 96.1 and 96.2 %, respectively. Strain 202T was found to differ from these two species, however, when investigated by multilocus sequence analysis, and it also differed in terms of some of its metabolic properties. On the basis of these observations, strain 202T is considered to represent a novel species in the genus Lactobacillus, for which the name Lactobacillus gigeriorum sp. nov. is proposed; the type strain is 202T ( = CRBIP 24.85T = DSM 23908T).
Actinoallomurus radicium sp. nov., isolated from the roots of two plant species
Authors: Matsumoto Atsuko , Fukuda Asami , Inahashi Yuki , Ōmura Satoshi , Takahashi YŌko
Published: March 2011

Three strains, K08-0182T, K08-0178 and K08-0195 were isolated from the paste of ground plant roots collected in Kanagawa Prefecture, Japan. These strains contained meso-diaminopimelic acid and lysine as the diamino acids in cell-wall peptidoglycan, and MK-9(H6) and MK-9(H8) as the predominant menaquinones. The G+C contents of the DNA were 72–73 mol%. Taken together, these characteristics combined with 16S rRNA gene sequence analyses revealed that the isolated strains belong to the genus Actinoallomurus. DNA–DNA hybridization values showed that the three strains belonged to a novel species of the genus Actinoallomurus. Therefore strains K08-0182T, K08-0178 and K08-0195 are proposed as representatives of a novel species, Actinoallomurus radicium sp. nov. The type strain is K08-0182T ( = DSM 45523T  = NBRC 107678T  = JCM 17294T).
Helicobacter heilmannii sp. nov., isolated from feline gastric mucosa
Authors: Smet A. , Flahou B. , D’Herde K. , Vandamme P. , Cleenwerck I. , Ducatelle R. , Pasmans F. , Haesebrouck F.
Published: March 2011

Three Gram-negative, microaerophilic bacteria, strains ASB1T, ASB2 and ASB3, with a corkscrew-like morphology isolated from the gastric mucosa of cats were studied using a polyphasic taxonomic approach. The isolates grew on biphasic culture plates under microaerobic conditions at 37 °C and exhibited urease, oxidase and catalase activities. They were also able to grow in colonies on dry agar plates. Based on 16S rRNA gene sequence analysis, ASB1T, ASB2 and ASB3 were identified as members of the genus Helicobacter and showed 98 to 99 % sequence similarity to strains of Helicobacter felis, Helicobacter bizzozeronii, ‘Candidatus Helicobacter heilmannii’, Helicobacter cynogastricus, Helicobacter baculiformis and Helicobacter salomonis, six related Helicobacter species previously detected in feline or canine gastric mucosa. Sequencing of the partial hsp60 gene demonstrated that ASB1T, ASB2 and ASB3 constitute a separate taxon among the feline and canine Helicobacter species. The urease gene sequences of ASB1T, ASB2 and ASB3 showed approximately 91 % similarity to those of ‘Candidatus Helicobacter heilmannii’. Protein profiling, the absence of alkaline phosphatase activity and several other biochemical characteristics also allowed strains ASB1T, ASB2 and ASB3 to be differentiated from other Helicobacter species of feline or canine gastric origin. The results of this polyphasic taxonomic study show that the cultured isolates constitute a new taxon corresponding to ‘Candidatus Helicobacter heilmannii’, which was previously demonstrated in the stomach of humans, wild felidae, cats and dogs. The name Helicobacter heilmannii sp. nov. is proposed for these isolates; the type strain is ASB1T ( = DSM 23983T = LMG 26292T).
Motilibacter peucedani gen. nov., sp. nov., isolated from rhizosphere soil
Authors: Lee Soon Dong
Published: March 2011

A novel actinomycete strain, designated RP-AC37T, was isolated from rhizosphere soil collected on Mara Island of Jeju, Republic of Korea. Cells were aerobic, Gram-positive, oxidase-negative, catalase-positive, non-mycelium-forming and motile rods (0.6–0.7×1.9–2.4 µm). Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism formed a distinct clade within the radiation occupied by the suborder Frankineae. 16S rRNA gene similarity values were less than 93.2 % to members of the suborder Frankineae and related taxa. The diamino acid isomer in the cell-wall peptidoglycan was ll-diaminopimelic acid. The major whole-cell sugars were glucose, galactose and xylose. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The cellular fatty acids were straight-chain, unsaturated and saturated, with a significant amount of tuberculostearic acid (10-methyl-C18 : 0). The DNA G+C content was 73.2 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly separate the isolate from members of known genera of the suborder Frankineae and related taxa, suggesting that the isolate represents a novel species in a new genus in this suborder, for which the name Motilibacter peucedani gen. nov., sp. nov. is proposed; the type strain is RP-AC37T ( = KCTC 19630T = DSM 45328T).
Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow’s milk
Authors: Wolfgang William J. , Coorevits An , Cole Jocelyn A. , De Vos Paul , Dickinson Michelle C. , Hannett George E. , Jose Reashma , Nazarian Elizabeth J. , Schumann Peter , Van Landschoot Anita , Wirth Samantha E. , Musser Kimberlee A.
Published: March 2011

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T  = DSM 23544T  = CCUG 59649T  = LMG 26022T) is proposed.
Knoellia locipacati sp. nov., from soil of the Demilitarized Zone in South Korea
Authors: Shin Na-Ri , Roh Seong Woon , Kim Min-Soo , Jung Mi-Ja , Whon Tae Woong , Bae Jin-Woo
Published: March 2011

A Gram-positive, aerobic, rod- or coccus-shaped, non-motile bacterium, designated DMZ1T, was isolated from soil of the Demilitarized Zone, South Korea. Strain DMZ1Tgrew optimally at 30 °C, at pH 7–8 and with 1 % (w/v) NaCl. The isolate showed high 16S rRNA gene sequence similarity withKnoellia aerolata5317S-21T(98.2 %). The cell-wall sugars were glucose and ribose. The peptidoglycan amino acids weremeso-diaminopimelic acid, glutamic acid and glycine. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0and iso-C14 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and five unknown phospholipids. The isolate did not contain mycolic acids. The DNA G+C content was 72.6 mol%. The isolate showed <28 % DNA–DNA relatedness with members of the genusKnoellia. Phylogenetic, phenotypic and genotypic analysis indicated that strain DMZ1Trepresents a novel species of the genusKnoellia, for which the nameKnoellia locipacatisp. nov. is proposed. The type strain is DMZ1T( = KACC 15114T = JCM 17313T).