bluuebunny/crossref_metadata_2025 huggingface dataset:
Vacancy island creation and coalescence using automated scanning tunneling microscopy
Authors: Lake R. E. , Dean A. , Maheswaranathan N. , Lange A. P. , Ray M. P. , Sosolik C. E.
Published: January 2008

We demonstrate that scanning tunneling microscope tip-surface crash events can be utilized as an efficient means for the creation of predefined island configurations for diffusion studies. Using this method, islands of varying size can be created and placed in close proximity, increasing the probability of initiating and observing coalescence events. Data obtained from crash initiated events on a Ag(111) surface are presented. Relaxation time exponents extracted from these data confirm that our method gives results consistent with previous, sputter-obtained island coalescence studies. We also describe an instrument-control routine developed for these measurements that utilizes commercial imaging and off-the-shelf automation software to automate the tracking of islands or other features by the microscope.
Time-of-flight studies on TiO2/CuInS2 heterojunctions
Authors: Hofhuis Joris , Schoonman Joop , Goossens Albert
Published: January 2008

Time-of-Flight (TOF) measurements have been performed on n-type TiO2/p-type CuInS2 heterojunctions. The TiO2 film thickness has been varied between 200 and 400 nm, while the CuInS2 film thickness has been fixed at 500 nm. The TOF response can be accurately modeled, if the potential drop across the p-n heterojunction with a large density of interface states is properly accounted for. Also electron transport in a space-charge region for a not fully depleted semiconductor has to be considered. The electron mobility in TiO2 is found to be 10−2 cm2 V−1 s−1, independent of the TiO2 layer thickness. The interface-state densities are 5×1011, 2×1012, and 6×1012 eV−1 cm−2 for 200, 300, and 400 nm thick TiO2 films, respectively.
Current-excited magnetization reversal under in-plane magnetic field in a nanoscaled ferromagnetic wire
Authors: Togawa Yoshihiko , Kimura Takashi , Harada Ken , Matsuda Tsuyoshi , Tonomura Akira , Otani Yoshichika , Akashi Tetsuya
Published: January 2008

We microscopically demonstrate that the magnetic domain is controllably nucleated and erased in the uniformly magnetized wire using a current pulse in small magnetic fields. Lorentz microscopy is performed in Permalloy nanowires with in-plane anisotropy. The stochastic nature of the magnetization reversal due to spin wave and thermal excitations in the absence of magnetic field completely disappears and turns into deterministic in the presence of small magnetic field, which enables the magnetization reversal control. We interpret that the phenomena are associated with Zeeman energy stabilization.
Growth of layered LiNi0.5Mn0.5O2 thin films by pulsed laser deposition for application in microbatteries
Authors: Xia Hui , Lu Li , Meng Ying Shirley
Published: January 2008

Li Ni 0.5 Mn 0.5 O 2 films were prepared by pulsed laser deposition on stainless steel (SS) and Au substrates. The substrate was found to play an important role in determining the growth of films. Although similar x-ray diffraction spectra were observed for both types of substrates, Raman spectra exhibited different features. The charge-discharge behavior of the film on the SS substrate indicates a spinel structure while the charge-discharge behavior of the film on the Au substrate indicates a layered structure. The secondary ion mass spectrometry depth-profiling results indicate interdiffusion between the film and the substrate, which inhibits the formation of pure layered LiNi0.5Mn0.5O2 phase.
Formation and electrical bistability properties of ZnO nanoparticles embedded in polyimide nanocomposites sandwiched between two C60 layers
Authors: Li Fushan , Kim Tae Whan , Dong Wenguo , Kim Young-Ho
Published: January 2008

The electrical bistability of the memory device based on ZnO nanoparticles embedded in a polyimide (PI) layer was investigated. Transmission electron microscopy and selected area electron diffraction pattern measurements showed that ZnO nanocrystals were formed inside the PI layer. Current-voltage measurements on Al∕C60∕ZnO nanoparticles embedded in PI layer/C60/indium tin oxide structures at 300K showed a current bistability with a large on/off ratio of 104. The current-voltage hysteresis characteristics at negative voltages could be modified by varying the applied positive erasing voltage. The memory device fabricated utilizing ZnO nanoparticles embedded in a PI layer exhibited excellent environmental stability at ambient conditions.
Characterization of doped silicon in low carrier density region by terahertz frequency Faraday effect
Authors: Ikebe Yohei , Shimano Ryo
Published: January 2008

We report on optical characterization of doped semiconductors by using terahertz Faraday rotation measurements in Cross-Nicole configuration. The detection sensitivity of Faraday rotation angle as small as 0.5mrad is obtained. The scheme is applied to an n-type silicon wafer of 525μm thickness in carrier freeze-out temperature region. The carrier density below N=1×1014cm−3 is evaluated under magnetic field B=1T.
Enhanced charge carrier generation in dye sensitized solar cells by nanoparticle plasmons
Authors: Hägglund Carl , Zäch Michael , Kasemo Bengt
Published: January 2008

An interesting possibility to improve the conversion and cost efficiencies of photovoltaic solar cells is to exploit the large optical cross sections of localized (nanoparticle) surface plasmon resonances (LSPRs). We have investigated this prospect for dye sensitized solar cells. Photoconductivity measurements were performed on flat TiO2 films, sensitized by a combination of dye molecules and arrays of nanofabricated elliptical gold disks. An enhanced dye charge carrier generation rate was found and shown to derive from the LSPR contribution by means of the polarization dependent resonance frequency in the anisotropic, aligned gold disks.
Optical waveguide cantilever actuated by light
Authors: Zinoviev Kirill , Dominguez Carlos , Plaza Jose Antonio , Lechuga Laura M.
Published: January 2008

We present experimental studies and theoretical analysis of a microcantilever working as an optical waveguide metallized from one side and actuated by light propagating inside it. Light absorbed in the metallic layer increases the temperature of the bimetallic structure and induces the cantilever bending. Dynamical properties of the cantilevers were studied using actuation by light modulated at frequencies of up to 800Hz. The deflection of the cantilever by 400nm was obtained while 0.25mW of light power was coupled inside it.
Reversible photoinduced change of refractive index in ion-conducting chalcohalide glass
Authors: Ren Jing , Wagner Tomas , Orava Jiri , Frumar Miloslav , Frumarova Bozena
Published: January 2008

When irradiated by the focused Ar+ ion laser of below band-gap photon energy (2.41 and 2.54eV), a large increase of refractive index (e.g., Δn=6% at 1550nm) was observed in 60GeS2–20Ga2S3–20AgI bulk glass (with bandgap of 2.71eV). We found it surprisingly that such a large Δn quickly smeared out after the illumination even at room temperature, i.e., the refractive index will return to almost initial value within only 2h. It is fairly rare among chalcogenides ever reported. The plausible correlation between the photorefraction effect and the ion-conducting property of glasses was also suggested.
Comparitive Magnetospheres
Authors: Lanzerotti Louis J. , Krimigis Stamatios M.
Published: January 2008

A major discovery to emerge from the era of spacecraft investigations of the solar system is the high degree to which planetary magnetic fields organize ionized matter. The spectacular images of planetary surfaces, atmospheres and satellites beamed to Earth by unmanned spacecraft have attracted much attention. However, the discovery of unexpected large-scale plasma formations within the magnetospheres of the planets is equally important because the behavior of these plasmas gives us insight into the way plasmas behave on cosmological scales.
The Physics Classroom Revisited: Have We Learned Our Lesson?
Authors: Pallrand George , Lindenfeld Peter
Published: January 2008

Science is regarded as a difficult subject by students, and most graduate from high school with only a very limited knowledge about it. The study of science in secondary schools can be compared to a pyramid with physics at the apex. It is nice to be on top. Unfortunately, though, there are not many there to keep each other company.
Werner Heisenberg and the Beginning of Nuclear Physics
Authors: Miller Arthur I.
Published: January 2008

Great advances in science alter our view of the world. Galileo Galilei's theory of motion, Albert Einstein's theory of special relativity and Werner Heisenberg's invention of quantum mechanics, with its subsequent interpretation by Niels Bohr and Heisenberg himself, spring immediately to mind (figure 1). In exploring these episodes we must recognize that historical narrative without investigation of conceptual transformation is just chronology.
Between Two and Three Dimensions
Authors: Dash J. G.
Published: January 2008

One of the most glamorous aspects of monolayer films is their thinness, and another is their two dimensionality. These properties are not the same, of course, although it might seem that each implies the other. We know some monolayers that are not two dimensional, and some much thicker films that are nearly so. Even more confusing is that a film can be two dimensional and three dimensional—and some-where in between—at the same time. A simple change of temperature can change a film's dimensionality.
Photoelectron Spectroscopy
Authors: Himpsel Franz J. , Smith Neville V.
Published: January 2008

The electronic structure of materials not only is fascinating from a theoretical point of view, but also has tremendous implications for technology. Electronic-structure studies, in fact, account for the majority of uses of uv radiation from synchrotron sources. Most of these studies involve photoelectron spectroscopy, a measurement technique that goes to the heart of many problems in atomic, molecular and condensed-matter physics. For example, photoelectron spectroscopy permits direct measurement of all quantum numbers of the electronic states in a material, and in particular determination of its band structure—that is, the relationship between energy and momentum of electrons in the material.
Asteroids and Comets
Authors: Gehrels Tom
Published: January 2008

Asteroids that orbit the Sun in a belt between the orbits of Mars and Jupiter are well known. A few other asteroids cross Earth's orbit, and, from time to time, one collides with our planet, as figure 1 so clearly indicates. What are they made of? How did they originate? We suspect that material much like the asteroids played a part in the origin of the solar system—can we see similar forces at work elsewhere?
Neutron Scattering with Spallation Sources
Authors: Lander Gerard H. , Price David L.
Published: January 2008

The other articles in this issue are concerned with the variety of science that goes on at reactor-based neutron sources. Such sources, based on nuclear fission, have been available since 1942. It has been known since the 1930s that neutrons could be produced through spallation by sending a charged beam of accelerated protons or electrons into a target. However, it has only been in the last few years that the intensity of these spallation sources has been sufficient for the range of sophisticated experiments required to study the properties of condensed matter. Today there are a number of operating spallation neutron sources, and more with higher intensity are planned (see the table). In this article we want to explain the difference between doing experiments at steady-state and at pulsed sources, illustrate what has been done with the modest sources now available, and speculate on some future experimental efforts. We do not have space to describe how a spallation source works: this information is presented in detail in earlier articles.
Homeostatic regulation of AMPA receptor expression at single hippocampal synapses
Authors: Hou Qingming , Zhang Dawei , Jarzylo Larissa , Huganir Richard L. , Man Heng-Ye
Published: January 2008

Homeostatic synaptic response is an important measure in confining neuronal activity within a narrow physiological range. Whether or not homeostatic plasticity demonstrates synapse specificity, a key feature characteristic of Hebbian-type plasticity, is largely unknown. Here, we report that in cultured hippocampal neurons, α-amino-3-hydroxy-5-methyl-isoxazole-4-propionic acid subtype glutamate receptor (AMPAR) accumulation is increased selectively in chronically inhibited single synapses, whereas the neighboring normal synapses remain unaffected. This synapse-specific homeostatic regulation depends on the disparity of synaptic activity and is mediated by GluR2-lacking AMPARs and PI3-kinase signaling. These results demonstrate the existence of synaptic specificity and the crucial role of AMPAR-gated calcium in homeostatic plasticity in central neurons.
Thai Speech and Language Test for children between 1 and 2 years of age
Authors: Prathanee Benjamas , Pongjanyakul Amornrat , Chano Jiraporn
Published: January 2008

Background: Children with delayed speech and language development are at considerable risk for later language impairment, social and behavioural problems, and illiteracy. Early diagnosis is needed for intervention planning and prevention. However, a speech and language test for Thai children has not been available.

Aims: To establish a Thai Speech and Language Test for Thai children between zero and 2 years of age.

Methods & Procedures: The authors reviewed both Thai and international speech and language development tests and studies related to factors associated with speech and language development. A Thai Speech and Language Test for children between zero and 2 years of age (TSLT2) was then formulated. The test was used with 419 typically developing Thai children in Khon Kaen, north‐east Thailand.

Outcome & Results: Language quotients were calculated to quantify/qualify Thai language development norms. Inter‐rater reliability of the test ranged between 0.64 and 1, while internal consistencies ranged between 0.83 and 0.95 for tests on children between 1 and 2 years of age.

Conclusions: Professionals or paraprofessionals can use the Thai Speech and Language Test for children between 1 and 2 years of age, which is the first Thai tool for the assessment, diagnosis and remediation planning of children with delayed speech and language development. It should be also adapted for use in other regions in Thailand. However, the test for children aged between 3 and 9 months should be revised and continue to be developed.
Concordance rates between parent and teacher clinical evaluation of language fundamentals observational rating scale
Authors: Massa Jacqueline , Gomes Hilary , Tartter Vivien , Wolfson Virginia , Halperin Jeffrey M.
Published: January 2008

Background: Research has shown that early identification of children with language issues is critical for effective intervention, and yet many children are not identified until school age. The use of parent‐completed rating scales, especially in urban, minority populations, might improve early identification if parent ratings are found to be reliable and valid.

Aims: To evaluate the reliability and validity of the Observational Rating Scale (ORS) in an urban setting where it may be difficult to distinguish language difficulties from cultural language differences.

Methods & Procedures: The present study examined the degree to which parent and teacher ORS scores for 73 7–10‐year‐old children (47 boys) had concordance for the four ORS dimensions of Listening, Speaking, Reading, and Writing, as well as for a composite ORS score. The relationship between the ORS ratings and the children's scores on the CELF‐3, or CELF‐4 Receptive and Expressive scores, and the WIAT Reading Composite scores were also examined.

Outcomes & Results: Parent and teacher concordance rates for the ORS were significant, but moderate for the Speaking, Reading, and Writing categories and for the overall ORS score. There were also significant relationships between the ORS scores and performance on standardized language and reading tests supporting the validity of the ORS.

Conclusions: The reliability and validity of the ORS have been replicated and extended to a diverse, urban population. Further, parent ratings were shown to provide as least as good information about language function as teacher ratings. Finally, it was suggested that an overall ORS score may provide a better indicator of overall language function than the domain scores.
Sentence production in students with dyslexia
Authors: Altmann Lori J. P. , Lombardino Linda J. , Puranik Cynthia
Published: January 2008

Background:While spoken language deficits have been identified in children with developmental dyslexia, microanalysis of sentence production proficiency in these children is a largely unexplored area.

Aims:The current study examines proficiency of syntactic production in children and young adults with dyslexia and typically developing age‐matched controls on a constrained sentence production task targeting two advanced argument structures, theme–experiencer verbs and irregular past participles.

Methods & Procedures:Participants aged between 8 and 22 years produced sentences that included three stimulus words, a proper name, an inanimate noun and a verb from one of three categories: control verbs (agent–patient verbs with regular morphology); theme–experiencer verbs, which require an inanimate subject in active sentences (e.g. The bookboredSarah); and irregular past participles, which require awareness of the syntactic requirements associated with the ‐enpast participle ending, i.e. that this verb form cannot be used as a simple past tense (e.g. *Mary ___ hidden the candy).

Outcomes & Results:Students with dyslexia produced more dysfluent, ungrammatical and incomplete responses than normal readers; however, the developmental trajectories of the verb types varied between groups. Normal readers performed similarly with both experimental verb types, but those with dyslexia were particularly impaired using irregular past participles in sentences.

Conclusions:The findings support a model of lexical representation in which development of grammar hinges on the acquisition of lexical knowledge. Furthermore, the data suggest that individuals with dyslexia may have difficulties with sentence formulation that persist into adulthood.
Serial Memory for Sound-Specified Locations: Effects of Spatial Uncertainty and Motor Suppression
Authors: Groeger J. A. , Banks A. P. , Simpson P. J.
Published: January 2008

According to Parmentier and Jones (2000), serial recall of locations that are specified by a sequence of sounds is prone to temporal error and is unaffected by motor suppression during retention. Experiments are reported here that show that with increased spatial uncertainty at recall (Experiment 1) and presentation (Experiment 2), spatial rather than temporal errors predominate. This is also the case when serial recall of sound-specified locations is subject to interference from a motor suppression task (Experiment 3). Contrary to Parmentier and Jones's (2000) original report, these results suggest that the memory representation for location is not necessarily amodal but is influenced by the representational requirements of the task being performed. This is consistent with recent findings that provide evidence for a distinct spatial working memory.
Short Article: Semantic Anomalies at the Borderline of Consciousness: An Eye-Tracking Investigation
Authors: Bohan Jason , Sanford Anthony
Published: January 2008

We report an eye-tracking study in which participants read passages containing difficult-to-detect semantic anomalies. Would there be any evidence of the registration of the anomaly within the comprehension system (reflected in eye tracking) when anomalies were not noticed? Using early and late processing measures, there was no evidence for registration independent of conscious detection. Comparisons were made between detected and undetected anomalies and between these and nonanomalous controls. There was evidence of disruption to the tracking measures only when a conscious report was also made. These data fit the view that shallow semantic processing underlies the failure to detect anomalies. Implications for language processing are discussed.
Can Colour be Reduced to Anything?
Authors: Dedrick Don
Published: January 2008

C. L. Hardin has argued that the colour opponency of the vision system leads to chromatic subjectivism: chromatic sensory states reduce to neurophysiological states. Much of the force of Hardin's argument derives from a critique of chromatic objectivism. On this view chromatic sensory states are held to reduce to an external property. While I agree with Hardin's critique of objectivism it is far from clear that the problems which beset objectivism do not apply to the subjectivist position as well. I develop a critique of subjectivism that parallels Hardin's antiobjectivist argument.
Theories in Children and the Rest of Us
Authors: Schwitzgebel Eric
Published: January 2008

I offer an account of theories useful in addressing the question of whether children are young theoreticians whose development can be regarded as the product of theory change. I argue that to regard a set of propositions as a theory is to be committed to evaluating that set in terms of its explanatory power. If theory change is the substance of cognitive development, we should see patterns of affect and arousal consonant with the emergence and resolution of explanation-seeking curiosity. Affect has largely been ignored as a potential source of support or disconfirmation for the “theory theory” of development.
On the Use of Visualizations in the Practice of Science
Authors: Sargent Pauline
Published: January 2008

Visualizations used in the practice of neuroscience, as one example of a scientific practice, can be sorted according to whether they represent (A) actual things, (B) theoretical models, or (C) some integration of these two. In this paper I hypothesize that an assessment of a chain of visual representations from (A) through (C) to (B) (and back again) is used, as part of the practice of scientific judgment, to assess the adequacy of the “working fit” between the theoretical model and the actual thing or process that the model is intended to explain.
Tensor Products and Split-Level Architecture: Foundational Issues in The Classicism-Connectionism Debate
Authors: Guarini Marcello
Published: January 2008

This paper responds to criticisms levelled by Fodor, Pylyshyn, and McLaughlin against connectionism. Specifically, I will rebut the charge that connectionists cannot account for representational systematicity without implementing a classical architecture. This will be accomplished by drawing on Paul Smolensky's Tensor Product model of representation and on his insights about split-level architectures.
Message from the Editor
Authors: Thomas Paul
Published: January 2008

To begin, I would like to wish our readers, authors, referees and Board of Editors a successful and happy 2008 and thank them for their contributions to Nuclear Fusion in 2007.

I took over the editorship of Nuclear Fusion in January, and the year has been one in which the community as a whole has been busier than ever with a variety of duties associated with the ITER project.

It was with pride that we published the Progress in the ITER Physics Basis in the June issue of the journal (stacks.iop.org/NF/47/i=6). The task undertaken by the coordinators, authors and referees was a daunting one but one which led to an outstandingly successful issue. The response from readers has been phenomenal and there were in the region of 10 000 downloads of papers in the first month following publication.

Looking to 2008 and beyond, the journal will endeavour to continue to support the work of the fusion community.

Refereeing

As we have done since January 2005, we would like to thank our top ten most loyal referees who have helped the journal with its double-referee peer-review procedure in the past year. At the Nuclear Fusion Editorial Office we are fully aware of the load we put on the shoulders of our referees. At the end of 2004 the Editorial Board decided that a gesture of gratitude should be made to our most loyal referees. We offer them a personal subscription to Nuclear Fusion with electronic access for one year, free of charge.

To select the top referees we have adopted the criterion that a researcher should have acted as a referee or adjudicator for at least three different manuscripts during the period from summer 2006 to the end of 2007. We have excluded our Board members and those referees who were already listed in the top ten in the last two years.

According to our records the following people met this criterion. Congratulations and many, many thanks!

H.L. Berk (Texas University, USA)

J.S. DeGrassie (GAT, USA)

C. Deutsch (Paris University, France)

N. Hayashi (JAEA, Japan)

P. Ghendrih (CEA, France)

E. Gusakov (Ioffe Institute, Russia)

T.C. Luce (GAT, USA)

N. Oyama (JAEA, Japan)

J.J. Ramos (MIT, USA)

H. Takenaga (JAEA, Japan)

In addition there is a group of several hundred referees who have helped us in the past year to maintain the high scientific standard of Nuclear Fusion. At the end of this issue we give the full list of all referees for 2007. Our thanks to them!

Peer-review process

We are pleased to report that further progress has been made in speeding up our publishing process, without any compromise of quality. Those authors who regularly submit work based on contributions to the Fusion Energy Conference (FEC) will, perhaps, have noticed the reduction in times compared to earlier years.

We believe that Nuclear Fusion maintains its position in the field because of the perceived high quality of the submissions, the refereeing and the editorial processes. This position of strength will be built upon as we endeavour to further improve the service to the journal's authors and readers.
Beta limit due to m/n = 2/1 tearing mode onset in the DIII-D hybrid scenario
Authors: La Haye R.J. , Politzer P.A. , Brennan D.P.
Published: January 2008

The performance (βN≈ 3,q95≈ 4.4,fBS≈ 0.5,H89> 2) of hybrid scenario plasmas in DIII-D (Luxon2002Nucl. Fusion42614) is limited bym/n= 2/1 tearing modes. Unlike conventional plasmas (Henderet al2004Nucl. Fusion44798), the linear dependence scaling of the global beta for onset of the instability with normalized local ion gyroradiusis modified as then= 1 ideal kink beta limit is approached, suggesting that small island neoclassical tearing mode (NTM) threshold physics does not impose the dominant criterion for NTM stability. The hybrid scenario tends to go unstable just at or below the no walln= 1 ideal kink beta limit of about 4ℓi. Experimentally 4ℓidecreases with beta as. Thus the ‘ceiling’ in beta due to coupling of tearing to the ideal kink comes down as beta is increased. Scaling of the tearing unstable beta that combines both NTM threshold physics and a pole in Δ′rdue to coupling to the ideal kink is presented.
Summary of the 8th IAEA Technical Meeting on Fusion Power Plant Safety
Authors: Girard J.Ph. , Gulden W. , Kolbasov B. , Louzeiro-Malaquias A.-J. , Petti D. , Rodriguez-Rodrigo L.
Published: January 2008

Reports were presented covering a selection of topics on the safety of fusion power plants. These included a review on licensing studies developed for ITER site preparation surveying common and non-common issues (i.e. site dependent) as lessons to a broader approach for fusion power plant safety. Several fusion power plant models, spanning from accessible technology to more advanced-materials based concepts, were discussed. On the topic related to fusion-specific technology, safety studies were reported on different concepts of breeding blanket modules, tritium handling and auxiliary systems under normal and accident scenarios' operation. The testing of power plant relevant technology in ITER was also assessed in terms of normal operation and accident scenarios, and occupational doses and radioactive releases under these testings have been determined. Other specific safety issues for fusion have also been discussed such as availability and reliability of fusion power plants, dust and tritium inventories and component failure databases. This study reveals that the environmental impact of fusion power plants can be minimized through a proper selection of low activation materials and using recycling technology helping to reduce waste volume and potentially open the route for its reutilization for the nuclear sector or even its clearance into the commercial circuit. Computational codes for fusion safety have been presented in support of the many studies reported. The on-going work on establishing validation approaches aiming at improving the prediction capability of fusion codes has been supported by experimental results and new directions for development have been identified. Fusion standards are not available and fission experience is mostly used as the framework basis for licensing and target design for safe operation and occupational and environmental constraints. It has been argued that fusion can benefit if a specific fusion approach is implemented, in particular for materials selection which will have a large impact on waste disposal and recycling and in the real limits of radiation releases if indexed to the real impact on individuals and the environment given the differences in the types of radiation emitted by tritium when compared with the fission products. Round table sessions resulted in some common recommendations. The discussions also created the awareness of the need for a larger involvement of the IAEA in support of fusion safety standards development.
A note on difficult structure alignment problems
Authors: Sippl Manfred J. , Wiederstein Markus
Published: January 2008

Summary: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples.

Availability: TopMatch is available as a public web service at http://services.came.sbg.ac.at

Contact:  sippl@came.sbg.ac.at
NetworkBLAST: comparative analysis of protein networks
Authors: Kalaev Maxim , Smoot Mike , Ideker Trey , Sharan Roded
Published: January 2008

Summary: The identification of protein complexes is a fundamental challenge in interpreting protein–protein interaction data. Cross-species analysis allows coping with the high levels of noise that are typical to these data. The NetworkBLAST web-server provides a platform for identifying protein complexes in protein-protein interaction networks. It can analyze a single network or two networks from different species. In the latter case, NetworkBLAST outputs a set of putative complexes that are evolutionarily conserved across the two networks.

Availability: NetworkBLAST is available as web-server at: www.cs.tau.ac.il/~roded/networkblast.htm

Contact:  kalaevma@post.tau.ac.il; roded@post.tau.ac.il
Decomp—from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Authors: Böcker Sebastian , Lipták Zsuzsanna , Martin Marcel , Pervukhin Anton , Sudek Henner
Published: January 2008

Summary: We introduce Decomp, a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises frequently in biochemistry and mass spectrometry (MS), when we know the molecular mass of a protein, DNA or metabolite fragment but have no other information. A closely related problem is known as the Money Changing Problem (MCP), where all masses are positive integers. Recently, efficient algorithms have been developed for the MCP, in which Decomp applies to real-valued MS data. The excellent performance of this method on proteomic and metabolomic MS data has recently been demonstrated. Decomp has an easy-to-use graphical interface, which caters for both types of users: those interested in solving MCP instances and those submitting MS data.

Availability: Decomp is freely accessible at http://bibiserv.techfak.uni-bielefeld.de/decomp/

Contact:  anton.pervukhin@minet.uni-jena.de
ATP sensitivity of preBötzinger complex neurones in neonatal ratin vitro: mechanism underlying a P2 receptor‐mediated increase in inspiratory frequency
Authors: Lorier A. R. , Lipski J. , Housley G. D. , Greer J. J. , Funk G. D.
Published: January 2008

P2 receptor (R) signalling plays an important role in the central ventilatory response to hypoxia. The frequency increase that results from activation of P2Y1Rs in the preBötzinger complex (preBötC; putative site of inspiratory rhythm generation) may contribute, but neither the cellular nor ionic mechanism(s) underlying these effects are known. We applied whole‐cell recording to rhythmically‐active medullary slices from neonatal rat to define, in preBötC neurones, the candidate cellular and ionic mechanisms through which ATP influences rhythm, and tested the hypothesis that putative rhythmogenic preBötC neurones are uniquely sensitive to ATP. ATP (1 mm) evoked inward currents in all non‐respiratory neurones and the majority of respiratory neurons, which included inspiratory, expiratory and putative rhythmogenic inspiratory neurones identified by sensitivity to substance P (1 μm) and DAMGO (50 μm) or by voltage‐dependent pacemaker‐like activity. ATP current densities were similar in all classes of preBötC respiratory neurone. Reversal potentials and input resistance changes for ATP currents in respiratory neurones suggested they resulted from either inhibition of a K+channel or activation of a mixed cationic conductance. The P2YR agonist 2MeSADP (1 mm) evoked only the latter type of current in inspiratory and pacemaker‐like neurones. In summary, putative rhythmogenic preBötC neurones were sensitive to ATP. However, this sensitivity was not unique; ATP evoked similar currents in all types of preBötC respiratory neurone. The P2Y1R‐mediated frequency increase is therefore more likely to reflect activation of a mixed cationic conductance in multiple types of preBötC neurone than excitation of one, highly sensitive group.
Effect of dexamethasone on skeletal muscle Na+,K+ pump subunit specific expression and K+ homeostasis during exercise in humans
Authors: Nordsborg Nikolai , Ovesen Jakob , Thomassen Martin , Zangenberg Mathias , Jøns Christian , Iaia F. Marcello , Nielsen Jens Jung , Bangsbo Jens
Published: January 2008

The effect of dexamethasone on Na+,K+ pump subunit expression and muscle exchange of K+ during exercise in humans was investigated. Nine healthy male subjects completed a randomized double blind placebo controlled protocol, with ingestion of dexamethasone (Dex: 2 × 2 mg per day) or placebo (Pla) for 5 days. Na+,K+ pump catalytic α1 and α2 subunit expression was ∼17% higher (P < 0.05) and the structural β1 and β2 subunit expression was ∼6–8% higher (P < 0.05) after Dex compared with Pla. During one‐legged knee‐extension for 10 min at low intensity (LI; 18.6 ± 1.0 W), two moderate intensity (51.7 ± 2.4 W) exercise bouts (MI1: 5 min; 2 min recovery; MI2: exhaustive) and two high‐intensity (71.7 ± 2.5 W) exercise bouts (HI1: 1 min 40 s; 2 min recovery; HI2: exhaustive), femoral venous K+ was lower (P < 0.05) in Dex compared with Pla. Thigh K+ release was lower (P < 0.05) in Dex compared with Pla in LI and MI, but not in HI. Time to exhaustion in MI2 tended to improve (393 ± 50 s versus 294 ± 41 s; P= 0.07) in Dex compared with Pla, whereas no difference was detected in HI2 (106 ± 10 s versus 108 ± 9 s). The results indicate that an increased Na+,K+ pump expression per se is of importance for thigh K+ reuptake at the onset of low and moderate intensity exercise, but less important during high intensity exercise.
Kv7.1 (KCNQ1) properties and channelopathies
Authors: Peroz David , Rodriguez Nicolas , Choveau Frank , Baró Isabelle , Mérot Jean , Loussouarn Gildas
Published: January 2008

KCNQ1 is the pore‐forming subunit of a channel complex whose expression and function have been rather well characterized in the heart. Almost 300 mutations of KCNQ1 have been identified in patients and a vast majority of the described mutations are linked to the long QT syndrome. Only a few mutations are linked to other pathologies such as atrial fibrillation and the short QT syndrome. However, a considerable amount of work remains to be done to get a clear picture of the molecular mechanisms responsible for the pathogenesis related to each mutation. The present review gives three examples of recent studies towards this goal and illustrates the diversity of the molecular mechanisms involved.
Kv7 channels: interaction with dopaminergic and serotonergic neurotransmission in the CNS
Authors: Hansen Henrik H. , Waroux Olivier , Seutin Vincent , Jentsch Thomas J. , Aznar Susana , Mikkelsen Jens D.
Published: January 2008

Neuronal Kv7 channels (also termed KCNQ channels) are the molecular correlate of the M‐current. The Kv7 channels activate at rather negative membrane potentials (≤ 60 mV), thereby ‘fine‐tuning’ the resting membrane potential. The Kv7 channels are widely expressed in the brain with the Kv7.2, Kv7.3 and Kv7.5 channels being the most abundant. The Kv7.4 subunit has the most restricted brain regional expression being present in discrete nuclei of brainstem only. Kv7 channels are expressed at different subcellular locations, being on both somatodendritic, axonal and terminal sites. This complex subcellular distribution of Kv7 channels enables them to participate in both pre‐ and postsynaptic modulation of basal and stimulated excitatory neurotransmission. Activation of neuronal Kv7 channels limits repetitive firing thereby potentially limiting the generation of long bursts, with subsequent inhibition of monoaminergic neurotransmitter release. In this review, we focus on the influence of Kv7 channels on dopaminergic and serotonergic neurotransmission. The data suggest a novel action of Kv7 channel openers which could translate into having therapeutic value in the treatment of disease states characterized by overactivity of dopaminergic (e.g. schizophrenia and drug abuse) and serotonergic neurotransmission (e.g. anxiety).
Priming and sentence context support listening to noise-vocoded speech by younger and older adults
Authors: Sheldon Signy , Pichora-Fuller M. Kathleen , Schneider Bruce A.
Published: January 2008

Older adults are known to benefit from supportive context in order to compensate for age-related reductions in perceptual and cognitive processing, including when comprehending spoken language in adverse listening conditions. In the present study, we examine how younger and older adults benefit from two types of contextual support, predictability from sentence context and priming, when identifying target words in noise-vocoded sentences. In the first part of the experiment, benefit from context based on primarily semantic knowledge was evaluated by comparing the accuracy of identification of sentence-final target words that were either highly predictable or not predictable from the sentence context. In the second part of the experiment, benefit from priming was evaluated by comparing the accuracy of identification of target words when noise-vocoded sentences were either primed or not by the presentation of the sentence context without noise vocoding and with the target word replaced with white noise. Younger and older adults benefited from each type of supportive context, with the most benefit realized when both types were combined. Supportive context reduced the number of noise-vocoded bands needed for 50% word identification more for older adults than their younger counterparts.
Comment on “A geometric representation of spectral and temporal vowel features: Quantification of vowel overlap in three linguistic varieties” [J. Acoust. Soc. Am. 119, 2334–2350 (2006)]
Authors: Morrison Geoffrey Stewart
Published: January 2008

In a recent paper by Wassink [J. Acoust Soc. Am. 119, 2334–2350 (2006)] the spectral overlap assessment metric (SOAM) was proposed for quantifying the degree of acoustic overlap between vowels. The SOAM does not fully take account of probability densities. An alternative metric is proposed which is based on quadratic discriminant analysis and takes account of probability densities in the form of a posteriori probabilities. Unlike the SOAM, the a posteriori probability-based metric allows for a direct comparison of vowel overlaps calculated using different numbers of dimensions, e.g., three dimensions (Fl, F2, and duration) versus two dimensions (Fl and F2).
Reconciling the origin of the transient evoked ototacoustic emission in humans
Authors: Withnell Robert H. , Hazlewood Chantel , Knowlton Amber
Published: January 2008

A pervasive theme in the literature for the transient evoked otoacoustic emission (TEOAE) measured from the human ear canal has been one of the emission arising solely (or largely) from a single, place-fixed mechanism. Here TEOAEs are reported measured in the absence of significant stimulus contamination at stimulus onset, providing for the identification of a TEOAE response beginning within the time window that is typically removed by windowing. Contrary to previous studies, it was found that in humans, as has previously been found in guinea pig, the TEOAE appears to arise from two generation mechanisms, the relative contributions of these two mechanisms being time and stimulus-level dependent. The method of windowing the earliest part of the ear canal measurement to remove stimulus artifact removes part of the TEOAE i.e., much of the component arising from a nonlinear generation mechanism. This reconciliation of TEOAE origin is consistent with all OAEs in mammals arising in a stimulus-level dependent manner from two mechanisms of generation, one linear, one nonlinear, as suggested by Shera and Guinan [J. Acoust. Soc. Am. 105, 782–798 (1999)].
Influences of auditory object formation on phonemic restoration
Authors: Shinn-Cunningham Barbara G. , Wang Dali
Published: January 2008

In phonemic restoration, intelligibility of interrupted speech is enhanced when noise fills the speech gaps. When the broadband envelope of missing speech amplitude modulates the intervening noise, intelligibility is even better. However, this phenomenon represents a perceptual failure: The amplitude modulation, a noise feature, is misattributed to the speech. Experiments explored whether object formation influences how information in the speech gaps is perceptually allocated. Experiment 1 replicates the finding that intelligibility is enhanced when speech-modulated noise rather than unmodulated noise is presented in the gaps. In Experiment 2, interrupted speech was presented diotically, but intervening noises were presented either diotically or with an interaural time difference leading in the right ear, causing the noises to be perceived to the side of the listener. When speech-modulated noise and speech are perceived from different directions, intelligibility is no longer enhanced by the modulation. However, perceived location has no effect for unmodulated noise, which contains no speech-derived information. Results suggest that enhancing object formation reduces misallocation of acoustic features across objects, and demonstrate that our ability to understand noisy speech depends on a cascade of interacting processes, including glimpsing sensory inputs, grouping sensory inputs into objects, and resolving ambiguity through top-down knowledge.
A ray model for hard parallel noise barriers in high-rise cities
Authors: Li Kai Ming , Kwok Man Pun , Law Ming Kan
Published: January 2008

A ray model is developed and validated for prediction of the insertion loss of hard parallel noise barriers placed in an urban environment either in front of a row of tall buildings or in a street canyon. The model is based on the theory of geometrical acoustics for sound diffraction at the edge of a barrier and multiple reflections by the ground, barrier and façade surfaces. It is crucial to include the diffraction and multiple reflection effects in the ray model as they play important roles in determining the overall sound pressure levels for receivers located between the façade and the near-side barrier. Comparisons of the ray model with a wave-based boundary element formulation show reasonably good agreement over a broad frequency range. Results of scale model experimental studies are also presented. It is demonstrated that the ray model agrees tolerably well with the scale model experimental data.
Spectral structure across the syllable specifies final-stop voicing for adults and children alike
Authors: Nittrouer Susan , Lowenstein Joanna H.
Published: January 2008

Traditional accounts of speech perception generally hold that listeners use isolable acoustic “cues” to label phonemes. For syllable-final stops, duration of the preceding vocalic portion and formant transitions at syllable’s end have been considered the primary cues to voicing decisions. The current experiment tried to extend traditional accounts by asking two questions concerning voicing decisions by adults and children: (1) What weight is given to vocalic duration versus spectral structure, both at syllable’s end and across the syllable? (2) Does the naturalness of stimuli affect labeling? Adults and children (4, 6, and 8 years old) labeled synthetic stimuli that varied in vocalic duration and spectral structure, either at syllable’s end or earlier in the syllable. Results showed that all listeners weighted dynamic spectral structure, both at syllable’s end and earlier in the syllable, more than vocalic duration, and listeners performed with these synthetic stimuli as listeners had performed previously with natural stimuli. The conclusion for accounts of human speech perception is that rather than simply gathering acoustic cues and summing them to derive strings of phonemic segments, listeners are able to attend to global spectral structure, and use it to help recover explicitly phonetic structure.
Absorption of reliable spectral characteristics in auditory perception
Authors: Kiefte Michael , Kluender Keith R.
Published: January 2008

Several experiments are described in which synthetic monophthongs from series varying between /i/ and /u/ are presented following filtered precursors. In addition to F2, target stimuli vary in spectral tilt by applying a filter that either raises or lowers the amplitudes of higher formants. Previous studies have shown that both of these spectral properties contribute to identification of these stimuli in isolation. However, in the present experiments we show that when a precursor sentence is processed by the same filter used to adjust spectral tilt in the target stimulus, listeners identify synthetic vowels on the basis of F2 alone. Conversely, when the precursor sentence is processed by a single-pole filter with center frequency and bandwidth identical to that of the F2 peak of the following vowel, listeners identify synthetic vowels on the basis of spectral tilt alone. These results show that listeners ignore spectral details that are unchanged in the acoustic context. Instead of identifying vowels on the basis of incorrect acoustic information, however (e.g., all vowels are heard as /i/ when second formant is perceptually ignored), listeners discriminate the vowel stimuli on the basis of the more informative spectral property.