bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing phonological skills and spelling abilities in children with reading and language impairments
Authors: Larkin Rebecca F. , Snowling Margaret J.
Published: January 2008

Background: Bishop and Snowling (2004) proposed that children with language impairments (LI) and children with reading difficulties (RD) can be considered to be on a (phonological) continuum of risk for reading impairments.

Aims: The first aim of the present study was to address two specific hypotheses about the relationship between RD and LI. The severity hypothesis proposes that LI is a more severe form of RD. In contrast, the dyslexia‐plus hypothesis proposes that children with LI share the same phonological deficit as children with RD, but also have impairments in non‐phonological language skills. The second aim of the study was to further our understanding of the spelling skills of children with LI.

Methods & Procedures: Twenty‐three children with primary language impairments (LI) and 22 children with primary reading impairments (RD) matched on chronological and reading age were compared with typically developing children. The children's performance on tests of phoneme deletion, phonological memory, and spelling accuracy and phonetic spelling was compared.

Outcomes & Results: Children with LI showed poorer phonological memory performance than children with RD and age controls, whereas both clinical groups performed significantly worse than the age controls on the phoneme deletion task and comparably to reading‐age controls. Children with LI and RD were impaired for their age at phonetic spelling, the children with LI showing the more severe impairment. Further exploration of the data identified two different profiles among children with LI; some of these children had poorer phonological skills than predicted from receptive vocabulary, supporting the severity hypothesis. The other group showed a profile with concurrent impairments in vocabulary and phonological skills, in line with the dyslexia‐plus hypothesis.

Conclusions: The findings suggest that a subgroup of children with LI may be experiencing a severe form of dyslexia. The results further suggest that children with LI have difficulty producing phonologically plausible spellings.
Concreteness Effects in Different Tasks: Implications for Models of Short-Term Memory
Authors: Romani Cristina , Mcalpine Sheila , Martin Randi C.
Published: January 2008

This study investigates concreteness effects in tasks requiring short-term retention. Concreteness effects were assessed in serial recall, matching span, order reconstruction, and free recall. Each task was carried out both in a control condition and under articulatory suppression. Our results show no dissociation between tasks that do and do not require spoken output. This argues against the redintegration hypothesis according to which lexical-semantic effects in short-term memory arise only at the point of production. In contrast, concreteness effects were modulated by task demands that stressed retention of item versus order information. Concreteness effects were stronger in free recall than in serial recall. Suppression, which weakens phonological representations, enhanced the concreteness effect with item scoring. In a matching task, positive effects of concreteness occurred with open sets but not with closed sets of words. Finally, concreteness effects reversed when the task asked only for recall of word positions (as in the matching task), when phonological representations were weak (because of suppression), and when lexical semantic representations overactivated (because of closed sets). We interpret these results as consistent with a model where phonological representations are crucial for the retention of order, while lexical-semantic representations support maintenance of item identity in both input and output buffers.
Action Planning in Sequential Skills: Relations to Music Performance
Authors: Keller Peter E. , Koch Iring
Published: January 2008

The hypothesis that planning music-like sequential actions involves anticipating their auditory effects was investigated in a series of experiments. Participants with varying levels of musical experience responded to each of four colour-patch stimuli by producing a unique sequence of three taps on three vertically aligned keys. Each tap triggered a tone in most experimental conditions. Response–effect (key-to-tone) mapping was either compatible—taps on the top, middle, and bottom keys triggered high, medium, and low pitched tones, respectively—or incompatible—key-to-tone mapping was scrambled, reversed, or neutral (taps on different keys triggered the same tone). The results suggest that action planning was faster with compatible than with incompatible mappings (and faster than with no tones). Furthermore, the size of this compatibility effect grew with increasing musical experience, which suggests that improvements in auditory imagery ability that typically accompany musical training may augment the role of anticipatory auditory-effect representations during planning.
Short Article: Backward Blocking: The Role of Within-Compound Associations and Interference between Cues Trained Apart
Authors: Vadillo Miguel A. , Castro Leyre , Matute Helena , Wasserman Edward A.
Published: January 2008

Most theoretical accounts of backward blocking place heavy stress on the necessity of the target cue having been trained in compound with the competing cue to produce a decrement in responding. Yet, other evidence suggests that a similar reduction in responding to the target cue can be observed when the outcome is later paired with a novel cue never trained in compound with the target cue (interference between cues trained apart). The present experiment shows that pairing another nonassociated cue with the same outcome may be sufficient to produce a decremental effect on the target cue, but the presence of a within-compound association between the target and the competing cue adds to this effect. Thus, both interference between cues trained apart and within-compound associations independently contribute to backward blocking.
Short Article: Why do the Effects of Delaying Reinforcement in Animals and Delaying Feedback in Humans Differ? A Working-Memory Analysis
Authors: Lieberman David A. , Vogel A. Carina M. , Nisbet Jaime
Published: January 2008

Animal research has shown that reinforcement is substantially less effective when it is delayed, but in studies of human motor learning delays in providing feedback typically have much less effect. One possible explanation is that in human research participants know the response to be learned and can thus focus on it during the delay; that is not the case in experiments on animals. We tested this hypothesis using a task in which participants had minimal information on what movement was correct and found that, as in animal experiments, participants learned only when feedback was immediate. A second experiment confirmed that the effects of the delay depended on how many responses had to be held in working memory: the greater the memory load, the poorer the learning. The results point to the importance of activity during a delay on learning; implications for the teaching of motor skills are discussed.
Short Article: Sequence Learning at Optimal Stimulus–Response Mapping: Evidence from a Serial Reaction Time Task
Authors: Kinder Annette , Rolfs Martin , Kliegl Reinhold
Published: January 2008

We propose a new version of the serial reaction time (SRT) task in which participants merely looked at the target instead of responding manually. As response locations were identical to target locations, stimulus–response compatibility was maximal in this task. We demonstrated that saccadic response times decreased during training and increased again when a new sequence was presented. It is unlikely that this effect was caused by stimulus–response (S–R) learning because bonds between (visual) stimuli and (oculomotor) responses were already well established before the experiment started. Thus, the finding shows that the building of S–R bonds is not essential for learning in the SRT task.
Short Article: Asymmetrical Learning between a Tactile and Visual Serial RT Task
Authors: Abrahamse Elger L. , Van Der Lubbe Rob H. J. , Verwey Willem B.
Published: January 2008

According to many researchers, implicit learning in the serial reaction-time task is predominantly motor based and therefore should be independent of stimulus modality. Previous research on the task, however, has focused almost completely on the visual domain. Here we investigated sequence learning when the imperative stimuli were presented tactilely to the fingers. Learning in this task was compared to sequence learning in a typical visual task, using very similar experimental conditions. The results indicate that sequential learning occurs in the tactile task, though to a lesser degree than in its visual counterpart. Furthermore, there was similar cross-modal transfer in both directions, meaning that transfer from the visual to the tactile task was partial. It is proposed that sequence learning involves a stimulus-specific component in the visual but not in the tactile task.
Short Article: Acquired Flavour Preferences: Contextual Control of Adaptation-Level Effects
Authors: Albertella Lucy , Harris Justin A. , Boakes Robert A.
Published: January 2008

This experiment investigated the role of context in the expression of conditioned flavour preferences. Rats were trained on a mixture of almond and sucrose and were then given intermixed exposures to almond in one context (Context A) and to sucrose in a second context (Context S). Finally, choice tests were given in both contexts, with one group given almond-versus-water tests and the other almond + sucrose-versus-sucrose tests. Preference for almond over water was greater in Context A than in Context S. Conversely, preference for almond + sucrose over sucrose was greater in Context S than in Context A. These results suggest that the perceived sweetness of a flavour depends on the context in which it is presented and confirm that expression of a flavour preference depends on the type of test employed.
Borrelia burgdorferi basic membrane proteins A and B participate in the genesis of Lyme arthritis
Authors: Pal Utpal , Wang Penghua , Bao Fukai , Yang Xiuli , Samanta Swapna , Schoen Robert , Wormser Gary P. , Schwartz Ira , Fikrig Erol
Published: January 2008

Lyme arthritis results from colonization of joints by Borrelia burgdorferi and the ensuing host response. Using gene array–based differential analysis of B. burgdorferi gene expression and quantitative reverse trancription-polymerase chain reaction, we identified two paralogous spirochete genes, bmpA and bmpB, that are preferentially up-regulated in mouse joints compared with other organs. Transfer of affinity-purified antibodies against either BmpA or BmpB into B. burgdorferi–infected mice selectively reduced spirochete numbers and inflammation in the joints. B. burgdorferi lacking bmpA/B were therefore generated to further explore the role of these proteins in the pathogenesis of Lyme disease. B. burgdorferi lacking bmpA/B were infectious in mice, but unable to persist in the joints, and they failed to induce severe arthritis. Complementation of the mutant spirochetes with a wild-type copy of the bmpA and bmpB genes partially restored the original phenotype. These data delineate a role for differentially produced B. burgdorferi antigens in spirochete colonization of mouse joints, and suggest new strategies for the treatment of Lyme arthritis.
Discovery of a novel class of highly conserved vaccine antigens using genomic scale antigenic fingerprinting of pneumococcus with human antibodies
Authors: Giefing Carmen , Meinke Andreas L. , Hanner Markus , Henics Tamás , Minh Duc Bui , Gelbmann Dieter , Lundberg Urban , Senn Beatrice M. , Schunn Michael , Habel Andre , Henriques-Normark Birgitta , Örtqvist Åke , Kalin Mats , von Gabain Alexander , Nagy Eszter
Published: January 2008

Pneumococcus is one of the most important human pathogens that causes life-threatening invasive diseases, especially at the extremities of age. Capsular polysaccharides (CPSs) are known to induce protective antibodies; however, it is not feasible to develop CPS-based vaccines that cover all of the 90 disease-causing serotypes. We applied a genomic approach and described the antibody repertoire for pneumococcal proteins using display libraries expressing 15–150 amino acid fragments of the pathogen's proteome. Serum antibodies of exposed, but not infected, individuals and convalescing patients identified the ANTIGENome of pneumococcus consisting of ∼140 antigens, many of them surface exposed. Based on several in vitro assays, 18 novel candidates were preselected for animal studies, and 4 of them showed significant protection against lethal sepsis. Two lead vaccine candidates, protein required for cell wall separation of group B streptococcus (PcsB) and serine/threonine protein kinase (StkP), were found to be exceptionally conserved among clinical isolates (>99.5% identity) and cross-protective against four different serotypes in lethal sepsis and pneumonia models, and have important nonredundant functions in bacterial multiplication based on gene deletion studies. We describe for the first time opsonophagocytic killing activity for pneumococcal protein antigens. A vaccine containing PcsB and StkP is intended for the prevention of infections caused by all serotypes of pneumococcus in the elderly and in children.
Secretory IgA mediates retrotranscytosis of intact gliadin peptides via the transferrin receptor in celiac disease
Authors: Matysiak-Budnik Tamara , Moura Ivan Cruz , Arcos-Fajardo Michelle , Lebreton Corinne , Ménard Sandrine , Candalh Céline , Ben-Khalifa Karima , Dugave Christophe , Tamouza Houda , van Niel Guillaume , Bouhnik Yoram , Lamarque Dominique , Chaussade Stanislas , Malamut Georgia , Cellier Christophe , Cerf-Bensussan Nadine , Monteiro Renato C. , Heyman Martine
Published: January 2008

Celiac disease (CD) is an enteropathy resulting from an abnormal immune response to gluten-derived peptides in genetically susceptible individuals. This immune response is initiated by intestinal transport of intact peptide 31-49 (p31-49) and 33-mer gliadin peptides through an unknown mechanism. We show that the transferrin receptor CD71 is responsible for apical to basal retrotranscytosis of gliadin peptides, a process during which p31-49 and 33-mer peptides are protected from degradation. In patients with active CD, CD71 is overexpressed in the intestinal epithelium and colocalizes with immunoglobulin (Ig) A. Intestinal transport of intact p31-49 and 33-mer peptides was blocked by polymeric and secretory IgA (SIgA) and by soluble CD71 receptors, pointing to a role of SIgA–gliadin complexes in this abnormal intestinal transport. This retrotranscytosis of SIgA–gliadin complexes may promote the entry of harmful gliadin peptides into the intestinal mucosa, thereby triggering an immune response and perpetuating intestinal inflammation. Our findings strongly implicate CD71 in the pathogenesis of CD.
Strange Couplings and Space-Time Structure
Authors: Weinstein Steven
Published: January 2008

General relativity is commonly thought to imply the existence of a unique metric structure for space-time. A simple example is presented of a general relativistic theory with ambiguous metric structure. Brans-Dicke theory is then presented as a further example of a space-time theory in which the metric structure is ambiguous. Other examples of theories with ambiguous metrical structure are mentioned. Finally, it is suggested that several new and interesting philosophical questions arise from the sorts of theories discussed.
Why General Relativity Does Need an Interpretation
Authors: Belot Gordon
Published: January 2008

There is a widespread impression that General Relativity, unlike Quantum Mechanics, is in no need of an interpretation. I present two reasons for thinking that this is a mistake. The first is the familiar hole argument. I argue that certain skeptical responses to this argument are too hasty in dismissing it as being irrelevant to the interpretative enterprise. My second reason is that interpretative questions about General Relativity are central to the search for a quantum theory of gravity. I illustrate this claim by examining the interpretative consequences of a particular technical move in canonical quantum gravity.
The Empirical Character of Methodological Rules
Authors: Schmaus Warren
Published: January 2008

Critics of Laudan's normative naturalism have questioned whether methodological rules can be regarded as empirical hypotheses about relations between means and ends. Drawing on Laudan's defense that rules of method are contingent on assumptions about the world, I argue that even if such rules can be shown to be analytic in principle (Kaiser 1991), in practice the warrant for such rules will be empirical. Laudan's naturalism, however, acquires normative force only by construing both methods and epistemic goals as instrumental to practical concerns, and issues only in context-specific and not general methodological principles.
Instrumental Rationality and Naturalized Philosophy of Science
Authors: Siegel Harvey
Published: January 2008

In two recent papers, I criticized Ronald N. Giere's and Larry Laudan's arguments for ‘naturalizing’ the philosophy of science (Siegel 1989, 1990). Both Giere and Laudan replied to my criticisms (Giere 1989, Laudan 1990b). The key issue arising in both interchanges is these naturalists' embrace of instrumental conceptions of rationality, and their concomitant rejection of non-instrumental conceptions of that key normative notion. In this reply I argue that their accounts of science's rationality as exclusively instrumental fail, and consequently that their cases for ‘normatively naturalizing’ the philosophy of science fail as well.
Oracles, Aesthetics, and Bayesian Consensus
Authors: Barrett Jeffrey A.
Published: January 2008

In order for Bayesian inquiry to count as objective, one might argue that it must lead to a consensus among those who use it and share evidence, but presumably this is not enough. It has been proposed that one should also require that the consensus be reached from very different initial opinions by conditioning only on basic experimental evidence, evidence free from subjective, social, or psychological influence. I will argue here, however, that this notion of objectivity in Bayesian inquiry is too narrow.
Assessment of current drive efficiency and the synergetic effect for ECCD and LHCD and the possibility of long pulse operation in ITER
Authors: Polevoi A. , Zvonkov A. , Oikawa T. , Kuyanov A. , Shimada M. , Saveliev A. , Gribov Yu.
Published: January 2008

Steady state operation is preferable for fusion reactors. The possibility of extending the pulse length in ITER is considered taking into account the capabilities of the planned electron-cyclotron current drive (ECCD) and low-hybrid current drive (LHCD). The ECCD efficiency for current drive at different locations is assessed. The possibility of extending the pulse length by the increase in the current drive efficiency due to the synergetic effect for combined ECCD and LHCD at the same location is assessed. The calculated synergetic effect of ECCD and LHCD on the current drive efficiency is less than 10% for ITER parameters. Long pulse operation with the energy multiplication factorPfus/Paux=Q> 5 and durationt> 3000 s will be possible in the case of enhanced confinement with respect to the ELMy H-mode scalingHH98y,2∼ 1.3–1.4.
Formation, sustainment and characteristics of current hole plasmas in DIII-D discharges
Authors: Jayakumar R.J. , Austin M.A. , Greenfield C.M. , Hawkes N.C. , Kinsey J.E. , Lao L.L. , Parks P.B. , Solano E.R. , Taylor T.S.
Published: January 2008

Plasmas with zero or near-zero current density in a wide region of the core have been produced in DIII-D discharges. The discharges were obtained with early neutral beam and electron cyclotron heating (ECH) during the plasma current ramp. Wide current holes (CHs) with a near-zero field over about 23% of the plasma width and narrow CHs with a duration of up to 1.1 s (comparable to the current relaxation time) have been obtained. Equilibria and pressure profiles were obtained by including kinetic and motional Stark effect (MSE) data using the code TRANSP. Agreement between calculated and measured neutron fluxes is obtained only when the fast-ion diffusion coefficient is set to very high values which results in considerable fast-ion redistribution and a broadened pressure profile. The MSE-only equilibrium fits are in good agreement with such kinetic fits. While CHs collapse due to tearing modes, bursty MHD activity coherent with electron temperature relaxation events is observed when the CHs are sustained. Some collapse events also appear to be coincident with edge localized modes. The CH phase seems to have been limited by the no-wall beta limit. In the present set of discharges, wider CHs (steeper temperature gradients) appear to collapse at somewhat lower β. Tearing modes are seen to cause shrinking of the CH. While early electron heating is strongly dependent on the timing and power of the neutral beam and by the ECH power, it is seen that larger neutral beam powers are correlated with wider CHs which do not decay significantly. An extensive and perhaps difficult analysis of current transport is required to check whether a neoclassical poloidal flux evolution (diffusive EMF) is either consistent with a stationary current profile or that an additional or anomalous EMF is present.
Hypervelocity dust impacts in FTU scrape-off layer
Authors: Ratynskaia S. , Castaldo C. , Rypdal K. , Morfill G. , de Angelis U. , Pericoli-Ridolfini V. , Rufoloni A. , Giovannozzi E.
Published: January 2008

The first evidence of dust-impact ionization processes in the scrape-off layer of the Frascati tokamak upgrade (FTU) was reported inNucl. Fusion47L5 (2007). In this work an extended data analysis (both of electrostatic probe signals and probe surface analysis) is presented, using results of empirical studies of hypervelocity impacts. Within the accuracy and limits of application of such results to tokamak plasma environment, the data are shown to be consistent with occurrence of impacts by micrometre size iron particles at velocities of the order of 10 km s−1.
Natural similarity measures between position frequency matrices with an application to clustering
Authors: Pape Utz J. , Rahmann Sven , Vingron Martin
Published: January 2008

Motivation: Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied problem in computational biology. The binding sites for one TF are represented by a position frequency matrix (PFM). The discovery of new PFMs requires the comparison to known PFMs to avoid redundancies. In general, two PFMs are similar if they occur at overlapping positions under a null model. Still, most existing methods compute similarity according to probabilistic distances of the PFMs. Here we propose a natural similarity measure based on the asymptotic covariance between the number of PFM hits incorporating both strands. Furthermore, we introduce a second measure based on the same idea to cluster a set of the Jaspar PFMs.

Results: We show that the asymptotic covariance can be efficiently computed by a two dimensional convolution of the score distributions. The asymptotic covariance approach shows strong correlation with simulated data. It outperforms three alternative methods. The Jaspar clustering yields distinct groups of TFs of the same class. Furthermore, a representative PFM is given for each class. In contrast to most other clustering methods, PFMs with low similarity automatically remain singletons.

Availability: A website to compute the similarity and to perform clustering, the source code and Supplementary Material are available at http://mosta.molgen.mpg.de

Contact:  utz.pape@molgen.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
PRALINE™: a strategy for improved multiple alignment of transmembrane proteins
Authors: Pirovano Walter , Feenstra K. Anton , Heringa Jaap
Published: January 2008

Motivation: Membrane-bound proteins are a special class of proteins. The regions that insert into the cell-membrane have a profoundly different hydrophobicity pattern compared with soluble proteins. Multiple alignment techniques use scoring schemes tailored for sequences of soluble proteins and are therefore in principle not optimal to align membrane-bound proteins.

Results: Transmembrane (TM) regions in protein sequences can be reliably recognized using state-of-the-art sequence prediction techniques. Furthermore, membrane-specific scoring matrices are available. We have developed a new alignment method, called PRALINE™, which integrates these two features to enhance multiple sequence alignment. We tested our algorithm on the TM alignment benchmark set by Bahr et al. (2001), and showed that the quality of TM alignments can be significantly improved compared with the quality produced by a standard multiple alignment technique. The results clearly indicate that the incorporation of these new elements into current state-of-the-art alignment methods is crucial for optimizing the alignment of TM proteins.

Availability: A webserver is available at http://www.ibi.vu.nl/programs/pralinewww.

Contact:  heringa@cs.vu.nl
Parabolic equation solution of seismo-acoustics problems involving variations in bathymetry and sediment thickness
Authors: Collis Jon M. , Siegmann William L. , Jensen Finn B. , Zampolli Mario , Küsel Elizabeth T. , Collins Michael D.
Published: January 2008

Recent improvements in the parabolic equation method are combined to extend this approach to a larger class of seismo-acoustics problems. The variable rotated parabolic equation [J. Acoust. Soc. Am. 120, 3534–3538 (2006)] handles a sloping fluid-solid interface at the ocean bottom. The single-scattering solution [J. Acoust. Soc. Am. 121, 808–813 (2007)] handles range dependence within elastic sediment layers. When these methods are implemented together, the parabolic equation method can be applied to problems involving variations in bathymetry and the thickness of sediment layers. The accuracy of the approach is demonstrated by comparing with finite-element solutions. The approach is applied to a complex scenario in a realistic environment.
Modal group time spreads in weakly range-dependent deep ocean environments
Authors: Udovydchenkov Ilya A. , Brown Michael G.
Published: January 2008

The temporal spread of modal group arrivals in weakly range-dependent deep ocean environments is considered. It is assumed that the range dependence is sufficiently weak that mode coupling is predominantly local in mode number. The phrase “modal group arrival” is taken here to mean the contribution to a transient wave field corresponding to a fixed mode number. There are three contributions to modal group time spreads which combine approximately in quadrature. These are the reciprocal bandwidth (the minimal pulse width), a deterministic dispersive contribution that is proportional to bandwidth and grows like range r, and a scattering-induced contribution that grows approximately like r3∕2. The latter two contributions are shown to be proportional to the waveguide invariant β, a property of the background sound speed profile. The results presented, based mostly on asymptotic theory, are shown to agree well with full-wave numerical wave field simulations and available exact mode theoretical results. Simulations are shown that correspond approximately to conditions during the LOAPEX acoustic propagation experiment.
Guided wave arrays for high resolution inspection
Authors: Velichko Alexander , Wilcox Paul D.
Published: January 2008

The paper describes a general approach for processing data from a guided wave transducer array on a plate-like structure. The raw data set from such an array contains time-domain signals from each transmitter–receiver combination. The technique is based on linear superposition of signals in the frequency domain with some amplitude and phase factors and can be applied to any array geometry and any types of array elements. The problem of finding optimal coefficients, which allow the best resolution to be achieved with the minimum number of array elements, is investigated. It is shown that improvements in resolution are obtained at the expense of sensitivity to noise. A method of quantifying this sensitivity is presented. Results are shown that illustrate the application of the technique to a linear array and an array of circular geometry (containing a single ring of elements). Experimental data obtained from a guided wave array containing electromagnetic acoustic transducer elements for exciting and detecting the S0 Lamb wave mode in a 5-mm-thick aluminum plate are processed with different algorithms and the results are discussed. Generalization of the technique for the case of multimode media is suggested.
Mechanical response measurements of real and artificial brass players lips
Authors: Newton Michael J. , Campbell Murray , Gilbert Jöel
Published: January 2008

Mechanical frequency responses of human and artificial lips in brass instrument playing have been measured using a high-speed digital video technique, in an attempt to classify the true nature of the “lip-reed.” Four semiprofessional human players were used, and three notes played on a trombone were studied. All measurements revealed a strong mechanical resonance with “outward striking” behavior; the played note always sounded above this frequency. Several measurements also showed a weaker second resonance, above the played frequency, with “inward striking” behavior. The Q values of the dominant resonances in human lips were lower than those typical of artificial lips.
On boundary conditions for the diffusion equation in room-acoustic prediction: Theory, simulations, and experiments
Authors: Jing Yun , Xiang Ning
Published: January 2008

This paper proposes a modified boundary condition to improve the room-acoustic prediction accuracy of a diffusion equation model. Previous boundary conditions for the diffusion equation model have certain limitations which restrict its application to a certain number of room types. The boundary condition employing the Sabine absorption coefficient [V. Valeau et al., J. Acoust. Soc. Am. 119, 1504–1513 (2006)] cannot predict the sound field well when the absorption coefficient is high, while the boundary condition employing the Eyring absorption coefficient [Y. Jing and N. Xiang, J. Acoust. Soc. Am. 121, 3284–3287 (2007); A. Billon et al., Appl. Acoust. 69, (2008)] has a singularity whenever any surface material has an absorption coefficient of 1.0. The modified boundary condition is derived based on an analogy between sound propagation and light propagation. Simulated and experimental data are compared to verify the modified boundary condition in terms of room-acoustic parameter prediction. The results of this comparison suggest that the modified boundary condition is valid for a range of absorption coefficient values and successfully eliminates the singularity problem.
Hearing sensitivity during target presence and absence while a whale echolocates
Authors: Supin Alexander Ya. , Nachtigall Paul E. , Breese Marlee
Published: January 2008

Hearing sensitivity was measured in a false killer whale during echolocation. Sensitivity was measured using probe stimuli as sinusoidally amplitude modulated signals with a 22.5-kHz carrier frequency and recording auditory evoked potentials as envelope-following responses. The probes were presented and responses were recorded during short 2-s periods when the animal echolocated to detect the presence or absence of a target in a go/no-go paradigm. In the target-absent trials, a hearing threshold of 90.4dB re 1μPa was found; in the target-present trials, the threshold was 109.8dB. Thus, a 19.4-dB difference was found between thresholds in the target-present and target-absent trials. To check the possibility that this difference was the result of different masking degree of the probe by the emitted sonar clicks, click statistics were investigated in similar trials. No indication was found that the energy of the emitted clicks was higher in the target-present than in target-absent trials; on the contrary, mean click level, mean number of clicks per train, and overall train energy was slightly higher in the target-absent trials. Thus the data indicate that the hearing sensitivity of the whale varied depending on target presence or absence.
Estimating bottlenose dolphin (Tursiops truncatus) hearing thresholds from single and multiple simultaneous auditory evoked potentials
Authors: Finneran James J. , Houser Dorian S. , Blasko Dave , Hicks Christie , Hudson Jim , Osborn Mike
Published: January 2008

Hearing thresholds were estimated in four bottlenose dolphins by measuring auditory evoked responses to single and multiple sinusoidal amplitude modulated tones. Subjects consisted of two males and two females with ages from 4 to 22 years. Testing was conducted in air using a “jawphone” transducer to couple sound into each subject’s lower right jaw. Carrier frequencies ranged from 10 to 160kHz in one-half octave steps. Amplitude modulated stimuli were presented individually and as the sum of four, five, and nine simultaneous tones with unique carrier and modulation frequencies. Evoked potentials were noninvasively recorded using surface electrodes embedded in silicon suction cups. The presence or absence of an evoked response at each modulation frequency was assessed by calculating the magnitude-squared coherence from the frequency spectra of the recorded sweeps. All subjects exhibited traditional “U-shaped” audiograms with upper cutoff frequencies above 113kHz. The time required for threshold estimates ranged from 23 to 37min for single stimuli to 5–9min for nine simultaneous stimuli. Agreement between thresholds estimated from single stimuli and multiple, simultaneous stimuli was generally good, indicating that multiple stimuli may be used for quick hearing assessment when time is limited.
The interplay between the auditory and visual modality for end-of-utterance detection
Authors: Barkhuysen Pashiera , Krahmer Emiel , Swerts Marc
Published: January 2008

The existence of auditory cues such as intonation, rhythm, and pausing that facilitate end-of-utterance detection is by now well established. It has been argued repeatedly that speakers may also employ visual cues to indicate that they are at the end of their utterance. This raises at least two questions, which are addressed in the current paper. First, which modalities do speakers use for signalling finality and nonfinality, and second, how sensitive are observers to these signals. Our goal is to investigate the relative contribution of three different conditions to end-of-utterance detection: the two unimodal ones, vision only and audio only, and their bimodal combination. Speaker utterances were collected via a novel semicontrolled production experiment, in which participants provided lists of words in an interview setting. The data thus collected were used in two perception experiments, which systematically compared responses to unimodal (audio only and vision only) and bimodal (audio-visual) stimuli. Experiment I is a reaction time experiment, which revealed that humans are significantly quicker in end-of-utterance detection when confronted with bimodal or audio-only stimuli, than for vision-only stimuli. No significant differences in reaction times were found between the bimodal and audio-only condition, and therefore a second experiment was conducted. Experiment II is a classification experiment, and showed that participants perform significantly better in the bimodal condition than in the two unimodal ones. Both the first and the second experiment revealed interesting differences between speakers in the various conditions, which indicates that some speakers are more expressive in the visual and others in the auditory modality.
Subjective and objective assessment of acoustical and overall environmental quality in secondary school classrooms
Authors: Astolfi Arianna , Pellerey Franco
Published: January 2008

A subjective survey on perceived environmental quality has been carried out on 51 secondary-school classrooms, some of which have been acoustically renovated, and acoustical measurements were carried out in eight of the 51 classrooms, these eight being representative of the different types of classrooms that are the subject of the survey. A questionnaire, which included items on overall quality and its single aspects such as acoustical, thermal, indoor air and visual quality, has been administered to 1006 students. The students perceived that acoustical and visual quality had the most influence on their school performance and, with the same dissatisfaction for acoustical, thermal and indoor air quality, they attributed more relevance, in the overall quality judgment, to the acoustical condition. Acoustical quality was correlated to speech comprehension, which was correlated to the speech transmission index, even though the index does not reflect all the aspects by which speech comprehension can be influenced. Acoustical satisfaction was lower in nonrenovated classrooms, and one of the most important consequences of poor acoustics was a decrease in concentration. The stronger correlation between average noise disturbance scores and LAmax levels, more than LAeq and LA90, showed that students were more disturbed by intermittent than constant noise.
Comparison of adaptive psychometric procedures motivated by the Theory of Optimal Experiments: Simulated and experimental results
Authors: Remus Jeremiah J. , Collins Leslie M.
Published: January 2008

The wide use of psychometric assessments and the time necessary to conduct comprehensive psychometric tests has motivated significant research into the development of psychometric testing procedures that will provide accurate and efficient estimates of the parameters of interest. One potential framework for developing adaptive psychometric procedures is the Theory of Optimal Experiments. The Theory of Optimal Experiments provides several metrics for determining informative stimulus values based on a model of the psychometric function to be provided by the investigator. In this study, two methods based on a previous implementation of the Theory of Optimal Experiments are presented for comparison to two fixed step size staircase methods and also an existing adaptive method that utilizes a Bayesian framework. The psychometric procedures were used to measure detection thresholds and discrimination limens on two separate psychoacoustic tasks with normal-hearing subjects. Computer simulations were performed based on the outcomes of the experimental psychoacoustic detection task to analyze performance over a large sample size in the case of known truth. Results suggest that the proposed stimulus selection rules motivated by the Theory of Optimal Experiments perform better than previous techniques and also extend estimation to multiple parameters.
Power-output regularization in global sound equalization
Authors: Stefanakis Nick , Sarris John , Cambourakis George , Jacobsen Finn
Published: January 2008

The purpose of equalization in room acoustics is to compensate for the undesired modification that an enclosure introduces to signals such as audio or speech. In this work, equalization in a large part of the volume of a room is addressed. The multiple point method is employed with an acoustic power-output penalty term instead of the traditional quadratic source effort penalty term. Simulation results demonstrate that this technique gives a smoother decline of the reproduction performance away from the control points.
Spectral envelope sensitivity of musical instrument sounds
Authors: Gunawan David , Sen D.
Published: January 2008

It is well known that the spectral envelope is a perceptually salient attribute in musical instrument timbre perception. While a number of studies have explored discrimination thresholds for changes to the spectral envelope, the question of how sensitivity varies as a function of center frequency and bandwidth for musical instruments has yet to be addressed. In this paper a two-alternative forced-choice experiment was conducted to observe perceptual sensitivity to modifications made on trumpet, clarinet and viola sounds. The experiment involved attenuating 14 frequency bands for each instrument in order to determine discrimination thresholds as a function of center frequency and bandwidth. The results indicate that perceptual sensitivity is governed by the first few harmonics and sensitivity does not improve when extending the bandwidth any higher. However, sensitivity was found to decrease if changes were made only to the higher frequencies and continued to decrease as the distorted bandwidth was widened. The results are analyzed and discussed with respect to two other spectral envelope discrimination studies in the literature as well as what is predicted from a psychoacoustic model.
Faxén relations in solids—a generalized approach to particle motion in elasticity and viscoelasticity
Authors: Norris Andrew N.
Published: January 2008

A movable inclusion in an elastic material oscillates as a rigid body with six degrees of freedom. Displacement/rotation and force/moment tensors which express the motion of the inclusion in terms of the displacement and force at arbitrary exterior points are introduced. Using reciprocity arguments two general identities are derived relating these tensors. Applications of the identities to spherical particles provide several new results, including simple expressions for the force and moment on the particle due to plane wave excitation.
Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
Authors: Greenleaf William J. , Frieda Kirsten L. , Foster Daniel A. N. , Woodside Michael T. , Block Steven M.
Published: January 2008

Riboswitches regulate genes through structural changes in ligand-binding RNA aptamers. With the use of an optical-trapping assay based on in situ transcription by a molecule of RNA polymerase, single nascent RNAs containing
pbuE
adenine riboswitch aptamers were unfolded and refolded. Multiple folding states were characterized by means of both force-extension curves and folding trajectories under constant force by measuring the molecular contour length, kinetics, and energetics with and without adenine. Distinct folding steps correlated with the formation of key secondary or tertiary structures and with ligand binding. Adenine-induced stabilization of the weakest helix in the aptamer, the mechanical switch underlying regulatory action, was observed directly. These results provide an integrated view of hierarchical folding in an aptamer, demonstrating how complex folding can be resolved into constituent parts, and supply further insights into tertiary structure formation.
Human Papillomavirus (HPV) in Atypical Squamous Cervical Cytology: the Invader HPV Test as a New Screening Assay
Authors: Wong Anna K. , Chan Raymond C.-K. , Nichols W. Stephen , Bose Shikha
Published: January 2008

In surveillance for cervical neoplasia, a diagnosis of cytologically atypical squamous cells of undetermined significance (ASCUS) presents a significant clinical issue, often dependent on testing for high-risk (HR) human papillomavirus (HPV) for the triage of patients. HPV type 16 now appears to be a critical concern in the follow-up of patients with ASCUS. The Invader HPV (Inv2) test, by Third Wave Technologies, Inc., is a recently developed analyte-specific reagent assay that uses probe sets for the detection of 14 HR HPV subtypes. These probe sets are A5/A6 (HPV types 51, 56, and 66), A7 (HPV types 18, 39, 45, 59, and 68), and A9 (HPV types 16, 31, 33, 35, 52, and 58). This report describes the performance characteristics of the Inv2 test in the screening of ASCUS cervical cytology specimens and correlates the results of the Inv2 test with those of the Hybrid Capture II HPV (HC2) test by Digene. The linear array HPV genotyping test (Roche Molecular Systems) was used as a reference method for the testing of samples with discordant results. Ninety-four Pap smear samples with a cytological diagnosis of ASCUS and 39 samples with a negative diagnosis were tested. The results of the Inv2 test demonstrated a good (86.6%) concordance with those of the HC2 test, with an overall sensitivity and specificity of 96% for the Inv2 test. Additionally, the Inv2 assay, which offers high-throughput, semiautomated DNA extraction, allows the subgrouping of HPV types by differential probe sets, could provide a useful test for screening for HPV, and has the potential to provide an improved means of risk stratification and the selection of patients for further HPV subtyping.
Comparison of a Lateral-Flow Immunochromatography Assay with Real-Time Reverse Transcription-PCR for Detection of Human Metapneumovirus
Authors: Kikuta Hideaki , Sakata Chikako , Gamo Reiko , Ishizaka Akihito , Koga Yasutsugu , Konno Mutsuko , Ogasawara Yoshinori , Sawada Hiroyuki , Taguchi Yuichi , Takahashi Yutaka , Yasuda Kazue , Ishiguro Nobuhisa , Hayashi Akio , Ishiko Hiroaki , Kobayashi Kunihiko
Published: January 2008

A lateral-flow immunochromatography (IC) assay for the detection of human metapneumovirus (hMPV) has been developed by using two mouse monoclonal antibodies to the nucleocapsid protein of hMPV. The purpose of this study was to compare the virus detection rate in nasopharyngeal secretions by the IC assay with that by real-time reverse transcription-PCR (RT-PCR). We collected nasopharyngeal swab samples from 247 children with respiratory symptoms in Sapporo, Japan, during the period from April to July 2007. Sixty-eight of the 247 children were positive for hMPV by real-time RT-PCR. When the real-time RT-PCR was used as the reference standard, the IC assay results were positive for 48 of the 68 real-time RT-PCR-positive children (70.6% sensitivity) and 8 of the 179 real-time RT-PCR-negative children (95.5% specificity). Although the sensitivity of the IC assay is lower than that of real-time RT-PCR, the IC assay is a rapid and useful test for the diagnosis of hMPV infections in children.
NON-UNIFORM MIXING OF QUANTUM WALK ON CYCLES
Authors: ADAMCZAK WILLIAM , ANDREW KEVIN , BERGEN LEON , ETHIER DILLON , HERNBERG PETER , LIN JENNIFER , TAMON CHRISTINO
Published: January 2008

A classical lazy random walk on cycles is known to mix with the uniform distribution. In contrast, we show that a continuous-time quantum walk on cycles exhibits strong non-uniform mixing properties. First, we prove that the instantaneous distribution of a quantum walk on most even-length cycles is never uniform. More specifically, we prove that a quantum walk on a cycle Cnis not instantaneous uniform mixing, whenever n satisfies either: (a) n = 2u, for u ≥ 3; or (b) n = 2uq, for u ≥ 1 and q ≡ 3 (mod 4). Second, we prove that the average distribution of a quantum walk on any Abelian circulant graph is never uniform. As a corollary, the average distribution of a quantum walk on any standard circulant graph, such as the cycles, complete graphs, and even hypercubes, is never uniform. Nevertheless, we show that the average distribution of a quantum walk on the cycle Cnis O(1/n)-uniform.
PROPERTIES OF NONFREENESS: AN ENTROPY MEASURE OF ELECTRON CORRELATION
Authors: GOTTLIEB ALEX D. , MAUSER NORBERT J.
Published: January 2008

The "nonfreeness" of a many-fermion state ω is the entropy of ω relative to the free state that has the same 1-particle statistics as ω. The nonfreeness of a pure state is the same as its "particle-hole symmetric correlation entropy", a variant of an established measure of electron correlation. However, nonfreeness is also defined for mixed states, and this allows one to compare the nonfreeness of subsystems to the nonfreeness of the whole. Nonfreeness of a part does not exceed that in the whole; nonfreeness is additive over independent subsystems; and nonfreeness is superadditive over subsystems that are independent on the 1-particle level.