Effects of stimulus naturalness and contralateral interferers on lexical bias in consonant identification

Lexical bias is the tendency to perceive an ambiguous speech sound as a phoneme completing a word; more ambiguity typically causes greater reliance on lexical knowledge. A speech sound ambiguous between /g/ and /k/ is more likely to be perceived as /g/ before /ɪft/ and as /k/ before /ɪs/. The magnitude of this difference-the Ganong shift-increases when high cognitive load limits available processing resources. The effects of stimulus naturalness and informational masking on Ganong shifts and reaction times were explored. Tokens between /gɪ/ and /kɪ/ were generated using morphing software, from which two continua were created ("giss"-"kiss" and "gift"-"kift"). In experiment 1, Ganong shifts were considerably larger for sine- than noise-vocoded versions of these continua, presumably because the spectral sparsity and unnatural timbre of the former increased cognitive load. In experiment 2, noise-vocoded stimuli were presented alone or accompanied by contralateral interferers with constant within-band amplitude envelope, or within-band envelope variation that was the same or different across bands. The latter, with its implied spectro-temporal variation, was predicted to cause the greatest cognitive load. Reaction-time measures matched this prediction; Ganong shifts showed some evidence of greater lexical bias for frequency-varying interferers, but were influenced by context effects and diminished over time.

Mandatory dichotic integration of second-formant information: Contralateral sine bleats have predictable effects on consonant place judgments

Speech-on-speech informational masking arises because the interferer disrupts target processing (e.g., capacity limitations) or corrupts it (e.g., intrusions into the target percept); the latter should produce predictable errors. Listeners identified the consonant in monaural buzz-excited three-formant analogues of approximant-vowel syllables, forming a place of articulation series (/w/-/l/-/j/). There were two 11-member series; the vowel was either high-front or low-back. Series members shared formant-amplitude contours, fundamental frequency, and F1+F3 frequency contours; they were distinguished solely by the F2 frequency contour before the steady portion. Targets were always presented in the left ear. For each series, F2 frequency and amplitude contours were also used to generate interferers with altered source properties-sine-wave analogues of F2 (sine bleats) matched to their buzz-excited counterparts. Accompanying each series member with a fixed mismatched sine bleat in the contralateral ear produced systematic and predictable effects on category judgments; these effects were usually largest for bleats involving the fastest rate or greatest extent of frequency change. Judgments of isolated sine bleats using the three place labels were often unsystematic or arbitrary. These results indicate that informational masking by interferers involved corruption of target processing as a result of mandatory dichotic integration of F2 information, despite the grouping cues disfavoring this integration.

Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer

BACKGROUND & AIMS

Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC.

METHODS

We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids.

RESULTS

Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency.

CONCLUSIONS

Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.

Using Chromatin Accessibility to Delineate Therapeutic Subtypes in Pancreatic Cancer Patient-Derived Cell Lines

Disrupted chromatin regulatory processes contribute to the development of cancer, in particular pancreatic ductal adenocarcinoma. The assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) is typically used to study chromatin organization. Here, we present a revised ATAC-seq protocol to study chromatin accessibility in adherent patient-derived cell lines. We provide details on how to calculate the library molarity using Agilent's Bioanalyzer and an analysis pipeline for peak calling and transcription factor mapping. For complete details on the use and execution of this protocol, please refer to Brunton et al. (2020).

HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) can be divided into transcriptomic subtypes with two broad lineages referred to as classical (pancreatic) and squamous. We find that these two subtypes are driven by distinct metabolic phenotypes. Loss of genes that drive endodermal lineage specification, HNF4A and GATA6, switch metabolic profiles from classical (pancreatic) to predominantly squamous, with glycogen synthase kinase 3 beta (GSK3β) a key regulator of glycolysis. Pharmacological inhibition of GSK3β results in selective sensitivity in the squamous subtype; however, a subset of these squamous patient-derived cell lines (PDCLs) acquires rapid drug tolerance. Using chromatin accessibility maps, we demonstrate that the squamous subtype can be further classified using chromatin accessibility to predict responsiveness and tolerance to GSK3β inhibitors. Our findings demonstrate that distinct patterns of chromatin accessibility can be used to identify patient subgroups that are indistinguishable by gene expression profiles, highlighting the utility of chromatin-based biomarkers for patient selection in the treatment of PDAC.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

On the Strategic Weighting of Spectral Information in Consonant Identification

When identifying speech sounds, do listeners direct attention specifically to those frequency regions in which distinctive phonetic information is located? Scharf, Dai, and Miller (1988) concluded that they do, based on an experiment that involved listeners identifying the members of a pair of voiced stop consonants differing primarily in their third-formant transitions. Adding extra contrastive acoustic energy to the third-formant region of one of the consonants enhanced performance more than did adding energy to a region where the consonants were otherwise identical. The present experiments extended this paradigm to reveal evidence of an interaction between the frequency region in which extra distinctive energy was added and the class of consonant to which it was added. The results were more consistent with an account in terms of the effects of added energy on phonetic identity than one based on spectral selective attention.

Defining the molecular pathology of pancreatic body and tail adenocarcinoma

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) remains a dismal disease, with very little improvement in survival over the past 50 years. Recent large-scale genomic studies have improved understanding of the genomic and transcriptomic landscape of the disease, yet very little is known about molecular heterogeneity according to tumour location in the pancreas; body and tail PDACs especially tend to have a significantly worse prognosis. The aim was to investigate the molecular differences between PDAC of the head and those of the body and tail of the pancreas.

METHODS

Detailed correlative analysis of clinicopathological variables, including tumour location, genomic and transcriptomic data, was performed using the Australian Pancreatic Cancer Genome Initiative (APGI) cohort, part of the International Cancer Genome Consortium study.

RESULTS

Clinicopathological data were available for 518 patients recruited to the APGI, of whom 421 underwent genomic analyses; 179 of these patients underwent whole-genome and 96 RNA sequencing. Patients with tumours of the body and tail had significantly worse survival than those with pancreatic head tumours (12·1 versus 22·0 months; P = 0·001). Location in the body and tail was associated with the squamous subtype of PDAC. Body and tail PDACs enriched for gene programmes involved in tumour invasion and epithelial-to-mesenchymal transition, as well as features of poor antitumour immune response. Whether this is due to a molecular predisposition from the outset, or reflects a later time point on the tumour molecular clock, requires further investigation using well designed prospective studies in pancreatic cancer.

CONCLUSION

PDACs of the body and tail demonstrate aggressive tumour biology that may explain worse clinical outcomes.

Hypermutation In Pancreatic Cancer

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer.

Across-formant integration and speech intelligibility: Effects of acoustic source properties in the presence and absence of a contralateral interferer

The role of source properties in across-formant integration was explored using three-formant (F1+F2+F3) analogues of natural sentences (targets). In experiment 1, F1+F3 were harmonic analogues (H1+H3) generated using a monotonous buzz source and second-order resonators; in experiment 2, F1+F3 were tonal analogues (T1+T3). F2 could take either form (H2 or T2). Target formants were always presented monaurally; the receiving ear was assigned randomly on each trial. In some conditions, only the target was present; in others, a competitor for F2 (F2C) was presented contralaterally. Buzz-excited or tonal competitors were created using the time-reversed frequency and amplitude contours of F2. Listeners must reject F2C to optimize keyword recognition. Whether or not a competitor was present, there was no effect of source mismatch between F1+F3 and F2. The impact of adding F2C was modest when it was tonal but large when it was harmonic, irrespective of whether F2C matched F1+F3. This pattern was maintained when harmonic and tonal counterparts were loudness-matched (experiment 3). Source type and competition, rather than acoustic similarity, governed the phonetic contribution of a formant. Contrary to earlier research using dichotic targets, requiring across-ear integration to optimize intelligibility, H2C was an equally effective informational masker for H2 as for T2.

Abstract 1980: Long-range regulation of HOTAIR identifies novel biomarkers of breast cancer outcome and suggests a role in genome instability

Long-range regulators of gene expression are emerging as promising new biomarkers and therapeutic targets for human diseases including cancer. As current breast cancer biomarkers have limited power for predicting disease progression and response to therapy, we have explored the potential of long-range regulators of non-coding RNAs to be useful in the prognostication of breast cancer. HOTAIR is a long non-coding RNA that is overexpressed, promotes metastasis, and is predictive of poor prognosis in breast cancer. Here we describe a long-range transcriptional enhancer of the HOTAIR gene that binds several hormone receptors and associated transcription factors, interacts with the HOTAIR promoter and augments HOTAIR transcription. This enhancer is dependent on FOXA1 and FOXM1 transcription factors and functionally interacts with a novel alternate HOTAIR promoter. Analysis of breast cancer gene expression data indicates that HOTAIR is co-expressed with FOXA1 and FOXM1 in HER2-enriched tumours, and these factors enhance the prognostic power of HOTAIR in this subtype of breast cancer. The combination of HOTAIR and FOXM1 also enables better predictions of response to endocrine therapy for ER+ breast cancer. FOXM1 is a member of the recently described chromosome instability module and consistent with this, the expression of HOTAIR and FOXM1 is associated with increased frequency of copy number alterations and somatic non-synonymous mutations. Our study corroborates the importance of enhancers in breast cancer, elucidates the transcriptional regulation of HOTAIR, suggests HOTAIR as a novel biomarker of patient response to endocrine therapy, and implicates HOTAIR in chromosome instability.

Citation Format: Michael J. Milevskiy, Fares Al-Ejeh, Jodi M. Saunus, Korinne S. Northwood, Amy E. McCart-Reed, Eloise Dray, Kenneth Nephew, Peter J. Bailey, Joshua A. Betts, Andrew Stone, Julia M W Gee, Annette M. Shewan, Juliet D. French, Stacey L. Edwards, Susan J. Clark, Sunil R. Lakhani, Melissa A. Brown. Long-range regulation of HOTAIR identifies novel biomarkers of breast cancer outcome and suggests a role in genome instability. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1980.

Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer

Predicting response to endocrine therapy and survival in oestrogen receptor positive breast cancer is a significant clinical challenge and novel prognostic biomarkers are needed. Long-range regulators of gene expression are emerging as promising biomarkers and therapeutic targets for human diseases, so we have explored the potential of distal enhancer elements of non-coding RNAs in the prognostication of breast cancer survival. HOTAIR is a long non-coding RNA that is overexpressed, promotes metastasis and is predictive of decreased survival. Here, we describe a long-range transcriptional enhancer of the HOTAIR gene that binds several hormone receptors and associated transcription factors, interacts with the HOTAIR promoter and augments transcription. This enhancer is dependent on Forkhead-Box transcription factors and functionally interacts with a novel alternate HOTAIR promoter. HOTAIR expression is negatively regulated by oestrogen, positively regulated by FOXA1 and FOXM1, and is inversely correlated with oestrogen receptor and directly correlated with FOXM1 in breast tumours. The combination of HOTAIR and FOXM1 enables greater discrimination of endocrine therapy responders and non-responders in patients with oestrogen receptor positive breast cancer. Consistent with this, HOTAIR expression is increased in cell-line models of endocrine resistance. Analysis of breast cancer gene expression data indicates that HOTAIR is co-expressed with FOXA1 and FOXM1 in HER2-enriched tumours, and these factors enhance the prognostic power of HOTAIR in aggressive HER2+ breast tumours. Our study elucidates the transcriptional regulation of HOTAIR, identifies HOTAIR and its regulators as novel biomarkers of patient response to endocrine therapy and corroborates the importance of transcriptional enhancers in cancer.

Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Whole-genome characterization of chemoresistant ovarian cancer

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Acoustic source characteristics, across-formant integration, and speech intelligibility under competitive conditions

An important aspect of speech perception is the ability to group or select formants using cues in the acoustic source characteristics—for example, fundamental frequency (F0) differences between formants promote their segregation. This study explored the role of more radical differences in source characteristics. Three-formant (F1+F2+F3) synthetic speech analogues were derived from natural sentences. In Experiment 1, F1+F3 were generated by passing a harmonic glottal source (F0 = 140 Hz) through second-order resonators (H1+H3); in Experiment 2, F1+F3 were tonal (sine-wave) analogues (T1+T3). F2 could take either form (H2 or T2). In some conditions, the target formants were presented alone, either monaurally or dichotically (left ear = F1+F3; right ear = F2). In others, they were accompanied by a competitor for F2 (F1+F2C+F3; F2), which listeners must reject to optimize recognition. Competitors (H2C or T2C) were created using the time-reversed frequency and amplitude contours of F2. Dichotic presentation of F2 and F2C ensured that the impact of the competitor arose primarily through informational masking. In the absence of F2C, the effect of a source mismatch between F1+F3 and F2 was relatively modest. When F2C was present, intelligibility was lowest when F2 was tonal and F2C was harmonic, irrespective of which type matched F1+F3. This finding suggests that source type and context, rather than similarity, govern the phonetic contribution of a formant. It is proposed that wideband harmonic analogues are more effective informational maskers than narrowband tonal analogues, and so become dominant in across-frequency integration of phonetic information when placed in competition.

Formant-frequency variation and informational masking of speech by extraneous formants: evidence against dynamic and speech-specific acoustical constraints

How speech is separated perceptually from other speech remains poorly understood. Recent research indicates that the ability of an extraneous formant to impair intelligibility depends on the variation of its frequency contour. This study explored the effects of manipulating the depth and pattern of that variation. Three formants (F1+F2+F3) constituting synthetic analogues of natural sentences were distributed across the 2 ears, together with a competitor for F2 (F2C) that listeners must reject to optimize recognition (left = F1+F2C; right = F2+F3). The frequency contours of F1 - F3 were each scaled to 50% of their natural depth, with little effect on intelligibility. Competitors were created either by inverting the frequency contour of F2 about its geometric mean (a plausibly speech-like pattern) or using a regular and arbitrary frequency contour (triangle wave, not plausibly speech-like) matched to the average rate and depth of variation for the inverted F2C. Adding a competitor typically reduced intelligibility; this reduction depended on the depth of F2C variation, being greatest for 100%-depth, intermediate for 50%-depth, and least for 0%-depth (constant) F2Cs. This suggests that competitor impact depends on overall depth of frequency variation, not depth relative to that for the target formants. The absence of tuning (i.e., no minimum in intelligibility for the 50% case) suggests that the ability to reject an extraneous formant does not depend on similarity in the depth of formant-frequency variation. Furthermore, triangle-wave competitors were as effective as their more speech-like counterparts, suggesting that the selection of formants from the ensemble also does not depend on speech-specific constraints.

Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events

BACKGROUND

Breast cancer outcome, including response to therapy, risk of metastasis and survival, is difficult to predict using currently available methods, highlighting the urgent need for more informative biomarkers. Androgen receptor (AR) has been implicated in breast carcinogenesis however its potential to be an informative biomarker has yet to be fully explored. In this study, AR protein levels were determined in a cohort of 73 Grade III invasive breast ductal adenocarcinomas.

METHODS

The levels of Androgen receptor protein in a cohort of breast tumour samples was determined by immunohistochemistry and the results were compared with clinical characteristics, including survival. The role of defects in the regulation of Androgen receptor gene expression were examined by mutation and methylation screening of the 5' end of the gene, reporter assays of the 5' and 3' end of the AR gene, and searching for miRNAs that may regulate AR gene expression.

RESULTS

AR was expressed in 56% of tumours and expression was significantly inversely associated with 10-year survival (P = 0.004). An investigation into the mechanisms responsible for the loss of AR expression revealed that hypermethylation of the AR promoter is associated with loss of AR expression in breast cancer cells but not in primary breast tumours. In AR negative breast tumours, mutation screening identified the same mutation (T105A) in the 5'UTR of two AR negative breast cancer patients but not reported in the normal human population. Reporter assay analysis of this mutation however found no evidence for a negative impact on AR 5'UTR activity. The role of miR-124 in regulating AR expression was also investigated, however no evidence for this was found.

CONCLUSION

This study highlights the potential for AR expression to be an informative biomarker for breast cancer survival and sets the scene for a more comprehensive investigation of the molecular basis of this phenomenon.

Effects of the rate of formant-frequency variation on the grouping of formants in speech perception

How speech is separated perceptually from other speech remains poorly understood. Recent research suggests that the ability of an extraneous formant to impair intelligibility depends on the modulation of its frequency, but not its amplitude, contour. This study further examined the effect of formant-frequency variation on intelligibility by manipulating the rate of formant-frequency change. Target sentences were synthetic three-formant (F1 + F2 + F3) analogues of natural utterances. Perceptual organization was probed by presenting stimuli dichotically (F1 + F2C + F3C; F2 + F3), where F2C + F3C constitute a competitor for F2 and F3 that listeners must reject to optimize recognition. Competitors were derived using formant-frequency contours extracted from extended passages spoken by the same talker and processed to alter the rate of formant-frequency variation, such that rate scale factors relative to the target sentences were 0, 0.25, 0.5, 1, 2, and 4 (0 = constant frequencies). Competitor amplitude contours were either constant, or time-reversed and rate-adjusted in parallel with the frequency contour. Adding a competitor typically reduced intelligibility; this reduction increased with competitor rate until the rate was at least twice that of the target sentences. Similarity in the results for the two amplitude conditions confirmed that formant amplitude contours do not influence across-formant grouping. The findings indicate that competitor efficacy is not tuned to the rate of the target sentences; most probably, it depends primarily on the overall rate of frequency variation in the competitor formants. This suggests that, when segregating the speech of concurrent talkers, differences in speech rate may not be a significant cue for across-frequency grouping of formants.

A note about insensitivity to pitch-change direction

Some listeners are insensitive to the direction of pure-tone frequency changes when the standard frequency is roved widely over trials, but less so when the standard frequency is fixed and trial-by-trial feedback is provided. The present experiment tested the hypothesis that fixing the standard frequency and providing feedback is advantageous for direction-impaired listeners because under these conditions the listeners can learn to respond correctly without genuinely perceiving frequency-change direction. This hypothesis was ruled out by the experiment. It appears instead that direction-impaired listeners find it difficult to ignore the irrelevant frequency changes introduced by roving.

Effects of differences in fundamental frequency on across-formant grouping in speech perception

In an isolated syllable, a formant will tend to be segregated perceptually if its fundamental frequency (F0) differs from that of the other formants. This study explored whether similar results are found for sentences, and specifically whether differences in F0 (ΔF0) also influence across-formant grouping in circumstances where the exclusion or inclusion of the manipulated formant critically determines speech intelligibility. Three-formant (F1 + F2 + F3) analogues of almost continuously voiced natural sentences were synthesized using a monotonous glottal source (F0 = 150 Hz). Perceptual organization was probed by presenting stimuli dichotically (F1 + F2C + F3; F2), where F2C is a competitor for F2 that listeners must resist to optimize recognition. Competitors were created using time-reversed frequency and amplitude contours of F2, and F0 was manipulated (ΔF0 = ± 8, ± 2, or 0 semitones relative to the other formants). Adding F2C typically reduced intelligibility, and this reduction was greatest when ΔF0 = 0. There was an additional effect of absolute F0 for F2C, such that competitor efficacy was greater for higher F0s. However, competitor efficacy was not due to energetic masking of F3 by F2C. The results are consistent with the proposal that a grouping "primitive" based on common F0 influences the fusion and segregation of concurrent formants in sentence perception.

The intelligibility of noise-vocoded speech: spectral information available from across-channel comparison of amplitude envelopes

Noise-vocoded (NV) speech is often regarded as conveying phonetic information primarily through temporal-envelope cues rather than spectral cues. However, listeners may infer the formant frequencies in the vocal-tract output-a key source of phonetic detail-from across-band differences in amplitude when speech is processed through a small number of channels. The potential utility of this spectral information was assessed for NV speech created by filtering sentences into six frequency bands, and using the amplitude envelope of each band (≤30 Hz) to modulate a matched noise-band carrier (N). Bands were paired, corresponding to F1 (≈N1 + N2), F2 (≈N3 + N4) and the higher formants (F3' ≈ N5 + N6), such that the frequency contour of each formant was implied by variations in relative amplitude between bands within the corresponding pair. Three-formant analogues (F0 = 150 Hz) of the NV stimuli were synthesized using frame-by-frame reconstruction of the frequency and amplitude of each formant. These analogues were less intelligible than the NV stimuli or analogues created using contours extracted from spectrograms of the original sentences, but more intelligible than when the frequency contours were replaced with constant (mean) values. Across-band comparisons of amplitude envelopes in NV speech can provide phonetically important information about the frequency contours of the underlying formants.

The perceptual organization of sine-wave speech under competitive conditions

Speech comprises dynamic and heterogeneous acoustic elements, yet it is heard as a single perceptual stream even when accompanied by other sounds. The relative contributions of grouping "primitives" and of speech-specific grouping factors to the perceptual coherence of speech are unclear, and the acoustical correlates of the latter remain unspecified. The parametric manipulations possible with simplified speech signals, such as sine-wave analogues, make them attractive stimuli to explore these issues. Given that the factors governing perceptual organization are generally revealed only where competition operates, the second-formant competitor (F2C) paradigm was used, in which the listener must resist competition to optimize recognition [Remez, R. E., et al. (1994). Psychol. Rev. 101, 129-156]. Three-formant (F1+F2+F3) sine-wave analogues were derived from natural sentences and presented dichotically (one ear=F1+F2C+F3; opposite ear=F2). Different versions of F2C were derived from F2 using separate manipulations of its amplitude and frequency contours. F2Cs with time-varying frequency contours were highly effective competitors, regardless of their amplitude characteristics. In contrast, F2Cs with constant frequency contours were completely ineffective. Competitor efficacy was not due to energetic masking of F3 by F2C. These findings indicate that modulation of the frequency, but not the amplitude, contour is critical for across-formant grouping.

Stimulus uncertainty and insensitivity to pitch-change direction

In a series of experiments, Semal and Demany [(2006). J. Acoust. Soc. Am. 120, 3907-3915] demonstrated that some normally hearing listeners are unable to determine the direction of small but detectable differences in frequency between pure tones. Unlike studies demonstrating similar effects in patients with brain damage, the authors used stimuli in which the standard frequency of the tones was highly uncertain (roved) over trials. In Experiment 1, listeners were identified as insensitive to the direction of pitch changes using stimuli with frequency roving. When listeners were retested using stimuli without roving in Experiment 2, impairments in pitch-direction identification were generally much less profound. In Experiment 3, frequency-roving range had a systematic effect on listeners' thresholds, and impairments in pitch-direction identification tended to occur only when the roving range was widest. In Experiment 4, the influence of frequency roving was similar for continuous frequency changes as for discrete changes. Possible explanations for the influence of roving on listeners' insensitivity to pitch-change direction are discussed.

Benefits of knowing who, where, and when in multi-talker listening

The benefits of prior information about who would speak, where they would be located, and when they would speak were measured in a multi-talker spatial-listening task. On each trial, a target phrase and several masker phrases were allocated to 13 loudspeakers in a 180 degrees arc, and to 13 overlapping time slots, which started every 800 ms. Speech-reception thresholds (SRTs) were measured as the level of target relative to masker phrases at which listeners reported key words at 71% correct. When phases started in pairs all three cues were beneficial ("who" 3.2 dB, "where" 5.1 dB, and "when" 0.3 dB). Over a range of onset asynchronies, SRTs corresponded consistently to a signal-to-noise ratio (SNR) of -2 dB at the start of the target phrase. When phrases started one at a time, SRTs fell to a SNR of -8 dB and were improved significantly, but only marginally, by constraining "who" (1.9 dB), and not by constraining "where" (1.0 dB) or "when" (0.01 dB). Thus, prior information about "who," "where," and "when" was beneficial, but only when talkers started speaking in pairs. Low SRTs may arise when talkers start speaking one at a time because of automatic orienting to phrase onsets and/or the use of loudness differences to distinguish target from masker phrases.

Concurrent sound segregation based on inharmonicity and onset asynchrony

To explore the neural processes underlying concurrent sound segregation, auditory evoked fields (AEFs) were measured using magnetoencephalography (MEG). To induce the segregation of two auditory objects we manipulated harmonicity and onset synchrony. Participants were presented with complex sounds with (i) all harmonics in-tune (ii) the third harmonic mistuned by 8% of its original value (iii) the onset of the third harmonic delayed by 160 ms compared to the other harmonics. During recording, participants listened to the sounds and performed an auditory localisation task whereas in another session they ignored the sounds and performed a visual localisation task. Active and passive listening was chosen to evaluate the contribution of attention on sound segregation. Both cues - inharmonicity and onset asynchrony - elicited sound segregation, as participants were more likely to report correctly on which side they heard the third harmonic when it was mistuned or delayed compared to being in-tune with all other harmonics. AEF activity associated with concurrent sound segregation was identified over both temporal lobes. We found an early deflection at approximately 75 ms (P75m) after sound onset, probably reflecting an automatic registration of the mistuned harmonic. Subsequent deflections, the object-related negativity (ORNm) and a later displacement (P230m) seem to be more general markers of concurrent sound segregation, as they were elicited by both mistuning and delaying the third harmonic. Results indicate that the ORNm reflects relatively automatic, bottom-up sound segregation processes, whereas the P230m is more sensitive to attention, especially with inharmonicity as the cue for concurrent sound segregation.

A global genomic transcriptional code associated with CNS-expressed genes

Highly conserved non-coding DNA regions (HCNR) occur frequently in vertebrate genomes, but their functional roles remain unclear. Here, we provide evidence that a large portion of HCNRs are enriched for binding sites for Sox, POU and Homeodomain transcription factors, and such HCNRs can act as cis-regulatory regions active in neural stem cells. Strikingly, these HCNRs are linked to several hundreds of genes expressed in the developing CNS and they may exert locus-wide regulatory effects on multiple genes flanking their genomic location. Moreover, these data imply a unifying transcriptional logic for a large set of CNS-expressed genes in which Sox and POU proteins act as generic promoters of transcription while Homeodomain proteins control the spatial expression of genes through active repression.

Some characteristics of auditory spatial attention revealed using rhythmic masking release

The tuning of auditory spatial attention with respect to interaural level and time difference cues (ILDs and ITDs) was explored using a rhythmic masking release (RMR) procedure. Listeners heard tone sequences defining one of two simple target rhythms, interleaved with arhythmic masking tones, presented over headphones. There were two conditions, which differed only in the ILD of the tones defining the target rhythm: For one condition, ILD was 0 dB and the perceived lateral position was central, and for the other, ILD was 4 dB and the perceived lateral position was to the right; target tone ITD was always zero. For the masking tones, ILD was fixed at 0 dB and ITDs were varied, giving rise to a range of lateral positions determined by ITD. The listeners' task was to attend to and identify the target rhythm. The data showed that target rhythm identification accuracy was low, indicating that maskers were effective, when target and masker shared spatial position, but not when they shared only ITD. A clear implication is that at least within the constraints of the RMR paradigm, overall spatial position, and not ITD, is the substrate for auditory spatial attention.

Auditory temporal order discrimination and backward recognition masking in adults with dyslexia

The ability of 20 adult dyslexic readers to extract frequency information from successive tone pairs was compared with that of IQ-matched controls using temporal order discrimination and auditory backward recognition masking (ABRM) tasks. In both paradigms, the interstimulus interval (ISI) between tones in a pair was either short (20 ms) or long (200 ms). Temporal order discrimination was better for both groups of listeners at long than at short ISIs, but no group differences in performance were observed at either ISI. Performance on the ABRM task was also better at long than at short ISIs and was influenced by variability in masker frequency and by the spectral proximity of target and masker. The only significant group difference was found in one condition of the ABRM task when the target-masker interval was 200 ms, but this difference was not reliable when the measure was of optimal performance. Moderate correlations were observed between auditory thresholds and phonological skill for the sample as a whole and within the dyslexic and control groups. However, although a small subgroup of dyslexic listeners with poor phonology was characterized by elevated thresholds across the auditory tasks, evidence for an association between auditory and phonological processing skills was weakened by the finding of a subgroup of control listeners with poor auditory processing and normal phonological processing skills.

A comparison of the effects of differences in temporal gating and ear of presentation on profile discrimination

The aim of the study was to examine the effects of differences in temporal gating and ear of presentation (both separately and in combination) on listeners' ability to detect an increment in the level of a 1 kHz component (the target) relative to that of four spectrally flanking components. The flanking components were always presented to the listeners' right ear, while the target component was either presented to the same ear (monaural presentation) or to the left ear (dichotic presentation). Similarly, the target and flanking components were either gated on and off at the same time (synchronous presentation), or else the target component began 100 ms before and terminated 100 ms after the four flanking components (asynchronous presentation). On average, thresholds were lowest in the synchronous, monaural condition, and highest in the two asynchronous conditions. Ear differences alone did result in elevated thresholds for most listeners. However, combining differences in gating and ear of presentation produced thresholds that were indistinguishable from those obtained when gating differences alone were employed. These results are consistent with the suggestion that differences in temporal gating lead to more complete segregation of concurrent frequency components than differences in spatial location.

Cyclin D-cdk4 activity modulates the subnuclear localization and interaction of MEF2 with SRC-family coactivators during skeletal muscle differentiation

Prior work has indicated that D-type cyclin-cdk4 complexes, which are only active in proliferating cells, can suppress the skeletal muscle differentiation program in proliferating myoblasts. In this study, we show that cyclin D-cdk activity can block the activity of the MEF2 family of transcriptional regulators, which are crucial regulators of skeletal muscle gene expression. We have found that cyclin D-cdk activity blocks the association of MEF2C with the coactivator protein GRIP-1 and thereby inhibits the activity of MEF2. During skeletal muscle differentiation, GRIP-1 is localized to punctate nuclear structures and can apparently tether MEF2 to such structures. Cotransfection of GRIP-1 can both potentiate the transcriptional activity of a Gal4-MEF2C construct and induce MEF2C localization to punctate nuclear structures. Consistent with the absence of punctate nuclear GRIP-1 in proliferating myoblasts, we have found that ectopic cyclin D-cdk4 expression disrupts the localization of both GRIP-1 and MEF2C to these punctate subnuclear structures. Our findings indicate that cyclin D-cdk4 activity represses skeletal muscle differentiation in proliferating cells by blocking the association of MEF2 with the coactivator GRIP-1 and concomitantly disrupts the association of these factors with punctate nuclear subdomains within the cell.

Auditory processing and the development of language and literacy

This paper considers evidence for basic auditory processing impairments associated with dyslexia and specific language impairment, against a back-drop of findings from studies of the normal development of auditory and phonological processing. A broad range of auditory impairments have been implicated in the aetiology of these language-learning disorders, including deficits in discriminating the temporal order of rapid sequences of auditory signals, elevated thresholds for frequency discrimination and for detection of amplitude and frequency modulation, impaired binaural processing and increased susceptibility to backward masking. Current evidence is inconsistent, but suggests that not all children with language difficulties have non-verbal auditory processing impairments, and for those that do, the impact on language development is poorly understood. Some implications for clinical practice are discussed.

Hydridotris(thioxotriazolyl)borate (Tt), an ambidentate (N(3)/S(3)) tripodal ligand. X-ray crystal structures of sodium, bismuth(III), tin(IV), and manganese(I) complexes

Treatment of the heterocycle 5-thioxo-4,5-dihydro-3,4-dimethyl-1,2,4-triazole (thioxotriazole) with sodium tetrahydroborate at 210 degrees C provides the new [N(3)/S(3)] ambidentate tripod ligand hydridotris(thioxotriazolyl)borate (Tt) as its sodium complex salt. Complexes of this ligand with sodium, bismuth(III), tin(IV), and manganese(I) have been synthesized and characterized by X-ray crystallography. The structures of these complexes illustrate the ambidentate character of the ligand with the softer metals bismuth and tin exhibiting sulfur coordination, while sodium and manganese(I) bond via the ligand nitrogen donors. In the [S(3)] coordination mode the ligand creates eight-membered chelate rings with the metal with the consequence that the metal ligand unit adopts a propeller-type conformation with C(3)-symmetry. However, in the [N(3)] mode six-membered chelate rings are formed analogous to the familiar hydrotris(pyrazolyl)borate (Tp) ligand.

Rapid auditory processing and phonological ability in normal readers and readers with dyslexia

According to a prominent theory, the phonological difficulties in dyslexia are caused by an underlying general impairment in the ability to process sequences of rapidly presented, brief sounds. Two studies examined this theory by exploring the relationships between rapid auditory processing and phonological processing in a sample of 82 normally reading children (Study 1) and by comparing 17 children with dyslexia to chronological-age and reading-age control participants on these tasks (Study 2). In the normal readers, moderate correlations were found between the measure of rapid auditory processing (Auditory Repetition Task, or ART) and phonological ability. On the ART, the dyslexia group performed at a level similar to that of the reading-age control group but obtained scores that were significantly below those of the chronological-age control group. This difference was due to a subgroup of 4 children in the dyslexia group who had particular difficulty with the ART. The phonological skills of these individuals were not worse than those of the children in the dyslexia group who were unimpaired on the ART. The discussion argues that there is no evidence that phonoogical difficulties are secondary to impairments of rapid auditory processing, as measured by the ART, and highlights the need to examine the strategic and cognitive demands involved in tasks of rapid auditory processing.

A dynamic role for HDAC7 in MEF2-mediated muscle differentiation

The overlapping expression profile of MEF2 and the class-II histone deacetylase, HDAC7, led us to investigate the functional interaction and relationship between these regulatory proteins. HDAC7 expression inhibits the activity of MEF2 (-A, -C, and -D), and in contrast MyoD and Myogenin activities are not affected. Glutathione S-transferase pulldown and immunoprecipitation demonstrate that the repression mechanism involves direct interactions between MEF2 proteins and HDAC7 and is associated with the ability of MEF2 to interact with the N-terminal 121 amino acids of HDAC7 that encode repression domain 1. The MADS domain of MEF2 mediates the direct interaction of MEF2 with HDAC7. MEF2 inhibition by HDAC7 is dependent on the N-terminal repression domain and surprisingly does not involve the C-terminal deacetylase domain. HDAC7 interacts with CtBP and other class-I and -II HDACs suggesting that silencing of MEF2 activity involves corepressor recruitment. Furthermore, we show that induction of muscle differentiation by serum withdrawal leads to the translocation of HDAC7 from the nucleus into the cytoplasm. This work demonstrates that HDAC7 regulates the function of MEF2 proteins and suggests that this class-II HDAC regulates this important transcriptional (and pathophysiological) target in heart and muscle tissue. The nucleocytoplasmic trafficking of HDAC7 and other class-II HDACs during myogenesis provides an ideal mechanism for the regulation of HDAC targets during mammalian development and differentiation.

Auditory spatial attention using interaural time differences

Previous probe-signal studies of auditory spatial attention have shown faster responses to sounds at an expected versus an unexpected location, making no distinction between the use of interaural time difference (ITD) cues and interaural-level difference cues. In 5 experiments, performance on a same-different spatial discrimination task was used in place of the reaction time metric, and sounds, presented over headphones, were lateralized only by an ITD. In all experiments, performance was better for signals lateralized on the expected side of the head, supporting the conclusion that ITDs can be used as a basis for covert orienting. The performance advantage generalized to all sounds within the spatial focus and was not dissipated by a trial-by-trial rove in frequency or by a rove in spectral profile. Successful use by the listeners of a cross-modal, centrally positioned visual cue provided evidence for top-down attentional control.

A comparison of the effects of quetiapine ('seroquel') and haloperidol in schizophrenic patients with a history of and a demonstrated, partial response to conventional antipsychotic treatment. PRIZE Study Group

Quetiapine ('Seroquel') is a well-tolerated, novel, atypical antipsychotic with consistent efficacy in the treatment of schizophrenia. To date, no clinical studies have evaluated the effect of quetiapine in patients who only partially respond to conventional antipsychotics, yet this type of patient is most frequently seen by psychiatrists. Therefore, this international, multicentre, double-blind study was conducted to compare the efficacy and tolerability of 8 weeks' treatment of quetiapine 600 mg/day with haloperidol 20 mg/day in 288 patients who had a history of partial response to conventional antipsychotics and displayed a partial or no response to 1 month of fluphenazine (20 mg/day) treatment. Patients on quetiapine tended to have greater improvement than those on haloperidol in the primary efficacy measure, mean Positive and Negative Symptom Scale (PANSS) score, after 4 weeks' treatment (-9.05, -5.82, respectively, P = 0.061) and at study end (-11.50, -8.87, respectively, P = 0.234). Similarly, there was a trend towards patients on quetiapine demonstrating greater improvements in the secondary efficacy measures (Clinical Global Impression, PANSS subscale and Brief Psychiatric Rating Scale scores) [week 4 (baseline) to week 12 (end)], but the difference between treatments did not reach significance. Significantly more patients on quetiapine than on haloperidol showed a clinical response-patient response rates, defined as > 20% reduction in PANSS total score between weeks 4 and 12, were 52.2% for quetiapine and 38.0% for haloperidol (P = 0.043). Patients receiving quetiapine required less anticholinergic medication (P < 0.011), had greater reduction in extrapyramidal symptoms (EPS) (P = 0.005) and fewer treatment-emergent EPS-related adverse events compared to those on haloperidol (P < 0.001). Serum prolactin concentrations were elevated at the end of fluphenazine treatment in 73% of patients. Between weeks 4 and 12, elevated serum prolactin concentrations significantly decreased in quetiapine-treated patients compared to those receiving haloperidol (P < 0.001). At the end of quetiapine treatment, 83% of patients had normal prolactin levels while only 21% of patients receiving haloperidol were within the normal range. These results suggest that quetiapine may make a valuable contribution to the management of patients with a history of partial response to conventional antipsychotics.

Auditory spatial attention using interaural time differences

Previous probe-signal studies of auditory spatial attention have shown faster responses to sounds at an expected versus an unexpected location, making no distinction between the use of interaural time difference (ITD) cues and interaural-level difference cues. In 5 experiments, performance on a same-different spatial discrimination task was used in place of the reaction time metric, and sounds, presented over headphones, were lateralized only by an ITD. In all experiments, performance was better for signals lateralized on the expected side of the head, supporting the conclusion that ITDs can be used as a basis for covert orienting. The performance advantage generalized to all sounds within the spatial focus and was not dissipated by a trial-by-trial rove in frequency or by a rove in spectral profile. Successful use by the listeners of a cross-modal, centrally positioned visual cue provided evidence for top-down attentional control.

Across-channel intensity discrimination in the presence of an interferer

Listeners' thresholds for discriminating changes in the relative intensities of two octave-spaced pure tones were measured in three conditions using a 2AFC procedure. In the baseline condition the tone pair was presented alone, while in the two interference conditions the tone pair was accompanied by four additional tones, with the frequency separation between adjacent components of the resultant six-component complex being one octave. In the interference conditions the flanking components were either gated synchronously with the target pair, or began 200 ms ahead. The level of the flanking components relative to the target was randomized on each presentation. The overall stimulus level was also randomized on each presentation to reduce the effectiveness of within-channel comparisons. Threshold elevations in the synchronous condition relative to the baseline ranged from approximately 5 to 17 decibels. By contrast, in the asynchronous condition only one listener showed significant (although substantially reduced) interference. The results complement previous observations that across-channel intensity comparisons are poorer between components that begin or end at different times, and are qualitatively consistent with the hypothesis that temporal misalignment promotes the perceptual segregation of simultaneous frequency components.

Repression of basal transcription by vitamin D receptor: evidence for interaction of unliganded vitamin D receptor with two receptor interaction domains in RIP13delta1

Repression of basal transcription of a 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3) responsive 25-hydroxyvitamin D3-24-hydroxylase (CYP24) promoter construct as observed in kidney cells in the absence of ligand and this repression was dependent on a functional vitamin D response element (VDRE). Basal repression was also seen with a construct where a consensus DR-3-type VDRE was fused to the thymidine kinase promoter. Expression of a dominant negative vitamin D receptor (VDR) isoform that strongly bound to the VDRE motif in the CYP24 promoter ablated basal repression. This VDR isoform lacked sequence in the hinge- and ligand-binding domains implicating one or both of these domains in basal repression. It is well known that thyroid hormone and retinoic acid receptors silence basal transcription of target genes in the absence of ligands and this repressor function can be mediated by the nuclear receptor corepressor N-CoR. Two variants of N-CoR have been described, RIP13a and RIP13delta1. N-CoR and the variants contain two receptor interaction domains, ID-I and ID-II, which are identical except region ID-II in RIP13delta1 has an internal deletion. We have used the mammalian two hybrid system to investigate whether VDR, in the absence of ligand 1,25-(OH)2D3, can interact with these domains. The data showed that unliganded VDR does not interact with either ID-I or ID-II from RIP13a and RIP13delta1, but does interact strongly with a composite domain of ID-I and ID-II from RIP13delta1 (but not from RIP13a) and this strong interaction is abrogated in the presence of ligand. This finding implicates RIP13delta1 in VDR-dependent basal repression of the promoter constructs under investigation. However, over-expression of RIP13delta1 in kidney cell lines did not alter basal expression of the CYP24 promoter construct. It is concluded that either the level of endogenous RIP13delta1 in these kidney cells permits maximal repression or that repression occurs by a mechanism that is independent of RIP13delta1. Alternatively, repression may be dependent on RIP13delta1 but requires an additional cofactor that is limiting in these cells.

Relative intensity comparisons between a tone and spectrally remote noise: effects of onset asynchrony

The present experiment investigated the effect of onset asynchrony on listeners' ability to make relative intensity comparisons between a 1-kHz tone and a band of noise high-pass filtered at 3 kHz. In the synchronous condition, the tone and noise were gated on and off simultaneously. In the two asynchronous conditions, either the tone was gated on before the noise or vice versa, both stimuli terminating simultaneously. In the sequential condition, the offset of the tone coincided with the onset of the noise. The task of the six listeners was to indicate in which of the two presentation intervals the level of the tone was incremented relative to that of the noise. To deter the use of strategies based on successive, within-channel level comparisons, the overall level of the stimuli was randomized on each presentation. For all listeners thresholds were lowest in the synchronous condition, and highest in the sequential condition, the difference ranging from approximately 7 to 18 dB (signal re: pedestal amplitude). Furthermore, five of the six listeners had significantly lower thresholds in the noise-leading condition than in the tone-leading condition, the average difference across listeners being approximately 5 dB. The results are discussed in terms of auditory grouping and the possible strategies available to the listeners.