Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets

Despite remarkable progress in DNA sequencing technologies there remains a trade-off between short-read platforms, having limited ability to sequence homopolymers, repeated motifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or throughput. Moreover, current methods do not allow direct readout of epigenetic modifications from a single read. With the aim of addressing these limitations, we have developed an optical electrowetting sequencing platform that uses step-wise nucleotide triphosphate (dNTP) release, capture and detection in microdroplets from single DNA molecules. Each microdroplet serves as a reaction vessel that identifies an individual dNTP based on a robust fluorescence signal, with the detection chemistry extended to enable detection of 5-methylcytosine. Our platform uses small reagent volumes and inexpensive equipment, paving the way to cost-effective single-molecule DNA sequencing, capable of handling widely varying GC-bias, and demonstrating direct detection of epigenetic modifications.

Machine-Assisted Organic Synthesis

In this Review we describe how the advent of machines is impacting on organic synthesis programs, with particular emphasis on the practical issues associated with the design of chemical reactors. In the rapidly changing, multivariant environment of the research laboratory, equipment needs to be modular to accommodate high and low temperatures and pressures, enzymes, multiphase systems, slurries, gases, and organometallic compounds. Additional technologies have been developed to facilitate more specialized reaction techniques such as electrochemical and photochemical methods. All of these areas create both opportunities and challenges during adoption as enabling technologies.

Organic synthesis: march of the machines

Organic synthesis is changing; in a world where budgets are constrained and the environmental impacts of practice are scrutinized, it is increasingly recognized that the efficient use of human resource is just as important as material use. New technologies and machines have found use as methods for transforming the way we work, addressing these issues encountered in research laboratories by enabling chemists to adopt a more holistic systems approach in their work. Modern developments in this area promote a multi-disciplinary approach and work is more efficient as a result. This Review focuses on the concepts, procedures and methods that have far-reaching implications in the chemistry world. Technologies have been grouped as topics of opportunity and their recent applications in innovative research laboratories are described.

The rapid synthesis of oxazolines and their heterogeneous oxidation to oxazoles under flow conditions

A flow process to access oxazolines and oxazoles via a rapid and practical protocol is described.

Cyclopropanation using flow-generated diazo compounds

A practical and mild protocol for the cyclopropanation of unstabilised diazo compounds is reported.

A systems approach towards an intelligent and self-controlling platform for integrated continuous reaction sequences

Performing reactions in flow can offer major advantages over batch methods. However, laboratory flow chemistry processes are currently often limited to single steps or short sequences due to the complexity involved with operating a multi-step process. Using new modular components for downstream processing, coupled with control technologies, more advanced multi-step flow sequences can be realized. These tools are applied to the synthesis of 2-aminoadamantane-2-carboxylic acid. A system comprising three chemistry steps and three workup steps was developed, having sufficient autonomy and self-regulation to be managed by a single operator.

Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

Here we describe the use of a new open-source software package and a Raspberry Pi^® computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide – a component of Rifater^®, used in the treatment of tuberculosis – and its reduced derivative piperazine-2-carboxamide.

Machine-assisted synthesis of modulators of the histone reader BRD9 using flow methods of chemistry and frontal affinity chromatography

Novel technologies were developed and used for the synthesis and evaluation of new triazolopyridazine BRD9 inhibitors.

Camera-enabled techniques for organic synthesis

A great deal of time is spent within synthetic chemistry laboratories on non-value-adding activities such as sample preparation and work-up operations, and labour intensive activities such as extended periods of continued data collection. Using digital cameras connected to computer vision algorithms, camera-enabled apparatus can perform some of these processes in an automated fashion, allowing skilled chemists to spend their time more productively. In this review we describe recent advances in this field of chemical synthesis and discuss how they will lead to advanced synthesis laboratories of the future.

An analysis of a token economy in stuttering therapy

A stuttering therapy program in which adult stutterers were hospitalized and treated in small groups (n = 4) under token economy conditions is described. The Token System reinforced reductions and penalized increases in stuttering during conversation. The therapy program was divided into three stages. Initially, subjects were treated by the token system, which was then integrated with a delayed auditory feedback schedule designed to instate and shape a prolonged speech pattern into normal fluent speech. Finally, subjects passed through a speech situation hierarchy while under token control conditions. Experiments conducted in the first two stages of treatment are described. The first-stage experiments examined the design of the token system; the second-stage experiment assessed the effect of a contingent punishment schedule integrated with the delayed auditory feedback procedure in order to shape rate of speaking as well as fluency.

A study of the reproducibility and etiology of diffusion anisotropy differences in developmental stuttering: a potential role for impaired myelination

Several diffusion tensor imaging (DTI) studies have reported fractional anisotropy (FA) reductions within the left perisylvian white matter (WM) of persistent developmental stutterers (PSs). However, these studies have not reached the same conclusions in regard to the presence, spatial distribution (focal/diffuse), and directionality (elevated/reduced) of FA differences outside of the left perisylvian region. In addition, supplemental DTI measures (axial and radial diffusivities, diffusion trace) have yet to be utilized to examine the potential etiology of these FA reductions. Therefore, the present study sought to reexamine earlier findings through a sex- and age-controlled replication analysis and then to extend these findings with the aforementioned non-FA measures. The replication analysis showed that robust FA reductions in PSs were largely focal, left hemispheric, and within late-myelinating associative and commissural fibers (division III of the left superior longitudinal fasciculus, callosal body, forceps minor of the corpus callosum). Additional DTI measures revealed that these FA reductions were attributable to an increase in diffusion perpendicular to the affected fiber tracts (elevated radial diffusivity). These findings suggest a hypothesis that will be testable in future studies: that myelogenesis may be abnormal in PSs within left-hemispheric fiber tracts that begin a prolonged course of myelination in the first postnatal year.

The Shb signalling scaffold binds to and regulates constitutive signals from the Epstein–Barr virus LMP2A membrane protein

The Epstein-Barr virus latency-associated membrane protein LMP2A has been shown to activate the survival kinase Akt in epithelial and B cells in a phosphoinositide 3-kinase-dependent fashion. In this study, we demonstrate that the signalling scaffold Shb associates through SH2 and PTB domain interactions with phosphorylated tyrosine motifs in the LMP2A N-terminal tail. Additionally, we show that mutation of tyrosines in these motifs as well as shRNA-mediated downregulation of Shb leads to a loss of constitutive Akt-activation in LMP2A-expressing cells. Furthermore, utilization by Shb of the LMP2A ITAM motif regulates stability of the Syk tyrosine kinase in LMP2A-expressing cells. Our data set the precedent for viral utilization of the Shb signalling scaffold and implicate Shb as a regulator of LMP2A-dependent Akt activation.

Hypophonia in Parkinson's disease: neural correlates of voice treatment revealed by PET

OBJECTIVE

To investigate the neural correlates of hypophonia in individuals with idiopathic PD (IPD) before and after voice treatment with the Lee Silverman Voice Treatment method (VT) using (15)O-H(2)O PET.

METHODS

Regional cerebral blood flow (rCBF) changes associated with overt speech-motor tasks relative to the resting state were measured in the IPD subjects before and after VT, and in a group of healthy control volunteers.

RESULTS

Behavioral measures of voice loudness significantly improved following treatment. Before VT, patients had strong speech-related activations in motor and premotor cortex (M1-mouth, supplementary motor cortex [SMA], and inferior lateral premotor cortex [ILPm]), which were significantly reduced post-VT. Similar to the post-treatment session, premotor activations were absent (SMA) or below statistical threshold (M1-mouth) in the healthy control group. In addition, following VT treatment, significant right-sided activations were present in anterior insular cortex, caudate head, putamen, and dorsolateral prefrontal cortex (DLPFC). Finally, the VT-induced neural changes were not present with transient experimenter-cued increases of loudness in VT-untreated patients.

CONCLUSIONS

Effective improvement of IPD hypophonia following voice treatment with VT was accompanied by a reduction of cortical motor-premotor activations, resembling the functional pattern observed in healthy volunteers and suggesting normalization, and additional recruitment of right anterior insula, caudate head, putamen, and DLPFC. This treatment-dependent functional reorganization suggests a shift from an abnormally effortful (premotor cortex) to a more automatic (basal ganglia, anterior insula) implementation of speech-motor actions.

Evaluation of a stuttering treatment based on reduction of short phonation intervals

This paper reports the results of an efficacy study of a stuttering treatment program known as Modifying Phonation Intervals (MPI), which trains stuttering speakers to reduce the frequency of relatively short phonation intervals (PIs) during connected speech across speaking tasks and situations. Five young adult male stuttering speakers were treated in this computer-based program that systematically trains speakers to reduce selected short PIs found to functionally control stuttering. The treatment process was evaluated using multiple-baseline designs. Treatment was largely self-managed and based on a performance-contingent schedule of within-clinic speaking tasks (Establishment), beyond-clinic speaking tasks (Transfer), and systematic decreases in assessment occasions (Maintenance). Assessments were made at regular intervals before, during, and after treatment. All speakers achieved stutter-free and natural-sounding speech during within- and beyond-clinic speaking tasks at the completion of Maintenance. All were tested 12 months after completion of Maintenance, and all maintained the results. The findings from this study suggest that this procedure may make a significant contribution to stuttering treatment practice.

Brain imaging studies of developmental stuttering

This paper reviews recent brain imaging research on stuttering against a background of studies that the writer and colleagues have been conducting at the University of Texas Health Science Center in San Antonio. The paper begins by reviewing some pertinent background to recent neuroimaging investigations of developmental stuttering. It then outlines the findings from four brain imaging studies that the San Antonio group has conducted using H2(15)O positron emission tomography (PET). Finally, some of the principal findings that are emerging across brain imaging studies of stuttering are reviewed, while also highlighting--and attempting to resolve--some apparent across-study inconsistencies among the findings. Research on stuttering using magnetoencephalogaphy (MEG) and transcranial magnetic stimulation (TMS) is also considered. The findings increasingly point to a failure of normal temporal lobe activation during speech that may either contribute to (or is the result of) a breakdown in the sequencing of processing among premotor regions implicated in phonologic planning.

LEARNING OUTCOMES

As a result of this activity, the participant will become familiar with some recent neurophysiological correlates of stuttering and what they suggest about the nature of this disorder.

The modification of speech naturalness during rhythmic stimulation treatment of stuttering

This study investigated the modification of speech naturalness during stuttering treatment. It systematically replicated an earlier study (Ingham & Onslow, 1985) that demonstrated that unnatural-sounding stutter-free speech could be shaped into more natural-sounding stutter-free speech by using regular feedback of speech-naturalness ratings during speaking tasks. In the present study, the some procedure was used with three persons who stutter-2 adolescent girls and 1 adult man-during rhythmic stimulation conditions. The two adolescent participants spoke only English, but Spanish was the first and English the second language (ESL) of the adult participant. For the 2 adolescents, it was demonstrated that their unnatural-sounding rhythmic speech could be shaped to levels found among normally fluent speakers without losing the fluency-inducing benefits of rhythmic speech. The findings indicate that speech-naturalness feedback may be a powerful procedure for overcoming a problematic aspect of rhythmic speech treatments of stuttering. However, it was not possible to deliver reliable speech-naturalness feedback to the adult ESL speaker, who also displayed a strong dialect. The study highlights the need to find strategies to improve interjudge agreement when using speech naturalness ratings with speakers who display a strong dialect.

The Gab1 docking protein links the b cell antigen receptor to the phosphatidylinositol 3-kinase/Akt signaling pathway and to the SHP2 tyrosine phosphatase

B cell antigen receptor (BCR) signaling causes tyrosine phosphorylation of the Gab1 docking protein. This allows phosphatidylinositol 3-kinase (PI3K) and the SHP2 tyrosine phosphatase to bind to Gab1. In this report, we tested the hypothesis that Gab1 acts as an amplifier of PI3K- and SHP2-dependent signaling in B lymphocytes. By overexpressing Gab1 in the WEHI-231 B cell line, we found that Gab1 can potentiate BCR-induced phosphorylation of Akt, a PI3K-dependent response. Gab1 expression also increased BCR-induced tyrosine phosphorylation of SHP2 as well as the binding of Grb2 to SHP2. We show that the pleckstrin homology (PH) domain of Gab1 is required for BCR-induced phosphorylation of Gab1 and for Gab1 participation in BCR signaling. Moreover, using confocal microscopy, we show that BCR ligation can induce the translocation of Gab1 from the cytosol to the plasma membrane and that this requires the Gab1 PH domain as well as PI3K activity. These findings are consistent with a model in which the binding of the Gab1 PH domain to PI3K-derived lipids brings Gab1 to the plasma membrane, where it can be tyrosine-phosphorylated and then act as an amplifier of BCR signaling.

Is overt stuttered speech a prerequisite for the neural activations associated with chronic developmental stuttering?

Four adult right-handed chronic stutterers and four age-matched controls completed H(2)(15)O PET scans involving overt and imagined oral reading tasks. During overt stuttered speech prominent activations occurred in SMA (medial), BA 46 (right), anterior insula (bilateral), and cerebellum (bilateral) plus deactivations in right A2 (BA 21/22). These activations and deactivations also occurred when the same stutterers imagined they were stuttering. Some parietal regions were significantly activated during imagined stuttering, but not during overt stuttering. Most regional activations changed in the same direction when overt stuttering ceased (during chorus reading) and when subjects imagined that they were not stuttering (also during chorus reading). Controls displayed fewer similarities between regional activations and deactivations during actual and imagined oral reading. Thus overt stuttering appears not to be a prerequisite for the prominent regional activations and deactivations associated with stuttering.

Brain correlates of stuttering and syllable production. A PET performance-correlation analysis

To distinguish the neural systems of normal speech from those of stuttering, PET images of brain blood flow were probed (correlated voxel-wise) with per-trial speech-behaviour scores obtained during PET imaging. Two cohorts were studied: 10 right-handed men who stuttered and 10 right-handed, age- and sex-matched non-stuttering controls. Ninety PET blood flow images were obtained in each cohort (nine per subject as three trials of each of three conditions) from which r-value statistical parametric images (SPI¿r¿) were computed. Brain correlates of stutter rate and syllable rate showed striking differences in both laterality and sign (i.e. positive or negative correlations). Stutter-rate correlates, both positive and negative, were strongly lateralized to the right cerebral and left cerebellar hemispheres. Syllable correlates in both cohorts were bilateral, with a bias towards the left cerebral and right cerebellar hemispheres, in keeping with the left-cerebral dominance for language and motor skills typical of right-handed subjects. For both stutters and syllables, the brain regions that were correlated positively were those of speech production: the mouth representation in the primary motor cortex; the supplementary motor area; the inferior lateral premotor cortex (Broca's area); the anterior insula; and the cerebellum. The principal difference between syllable-rate and stutter-rate positive correlates was hemispheric laterality. A notable exception to this rule was that cerebellar positive correlates for syllable rate were far more extensive in the stuttering cohort than in the control cohort, which suggests a specific role for the cerebellum in enabling fluent utterances in persons who stutter. Stutters were negatively correlated with right-cerebral regions (superior and middle temporal gyrus) associated with auditory perception and processing, regions which were positively correlated with syllables in both the stuttering and control cohorts. These findings support long-held theories that the brain correlates of stuttering are the speech-motor regions of the non-dominant (right) cerebral hemisphere, and extend this theory to include the non-dominant (left) cerebellar hemisphere. The present findings also indicate a specific role of the cerebellum in the fluent utterances of persons who stutter. Support is also offered for theories that implicate auditory processing problems in stuttering.

Targets of B-cell antigen receptor signaling: the phosphatidylinositol 3-kinase/Akt/glycogen synthase kinase-3 signaling pathway and the Rap1 GTPase

In this review, we discuss the role of phosphatidylinositol 3-kinase (PI3K) and Rap 1 in B-cell receptor (BCR) signaling. PI3K produces lipids that recruit pleckstrin homology domain-containing proteins to the plasma membrane. Akt is a kinase that the BCR activates in this manner. Akt phosphorylates several transcription factors as well as proteins that regulate apoptosis and protein synthesis. Akt also regulates glycogen synthase kinase-3, a kinase whose substrates include the nuclear factor of activated T cells (NF-AT)cl and beta-catenin transcriptional activators. In addition to Akt, PI3K-derived lipids also regulate the activity and localization of other targets of BCR signaling. Thus, a key event in BCR signaling is the recruitment of PI3K to the plasma membrane where its substrates are located. This is mediated by binding of the Src homology (SH) 2 domains in PI3K to phosphotyrosine-containing sequences on membrane-associated docking proteins. The docking proteins that the BCR uses to recruit PI3K include CD19, Cbl, Gab1, and perhaps Gab2. We have shown that Gab1 colocalizes PI3K with SH2 domain-containing inositol phosphatase (SHIP) and SHP2, two enzymes that regulate PI3K-dependent signaling. In contrast to PI3K, little is known about the Rap1 GTPase. We showed that the BCR activates Rap1 via phospholipase C-dependent production of diacylglycerol. Since Rap1 is thought to regulate cell adhesion and cell polarity, it may be involved in B-cell migration.

Tyrosine phosphorylation of shc in response to B cell antigen receptor engagement depends on the SHIP inositol phosphatase

Tyrosine phosphorylation of Shc in response to B cell Ag receptor (BCR) engagement creates binding sites for the Src homology 2 (SH2) domain of Grb2. This facilitates the recruitment of both Grb2. Sos complexes and Grb2. SHIP complexes to the plasma membrane where Sos can activate Ras and SH2 domain-containing inositol phosphatase (SHIP) can dephosphorylate phosphatidylinositol 3,4,5-trisphosphate. Given the importance of Shc phosphorylation, we investigated the mechanism by which the BCR stimulates this response. We found that both the SH2 domain and phosphotyrosine-binding (PTB) domain of Shc are important for BCR-induced tyrosine phosphorylation of Shc and the subsequent binding of Grb2 to Shc. The unexpected finding that the PTB domain of Shc is required for Shc phosphorylation was investigated further. Because the major ligand for the Shc PTB domain is SHIP, we asked whether the interaction of Shc with SHIP was required for BCR-induced tyrosine phosphorylation of Shc. Using SHIP-deficient DT40 cells, we show that SHIP is necessary for the BCR to induce significant levels of Shc tyrosine phosphorylation. BCR-induced tyrosine phosphorylation of Shc could be restored in the these cells by expressing wild-type SHIP but not by expressing a mutant form of SHIP that cannot bind to Shc. This suggests that BCR-induced tyrosine phosphorylation of Shc may depend on the binding of SHIP to the Shc PTB domain. Thus, we have described a novel role for SHIP in BCR signaling, promoting the tyrosine phosphorylation of Shc.

Effects of time-interval judgement training on real-time measurement of stuttering

The purpose of this study was to investigate whether a previously developed interval-based training program could improve judges' stuttering event judgments. Two groups of judges made real-time stuttering event judgments (computer-mouse button presses) in 3 to 6 trials before the response-contingent judgment training program and in another 3 to 6 trials after training, for recordings of 9 adults who stuttered. Their judgments were analyzed in terms of number of stuttering events, duration of stuttering, and 5-s intervals of speech that could be categorized as judged (or not judged) to contain stuttering. Results showed (a) changes in the amount of stuttering identified by the judges; (b) improved correspondence between the judges' identifications of stuttering events and interval-based standards previously developed from judgments made by experienced, authoritative judges; (c) improved correspondence between interval-based analyses of the judges' stuttering judgments and the previously developed standards; (d) improved intrajudge agreement; (e) improved interjudge agreement; and (f) convergence between the 2 judge groups, for samples and speakers used during training tasks and also for other speakers. Some implications of these findings for developing standardized procedures for the real-time measurement of stuttering are discussed.

The Gab1 protein is a docking site for multiple proteins involved in signaling by the B cell antigen receptor

Gab1 is a member of the docking/scaffolding protein family which includes IRS-1, IRS-2, c-Cbl, p130(cas), and p62(dok). These proteins contain a variety of protein-protein interaction motifs including multiple tyrosine residues that when phosphorylated can act as binding sites for Src homology 2 (SH2) domain-containing signaling proteins. We show in the RAMOS human B cell line that Gab1 is tyrosine-phosphorylated in response to B cell antigen receptor (BCR) engagement. Moreover, tyrosine phosphorylation of Gab1 correlated with the binding of several SH2-containing signaling proteins to Gab1 including Shc, Grb2, phosphatidylinositol 3-kinase, and the SHP-2 tyrosine phosphatase. Far Western analysis showed that the SH2 domains of Shc, SHP-2, and the p85 subunit of phosphatidylinositol 3-kinase could bind directly to tyrosine-phosphorylated Gab1 isolated from activated RAMOS cells. In contrast, the Grb2 SH2 domain did not bind directly to Gab1 but instead to the Shc and SHP-2 associated with Gab1. We also show that Gab1 is present in the membrane-enriched particulate fraction of RAMOS cells and that Gab1/signaling protein complexes are found in this fraction after BCR engagement. Thus, tyrosine-phosphorylated Gab1 may recruit cytosolic signaling proteins to cellular membranes where they can act on membrane-bound targets. This may be a critical step in the activation of multiple BCR signaling pathways.

Activation of the Rap1 GTPase by the B cell antigen receptor

The B cell antigen receptor (BCR) activates Ras, a GTPase that promotes cell proliferation by activating the Raf-1/MEK/ERK signaling module and other signaling enzymes. In its active GTP-bound form, the Rap1 GTPase may act as a negative regulator of Ras-mediated signaling by sequestering Ras effectors (e.g., Raf-1) and preventing their activation. In this report, we show that BCR engagement activates Rap1 and that this is dependent on production of diacylglycerol (DAG) by phospholipase C-gamma. Activation of Rap1 by the BCR was greatly reduced in phospholipase C-gamma-deficient B cells, whereas both a synthetic DAG and phorbol dibutyrate could activate Rap1 in B cells. We had previously shown that C3G, an activator of Rap1, associates with the Crk adaptor proteins in B cells and that BCR engagement causes Crk to bind to the Cas and Cbl docking proteins. However, the DAG-dependent pathway by which the BCR activates Rap1 apparently does not involve Crk signaling complexes since phorbol dibutyrate could activate Rap1 without inducing the formation of these complexes. Thus, the BCR activates Rap1 via a novel DAG-dependent pathway.

Children recovered from stuttering without formal treatment: perceptual assessment of speech normalcy

Current evidence suggests that young children who recover from stuttering are essentially stutter-free. However, there is no evidence to indicate if their speech is perceptually indistinguishable from normally fluent peers or whether they retain perceptually unusual speech. One important example of recovery from stuttering is children who have recovered without receiving formal treatment. An investigation was conducted to determine if the speech of these children is perceptually different from the speech of children who have never stuttered. Speakers consisted of 10 preschool and early school-age children documented as recovered from stuttering without benefit of formal treatment. In a series of studies they were compared with 10 children who had never stuttered. Three groups of judges-sophisticated, unsophisticated, and experienced-were separately asked, using videotaped speech samples of the children, to decide which samples were from children who used to stutter. Results revealed that the children who recovered from stuttering were perceptually indistinguishable from the normal controls. The same result was obtained regardless of whether the samples were presented in paired-stimulus or single-stimulus mode. Two of the groups of judges were also instructed to rate the speech naturalness of the speech samples. The speakers were not distinguished on this measure either. Methodological issues and the implications of the findings are discussed.

Identifying the authoritative judgments of stuttering: comparisons of self-judgments and observer judgments

Reliable and accurate stuttering measurement depends on the existence of unambiguous descriptions or exemplars of stuttered and nonstuttered speech. The development of clinically meaningful and useful exemplars, in turn, requires determining whether persons who stutter judge the same speech to be stuttered that other observers judge to be stuttered. The purpose of these experiments, therefore, was to compare stuttering judgements from several sources: 15 adults who stutter, judging their own spontaneous speech; the same adults who stutter, judging each other's speech; and a panel of 10 authorities on stuttering research and treatment. Judgments were mode under several conditions, including self-judgments made while the speaker was talking and self- and other-judgements made from recordings in continuous and interval formats. Results showed substantial differences in stuttering judgments across speakers, judges, and judgment conditions, but across-task comparisons were complicated by low self-agreement for many judges. Some intervals were judged consistently by all judges to be Stuttered or Nonstuttered, across multiple conditions, but many other intervals were either not assigned replicable judgments or were consistently judged to be Nonstuttered by the speaker who had produced them but were not assigned consistent judgments by other judges. The implications of these findings for stuttering measurement are considered.

Experimental investigation of the effects of frequency-altered auditory feedback on the speech of adults who stutter

A series of single-subject experiments evaluated the effects of frequency-altered auditory feedback (FAF) on the speech performance of four adult males who stutter. Using alterations of plus or minus one octave, FAF was compared with normal auditory feedback (NAF) in oral reading and spontaneous speech with measurements made of stuttered intervals, stutter-free speech rate, and speech naturalness. The effects of extended FAF conditions on spontaneous speech were also evaluated for two subjects who demonstrated a positive response to FAF. Results showed no consistencies across subjects in responses to FAF: One subject showed no response, another produced an initial temporary response, a third showed a deterioration in speech quality with minimal reductions in stuttering, and a fourth displayed substantial and sustained improvements in speech performance. Some implications of these findings for current research and theory about the relationship between stuttering and FAF are discussed.

Effect of speech dialect on speech naturalness ratings: a systematic replication of Martin, Haroldson, and Triden (1984)

This study investigated the effect of speech dialect on listeners' speech naturalness ratings by systematically replicating Martin, Haroldson, and Triden's (1984) study using three groups of speaker samples. Two groups consisted of speakers with General American dialect--one with persons who stutter and the other with persons who do not stutter. The third group also consisted of speakers who do not stutter but who spoke non-General American dialect. The results showed that speech naturalness ratings distinguished among the three speaker groups. The variables that appeared to influence speech naturalness ratings were type of dialect, speech fluency, and speaking rate, though they differed across speaker groups. The findings also suggested that strength of speech dialect may be a scaleable dimension that judges can rate with acceptable levels of reliability. Dialect may also be an important factor that needs to be incorporated or controlled within systems designed to train speech naturalness ratings. It may also be an important factor in determining the extent to which stuttering treatment produces natural sounding speech.

B cell antigen receptor signaling induces the formation of complexes containing the Crk adapter proteins

Crk proteins are Src homology (SH) 2/SH3-containing adapter proteins that can mediate the formation of signaling complexes. We show that engaging the B cell antigen receptor (BCR) on the RAMOS B cell line caused both Crk-L and Crk II to associate with several tyrosine-phosphorylated proteins. We identified two of these phosphoproteins as Cas and Cbl and showed that both bound to the Crk SH2 domain after BCR engagement. BCR ligation also increased the amount of Crk proteins in the particulate fraction of the cells and induced the formation of Crk.Cas and Crk.Cbl complexes in the particulate fraction. We propose that tyrosine phosphorylation of membrane-associated Cas and Cbl creates binding sites for the Crk SH2 domain and recruits Crk complexes to cellular membranes. Thus, Crk proteins may participate in BCR signaling by using their SH2 domains to direct the interactions and subcellular localization of proteins that bind to their SH3 domains. In RAMOS cells, we found that the SH3 domains of Crk-L and Crk II bound C3G. Since C3G activates Rap, a negative regulator of the Ras pathway, Crk proteins may participate in regulation of Ras signaling by the BCR.

Functional-lesion investigation of developmental stuttering with positron emission tomography

Positron emission tomographic (PET) H2(15)O measurements of resting-state regional cerebral blood flow (CBF) were obtained in 29 right-handed men, 10 of whom stuttered and 19 of whom did not. PET images were analyzed by sampling 74 regions of interest (ROIs), 37 per hemisphere. ROI placement was guided both physiologically and anatomically. Physiological ROI placement was based on speech motor activations. Anatomical ROIs were positioned by reference to a stereotactic, neurosurgical atlas with positions confirmed and finely adjusted by co-registered magnetic-resonance images (MRIs). For all subjects, PET and MR images were normal to visual inspection. Highly significant (p < 0.0001) between-region and between-hemisphere effects were found for both groups, as have been previously reported for normal subjects, but no significant between-group differences were found for any regional CBF values. Analysis by a laterality index found a weakly significant between-groups effect (p = 0.04) that was isolated to five regions, four of which are implicated in speech or hearing. However, these regional laterality effects showed no consistent directionality, nor did these regions have absolute differences in regional blood flow between groups. Present findings do not support recent suggestions that developmental stuttering is associated with abnormalities of brain blood flow at rest. Rather, our findings indicate an essentially normal functional brain terrain with a small number of minor differences in hemispheric symmetry.

A PET study of the neural systems of stuttering

The cause of stuttering is unknown. Failure to develop left-hemispheric dominance for speech is a long-standing theory although others implicated the motor system more broadly, often postulating hyperactivity of the right (language nondominant) cerebral hemisphere. As knowledge of motor circuitry has advanced, theories of stuttering have become more anatomically specific, postulating hyperactivity of premotor cortex, either directly or through connectivity with the thalamus and basal ganglia. Alternative theories target the auditory and speech production systems. By contrasting stuttering with fluent speech using positron emission tomography combined with chorus reading to induce fluency, we found support for each of these hypotheses. Stuttering induced widespread overactivations of the motor system in both cerebrum and cerebellum, with right cerebral dominance. Stuttered reading lacked left-lateralized activations of the auditory system, which are thought to support the self-monitoring of speech, and selectively deactivated a frontal-temporal system implicated in speech production. Induced fluency decreased or eliminated the overactivity in most motor areas, and largely reversed the auditory-system underactivations and the deactivation of the speech production system. Thus stuttering is a disorder affecting the multiple neural systems used for speaking.

Time-interval measurement of stuttering: establishing and modifying judgment accuracy

The purpose of this study was to determine whether accuracy training for interval judgments of stuttering might generalize to increased accuracy and/or interjudge agreement for intervals other than those used during training. Ten upper-division speech-language pathology students judged 5-s audiovisually recorded speech intervals as stuttered or nonstuttered in a series of group and single-subject experiments. Judgment accuracy was determined with respect to judgments provided previously by 10 recognized authorities on stuttering and its treatment. Training occurred within single-subject experiments that used multiple baselines across speakers and repeated generalization probes to assess training effects. Results showed that judgment accuracy tended to increase after training for speakers used during the training process as well as for unfamiliar speakers. Results also replicated previous findings of slight increases in interjudge and intrajudge agreement after interval-judgment training. The implications of these results for developing a valid and reliable stuttering measurement system are discussed.

Identifying the onset and offset of stuttering events

This study was designed to investigate the apparent contradiction between recent reports of physiological and interpersonal research on stuttering that claim or imply high agreement levels, and studies of stuttering judgment agreement itself that report much lower agreement levels. Four experienced stuttering researchers in one university department used laser videodisks of spontaneous speech, from persons whose stuttering could be described as mild to severe, to locate the precise onset and offset of individual stuttering events. Results showed a series of interjudge disagreements that raise serious questions about the reliability and validity of stuttering event onset and offset judgments. These results highlight the potentially poor reliability of a measurement procedure that is currently widespread in stuttering research. At the same time, they have isolated some few highly agreed stuttering events that might serve as the basis for the further development of either event-based or interval-based judgment procedures.

Stuttering includes both within-word and between-word disfluencies

A growing practice divides stuttered disfluencies from normal disfluencies by defining the former as "within-word" and the latter as "between-word." After reviewing the available logical and empirical evidence, this note concludes that the unstated implications of a strong form of this definition (that no between-word disfluencies are stuttering and that all within-word disfluencies are stuttering) cannot currently be supported. A weaker form of this definition might prove useful for the definition and measurement of stuttering, but only if such a definition can be both internally consistent and consistent with available clinical and empirical information.

Judgments of stuttered and nonstuttered intervals by recognized authorities in stuttering research

The study reported in this paper gathered judgments of stuttering on brief (5.0-sec) audiovisual speech samples taken from six adults who stuttered. Judgments were made by 10 highly experienced authorities on stuttering treatment and research, located in seven different universities or clinical research centers. Results showed considerable agreement between pairs of judges working in the same center, but large and potentially fundamental differences were identified in the amount of stuttering recorded in different centers. Approximately 40% of the 5.0-sec speech intervals used in this study were assigned the same judgment, either Stuttered or Nonstuttered, by all judges on two judgment occasions. The possibility that these intervals may serve as a core for establishing an across-center standard for behavioral judgments of stuttering is discussed.

Time-interval measurement of stuttering: effects of training with highly agreed or poorly agreed exemplars

This study required six groups of judges, three experimental groups and three control groups (all n = 5), to categorize consecutive 5.0-sec speech intervals as Stuttered or Nonstuttered on four judgment occasions. Between the second and third occasions, each experimental group was trained to categorize correctly one of three sets of speech intervals: agreed intervals, which had been unanimously prejudged to be Stuttered or Nonstuttered; disagreed intervals, which had been prejudged to be Stuttered by approximately half of a large group of judges; or randomly selected intervals, including both agreed and disagreed intervals. Results replicated and extended an earlier finding of improved interjudge agreement for judges trained with highly agreed intervals (Ingham, Cordes, & Gow, 1993): Training with highly agreed intervals was shown to be more effective than equivalent exposure to those intervals without feedback, and training with highly agreed intervals was shown to be more effective than training with, or exposure to, poorly agreed or randomly selected intervals.

Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes

We show that cross-linking the B cell AgR with anti-Ig Abs activates p56lck (Lck) in both the immature B cell line WEHI-231 and mature resting B cells from mouse spleen. Anti-Ig-stimulated Lck activity peaked after 1 to 2 min, but remained elevated for at least 15 min. Consistent with the proposed role for src family tyrosine kinases in AgR signaling, we found that Lck could phosphorylate the cytoplasmic tails of the Ig-alpha and Ig-beta components of the B cell AgR in vitro. Lck phosphorylated both of the tyrosines in the Ig-beta AgR homology motif and one of the two tyrosines in the Ig-alpha AgR homology motif. Finally, we show that AgR ligation in B cells caused a significant portion of the Lck to migrate with an apparent molecular mass of 60 kDa on SDS-PAGE gels. Conversion of p56lck to p60lck was maximal at 5 to 15 min, at which times Lck activity in the cells was decreasing. This Lck "band shift" has been observed previously in activated T cells and correlates with phosphorylation of Lck at serine 59. We show that the 60-kDa form of Lck induced by AgR cross-linking in B cells is also phosphorylated at serine 59. Phosphorylation of Lck at this site in vitro decreases its activity. Thus, in B cells, AgR cross-linking activates Lck and subsequently activates a kinase that phosphorylates Lck at serine 59, a potential negative regulatory site.

Activation and serine phosphorylation of the p56lck protein tyrosine kinase in response to antigen receptor cross-linking in B lymphocytes

We show that cross-linking the B cell AgR with anti-Ig Abs activates p56lck (Lck) in both the immature B cell line WEHI-231 and mature resting B cells from mouse spleen. Anti-Ig-stimulated Lck activity peaked after 1 to 2 min, but remained elevated for at least 15 min. Consistent with the proposed role for src family tyrosine kinases in AgR signaling, we found that Lck could phosphorylate the cytoplasmic tails of the Ig-alpha and Ig-beta components of the B cell AgR in vitro. Lck phosphorylated both of the tyrosines in the Ig-beta AgR homology motif and one of the two tyrosines in the Ig-alpha AgR homology motif. Finally, we show that AgR ligation in B cells caused a significant portion of the Lck to migrate with an apparent molecular mass of 60 kDa on SDS-PAGE gels. Conversion of p56lck to p60lck was maximal at 5 to 15 min, at which times Lck activity in the cells was decreasing. This Lck "band shift" has been observed previously in activated T cells and correlates with phosphorylation of Lck at serine 59. We show that the 60-kDa form of Lck induced by AgR cross-linking in B cells is also phosphorylated at serine 59. Phosphorylation of Lck at this site in vitro decreases its activity. Thus, in B cells, AgR cross-linking activates Lck and subsequently activates a kinase that phosphorylates Lck at serine 59, a potential negative regulatory site.

Time-interval measurement of stuttering: effects of interval duration

The study reported in this article used a binary forced-choice judgment procedure to investigate the effects of sample duration on observers' judgements of stuttering. Two groups of judges, differing in their previous experience with stuttering, categorized 270 speech intervals as stuttered or nonstuttered; the intervals were drawn from 30 persons who stuttered and ranged from 1 sec to 15 sec in duration. Results showed that judgments were consistently related to interval duration, with shorter intervals significantly more likely than longer intervals to be labeled nonstuttered. Interjudge agreement levels, however, were largely unaffected by the different interval durations for most speakers and for both judge groups, with the exception of the longest and shortest intervals drawn from speakers evidencing the mildest and most severe stuttering. An interval duration in the 3- to 5-sec region appeared to attract the most satisfactory level of agreement. The implications of these findings for interval-based clinical and experimental measurements of stuttering are discussed.

The reliability of observational data: II. Issues in the identification and measurement of stuttering events

Much attention has been directed recently toward the problem of measuring occurrences of stuttering with satisfactory levels of interjudge agreement. This paper reviews the prominent concepts of the stuttering event, arguing that they may be one cause of the stuttering measurement problem. The evidence that has led to concerns about the reliability of stuttering event measurements is also reviewed. Reliability and measurement issues that were discussed in the first paper of this series (Cordes, 1994) emerge as basic to the interpretation of much stuttering research, and it is argued that the stuttering measurement problem is not confined to research on stuttering judgments but actually permeates other important stuttering research areas. Some recent attempts to resolve the stuttering measurement problem are reviewed, and the implications of developing an improved measurement system for this disorder are discussed.

Stutterers' self-ratings of how natural speech sounds and feels

The efficacy of stuttering treatment has been a contentious issue in recent years. Two issues of primary concern include the treated stutterer's abnormal speech quality and the problem of continually self-monitoring fluency skills. One approach to addressing these issues is to obtain stutterers' self-ratings of speech quality and levels of speech monitoring. However, the reliability and validity of such self-ratings need to be assessed before they are suitable for use in stuttering treatment. The present study investigated one method of estimating the reliability and validity of stutterers' self-ratings of how natural their speech sounds (speech naturalness), and how natural they feel about the amount of attention they are paying to the way they are speaking (feel naturalness). Twelve adult stutterers were instructed to self-rate the speech and feel naturalness of their speech under a variety of rhythmic stimulation conditions across repeated rating occasions. With some qualifications, the results showed that stutterers were relatively consistent and valid self-raters of speech quality and levels of speech monitoring.

Purification and identification of tyrosine-phosphorylated proteins from B lymphocytes stimulated through the antigen receptor

The activation of protein tyrosine kinase (PTKs) and subsequent tyrosine phosphorylation of cellular proteins is a critical initial signal in the response of eukaryotic cells to mitogens, differentiative signals, and other stimuli. A number of PTK substrates have been identified and many of these are components of signal transduction pathways that regulate cell function. However, the majority of proteins that are tyrosine-phosphorylated in response to receptor signaling remain unidentified. As some of these unidentified PTK substrates may also be signal-transducing proteins, their identification and functional characterization is an important objective towards understanding receptor signaling. We describe the development of a comprehensive and general process for the isolation and structural characterization of tyrosine-phosphorylated proteins. The method involves enrichment by anti-phosphotyrosine affinity chromatography, electrophoretic concentration and separation, and proteolytic fragmentation of individual purified phosphoproteins. Resulting peptide fragments are separated by microbore reverse-phase high performance liquid chromatography (RP-HPLC) and a portion of the eluted peptides are subjected to electrospray-mass spectrometry (ES/MS) for accurate determination of peptide masses. Proteolytic fragmentation of a protein produces a characteristic set of peptide masses that can be used to rapidly identify the protein by searching databases containing the peptide mass "fingerprints" for all known proteins. The identity of the protein established by this method can be confirmed by sequence analysis of selected peptides. We have applied this procedure to the analysis of PTK substrates from B lymphocytes that have been stimulated through the B cell antigen receptor (BCR). Signaling by this receptor is involved in the generation of antibodies against foreign molecules (antigens). The BCR activates multiple PTKs which phosphorylate at least 30 different proteins. We have identified several of these tyrosine-phosphorylated proteins, including Syk, a PTK that is known to be tyrosine-phosphorylated in activated B cells. Thus, the procedure described here can be used to identify regulatory proteins of low abundance. The process consists of a logical succession of compatible steps that avoids pitfalls inherent to prior attempts to characterize low abundance phosphoproteins and should find wide use for the identification of tyrosine-phosphorylated proteins in other cell types.

Time-interval measurement of stuttering: systematic replication of Ingham, Cordes, and Gow (1993)

The study reported in this paper was designed to replicate and extend the results of an earlier study (Ingham, Cordes, & Gow, 1993) that investigated time-interval judgments of stuttering. Results confirmed earlier findings that interjudge agreement is higher for these interval-recording tasks than has been previously reported for event-based analyses of stuttering judgments or for time-interval analyses of event judgments. Results also confirmed an earlier finding that judges with intrajudge agreement levels of 90% or better show higher interjudge agreement than judges with lower intrajudge agreement scores. This study failed to find differences between audiovisual and audio-only judgment conditions; between relatively experienced and relatively inexperienced student judges; and, most importantly, between the judgments made, and the agreement levels achieved, by judges from two different clinical research settings. The implications of these findings for attempts to develop a reliable measurement method for stuttering are discussed.

Time-interval measurement of stuttering: modifying interjudge agreement

This paper reports the results of two experiments that investigated interval-by-interval inter- and intrajudge agreement for stuttered and nonstuttered speech intervals (4.0 sec). The first experiment demonstrated that interval-by-interval interjudge agreement could be significantly improved, and to satisfactory levels, by training judges to discriminate between experimenter-agreed intervals of stuttered and nonstuttered speech. The findings also showed that, independent of training, judges with relatively high intrajudge agreement also showed relatively higher interjudge agreement. The second experiment showed that interval-by-interval interjudge agreement was not significantly different if judges rated 4-sec speech intervals from different samples under three conditions: in random order, separated by 5-sec recording intervals; in correct order, also separated by 5-sec recording intervals; or after brief judgment signals that occurred every 4 sec during continuous samples. The implications of these findings for stuttering measurement are discussed.