Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting, stop-carry on, termination-reinitiation, and translational bypassing), the two most extensively employed by RNA viruses are Programmed Ribosomal Frameshifting (PRF) and Programmed Ribosomal Readthrough (PRT). While both PRT and PRF subvert normal decoding for expression of C-terminal extension products, the former involves an alteration of reading frame, and the latter requires decoding of a non-sense codon. Both processes occur at a low but defined frequency, and both require Recoding Stimulatory Elements (RSE) for regulation and optimum functionality. These stimulatory signals can be embedded in the RNA in the form of sequence or secondary structure, or trans-acting factors outside the mRNA such as proteins or micro RNAs (miRNA). Despite 40+ years of study, the precise mechanisms by which viral RSE mediate ribosome recoding for the synthesis of their proteins, or how the ratio of these products is maintained, is poorly defined. This study reveals that in addition to a long distance RNA:RNA interaction, three alternate conformations and a phylogenetically conserved pseudoknot regulate PRT in the carmovirus Turnip crinkle virus (TCV).

Addressing the needs of struggling literacy learners

Think back to your teaching experiences over the past four years. Were there a number of children or adolescents in your classes who seemed to have learning difficulties? What area of their learning seemed to be of greatest concern for these students? Did most of these struggling learners have difficulty with reading? Was expressing their thoughts in writing also a challenge? Did some of these students also have difficulty in listening to and following directions? And did some of these students seem hesitant when asked to speak to the class?

Sources of coding discrepancies in injury morbidity data: Implications for injury surveillance

Objective: To examine the sources of coding discrepancy for injury morbidity data and explore the implications of these sources for injury surveillance.-------- Method: An on-site medical record review and recoding study was conducted for 4373 injury-related hospital admissions across Australia. Codes from the original dataset were compared to the recoded data to explore the reliability of coded data aand sources of discrepancy.---------- Results: The most common reason for differences in coding overall was assigning the case to a different external cause category with 8.5% assigned to a different category. Differences in the specificity of codes assigned within a category accounted for 7.8% of coder difference. Differences in intent assignment accounted for 3.7% of the differences in code assignment.---------- Conclusions: In the situation where 8 percent of cases are misclassified by major category, the setting of injury targets on the basis of extent of burden is a somewhat blunt instrument Monitoring the effect of prevention programs aimed at reducing risk factors is not possible in datasets with this level of misclassification error in injury cause subcategories. Future research is needed to build the evidence base around the quality and utility of the ICD classification system and application of use of this for injury surveillance in the hospital environment.

The effects of L1 orthography on processing an artificial logographic script

To date, studies have focused on the acquisition of alphabetic second languages (L2s) in alphabetic first language (L1) users, demonstrating significant transfer effects. The present study examined the process from a reverse perspective, comparing logographic (Mandarin-Chinese) and alphabetic (English) L1 users in the acquisition of an artificial logographic script, in order to determine whether similar language-specific advantageous transfer effects occurred. English monolinguals, English-French bilinguals and Chinese-English bilinguals learned a small set of symbols in an artificial logographic script and were subsequently tested on their ability to process this script in regard to three main perspectives: L2 reading, L2 working memory (WM), and inner processing strategies. In terms of L2 reading, a lexical decision task on the artificial symbols revealed markedly faster response times in the Chinese-English bilinguals, indicating a logographic transfer effect suggestive of a visual processing advantage. A syntactic decision task evaluated the degree to which the new language was mastered beyond the single word level. No L1-specific transfer effects were found for artificial language strings. In order to investigate visual processing of the artificial logographs further, a series of WM experiments were conducted. Artificial logographs were recalled under concurrent auditory and visuo-spatial suppression conditions to disrupt phonological and visual processing, respectively. No L1-specific transfer effects were found, indicating no visual processing advantage of the Chinese-English bilinguals. However, a bilingual processing advantage was found indicative of a superior ability to control executive functions. In terms of L1 WM, the Chinese-English bilinguals outperformed the alphabetic L1 users when processing L1 words, indicating a language experience-specific advantage. Questionnaire data on the cognitive strategies that were deployed during the acquisition and processing of the artificial logographic script revealed that the Chinese-English bilinguals rated their inner speech as lower than the alphabetic L1 users, suggesting that they were transferring their phonological processing skill set to the acquisition and use of an artificial script. Overall, evidence was found to indicate that language learners transfer specific L1 orthographic processing skills to L2 logographic processing. Additionally, evidence was also found indicating that a bilingual history enhances cognitive performance in L2.

Reliability of routinely collected hospital data for child maltreatment surveillance

Background: Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. Methods: A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. Results: In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most ‘under-coded’ by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Conclusion: Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting.

Elements pour adapter les systemes de recherche d'information aux dyslexiques [Elements to adapt information retrieval systems to dyslexic users]

RÉSUMÉ. La prise en compte des troubles de la communication dans l’utilisation des systèmes de recherche d’information tels qu’on peut en trouver sur le Web est généralement réalisée par des interfaces utilisant des modalités n’impliquant pas la lecture et l’écriture. Peu d’applications existent pour aider l’utilisateur en difficulté dans la modalité textuelle. Nous proposons la prise en compte de la conscience phonologique pour assister l’utilisateur en difficulté d’écriture de requêtes (dysorthographie) ou de lecture de documents (dyslexie). En premier lieu un système de réécriture et d’interprétation des requêtes entrées au clavier par l’utilisateur est proposé : en s’appuyant sur les causes de la dysorthographie et sur les exemples à notre disposition, il est apparu qu’un système combinant une approche éditoriale (type correcteur orthographique) et une approche orale (système de transcription automatique) était plus approprié. En second lieu une méthode d’apprentissage automatique utilise des critères spécifiques , tels que la cohésion grapho-phonémique, pour estimer la lisibilité d’une phrase, puis d’un texte. ABSTRACT. Most applications intend to help disabled users in the information retrieval process by proposing non-textual modalities. This paper introduces specific parameters linked to phonological awareness in the textual modality. This will enhance the ability of systems to deal with orthographic issues and with the adaptation of results to the reader when for example the reader is dyslexic. We propose a phonology based sentence level rewriting system that combines spelling correction, speech synthesis and automatic speech recognition. This has been evaluated on a corpus of questions we get from dyslexic children. We propose a specific sentence readability measure that involves phonetic parameters such as grapho-phonemic cohesion. This has been learned on a corpus of reading time of sentences read by dyslexic children.

The acquisition of an artificial logographic script and bilingual working memory : Evidence for L1-specific orthographic processing skills transfer in Chinese-English bilinguals

Studies of orthographic skills transfer between languages focus mostly on working memory (WM) ability in alphabetic first language (L1) speakers when learning another, often alphabetically congruent, language. We report two studies that, instead, explored the transferability of L1 orthographic processing skills in WM in logographic-L1 and alphabetic-L1 speakers. English-French bilingual and English monolingual (alphabetic-L1) speakers, and Chinese-English (logographic-L1) speakers, learned a set of artificial logographs and associated meanings (Study 1). The logographs were used in WM tasks with and without concurrent articulatory or visuo-spatial suppression. The logographic-L1 bilinguals were markedly less affected by articulatory suppression than alphabetic-L1 monolinguals (who did not differ from their bilingual peers). Bilinguals overall were less affected by spatial interference, reflecting superior phonological processing skills or, conceivably, greater executive control. A comparison of span sizes for meaningful and meaningless logographs (Study 2) replicated these findings. However, the logographic-L1 bilinguals’ spans in L1 were measurably greater than those of their alphabetic-L1 (bilingual and monolingual) peers; a finding unaccounted for by faster articulation rates or differences in general intelligence. The overall pattern of results suggests an advantage (possibly perceptual) for logographic-L1 speakers, over and above the bilingual advantage also seen elsewhere in third language (L3) acquisition.

Use of a clay modeling task to reduce chocolate craving

Elaborated Intrusion theory (EI theory; Kavanagh, Andrade, & May, 2005) posits two main cognitive components in craving: associative processes that lead to intrusive thoughts about the craved substance or activity, and elaborative processes supporting mental imagery of the substance or activity. We used a novel visuospatial task to test the hypothesis that visual imagery plays a key role in craving. Experiment 1 showed that spending 10 min constructing shapes from modeling clay (plasticine) reduced participants' craving for chocolate compared with spending 10 min 'letting your mind wander'. Increasing the load on verbal working memory using a mental arithmetic task (counting backwards by threes) did not reduce craving further. Experiment 2 compared effects on craving of a simpler verbal task (counting by ones) and clay modeling. Clay modeling reduced overall craving strength and strength of craving imagery, and reduced the frequency of thoughts about chocolate. The results are consistent with EI theory, showing that craving is reduced by loading the visuospatial sketchpad of working memory but not by loading the phonological loop. Clay modeling might be a useful self-help tool to help manage craving for chocolate, snacks and other foods.

Supporting children's language and literacy skills : the effectiveness of shared book reading intervention strategies with parents

Parents are encouraged to read with their children from an early age because shared book reading helps children to develop their language and early literacy skills. A pragmatic Randomised Controlled Trial (RCT) research design was adopted to investigate the influence of two forms of a shared reading intervention (Dialogic Reading and Dialogic Reading with the addition of Print Referencing) on children’s language and literacy skills. Dialogic reading is a validated shared reading intervention that has been shown to improve children’s oral language skills prior to formal schooling (Whitehurst & Lonigan, 1998). Print referencing is another form of shared reading intervention that has the potential to have effects on children’s print knowledge as they begin school (Justice & Ezell, 2002). However, training parents to use print referencing strategies at home has not been researched extensively although research findings indicate its effectiveness when used by teachers in the early years of school. Eighty parents of Preparatory year children from three Catholic schools in low income areas in the outer suburbs of a metropolitan city were trained to deliver specific shared reading strategies in an eight-week home intervention. Parents read eight books to their children across the period of the intervention. Each book was requested to be read at least three times a week. There were 42 boys and 38 girls ranging in age from 4.92 years to 6.25 years (M=5.53, SD=0.33) in the sample. The families were randomly assigned to three groups: Dialogic Reading (DR); Dialogic Reading with the addition of Print Referencing (DR + PR); and a Control group. Six measures were used to assess children’s language skills at pre and post, and follow-up (three months after the intervention). These measures assessed oral language (receptive and expressive vocabulary), phonological awareness skills (rhyme, word completion), alphabet knowledge, and concepts about print. Results of the intervention showed that there were significant differences from pre to post between the two intervention groups and the control group on three measures: expressive vocabulary, rhyme, and concepts about print. The shared reading strategies delivered by parents of the dialogic reading, and dialogic reading with the addition of print referencing, showed promising results to develop children’s oral language skills in terms of expressive vocabulary and rhyme, as well as understanding of the concepts about print. At follow-up, when the children entered Year 1, the two intervention groups (DR and DR + PR) group had significantly maintained their knowledge of concepts about prints when compared with the control group. Overall, the findings from this intervention study did not show that dialogic reading with the addition of print referencing had stronger effects on children’s early literacy skills than dialogic reading alone. The research also explored if pre-existing family factors impacted on the outcomes of the intervention from pre to post. The relationships between maternal education and home reading practices prior to intervention and child outcomes at post were considered. However, there were no significant effects of maternal education and home literacy activities on child outcomes at post. Additionally, there were no significant effects for the level of compliance of parents with the intervention program in terms of regular weekly reading to children during the intervention period on child outcomes at post. These non-significant findings are attributed to the lack of variability in the recruited sample. Parents participating in the intervention had high levels of education, although they were recruited from schools in low socio-economic areas; parents were already highly engaged in home literacy activities at recruitment; and the parents were highly compliant in reading regularly to their child during the intervention. Findings of the current study did show that training in shared reading strategies enhanced children’s early language and literacy skills. Both dialogic reading and dialogic reading with the addition of print referencing improved children’s expressive vocabulary, rhyme, and concepts about print at post intervention. Further research is needed to identify how, and if, print referencing strategies used by parents at home can be effective over and above the use of dialogic reading strategies. In this research, limitations of sample size and the nature of the intervention to use print referencing strategies at home may have restricted the opportunities for this research study to find more effects on children’s emergent literacy skills or for the effectiveness of combining dialogic reading with print referencing strategies. However, these results did indicate that there was value in teaching parents to implement shared reading strategies at home in order to improve early literacy skills as children begin formal schooling.

Differential entrainment of neuroelectric delta oscillations in developmental dyslexia

Oscillatory entrainment to the speech signal is important for language processing, but has not yet been studied in developmental disorders of language. Developmental dyslexia, a difficulty in acquiring efficient reading skills linked to difficulties with phonology (the sound structure of language), has been associated with behavioural entrainment deficits. It has been proposed that the phonological ‘deficit’ that characterises dyslexia across languages is related to impaired auditory entrainment to speech at lower frequencies via neuroelectric oscillations (<10 Hz, ‘temporal sampling theory’). Impaired entrainment to temporal modulations at lower frequencies would affect the recovery of the prosodic and syllabic structure of speech. Here we investigated event-related oscillatory EEG activity and contingent negative variation (CNV) to auditory rhythmic tone streams delivered at frequencies within the delta band (2 Hz, 1.5 Hz), relevant to sampling stressed syllables in speech. Given prior behavioural entrainment findings at these rates, we predicted functionally atypical entrainment of delta oscillations in dyslexia. Participants performed a rhythmic expectancy task, detecting occasional white noise targets interspersed with tones occurring regularly at rates of 2 Hz or 1.5 Hz. Both groups showed significant entrainment of delta oscillations to the rhythmic stimulus stream, however the strength of inter-trial delta phase coherence (ITC, ‘phase locking’) and the CNV were both significantly weaker in dyslexics, suggestive of weaker entrainment and less preparatory brain activity. Both ITC strength and CNV amplitude were significantly related to individual differences in language processing and reading. Additionally, the instantaneous phase of prestimulus delta oscillation predicted behavioural responding (response time) for control participants only.

A shared reading intervention with parents to enhance young children’s early literacy skills

Parental reading to children from an early age has been shown to enhance children’s emergent literacy skills. A pragmatic randomized controlled trial (RCT) was used to investigate the effects of two forms of shared reading interventions on children’s language and literacy skills. Parents of 80 preparatory year children from outer suburban schools of an Australian metropolitan city were trained to use shared reading strategies in an eight-week home intervention. Families were assigned to one of three groups: Dialogic Reading (DR), Dialogic Reading with the addition of Print Referencing (DR + PR), or an attention-matched control group. The sample comprised 42 boys and 38 girls ranging in age from 4.9 years to 6.3 years (M = 5.5, SD = 0.3). Data were collected at pre, post, and at three months follow-up. Measures assessed children’s oral language (receptive and expressive vocabulary), phonological awareness (rhyme, word completion), alphabet knowledge, and concepts about print. Analyses of change from pre to post showed significant effects for the DR and DR + PR groups compared to the control group on three of the six measures: expressive language, rhyme, and concepts about print. At 3-month follow-up assessment, the two intervention groups maintained significantly better performance on the measure of concepts of print only. At both time points, there were no group differences between the DR and DR+PR conditions. These findings illustrate the potential of a brief home focused intervention on promoting children’s emergent literacy.

Recontextualising policy discourses : a Bernsteinian perspective on policy interpretation, translation, enactment

This paper contributes to critical policy research by theorising one aspect of policy enactment, the meaning making work of a cohort of mid-level policy actors. Specifically, we propose that Basil Bernstein’s work on the structuring of pedagogic discourse, in particular, the concept of recontextualisation, may add to understandings of the policy work of interpretation and translation. Recontextualisation refers to the relational processes of selecting and moving knowledge from one context to another, as well as to the distinctive re-organisation of knowledge as an instructional and regulative or moral discourse. Processes of recontextualisation necessitate an analysis of power and control relations, and therefore add to the Foucauldian theorisations of power that currently dominate the critical policy literature. A process of code elaboration (decoding and recoding) takes place in various recontextualising agencies, responsible for the production of professional development materials, teaching guidelines and curriculum resources. We propose that mid-level policy actors are crucial to the work of policy interpretation and translation because they are engaged in elaborating the condensed codes of policy texts to an imagined logic of teachers’ practical work. To illustrate our theoretical points we draw on data; collected for an Australian research project on the accounts of mid-level policy actors responsible for the interpretation of child protection and safety policies for staff in Queensland schools.

Dissociating verbal and nonverbal audiovisual object processing

This fMRI study investigates how audiovisual integration differs for verbal stimuli that can be matched at a phonological level and nonverbal stimuli that can be matched at a semantic level. Subjects were presented simultaneously with one visual and one auditory stimulus and were instructed to decide whether these stimuli referred to the same object or not. Verbal stimuli were simultaneously presented spoken and written object names, and nonverbal stimuli were photographs of objects simultaneously presented with naturally occurring object sounds. Stimulus differences were controlled by including two further conditions that paired photographs of objects with spoken words and object sounds with written words. Verbal matching, relative to all other conditions, increased activation in a region of the left superior temporal sulcus that has previously been associated with phonological processing. Nonverbal matching, relative to all other conditions, increased activation in a right fusiform region that has previously been associated with structural and conceptual object processing. Thus, we demonstrate how brain activation for audiovisual integration depends on the verbal content of the stimuli, even when stimulus and task processing differences are controlled.

The effect of prior visual information on recognition of speech and sounds

To identify and categorize complex stimuli such as familiar objects or speech, the human brain integrates information that is abstracted at multiple levels from its sensory inputs. Using cross-modal priming for spoken words and sounds, this functional magnetic resonance imaging study identified 3 distinct classes of visuoauditory incongruency effects: visuoauditory incongruency effects were selective for 1) spoken words in the left superior temporal sulcus (STS), 2) environmental sounds in the left angular gyrus (AG), and 3) both words and sounds in the lateral and medial prefrontal cortices (IFS/mPFC). From a cognitive perspective, these incongruency effects suggest that prior visual information influences the neural processes underlying speech and sound recognition at multiple levels, with the STS being involved in phonological, AG in semantic, and mPFC/IFS in higher conceptual processing. In terms of neural mechanisms, effective connectivity analyses (dynamic causal modeling) suggest that these incongruency effects may emerge via greater bottom-up effects from early auditory regions to intermediate multisensory integration areas (i.e., STS and AG). This is consistent with a predictive coding perspective on hierarchical Bayesian inference in the cortex where the domain of the prediction error (phonological vs. semantic) determines its regional expression (middle temporal gyrus/STS vs. AG/intraparietal sulcus).

Psycho-educational assessment of specific learning disabilities: Views and practices of Australian psychologists and guidance counsellors

This paper reports an investigation of the views and practices of 203 Australian psychologists and guidance counsellors with respect to psycho-educational assessment of students with Specific Learning Disabilities (SLDs). Results from an online survey indicated that practitioners draw upon a wide-range of theoretical perspectives when conceptualising and identifying SLDs, including both response to intervention and IQ – achievement discrepancy models. Intelligence tests (particularly the Wechsler scales) are commonly employed, with the main stated reasons for their use being ‘traditional’ perspectives (including IQ-achievement discrepancy-based definitions of SLDs), to exclude a diagnosis of intellectual disability, and to guide further assessment and intervention. In contrast participants reported using measures of academic achievement and tests of specific cognitive deficits known to predict SLDs (e.g., phonological awareness) relatively infrequently.