bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical activity and cancer risk
Authors: Hardman Adrianne E.
Published: September 2008

Evidence is accumulating that high levels of physical activity are associated with a reduced risk of some cancers. This evidence is most consistent for colon cancer, which is reduced by 40–50 % among the most active individuals, compared with the least active. The effect is evident in men and women, and appears to be independent of important confounding factors. However, there may be important interactions with body fatness; a high BMI has been reported to be associated with an increased risk of colon cancer in sedentary men but not in physically-active men. Whilst the evidence on breast cancer is less consistent, case–control studies typically suggest a reduction of 25–30 % among the most active women, although several studies have found no effect. Potential mechanisms include systemic influences and others relevant only to site-specific cancers. One unifying hypothesis is that physical inactivity reduces insulin sensitivity, leading to a growth-promotional environment which may facilitate neoplasia. The non-specific immune system may be improved by physical activity, possibly through the summative effects of repeated exercise bouts. Regular exercise, even at a recreational level, probably reduces exposure to oestrogen and thus decreases the risk of breast cancer. Increased colonic peristalsis, and thus reduced bowel transit time, might partly explain the lower risk of colon cancer in active people. Physical activity emerges as one of the few modifiable risk factors for some cancers and, as such, justifies further study.
Human nutrition in medical practice: the training of doctors
Authors: Jackson Alan A.
Published: September 2008

Nutritional advice from doctors and other health workers is held in high regard by the general public. It is important, therefore, to ensure that the advice given is sound and safe. Historically, the training in nutrition for the health professions has been piecemeal and selective. As a first step in the development of national standards, a core curriculum on nutrition for health professionals was developed as part of the National Nutrition Task Force. Designed for undergraduates, the curriculum sought to provide a standard for training which would ensure safe practice. The curriculum, which has been accepted by all undergraduate medical schools, identifies eighteen bullet points covering: the principles of nutritional science; public health nutrition; clinical nutrition and nutritional support. Postgraduate training for doctors is the responsibility of the Royal Colleges, who have formed an Intercollegiate Group on nutrition. This group has developed an intercollegiate foundation course in nutrition which lasts for 1 week and is offered at different centres around the country. Using the Intercollegiate Course as a base, individual Colleges are exploring how they might best develop the next level of training by identifying the educational needs for nutrition in different sub-specialities. There is some discussion as to whether it is timely to develop a defined clinical speciality in human nutrition. Within these developments, nutritionists and dietitians are identified as a resource to be called upon by other health professionals, and therefore it is important that in their own training they are suitably equipped to take on this challenge.
New food components and gastrointestinal health
Authors: Johnson Ian T.
Published: September 2008

Apart from its main functions of digestion, absorption and faecal processing, the human gastrointestinal tract has a complex pattern of muscular activity regulated by a largely autonomous nervous system, and its various organs contain large concentrations of immune and endocrine tissues. Any failure of these closely-integrated systems can lead to diseases ranging from the mildly irritating to the life threatening. Food contains a huge variety of chemical species, many of which are biologically active, and the distal regions of the gut are colonised by a rich and metabolically-active commensal flora that depend on nutrients derived ultimately from the host’s dietary residues. The present paper explores the evidence for significant effects of food ingredients on functional bowel disorders, intestinal infections, and aspects of epithelial cell physiology involved in the development of colo-rectal neoplasia. Various strategies, including the manipulation of the colo-rectal microflora with pre- and probiotics, and the development of new products and plant varieties containing biologically-active constituents, have the potential to underpin the development of novel functional food products. However, these products will need to be based on proven biological principles, and fully tested for efficacy and safety. The rapidly-developing fields of functional genomics and cell biology will open up new experimental strategies to explore these possibilities, and emerging processing technologies seem likely to provide novel methods for their exploitation.
Nutritional quality of organic food: shades of grey or shades of green?
Authors: Williams Christine M.
Published: September 2008

Consumer concern regarding possible adverse health effects of foods produced using intensive farming methods has led to considerable interest in the health benefits of organically-produced crops and animal products. There appears to be widespread perception amongst consumers that such methods result in foods of higher nutritional quality. The present review concludes that evidence that can support or refute such perception is not available in the scientific literature. A limited number of studies have compared the nutrient compositions of organically- and conventionally-produced crops, with a very small number of studies that have compared animal products (meat, milk and dairy products) produced under the two agricultural systems. Very few compositional differences have been reported, although there are reasonably consistent findings for higher nitrate and lower vitamin C contents of conventionally-produced vegetables, particularly leafy vegetables. Data concerning possible impacts on animal and human health of diets comprising organic or conventional produce are extremely sparse. Data from controlled studies in animal models, particularly within single species, are limited or poorly designed, and findings from these studies provide conflicting conclusions. There are no reports in the literature of controlled intervention studies in human subjects. Comparison of health outcomes in populations that habitually consume organically- or conventionally-produced foods are flawed by the large number of confounding factors that might contribute to any differences reported. If consumer perceptions regarding potential health benefits of organic foods are to be supported, more research of better quality is needed than that which is currently available.
Food allergen avoidance: risk assessment for life
Authors: Hazel Gowland M.
Published: September 2008

The skills and knowledge required to carry out food allergen avoidance are becoming increasingly sophisticated. It is not enough to know the names of a handful of dishes which contain a known allergen as an ingredient. Many lifestyles now depend on food prepared away from the home. New product development has introduced a wide range of ingredients and dishes which are labour saving, exciting and innovative. Product traceability now depends on advanced technological support as it struggles to keep up with foods manufactured, prepared and served in ever more complex circumstances. Consumers are now faced with ‘a jungle of choices’. However, those individuals who need to avoid a known allergen, particularly in trace quantities, often find that the food choice deemed suitable is poor, and the information available inadequate or even dangerously misleading. There are two important groups for whom this situation is a major concern. Thousands of families with young children are forced to live with the possibility that everyday foods may be contaminated by a known allergen which could kill in minutes. They live on their nerves, reading every packet and resorting to hyperprotective childcare and vigilance. In addition, the youngest independent consumers, teenagers and those in their twenties, may have little first-hand experience of food preparation. They may be ill-equipped in food-allergen risk assessment. Sadly, those who die from anaphylaxis or allergen-triggered asthma are often in this age-group. Current initiatives to support consumers at risk include a recognised standard for manufacturers seeking to eliminate an allergen from their production, and the integration of food allergy into training for caterers and food standards enforcement professionals.
Insulin resistance and glucose-induced thermogenesis in critical illness
Authors: Carlson Gordon L.
Published: September 2008

Critical illness is associated with a marked increase in metabolic rate and progressive wasting, despite aggressive nutritional support. The metabolic events which are responsible for these phenomena are unclear, but are characterised by marked impairment of the anabolic effects of insulin on glucose metabolism and excessive activation of the sympathetic nervous system. It has been suggested that critical illness may be associated with impaired carbohydrate oxidation and a marked increase in the loss of heat energy associated with glucose administration (glucose-induced thermogenesis). This situation may result in impaired efficiency of nutrient assimilation. Studies employing combinations of nutrient infusions both at clinically-relevant rates and in association with euglycaemic hyperinsulinaemia have, however, demonstrated that nutrient-induced thermogenesis is unaffected in critical illness in human subjects, and that defective glucose utilization occurs as a consequence of impaired insulin-mediated glucose storage rather than oxidation. Although the cellular and molecular mechanisms underlying these changes are controversial, the recent validation of a human model of insulin resistance in critical illness should provide a means of studying this response in future, and allow the identification of therapeutic targets. This information should increase the efficacy of nutritional support in some of our most seriously-ill patients.
Competition, cream‐skimming and department performance within secondary schools1
Authors: Davies Peter , Telhaj Shqiponje , Hutton David , Adnett Nick , Coe Robert
Published: September 2008

The performance of departments has been largely neglected in previous studies of subject choice in secondary schools. This is a significant omission because analysis at departmental level enables a fuller assessment of the effects of competition and specialisation on pupil performance. This paper examines relationships between both absolute and value‐added measures of departmental performance and the likelihood of students being entered for examination in a subject. It examines these relationships with reference to four option subjects: French, German, Geography and History. It utilises data from an Economic and Social Research Council‐funded study which examined trends and patterns in departmental effectiveness using a sample of 664 schools which participated in the Yellis monitoring system for a minimum of five years during the period 1995–2002.
Family Group Conferences—are they an effective and viable way of working with attendance and behaviour problems in schools?
Authors: Hayden Carol
Published: September 2008

Improving pupil attendance and behaviour are essential to improving teaching and learning in schools. Pupils who have the most problems in these respects are likely to need support that recognises the wider influences on these issues. Family Group Conferences (FGCs) are family‐led decision‐making meetings, that include the family and significant others in the formulation of a plan to help address the needs of a child. The research reported upon here included a quasi‐experimental element in the design in which levels of attendance and school exclusion were key before and after outcomes for the intervention (FGC) and comparison (Education Welfare Service, EWS) groups. The research shows that attendance and exclusion data did not improve in the FGC group but that the comparative gains made in attendance by the EWS were very modest. Nevertheless, responses to the survey of referral agents and interviews with Educational Welfare Officers and FGC coordinators suggest that FGCs are considered to be a viable approach in schools that may be effective in individual cases.
Language as capital, or language as identity? Chinese complementary school pupils' perspectives on the purposes and benefits of complementary schools
Authors: Francis Becky , Archer Louise , Mau Ada
Published: September 2008

Pupils' experiences of complementary education are neglected in the research literature, yet they are highly important in terms of understanding complementary schools and their impact on pupils' educational and social identities. This article explores British‐Chinese pupils' discursive constructions of the purposes and benefits of Chinese complementary schools, drawing on data from an Economic and Social Research Council (ESRC)‐funded study of six Chinese schools in England, including interviews with 60 of their British‐Chinese pupils. Findings demonstrate that British‐Chinese pupils overwhelmingly see the purpose of these schools as perpetuating the mother tongue. They produced a variety of explanations for the benefit of this perpetuation, and we analyse how these fall under two themes: instrumental benefits, and identity. In elaborating these themes we focus particularly on the ways in which language was constructed as identity, and draw out some theoretical implications for thinking around identity and ‘culture’.
Delivering the Lee Silverman Voice Treatment (LSVT) by web camera: a feasibility study
Authors: Howell Susan , Tripoliti Elina , Pring Tim
Published: September 2008

Background: Speech disorders are a feature of Parkinson's disease, typically worsening as the disease progresses. The Lee Silverman Voice Treatment (LSVT) was developed to address these difficulties. It targets vocal loudness as a means of increasing vocal effort and improving coordination across the subsystems of speech.

Aims: Currently LSVT is not widely available, and there are practical difficulties associated with the delivery of an intensive treatment in an environment of resource constraints in the National Health Service (NHS). Delivery of LSVT over the World‐Wide Web may address some of these difficulties.

Methods & Procedures: A feasibility study is reported in which three individuals with speech disorders resulting from Parkinson's disease received LSVT over the Internet, using broadband connection and a web camera. Participants were seen face to face for every fourth session in order to build a personal relationship, measure vocal sound pressure level (SPL) during treatment, and to review and prepare homework tasks. All other sessions were delivered over the Internet.

Outcomes & Results: Broadly similar treatment gains were found between individuals treated over the Internet and those treated face to face. Gains were maintained or improved at an assessment two months after the treatment.

Conclusions & Implications: This study demonstrates that delivery of LSVT over the Internet is feasible, and that a larger trial would be appropriate to establish cost and treatment effectiveness.
Unhelpful thoughts and beliefs linked to social anxiety in stuttering: development of a measure
Authors: St Clare Tamsen , Menzies Ross G. , Onslow Mark , Packman Ann , Thompson Robyn , Block Susan
Published: September 2008

Background: Those who stutter have a proclivity to social anxiety. Yet, to date, there is no comprehensive measure of thoughts and beliefs about stuttering that represent the cognitions associated with that anxiety.

Aims: The present paper describes the development of a measure to assess unhelpful thoughts and beliefs about stuttering.

Methods & Procedures: The Unhelpful Thoughts and Beliefs about Stuttering (UTBAS) self‐report measure contains 66 items that assess the frequency of unhelpful thoughts and beliefs. Items were constructed from a comprehensive file audit of all stuttering cases seen in a cognitive–behavior therapy based treatment programme over a ten‐year period.

Outcomes & Results: Preliminary investigations indicate that the UTBAS has high levels of test–retest reliability (r = 0.89) and internal consistency (Chronbach's alpha = 0.98). It has good known‐groups validity, being able to discriminate between stuttering and non‐stuttering participants on items that contain no reference to stuttering [t(38) = 8.06, p<0.0001], with a large effect size (d = 2.3). It has good convergent validity (r = 0.53–0.72) and discriminant validity (r = 0.24–0.27). The UTBAS sensitivity to change was supported by improvements in thoughts and beliefs related to social anxiety following cognitive–behavioural treatment for anxiety in stuttering [t(25) = 10.13, p<0.0001]. The effect size was large (d = 2.5).

Conclusions & Implications: Implications for the use of the UTBAS as an outcome measure and a clinical tool are discussed, along with the potential value of the UTBAS to explore the well‐documented social anxiety experienced by those who stutter.
Review of visual speech perception by hearing and hearing‐impaired people: clinical implications
Authors: Woodhouse Lynn , Hickson Louise , Dodd Barbara
Published: September 2008

Background: Speech perception is often considered specific to the auditory modality, despite convincing evidence that speech processing is bimodal. The theoretical and clinical roles of speech‐reading for speech perception, however, have received little attention in speech–language therapy.

Aims: The role of speech‐read information for speech perception is evaluated by considering evidence from hearing infants and adults, people with speech disorders, and those born profoundly hearing impaired.

Methods & Procedures: Research studies are evaluated for evidence on lip‐reading for speech perception: the mandatory role of speech‐reading for hearing adults' perception of the McGurk effect and hearing infants' awareness of the congruence between lip movements and speech sounds; brain neuroimaging studies of speech‐read and heard speech perception; the speech‐reading abilities of people with disordered speech; and the phonological coding abilities of people with profound pre‐lingual hearing loss. Theories of multimodal speech perception are explained.

Main Contributions: Five pieces of evidence indicate that speech‐reading is an integral part of speech processing. Hearing people's perception of speech is influenced by speech‐read cues, and those speech‐read cues cannot be ignored. Infants are aware that lip movements and speech sounds match from soon after birth and by four months of age have language specific speech‐reading skills. Studies of brain activity show that the brain processes speech‐read and heard speech similarly. Some children and adults with speech disorders are reported to rely less on speech‐read cues than people without speech disorders, and children who are profoundly hearing impaired from birth have concepts of rhyme, match homophones, and can repeat and spell nonsense words.

Conclusions & Implications: Speech‐reading, a mandatory part of speech perception, should be appropriately assessed and be considered when developing strategies for speech and language intervention.
The Peer Attitudes Toward Children who Stutter (PATCS) scale: an evaluation of validity, reliability and the negativity of attitudes
Authors: Langevin Marilyn , Kleitman Sabina , Packman Ann , Onslow Mark
Published: September 2008

Background:Persistent calls for school‐based education about stuttering necessitate a better understanding of peer attitudes toward children who stutter and a means to measure outcomes of such educational interventions. Langevin and Hagler in2004developed the Peer Attitudes Toward Children who Stutter scale (PATCS) to address these needs and gave preliminary evidence of reliability and construct validity.

Aims:To examine further the psychometric properties of PATCS and to examine the negativity of attitudes.

Methods & Procedures:PATCS was administered to 760 Canadian children in grades 3–6. Measures included reliability, a confirmatory factor analysis (CFA), a known groups analysis, convergent validity with the Pro‐Victim Scale of Rigby and Slee, and the negativity of attitudes.

Outcomes & Results:PATCS appears to tap a second‐order general attitude factor and three first‐order factors representing the constructs of Positive Social Distance (PSD), Social Pressure (SP), and Verbal Interaction (VI). In the known groups analysis, participants who had contact with someone who stutters had higher scores (more positive attitudes) than those who had not, and girls had higher scores than boys. PATCS correlated moderately (0.43,p<0.01) with the Pro‐Victim scale. Finally, one‐fifth (21.7%) of participants had scores that were somewhat to very negative.

Conclusions & Implications:Results provide evidence of the validity and reliability of PATCS and confirm the need for school‐based education about stuttering. The PSD and SP factors suggest that education include discussions about (1) similarities and differences among children who do and do not stutter in order to increase acceptance, and (2) making personal choices and handling peer pressure in thinking about children who stutter. The VI factor suggests that open discussion about stuttering may alleviate frustration experienced by listeners and provide the opportunity to give strategies for responding appropriately. Results also suggest that education involve contact with a person who stutters.
Optimizing speech production in the ventilator‐assisted individual following cervical spinal cord injury: a preliminary investigation
Authors: MacBean Naomi , Ward Elizabeth , Murdoch Bruce , Cahill Louise , Solley Maura , Geraghty Timothy , Hukins Craig
Published: September 2008

Background: Mechanical ventilation is commonly used during the acute management of cervical spinal cord injury, and is required on an ongoing basis in the majority of patients with injuries at or above C3. However, to date there have been limited systematic investigations of the options available to improve speech while ventilator‐assisted post‐cervical spinal cord injury.

Aims: To provide preliminary evidence of any benefits gained through the addition of positive end expiratory pressure (PEEP) and/or a tracheostomy speech valve to the condition of leak speech.

Methods & Procedures: Speech production in the three conditions was compared in two ventilator‐assisted participants using a series of instrumental and perceptual speech measures.

Outcomes & Results: The addition of PEEP or the use of a speech valve resulted in speech that was superior to leak speech for both participants; however, individual variation was present.

Conclusions & Implications: Leak speech alone or with the addition of PEEP or a tracheostomy speech valve can facilitate functional communication for the ventilated patient, though PEEP and valve speech were found to be superior in the current study. These findings will be of assistance for clinicians counselling the growing population of patients who may require tracheostomy positive pressure ventilation long‐term regarding communication options.
Cleft Audit Protocol for Speech (CAPS‐A): a comprehensive training package for speech analysis
Authors: Sell D. , John A. , Harding‐Bell A. , Sweeney T. , Hegarty F. , Freeman J.
Published: September 2008

Background:The previous literature has largely focused on speech analysis systems and ignored process issues, such as the nature of adequate speech samples, data acquisition, recording and playback. Although there has been recognition of the need for training on tools used in speech analysis associated with cleft palate, little attention has been paid to this issue.

Aims:To design, execute, and evaluate a training programme for speech and language therapists on the systematic and reliable use of the Cleft Audit Protocol for Speech‐Augmented (CAPS‐A), addressing issues of standardized speech samples, data acquisition, recording, playback, and listening guidelines.

Methods & Procedures:Thirty‐six specialist speech and language therapists undertook the training programme over four days. This consisted of two days' training on the CAPS‐A tool followed by a third day, making independent ratings and transcriptions on ten new cases which had been previously recorded during routine audit data collection. This task was repeated on day 4, a minimum of one month later. Ratings were made using the CAPS‐A record form with the CAPS‐A definition table. An analysis was made of the speech and language therapists' CAPS‐A ratings at occasion 1 and occasion 2 and the intra‐ and inter‐rater reliability calculated.

Outcomes & Results:Trained therapists showed consistency in individual judgements on specific sections of the tool. Intraclass correlation coefficients were calculated for each section with good agreement on eight of 13 sections. There were only fair levels of agreement on anterior oral cleft speech characteristics, non‐cleft errors/immaturities and voice. This was explained, at least in part, by their low prevalence which affects the calculation of the intraclass correlation coefficient statistic.

Conclusions & Implications:Speech and language therapists benefited from training on the CAPS‐A, focusing on specific aspects of speech using definitions of parameters and scalar points, in order to apply the tool systematically and reliably. Ratings are enhanced by ensuring a high degree of attention to the nature of the data, standardizing the speech sample, data acquisition, the listening process together with the use of high‐quality recording and playback equipment. In addition, a method is proposed for maintaining listening skills following training as part of an individual's continuing education.
Pragmatics fragmented: the factor structure of the Dutch Children's Communication Checklist (CCC)
Authors: Geurts Hilde M. , Hartman Catharina , Verté Sylvie , Oosterlaan Jaap , Roeyers Herbert , Sergeant Joseph A.
Published: September 2008

Background: A number of disorders are associated with pragmatic difficulties. Instruments that can make subdivisions within the larger construct of pragmatics could be important tools for disentangling profiles of pragmatic difficulty in different disorders. The deficits underlying the observed pragmatic difficulties may be different for different disorders.

Aims: To study the construct validity of a pragmatic language questionnaire.

Method & Procedures: The construct of pragmatics is studied by applying exploratory factor analysis (EFA) and confirmatory factor analysis to the parent version of the Dutch Children's Communication Checklist (CCC; Bishop 1998). Parent ratings of 1589 typically developing children and 481 children with a clinical diagnosis were collected. Four different factor models derived from the original CCC scales and five different factor models based on EFA were compared with each other. The models were cross‐validated.

Outcomes & Results: The EFA‐derived models were substantively different from the originally proposed CCC factor structure. EFA models gave a slightly better fit than the models based on the original CCC scales, though neither provided a good fit to the parent data. Coherence seemed to be part of language form and not of pragmatics, which is in line with the adaptation of the CCC, the CCC‐2 (Bishop 2003). Most pragmatic items clustered together in one factor and these pragmatic items also clustered with items related to social relationships and specific interests.

Conclusions & Implications: The nine scales of the original CCC do not reflect the underlying factor structure. Therefore, scale composition may be improved on and scores on subscale level need to be interpreted cautiously. Therefore, in interpreting the CCC profiles, the overall measure might be more informative than the postulated subscales as more information is needed to determine which constructs the suggested subscales are actually measuring.
Gesture and speech integration: an exploratory study of a man with aphasia
Authors: Cocks Naomi , Sautin Laetitia , Kita Sotaro , Morgan Gary , Zlotowitz Sally
Published: September 2008

Background: In order to comprehend fully a speaker's intention in everyday communication, information is integrated from multiple sources, including gesture and speech. There are no published studies that have explored the impact of aphasia on iconic co‐speech gesture and speech integration.

Aims: To explore the impact of aphasia on co‐speech gesture and speech integration in one participant with aphasia and 20 age‐matched control participants.

Methods & Procedures: The participant with aphasia and 20 control participants watched video vignettes of people producing 21 verb phrases in three different conditions, verbal only (V), gesture only (G), and verbal gesture combined (VG). Participants were required to select a corresponding picture from one of four alternatives: integration target, a verbal‐only match, a gesture‐only match, and an unrelated foil. The probability of choosing the integration target in the VG that goes beyond what is expected from the probabilities of choosing the integration target in V and G was referred to as multi‐modal gain (MMG).

Outcomes & Results: The participant with aphasia obtained a significantly lower multi‐modal gain score than the control participants (p<0.05). Error analysis indicated that in speech and gesture integration tasks, the participant with aphasia relied on gesture in order to decode the message, whereas the control participants relied on speech in order to decode the message. Further analysis of the speech‐only and gesture‐only tasks indicated that the participant with aphasia had intact gesture comprehension but impaired spoken word comprehension.

Conclusions & Implications: The results confirm findings by Records (1994) that reported that impaired verbal comprehension leads to a greater reliance on gesture to decode messages. Moreover, multi‐modal integration of information from speech and iconic gesture can be impaired in aphasia. The findings highlight the need for further exploration of the impact of aphasia on gesture and speech integration.
Untrained listeners' ratings of speech disorders in a group with cleft palate: a comparison with speech and language pathologists‚ ratings
Authors: Brunnegård Karin , Lohmander Anette , van Doorn Jan
Published: September 2008

Background:Hypernasal resonance, audible nasal air emission and/or nasal turbulence, and articulation errors are typical speech disorders associated with the speech of children with cleft lip and palate. Several studies indicate that hypernasal resonance tends to be perceived negatively by listeners. Most perceptual studies of speech disorders related to cleft palate are carried out with speech and language pathologists as listeners, whereas only a few studies have been conducted to explore how judgements by untrained listeners compare with expert assessments. These types of studies can be used to determine whether children for whom speech and language pathologists recommend intervention have a significant speech deviance that is also detected by untrained listeners.

Aims:To compare ratings by untrained listeners with ratings by speech and language pathologists for cleft palate speech.

Methods & Procedures:An assessment form for untrained listeners was developed using statements and a five‐point scale. The assessment form was tailored to facilitate comparison with expert judgements. Twenty‐eight untrained listeners assessed the speech of 26 speakers with cleft palate and ten speakers without cleft in a comparison group. This assessment was compared with the joint assessment of two expert speech and language pathologists.

Outcomes & Results:Listener groups generally agreed on which speakers were nasal. The untrained listeners detected hyper‐ and hyponasality when it was present in speech and considered moderate to severe hypernasality to be serious enough to call for intervention. The expert listeners assessed audible nasal air emission and/or nasal turbulence to be present in twice as many speakers as the untrained listeners who were much less sensitive to audible nasal air emission and/or nasal turbulence.

Conclusions & Implications:The results of untrained listeners' ratings in this study in the main confirm the ratings of speech and language pathologists and show that cleft palate speech disorders may have an impact in the everyday life of the speaker.
Evaluative expression in deaf children's written narratives
Authors: van Beijsterveldt Liesbeth Maria , van Hell Janet G.
Published: September 2008

Background: Deaf children vary in the use of and proficiency in signed language. The majority of studies on writing skills of children who are deaf did not assess deaf children's proficiency in signed language and/or grouped together deaf children with varying sign language skills.

Aims: Adopting a bimodal bilingual perspective, we examined evaluative expression, an important narrative tool in both oral/written languages and signed languages, in narratives written in Dutch by deaf children who are proficient in Sign Language of the Netherlands (SLN) and deaf children who are low‐proficient in SLN, and hearing monolingual and bilingual children. We hypothesized that deaf children who are proficient in signed language use their knowledge of evaluative expression in signed language to enrich their narratives in written Dutch, and more so than deaf children who are low‐proficient in signed language and hearing monolingual and bilingual children.

Methods & Procedures: We examined the use of eight different evaluative devices in narratives written by deaf proficiently and low‐proficiently signing children, and hearing monolingual and bilingual children. Narratives were also examined for morpho‐syntactic errors and use of complex sentences.

Outcomes & Results: The results show that proficiently signing deaf children's narratives contain more evaluative devices that enrich the referential structure of the narrative than narratives of low‐proficiently signing deaf children, and hearing bilingual and monolingual children.

Conclusions & Implications: We propose that proficiently signing deaf children use their knowledge of SLN to convey evaluation in their written narratives, and thus have an advantage in enriching their narratives. This study also shows that in order to gain insight into deaf people's writing, it is important to take variations in sign language proficiency into account.
Speech technology‐based assessment of phoneme intelligibility in dysarthria
Authors: Van Nuffelen Gwen , Middag Catherine , De Bodt Marc , Martens Jean‐Pierre
Published: September 2008

Background:Currently, clinicians mainly rely on perceptual judgements to assess intelligibility of dysarthric speech. Although often highly reliable, this procedure is subjective with a lot of intrinsic variables. Therefore, certain benefits can be expected from a speech technology‐based intelligibility assessment. Previous attempts to develop an automated intelligibility assessment mainly relied on automatic speech recognition (ASR) systems that were trained to recognize the speech of persons without known impairments. In this paper automatic speech alignment (ASA) systems are used instead. In addition, previous attempts only made use of phonemic features (PMF). However, since articulation is an important contributing factor to intelligibility of dysarthric speech and since phonological features (PLF) are shared by multiple phonemes, phonological features may be more appropriate to characterize and identify dysarthric phonemes.

Aims:To investigate the reliability of objective phoneme intelligibility scores obtained by three types of intelligibility models: models using only phonemic features (yielded by an automated speech aligner) (PMF models), models using only phonological features (PLF models), and models using a combination of phonemic and phonological features (PMF + PLF models).

Methods & Procedures:Correlations were calculated between the objective phoneme intelligibility scores of 60 dysarthric speakers and the corresponding perceptual phoneme intelligibility scores obtained by a standardized perceptual phoneme intelligibility assessment.

Outcomes & Results:The correlations between the objective and perceptual intelligibility scores range from 0.793 for the PMF models, over 0.828 for PLF models to 0.943 for PMF + PLF models. The features selected to obtain such high correlations can be divided into six main subgroups: (1) vowel‐related phonemic and phonological features, (2) lateral‐related features, (3) silence‐related features, (4) fricative‐related features, (5) velar‐related features and (6) plosive‐related features.

Conclusions & Implications:The phoneme intelligibility scores of dysarthric speakers obtained by the three investigated intelligibility model types are reliable. The highest correlation between the perceptual and objective intelligibility scores was found for models combining phonemic and phonological features. The intelligibility scoring system is now ready to be implemented in a clinical tool.
Mathematical Model of Mouse Embryonic Cardiomyocyte Excitation–Contraction Coupling
Authors: Korhonen Topi , Rapila Risto , Tavi Pasi
Published: September 2008

Excitation–contraction (E–C) coupling is the mechanism that connects the electrical excitation with cardiomyocyte contraction. Embryonic cardiomyocytes are not only capable of generating action potential (AP)-induced Ca2+ signals and contractions (E–C coupling), but they also can induce spontaneous pacemaking activity. The spontaneous activity originates from spontaneous Ca2+ releases from the sarcoplasmic reticulum (SR), which trigger APs via the Na+/Ca2+ exchanger (NCX). In the AP-driven mode, an external stimulus triggers an AP and activates voltage-activated Ca2+ intrusion to the cell. These complex and unique features of the embryonic cardiomyocyte pacemaking and E–C coupling have never been assessed with mathematical modeling. Here, we suggest a novel mathematical model explaining how both of these mechanisms can coexist in the same embryonic cardiomyocytes. In addition to experimentally characterized ion currents, the model includes novel heterogeneous cytosolic Ca2+ dynamics and oscillatory SR Ca2+ handling. The model reproduces faithfully the experimentally observed fundamental features of both E–C coupling and pacemaking. We further validate our model by simulating the effect of genetic modifications on the hyperpolarization-activated current, NCX, and the SR Ca2+ buffer protein calreticulin. In these simulations, the model produces a similar functional alteration to that observed previously in the genetically engineered mice, and thus provides mechanistic explanations for the cardiac phenotypes of these animals. In general, this study presents the first model explaining the underlying cellular mechanism for the origin and the regulation of the heartbeat in early embryonic cardiomyocytes.
Fabrication and analysis of a micro-machined tri-axis gyroscope
Authors: Tsai Nan-Chyuan , Sue Chung-Yang
Published: September 2008

This paper presents an innovative micro-gyroscope design. Solely by SOI (silicon on insulator) fabrication technology and wet etching, the proposed micro-gyroscope can be produced in batch and is capable of detecting three-axis angular rates. The induced motions of all individual seismic mass modules are designed to respond in the directions orthogonal to each other in order to decouple the obtained measurements. In our work, three pairs of high-resolution differential capacitors with signal processing circuits are employed to measure the angular velocity components in three axes. On the other hand, the drive electrode comb is used to constantly vibrate the outer-ring in the tangential direction by a sinusoidal voltage. The signal bandwidth is increased by distributed translational proof masses (DTPM), placed 90° apart orderly. Each individual proof mass of DTPM is designed with natural frequency discrepancy and constrained to move in the radial direction so that the superior mode matching can be easily, to some extent, achieved. The suspension flexures are particularly designed to resist planar displacements in the drive mode but increase the stroke of tilting angular displacement in the sense mode. By considering the complicated geometry of the suspension flexures, FEM (finite element method) is employed to examine the potential maximum induced mechanical stress. The dynamic equations of the proposed gyroscope are established so that the embedded gyroscopic effects are explicitly unveiled. More importantly, the efficacy of the drive and sense circuit modules are verified by commercial softwares Hspice and Multisim. By intensive computer simulations and preliminary experimental studies, the resolution, bandwidth and decoupling capability of the tri-axis gyroscope are expected to be fairly enhanced if a certain degree of trade-off is preset.

Corrections were made to figure 5 in this article on 3 October 2008. The corrected electronic version is identical to the print version.
Genome annotation in the presence of insertional RNA editing
Authors: Beargie Christina , Liu Tsunglin , Corriveau Mark , Lee Ha Youn , Gott Jonatha , Bundschuh Ralf
Published: September 2008

Motivation: Insertional RNA editing renders gene prediction very difficult compared to organisms without such RNA editing. A case in point is the mitochondrial genome of Physarum polycephalum in which only about one-third of the number of genes that are to be expected given its length are annotated. Thus, gene prediction methods that explicitly take into account insertional editing are needed for successful annotation of such genomes.

Results: We annotate the mitochondrial genome of P.polycephalum using several different approaches for gene prediction in organisms with insertional RNA editing. We computationally validate our annotations by comparing the results from different methods against each other and as proof of concept experimentally validate two of the newly predicted genes. We more than double the number of annotated putative genes in this organism and find several intriguing candidate genes that are not expected in a mitochondrial genome.

Availability: The C source code of the programs described here are available upon request from the corresponding author.

Contact:  bundschuh@mps.ohio-state.edu
Identifying differentially expressed subnetworks with MMG
Authors: Noirel Josselin , Sanguinetti Guido , Wright Phillip C.
Published: September 2008

Background: Mixture model on graphs (MMG) is a probabilistic model that integrates network topology with (gene, protein) expression data to predict the regulation state of genes and proteins. It is remarkably robust to missing data, a feature particularly important for its use in quantitative proteomics. A new implementation in C and interfaced with R makes MMG extremely fast and easy to use and to extend.

Availability: The original implementation (Matlab) is still available from http://www.dcs.shef.ac.uk/~guido/; the new implementation is available from http://wrightlab.group.shef.ac.uk/people_noirel.htm, from CRAN, and has been submitted to BioConductor, http://www.bioconductor.org/.

Contact:  j.noirel@sheffield.ac.uk
Physiological and Transcriptomic Evidence for a Close Coupling between Chloroplast Ontogeny and Cell Cycle Progression in the Pennate DiatomSeminavis robusta
Authors: Gillard Jeroen , Devos Valerie , Huysman Marie J.J. , De Veylder Lieven , D'Hondt Sofie , Martens Cindy , Vanormelingen Pieter , Vannerum Katrijn , Sabbe Koen , Chepurnov Victor A. , Inzé Dirk , Vuylsteke Marnik , Vyverman Wim
Published: September 2008

Despite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta  FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated.
Unique and Overlapping Expression Patterns among Members of Photosynthesis-Associated Nuclear Gene Families in Arabidopsis
Authors: Sawchuk Megan G. , Donner Tyler J. , Head Philip , Scarpella Enrico
Published: September 2008

Light provides crucial positional information in plant development, and the morphogenetic processes that are orchestrated by light signals are triggered by changes of gene expression in response to variations in light parameters. Control of expression of members of the RbcS and Lhc families of photosynthesis-associated nuclear genes by light cues is a paradigm for light-regulated gene transcription, but high-resolution expression profiles for these gene families are lacking. In this study, we have investigated expression patterns of members of the RbcS and Lhc gene families in Arabidopsis (Arabidopsis thaliana) at the cellular level during undisturbed development and upon controlled interference of the light environment. Members of the RbcS and Lhc gene families are expressed in specialized territories, including root tip, leaf adaxial, abaxial, and epidermal domains, and with distinct chronologies, identifying successive stages of leaf mesophyll ontogeny. Defined spatial and temporal overlap of gene expression fields suggest that the light-harvesting and photosynthetic apparatus may have a different polypeptide composition in different cells and that such composition could change over time even within the same cell.