Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes

We created a simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order. We used the simulation to compute the fitness of more than 105 mutants. We tested these computations by constructing and experimentally characterizing T7 mutants in which we repositioned gene 1, coding for T7 RNA polymerase. Computed protein synthesis rates for ectopic gene 1 strains were in moderate agreement with observed rates. Computed phage-doubling rates were close to observations for two of four strains, but significantly overestimated those of the other two. Computations indicate that the genome organization of wild-type T7 is nearly optimal for growth: only 2.8% of random genome permutations were computed to grow faster, the highest 31% faster, than wild type. Specific discrepancies between computations and observations suggest that a better understanding of the translation efficiency of individual mRNAs and the functions of qualitatively “nonessential” genes will be needed to improve the T7 simulation. In silico representations of biological systems can serve to assess and advance our understanding of the underlying biology. Iteration between computation, prediction, and observation should increase the rate at which biological hypotheses are formulated and tested.

Purification and Characterization of a Galactose-Rich Basic Glycoprotein in Tobacco1

We found a galactose-rich basic glycoprotein (GBGP) in the cell walls of cultured tobacco (Nicotiana tabacum) cells. GBGP and extensin were isolated as the major components of basic, salt-extracted cell wall glycoproteins. GBGP and extensin were separated by gel filtration in 6 m guanidine hydrochloride as 49- and 90-kD peaks, respectively, and further purified with reverse-phase chromatography. The protein moiety of GBGP constitutes about one-half of the molecule (w/w) and contains lysine (16%), proline (12%), hydroxyproline (10%), tyrosine (4%), alanine (7%), leucine (6%), and cystine (1.4%). Galactose accounted for 72% of the sugar moiety, arabinose content was low (17%), and a significant amount of mannose (7%) was found. No immunological cross-reaction was detected between GBGP and extensin. The antibody against native GBGP with sugar chains reacted with other glycoproteins on the gel blots, whereas the antibodies against deglycosylated GBGP and native extensin were highly specific. Immunolocalization analysis in tobacco stems showed that GBGP is specific to parenchyma tissue and that extensin localizes in the epidermis. This tissue-specific and exclusive distribution suggests important functions of these basic glycoproteins.

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.

Core promoter-specific function of a mutant transcription factor TFIID defective in TATA-box binding.

In conjunction with other general initiation factors, the TATA box-binding protein (TBP) can direct basal transcription by RNA polymerase II from TATA-containing promoters, but its stable interaction with TBP-associated factors (TAFs) in the TFIID complex is required both for activator-dependent transcription and for basal transcription directed by an initiator element. We have generated a TATA-binding-defective TFIID complex containing an amino acid substitution in the DNA-binding surface of its TBP subunit. This mutated TFIID is defective in both basal and activated transcription from core promoters containing only a TATA box but supports transcription from initiator-containing promoters independently of the presence or absence of a TATA sequence. Our results show that a functional initiator element is needed to bypass the requirement for an active TATA DNA-binding surface in TFIID and imply that gene-specific transcription can be achieved by modulating distinct core promoter-specific TFIID functions--e.g., TBP-TATA versus TAF-initiator interactions.

Processing of speech signals for physical and sensory disabilities.

Assistive technology involving voice communication is used primarily by people who are deaf, hard of hearing, or who have speech and/or language disabilities. It is also used to a lesser extent by people with visual or motor disabilities. A very wide range of devices has been developed for people with hearing loss. These devices can be categorized not only by the modality of stimulation [i.e., auditory, visual, tactile, or direct electrical stimulation of the auditory nerve (auditory-neural)] but also in terms of the degree of speech processing that is used. At least four such categories can be distinguished: assistive devices (a) that are not designed specifically for speech, (b) that take the average characteristics of speech into account, (c) that process articulatory or phonetic characteristics of speech, and (d) that embody some degree of automatic speech recognition. Assistive devices for people with speech and/or language disabilities typically involve some form of speech synthesis or symbol generation for severe forms of language disability. Speech synthesis is also used in text-to-speech systems for sightless persons. Other applications of assistive technology involving voice communication include voice control of wheelchairs and other devices for people with mobility disabilities.

Military and government applications of human-machine communication by voice.

This paper describes a range of opportunities for military and government applications of human-machine communication by voice, based on visits and contacts with numerous user organizations in the United States. The applications include some that appear to be feasible by careful integration of current state-of-the-art technology and others that will require a varying mix of advances in speech technology and in integration of the technology into applications environments. Applications that are described include (1) speech recognition and synthesis for mobile command and control; (2) speech processing for a portable multifunction soldier's computer; (3) speech- and language-based technology for naval combat team tactical training; (4) speech technology for command and control on a carrier flight deck; (5) control of auxiliary systems, and alert and warning generation, in fighter aircraft and helicopters; and (6) voice check-in, report entry, and communication for law enforcement agents or special forces. A phased approach for transfer of the technology into applications is advocated, where integration of applications systems is pursued in parallel with advanced research to meet future needs.

Saúde mental: concepções e práticas profissionais de um campo em tensão

A Reforma Psiquiátrica, atual política de saúde mental, redireciona os recursos da assistência psiquiátrica para o modelo de base comunitária, substituindo o modelo asilar. A abordagem proposta pela Reforma Psiquiátrica procura conjugar o esforço teórico e prático para a construção da Rede de Atenção Psicossocial. O presente trabalho objetivou desvelar concepções e práticas de trabalhadores da saúde mental, construídas na práxis de suas trajetórias profissionais e contextos de vida, em relação à incorporação do modelo de atenção psicossocial ou manutenção de princípios asilares, caracterizadores da tradicional prática profissional em saúde mental. Objetivou também identificar pontos de tensão, que caracterizam interesses de diferentes naturezas, como obstáculos e desafios à implementação da Reforma Psiquiátrica. A pesquisa, de natureza qualitativa, contou com 10 entrevistas de profissionais atuando na área, baseada na técnica de depoimento oral e em roteiro do tipo temático, sendo 3 enfermeiros, 3 psicólogos, 3 psiquiatras e 1 terapeuta ocupacional. Os relatos dos profissionais foram organizados em categorias gerais e específicas tendo em vista a interpretação das narrativas à luz da literatura especializada. Através dos discursos dos profissionais do campo da saúde mental é possível observar que um tensionamento ideológico marca fortemente o espaço da saúde. Alguns profissionais relataram a busca por construir práticas em equipe interdisciplinar, pautadas pelo modelo psicossocial; porém, referem à resistência de outros profissionais da equipe. Praticamente todos os profissionais apresentam discursos de humanização no campo da saúde mental, mas alguns não enunciam visões críticas aos modelos asilares. Alguns trabalhadores revelam a crença na possibilidade de coexistência integrada entre o Modo Asilar e Modo Psicossocial. Para estes trabalhadores de CAPS, é desejável a permanência dos hospitais psiquiátricos e é possível a humanização dos mesmos. Essa questão indica, ao que parece, que as práticas em saúde mental ainda operam sobre premissas epistemológicas diferenciando sujeitos que podem ou não circular no meio social. A existência dos hospitais psiquiátricos, considerados como instituições totais, é problematizada e questionada pela Luta Antimanicomial, indica a permanência da lógica asilar que respalda a continuidade dos hospitais, exclusivamente psiquiátricos, entre os serviços de atendimento, com o apoio de parte dos profissionais da rede de saúde mental. Concordantes com a possibilidade de coexistência do modelo asilar e modelo psicossocial, estes profissionais permitem-nos demonstrar que mesmo uma visão clínica pretensamente humanizadora, que defenda em seu discurso um tratamento digno, pode operar no modelo teórico-metodológico positivista e não está necessariamente vinculada a uma postura política de sujeitos de direitos e de cidadania. Os profissionais que apresentaram em suas narrativas a não concordância com a permanência dos hospitais psiquiátricos, defendem que as transformações sejam clínicas e políticas nos saberes e nas práticas em Saúde Mental. Estes trabalhadores já fizeram ou fazem parte de movimentos sociais, apontados como lugares de reflexão crítica sobre ideias instituídas contribuindo, ao que parece, para o processo de desnaturalização de concepções construídas culturalmente e orientadoras de práticas profissionais. Diante de tais constatações podemos indagar e refletir se a desinstitucionalização, concreta e simbólica, encontra-se no horizonte de uma política pública de atenção em Saúde Mental que realmente tenha como projeto a sua real implementação e se a permanência dos hospitais psiquiátricos e das comunidades terapêuticas estaria descaracterizando as propostas iniciais da construção da Atenção Psicossocial, considerando os interesses privados e a manutenção da lógica asilar, contrários aos princípios do SUS.

Can parents and teachers provide a reliable and valid report of behavioral inhibition?

Reliability and validity of parent and teacher report of behavioral inhibition (BI) was examined among children aged 3 to 5 years. Confirmatory factor analysis supported 6 correlated factors reflecting specific BI contexts, each loading on a single, higher order factor of BI. Internal consistency was acceptable, with moderate stability over 1 year and strong correlation with a brief inhibition subscale from a temperament questionnaire. Children who were rated by mothers and teachers as high BI took longer to initiate contact with a stranger, spoke less often and for shorter periods, and required more prompting to elicit speech compared with low-BI peers in a simulated stranger interaction task. Father report of BI was significantly associated with mean duration of speech and eye gaze.

Comparability of perceptual analysis of speech characteristics in Australian and Swedish speakers with multiple sclerosis

The aims of the present study were to compare the perceptual assessments of deviant speech signs (dysarthria) exhibited by Australian and Swedish speakers with multiple sclerosis (MS) and to explore whether judgements of dysarthria differed depending on whether the speakers and the judges spoke the same or different languages. Ten Australian and 10 Swedish individuals with MS (matched as closely as possible for age, gender, progression type and severity of dysarthria) were assessed by 2 Australian and 2 Swedish clinically experienced judges using a protocol including 33 speech parameters. Results show that the following perceptual dimensions were identified by both pairs of judges in both groups of speakers to a just noticeable or moderate degree: imprecise consonants, inappropriate pitch level, reduced general rate, and glottal fry. The reliability (Spearman rank-order correlation) of the consensus ratings from the Australian and the Swedish judges was high, with a mean rho of 85.7 for the Australian speakers and mean rho of 84.3 for the Swedish speakers. The most difficult perceptual parameters to assess (i.e. to agree on) included harshness, level of pitch and loudness, precision of consonants and general stress pattern. The study indicated that perceptual assessments of speech characteristics in individuals with MS are informative and can be achieved with high inter-judge reliability irrespective of the judge's knowledge of the speaker's language. Copyright (C) 2003 S. Karger AG, Basel.

Molecular introduction to head and neck cancer (HNSCC) carcinogenesis

Of all human cancers, HNSCC is the most distressing affecting pain, disfigurement, speech and the basic survival functions of breathing and swallowing. Mortality rates have not significantly changed in the last 40 years despite advances in radiotherapy and surgical treatment. Molecular markers are currently being identified that can determine prognosis preoperatively by routine tumour biopsy Leading to improved management of HNSCC patients. The approach could help decide which early stage patient should have adjuvant neck dissection and radiotherapy, and whether Later stage patients with operable lesions would benefit from resection and reconstructive surgery or adopt a conservative approach to patients with poor prognosis regardless of treatment. In the future, understanding these basic genetic changes in HNSCC would be important for the management of HNSCC. (C) 2004 The British Association of Plastic Surgeons. Published by Elsevier Ltd. All rights reserved.

Work activities of occupational therapists in Australian mental health services

The aim of this study was to obtain a profile of occupational therapists’ work activities in contemporary Australian mental health services so as to better understand the specific contribution of this profession. The study also aimed to determine whether or not actual work activity was congruent with the preferred roles of occupational therapists. A cross-sectional survey of 196 occupational therapists working in mental health was conducted. For the purposes of the study, a new instrument was developed that evaluated both actual and preferred work roles in four broad categories: administrative, general clinical skills, specialist clinical skills and community development. Respondents were engaged in a greater proportion of generic than discipline-specific work activities. They reported a preference for higher levels of activity in each of the work categories. These findings suggest that, contrary to some previous reports, not only are occupational therapists in Australia engaged in a broad spectrum of non-specialist mental health work activities, but these activities are mostly congruent with their expectations and wishes.

Clinical reporting by occupational therapists and speech pathologists: Therapists' intentions and parental satisfaction

This study employed a qualitative research design to explore therapists' and parents' perspectives of paediatric occupational therapy and speech pathology assessment reports. Aims of the study were to explore the intentions of therapists when writing reports, to expand upon existing literature on parental satisfaction and preferences with respect to paediatric clinical reports, to highlight documentation practices that would serve to maximize parental use of allied health reports, and to develop specific guidelines on how reports can be written to ensure they are useful and beneficial to therapists and parents. Participants were 15 parents of children who had been assessed at 1 of 2 university clinics and subsequently received a written report, and 11 therapists employed at the same university clinics. Questionnaires were used to seek information from therapists concerning the purpose of assessment reports and essential aspects to include when writing reports for parents. In-depth interviews were used to seek information about how understandable and beneficial clinical reports were to parents. The data were subjected to thematic analysis. From comments of therapists' intentions and parents' stated needs, and in accordance with literature reviewed, guidelines were identified for the production of parent-oriented reports. Conclusions drawn from this study can be specifically applied to services producing paediatric occupational therapy or speech pathology assessment reports, but are widely relevant to paediatric allied health services. (author abstract)

Suitability of acoustic perturbation measures in analysing periodic and nearly periodic voice signals

In recent years, acoustic perturbation measurement has gained clinical and research popularity due to the ease of availability of commercial acoustic analysing software packages in the market. However, because the measurement itself depends critically on the accuracy of frequency tracking from the voice signal, researchers argue that perturbation measures are not suitable for analysing dysphonic voice samples, which are aperiodic in nature. This study compares the fundamental frequency, relative amplitude perturbation, shimmer percent and noise-to-harmonic ratio between a group of dysphonic and non-dysphonic subjects. One hundred and twelve dysphonic subjects ( 93 females and 19 males) and 41 non-dysphonic subjects ( 35 females and 6 males) participated in the study. All the 153 voice samples were categorized into type I ( periodic or nearly periodic), type II ( signals with subharmonic frequencies that approach the fundamental frequency) and type III ( aperiodic) signals. Only the type I ( periodic and nearly periodic) voice signals were acoustically analysed for perturbation measures. Results revealed that the dysphonic female group presented significantly lower fundamental frequency, significantly higher relative amplitude perturbation and shimmer percent values than the non-dysphonic female group. However, none of these three perturbation measures were able to differentiate between male dysphonic and male non-dysphonic subjects. The noise-to-harmonic ratio failed to differentiate between the dysphonic and non-dysphonic voices for both gender groups. These results question the sensitivity of acoustic perturbation measures in detecting dysphonia and suggest that contemporary acoustic perturbation measures are not suitable for analysing dysphonic voice signals, which are even nearly periodic. Copyright (C) 2005 S. Karger AG, Basel.