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PubMed2005

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system.

BACKGROUND: Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. RESULTS: Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. CONCLUSION: This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists.

Algorithms↗
PubMed2001

Coding of the fundamental frequency in continuous interleaved sampling processors for cochlear implants.

In this study the perception of the fundamental frequency (F0) of periodic stimuli by cochlear implant users is investigated. A widely used speech processor is the Continuous Interleaved Sampling (CIS) processor, for which the fundamental frequency appears as temporal fluctuations in the envelopes at the output. Three experiments with four users of the LAURA (Registered trade mark of Philips Hearing Implants, now Cochlear Technology Centre Europe) cochlear implant were carried out to examine the influence of the modulation depth of these envelope fluctuations on pitch discrimination. In the first experiment, the subjects were asked to discriminate between two SAM (sinusoidally amplitude modulated) pulse trains on a single electrode channel differing in modulation frequency ( deltaf = 20%). As expected, the results showed a decrease in the performance for smaller modulation depths. Optimal performance was reached for modulation depths between 20% and 99%, depending on subject, electrode channel, and modulation frequency. In the second experiment, the smallest noticeable difference in F0 of synthetic vowels was measured for three algorithms that differed in the obtained modulation depth at the output: the default CIS strategy, the CIS strategy in which the F0 fluctuations in the envelope were removed (FLAT CIS), and a third CIS strategy, which was especially designed to control and increase the depth of these fluctuations (F0 CIS). In general, performance was poorest for the FLAT CIS strategy, where changes in F0 are only apparent as changes of the average amplitude in the channel outputs. This emphasizes the importance of temporal coding of F0 in the speech envelope for pitch perception. No significantly better results were obtained for the F0 CIS strategy compared to the default CIS strategy, although the latter results in envelope modulation depths at which sub-optimal scores were obtained in some cases of the first experiment. This indicates that less modulation is needed if all channels are stimulated with synchronous F0 fluctuations. This hypothesis is confirmed in a third experiment where subjects performed significantly better in a pitch discrimination task with SAM pulse trains, if three channels were stimulated concurrently, as opposed to only one.

Acoustic Stimulation↗
PubMed2001

Are the Twelve Steps more acceptable to drug users than to drinkers? A comparison of experiences of and attitudes to Alcoholics Anonymous (AA) and Narcotics Anonymous (NA) among 200 substance misusers attending inpatient detoxification.

The present study is a cross-sectional interview-based investigation comparing experiences of and attitudes towards Alcoholics Anonymous (AA) and Narcotics Anonymous (NA) in a sample of 200 patients attending inpatient substance misuse detoxification services. Two hundred consecutive admissions were recruited; 100 each from one drug and one alcohol in-patient treatment service in which attendance at AA/NA was a voluntary adjunct to a generic treatment programme. Although there were no differences in the history of AA/NA attendance, the drug users (who were on average younger) reported significantly more positive attitudes towards AA/NA, more willingness to attend during their in-patient treatment and greater intention to attend following completion of their detoxification. In particular, despite no differences in spiritual/religious orientation, the drug users reported more positive views of the Twelve Steps. As AA/NA remain popular and accessible forms of substance misuse support, it is critical that we develop a clearer understanding of their impact and of the scope for their integration with generic forms of substance misuse treatment.

Adult↗
PubMed2005

Adolescents' beliefs about marijuana use: a comparison of regular users, past users and never/occasional users.

A questionnaire investigating adolescents' opinions and experiences regarding marijuana use was administered to 163 adolescents and young adults (96 boys and 67 girls) aged 13 to 20 (mean age = 16.8, s.d. = 1.5). Items referred to marijuana and other substances' dangerousness, representations regarding the positive and negative consequences of marijuana use. Responses were compared according to marijuana use status (classified into never/occasional use, current regular use and past regular use). Results show that adolescents' opinions differ according to their experience with marijuana use. Current regular users evaluate marijuana as less dangerous, but alcohol and heroin as more dangerous in comparison with never/occasional and past users. Current and past users are more likely to define marijuana as a medical drug and a plant used in agriculture, and less likely to define it as an illegal drug. Current and past users evaluate marijuana use as a way to cope with stress, to relax to a greater extent than do never/occasional users do. The latter attribute more negative consequences to marijuana use such as diminished driving ability and school performance and a pathway to hard drugs.

Adolescent↗
PubMed1999

Mechanical failure of the latex condom in a cohort of women at high STD risk.

BACKGROUND AND OBJECTIVES: Mechanical failure may reduce the efficacy of condoms. Little is known about frequency and determinants of condom failure in groups at high risk of sexually transmitted diseases (STD). GOAL: To measure condom breakage and slippage rates and evaluate potential determinants of failure among women attending a public STD clinic. STUDY DESIGN: Women attending an STD clinic participated in a 6-month prospective study of barrier contraception for the prevention of STD. They completed sexual diaries that were reviewed at monthly follow-up visits. No data were collected from the male partners. Baseline characteristics of the participants and time-dependent behaviors were evaluated as potential determinants of condom failure. RESULTS: Of 21,852 condoms used by 892 women, 500 broke during intercourse (2.3%) and 290 slipped (1.3%). Breakage was more common among young, black, single nulliparae who engaged in high-risk behavior. Slippage was more common among married women with children. Failure rates decreased with condom use, with coital frequency, and with use of spermicides. CONCLUSION: User characteristics and experience are determinants of breakage and slippage, which are often regarded only as the effect of product design flaws. Attention to modifiable determinants of failure may improve user counseling and product labeling.

Adolescent↗
PubMed2005

Gait of stance control orthosis users: the dynamic knee brace system.

Individuals with weak or absent quadriceps who wish to walk independently are prescribed knee-ankle-foot orthoses (KAFOs). New stance control orthosis (SCO) designs automatically release the knee to allow swing phase flexion and extension while still locking the joint during stance. Twenty-one participants were fitted unilaterally with the Dynamic Knee Brace System (DKBS), a non-commercial SCO. Thirteen subjects were experienced KAFO users (average 28 +/- 18 years of experience) while eight were novice users. Novice users demonstrated increased velocity (55 vs. 71 cm/sec, p = 0.048) and cadence (77 vs. 85 steps/min, p < 0.05) when using the DKBS over the traditional locked KAFO. Experienced KAFO users tended to have reduced velocity and cadence measures when using the SCO (p < 0.10). Knee range of motion was significantly greater for the novice group than for the experienced group (55.2 +/- 4.8 vs. 42.6 +/- 3.8 degrees, p = 0.05). Peak knee extension moments tended to be greater for the experienced group (0.29 +/- 0.21 vs. 0.087 +/- 0.047 Nm/kg, p = 0.09). This report describes gait changes during the introductory phase of DKBS adoption. Experienced KAFO users undoubtedly had ingrained gait patterns designed to compensate for walking with a standard locked KAFO. These patterns may have limited the ability of those users from taking full and immediate advantage of the SCO capabilities. Also, alternate SCO systems may engender different results. Comparison studies and longer term field studies are needed to clarify benefits of the various bracing options.

Adolescent↗
PubMed2004

Adaptive interface for personalizing information seeking.

An adaptive interface autonomously adjusts its display and available actions to current goals and abilities of the user by assessing user status, system task, and the context. Knowledge content adaptability is needed for knowledge acquisition and refinement tasks. In the case of knowledge content adaptability, the requirements of interface design focus on the elicitation of information from the user and the refinement of information based on patterns of interaction. In such cases, the emphasis on adaptability is on facilitating information search and knowledge discovery. In this article, we present research on adaptive interfaces that facilitates personalized information seeking from a large data warehouse. The resulting proof-of-concept system, called source recommendation system (SRS), assists users in locating and navigating data sources in the repository. Based on the initial user query and an analysis of the content of the search results, the SRS system generates a profile of the user tailored to the individual's context during information seeking. The user profiles are refined successively and are used in progressively guiding the user to the appropriate set of sources within the knowledge base. The SRS system is implemented as an Internet browser plug-in to provide a seamless and unobtrusive, personalized experience to the users during the information search process. The rationale behind our approach, system design, empirical evaluation, and implications for research on adaptive interfaces are described in this paper.

Data Display↗
PubMed1992

User interactions with the PDQ cancer information system.

Searches by end users and intermediaries on the online PDQ (Physician Data Query) cancer information system were observed. With the National Library of Medicine (NLM) menu-based interface, end users (physicians) averaged fewer steps per question, while with the BRS command-drive interface, intermediaries appeared to be more efficient. Cancer Information Service (CIS) searchers, who have more PDQ experience than end users or intermediaries, made greater use of command stacking to anticipate menu selections. Retrieval was more complete in the NLM system, where both the menus and predefined print formats assisted the searchers.

Databases, Factual↗
PubMed1990

Attenuation performance of four hearing protectors under dynamic movement and different user fitting conditions.

An experiment was conducted to determine the effects of movement activities and alternative fitting procedures on protection levels afforded by four hearing protection devices (HPDs). Psychophysical attenuation measurements at nine one-third-octave bands from 125 to 8000 Hz were obtained prior to, during, and following a 2-hr wearing stint that included periods of either highly kinematic but controlled work activity or vigorous temporomandibular movement. The 40 subjects, who were nonusers of HPDs, initially fit the protectors according to either the instructions on the package (i.e., subject fit) or after receiving interactive training on proper fit (i.e., trained fit). Thereafter no further protector adjustments were allowed during the wearing period. The subject-fit condition resulted in significantly lower protection levels, from 4 to 14 dB, at 1000 Hz and below for a premolded polymer earplug, a user-molded foam earplug, and a double protector consisting of a muff over the foam plug. The muff alone was significantly more resilient to fitting effects on attenuation than were the plugs. Movement activity caused up to a 6-dB significant reduction in frequency-specific attenuation over time for the premolded plug, muff, and muff-plug combination. The compliant foam earplug was largely resistant to either type of movement effect but did benefit more than the other devices from use of the trained-fit procedure. Implications of the results for hearing protector testing protocol, device selection, and user training are discussed.

Adult↗
PubMed1995

Stimulation, data acquisition, spikes detection and time/rate analysis with a graphical programming system: an application to vision studies.

A Macintosh-based system performs stimulus control and data acquisition, and an off-line analysis, in experiments on visually driven neurons in frog. The stimulus is a target moved on a modified XY recorder. The computer is equipped with a multifunction input/output board to perform stimulus control and data acquisition. The graphical programming system LabVIEW 2 was used to develop the 'Vision 93' package made of 4 main 'virtual instruments' (VIs). By means of DOCS-Exp, the user controls the experiment via screen displays which look like front panels of electronic instruments. DOCS-Preproc performs a user-controlled spike detection and computes mean impulse rate values. DOCS-SAS displays the instantaneous frequency, mean impulse rate, spike counts or interspike time intervals as staircase histograms and/or spline smoothed curves. Finally, DOCS-x-Functions computes and graphs quantitative stimulus/response relationships in terms of velocity, diameter, orientation and configuration of the target. The functionalities of these main VIs are presented and original software components are detailed. System operation is illustrated by using the successive VIs to process a sample signal record.

Algorithms↗
PubMed1978

The effect of prior treatment on treatment success.

The characteristics of clients discharged from federally funded treatment facilities reporting to CODAP are analyzed in terms of several variables. These are the reasons for discharge (treatment completed, transfer or referral, or treatment not completed), the primary drug of abuse at admission (opiates and nonopiates), and the number of prior treatment experiences. Two independent replications using data for two consecutive quarters produced the same results, finding that the likelihood of completing treatment decreases as the number of prior treatment experiences increases. This relationship was found to apply to both opiate and nonopiate users. Although large differences exist in completion rates between opiate and nonopiate users without prior treatment experience, only small differences exist between opiate and nonopiate users who have had prior treatment. The largest difference in treatment outcome occurs between those with no prior treatment and those who have been treated before. Having one or more prior treatment experiences does not seem to have a major impact on the probability of completing treatment.

Heroin Dependence↗
PubMed1999

The quality of general dental care: public and users' perceptions.

BACKGROUND: Systematic evidence about how the public and users perceive and experience the quality of general dental care is in short supply, particularly in light of the recent changes in the general dental service. The study reported here attempted to fill this gap. OBJECTIVES: To identify the criteria the public and users adopt in evaluating the quality of general dental care, and to identify the extent and nature of perceived concerns with general dental care. DESIGN: Postal questionnaires were sent to random samples of adults living in an inner city area (I) and semi-rural area (R) in southern England. Fifty six per cent (1499) in area R and 48% (1388) in area I completed the questionnaire after four mailings. Follow up face-to-face interviews were done with a purposive subsample (n = 50) of responders from the postal survey. MAIN MEASURES: Public/user views about quality of dental care were measured through groups of questions about the importance of and satisfaction with different aspects of dental care (access/availability including cost; facilities; technical skills; and interpersonal care) and a scale (Dentsat) measuring general satisfaction was constructed from questions on different aspects of care. RESULTS: Evaluation of quality of general dental care from the users' point of view hinges on perceived technical skills, particularly pain management. Major dissatisfaction stems from concerns about costs of dental care and privatisation. CONCLUSIONS: The criteria adopted by the public/users to assess general dental care are similar to other areas of health care, apart from the priority placed on technical skills and pain management. However, the major source of decline in satisfaction with the quality of general dental care is the barrier to access created by the rising cost of dental care and the increasing involvement of dentists in private practice. This evidence suggests that the public and users find the drift towards private practice and away from NHS practice a major source of concern.

Consumer Behavior↗
PubMed2004

Improving software environments through usability and interaction design.

This paper introduces the fields of usability and interaction design in order to highlight their benefits and provide further resources for those that wish to find out more. It is hoped that this review will encourage medical illustrators to adopt certain principles and practices in their own project work, in order to strive towards (and ultimately produce) products and environments that provide more positive interactions for their users. Usability and interaction design are fields of study concerned with aims relating to ensuring that any given interactive product or environment is efficient, effective and safe to use, as well as easy to learn and remember. Of primary importance is the experience of the user whose interactions should be positive, as opposed to frustrating or counter-intuitive.

Equipment Design↗
PubMed2003

Inpatient chronic assisted ventilatory care: a 15-year experience.

STUDY OBJECTIVES: Ventilator users who are unable to leave the acute care setting may be transferred to a unit for chronic assisted ventilatory care (CAVC) with the goal of optimizing their level of function. In this report, we summarize the outcomes of all patients admitted to a CAVC unit between 1986 and 2001. PATIENTS AND METHODS: Fifty patients (24 with neuromuscular disease [NMD], 10 with spinal cord injury [SCI], 7 with thoracic restriction [TR], 7 with COPD, and 2 with parenchymal restriction [PR]) were reviewed. Thirty-eight patients were transferred to the CAVC unit from intensive care, 5 patients were transferred from inpatient respiratory rehabilitation, 4 patients came from home, and 3 patients came from pediatric long-term care. At the time of CAVC unit admission, all patients were receiving mechanical ventilation via a tracheostomy tube. RESULTS: Ventilator time increased gradually in patients with COPD from 16 h (SD, 5.6) to 22.9 h (SD, 3.0) per day (p < 0.05), and in patients with TR from 18.9 h (SD, 6.1) to 22.9 h (SD, 4.5) [not significant]. Five of the 10 patients with SCI were decannulated. Functional mobility, which decreased in patients with COPD and patients with TR, remained stable in NMD and PR and improved in SCI. Eighteen patients returned home or to an attendant care facility (COPD, n = 1; NMD, n = 10; SCI, n = 5; PR, n = 2); 11 patients died in the CAVC unit (COPD, n = 6; TR, n = 3; NMD, n = 1; SCI, n = 1); and 7 patients were transferred to intensive care, where they died. The average direct cost per patient per diem increased from $252 (Canadian) in 1988 to $335 in 2001. CONCLUSION: A CAVC unit can provide a safe environment for severely impaired, ventilator-dependent individuals, many of whom (36%) left for a more independent community-based environment. Better outcomes were seen among patients with SCI and NMD than in patients with COPD and TR.

Activities of Daily Living↗
PubMed2002

Chronic disease mortality in a cohort of smokeless tobacco users.

The purpose of this study was to characterize the relation between smokeless tobacco use and the risk of all-cause and disease-specific mortality. Using data from the First National Health and Nutrition Examination Survey Epidemiologic Followup Study, the authors assessed the 20-year mortality experience of smokeless tobacco users. Subjects aged 45 years or more at baseline (1971-1975) were categorized as either smokeless tobacco users (n = 1,068) or non-smokeless tobacco users (n = 5,737). Subjects were further stratified by smoking status and gender. Proportional hazard ratios were used to assess associations. After adjustment for confounders, no association between smokeless tobacco use and all-cause (hazard ratio = 1.1, 95% confidence interval (CI): 0.9, 1.3), all cancer (hazard ratio = 1.1, 95% CI: 0.6, 1.9), or all cardiovascular (hazard ratio = 1.1, 95% CI: 0.8, 1.5) mortality was found. There was an increase in all cancer mortality of borderline significance among female smokeless tobacco users (hazard ratio = 1.7, 95% CI: 1.0, 2.8). The lung cancer mortality rate among combined users (smokeless tobacco and cigarettes), based on the rates for exclusive smokeless tobacco users and exclusive smokers, was higher than expected, possibly because of heavier smoking among these subjects. The mortality experience of smokeless tobacco users was not significantly greater than that of non-tobacco users and was appreciably less than that of cigarette smokers. Furthermore, combined use of smokeless tobacco and cigarettes did not increase overall mortality beyond that expected from use of the individual products.

Adult↗
PubMedDate not supplied

Health sector reforms in sub-Saharan Africa: lessons of the last 10 years.

Over the past 10 years the poorest countries, especially in Africa, have struggled with worsening economic conditions and reduced public finance for health services. Some governments have responded in a piecemeal fashion, reacting to internal and external pressures. Others have embarked on major reforms of various aspects of their health systems. This paper reviews two specific types of strategy that have been initiated by governments: reform of financing strategies, and reform of public sector organization and procedures. Particular attention is paid to the experience of introducing user fees, community financing and decentralization since these have been some of the most popular strategies. The paper describes the nature, objectives and extent of reforms. It then presents an evaluation framework related to the criteria of efficiency and equity, and evaluates current reform experience using this framework. It concludes that assessment of the potential impact of reforms on efficiency and equity is undermined by the limited duration of many reforms and the limited nature of existing evaluations. It is clear, however, that a policy package is required rather than implementation of isolated reform strategies, and that in order to design an effective policy package, more needs to be known about the implementation and operation of reforms--particularly with respect to the influence of context, actors and processes.

Africa South of the Sahara↗
PubMed2026

The Soundtrack of Everyday Life: Real-world Music Listening Habits of Adult Cochlear Implant Users.

OBJECTIVE: Characterize real-world patterns of music listening and reward sensitivity among adult cochlear implant (CI) users compared with normal-hearing (NH) listeners. STUDY DESIGN: Cross-sectional observational study. SETTING: Online. PATIENTS: Adults (&#x2265;18&#xa0;y) with a CI or NH who used a music-streaming platform as their primary listening method. INTERVENTIONS: None. MAIN OUTCOME MEASURES: Objective measures included platform-derived audio features (acousticness, danceability, energy, tempo, and valence), listening volume, unique-song ratio, and decade preferences. Self-reported measures included listening habits and the Barcelona Music Reward Questionnaire (BMRQ). Group comparisons used ANCOVAs and mixed-effect models adjusting for age and gender; within-CI analyses compared prelingual versus postlingual deafness. RESULTS: Among 16 CI users (69% male, 39.0&#xb1;15.6&#xa0;y) and 29 NH listeners (38% male, 32.2&#xb1;11.3&#xa0;y), CI users demonstrated a higher unique-song ratio (&#x3b2;=-0.157, CI as reference; 95%CI [-0.281, -0.034]; P =0.014) and stronger preference for older music (Pillai trace=0.537; F8,35 =5.07; P <0.001), adjusting for age. No significant group differences were observed in weekly listening time, listening volume, audio features, or BMRQ scores (total and subscores). Equivalence was confirmed for Emotion Evocation and Sensory-Motor subscales. There were no statistically significant differences in listening environments after Holm correction. No statistically detectable differences were observed between pre- and postlingually deafened CI users. CONCLUSIONS: Musically active CI users showed no significant differences in listening volume or overall music-reward sensitivity compared with NH peers, but demonstrated higher unique-song ratios and a bias toward older music. Findings highlight the value of ecologically valid data in understanding real-world music experiences among CI users.

Adult↗