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Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.

BACKGROUND: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. RESULTS: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. CONCLUSION: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

Algorithms↗

Bleeding patterns and acceptability among Norplant users in Singapore.

Norplant contraceptive implants are silastic implants containing levonorgestrel. This study describes our experience with 100 acceptors of NORPLANT implants in Singapore. No pregnancies occurred during the first year of use. The majority found the method's ease of use to be the most attractive feature. Disruption of menstrual rhythm appeared to be the least liked feature. However the incidence of these menstrual irregularities appeared to diminish with time. Implant users have tolerated this early disruption of their menstrual rhythm well and the continuation rate at the end of the year was 97%. Thus it appears that Norplant is a safe, effective and acceptable method of contraception.

Adolescent↗

Stress detection in computer users through non-invasive monitoring of physiological signals.

he emerging discipline of Affective Computing pursues the development of computers that could interact with their users taking their affective states into account. For example, if a computer could detect when its user is experiencing stress, it could change the colors and sounds of its user interface to try to calm him/her down. Similarly, the pace of instruction in a computer-based training system could be adapted according to the stress level sensed in the pupil. The research described in this paper aims at the development of a stress detection approach based on automatic monitoring of physiological signals in the computer user. The paper describes the three main aspects of our work: experiment setup for physiological sensing, signal processing to detect the affective state and affective recognition using a learning system. Four signals: Galvanic Skin Response (GSR), Blood Volume Pulse (BVP), Pupil Diameter (PD) and Skin Temperature (ST) are monitored and analyzed to differentiate affective states in the user, in a non-invasive fashion. Results indicate that the physiological signals monitored do, in fact, have a strong correlation with the changes in emotional state of our experimental subjects when stress stimuli are applied to the interaction environment.

Adult↗

Ethical considerations in researching user views.

Researching user views has become a central plank of UK cancer and palliative care policy, not least because it is recognized that current systems for treatment reflect inadequately the experiences and concerns of cancer patients. This paper examines the process of accessing user views about cancer and palliative care from an ethical perspective, drawing by way of example on a study of outcomes associated with Macmillan nursing. A moral theory framework is used to discuss some of the issues involved in trying to achieve ethically sound practice and some essentially political issues that frame the process of accessing users' views are highlighted. The paper recommends that models of research be developed for accessing user views that are congruent with the values and philosophies of supportive and palliative care. This requires striking a fine balance between the ethical duties of providing care and support, nurturing independence and autonomy, and achieving research outcomes that are rigorous while also being accessible and meaningful to users. It also requires developing an understanding of the social, political and economic context of research enquiry with users.

Data Collection↗

Location-based health information services: a new paradigm in personalised information delivery.

Brute health information delivery to various devices can be easily achieved these days, making health information instantly available whenever it is needed and nearly anywhere. However, brute health information delivery risks overloading users with unnecessary information that does not answer their actual needs, and might even act as noise, masking any other useful and relevant information delivered with it. Users' profiles and needs are definitely affected by where they are, and this should be taken into consideration when personalising and delivering information to users in different locations. The main goal of location-based health information services is to allow better presentation of the distribution of health and healthcare needs and Internet resources answering them across a geographical area, with the aim to provide users with better support for informed decision-making. Personalised information delivery requires the acquisition of high quality metadata about not only information resources, but also information service users, their geographical location and their devices. Throughout this review, experience from a related online health information service, HealthCyberMap http://healthcybermap.semanticweb.org/, is referred to as a model that can be easily adapted to other similar services. HealthCyberMap is a Web-based directory service of medical/health Internet resources exploring new means to organise and present these resources based on consumer and provider locations, as well as the geographical coverage or scope of indexed resources. The paper also provides a concise review of location-based services, technologies for detecting user location (including IP geolocation), and their potential applications in health and healthcare.

Journal Article↗

preAssemble: a tool for automatic sequencer trace data processing.

BACKGROUND: Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. RESULTS: The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. CONCLUSION: preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Algorithms↗

Telecare at home: factors influencing technology choices and user acceptance.

Acceptance of telecare technologies in the home is strongly influenced by factors that relate to dwelling design and the ways in which independent living is promoted. The experience to date of personal response systems (and services) provides some indication of the reasons why users may either resist their introduction or not use such technologies after they have been introduced. Telecare systems and services are poised to incorporate medical and other sensors, so that the manner of their provision, installation and control becomes an important consideration for service providers. A clear ethical framework is called for.

Cost-Benefit Analysis↗

Effects of modafinil on sustained attention performance and quality of life in OSA patients with residual sleepiness while being treated with nCPAP.

BACKGROUND: Some patients with obstructive sleep apnea/hypopnea syndrome (OSA/HS) who are regular users of nasal continuous positive airway pressure (nCPAP) therapy continue to experience daytime sleepiness that impairs performance and quality of life. A randomized, double-blind, placebo-controlled, parallel-group study was conducted to determine the effect of modafinil on sustained attention performance and functional quality of life in OSA/HS patients with residual daytime sleepiness, who were regular users of nCPAP therapy. METHODS: Seventy-seven patients received modafinil (200 mg/day, week 1; 400 mg/day, weeks 2-4) and 80 patients received matching placebo once daily for 4 weeks. Sustained attention performance on the psychomotor vigilance task (PVT) and functional status and quality of life using the Functional Outcomes of Sleep Questionnaire (FOSQ) were measured. RESULTS: The frequency of lapses of attention during PVT performance was significantly decreased, and both the median and slowest reaction times were significantly improved in patients receiving nCPAP plus modafinil compared with those receiving nCPAP plus placebo (P=0.010 for the number of lapses [transformed], P=0.023 for the median reaction time, and P=0.014 for the reciprocal of the 10% slowest reaction times). Treatment with nCPAP plus modafinil significantly improved the FOSQ total score (weeks 1 and 4), the vigilance subscale score (weeks 1 and 4), and the activity level subscale score (week 4) compared with treatment with nCPAP plus placebo (all P<0.05). CONCLUSIONS: Consistent with previous results for objective and subjective measures of sleepiness, modafinil used adjunctively improved performance on a test of behavioral alertness and reduced functional impairments in patients with OSA/HS who were regular users of nCPAP therapy but still experiencing sleepiness.

Adult↗

'Getting somewhere', feeling cared for: patients' perspectives on complementary therapies in the NHS.

OBJECTIVE: To examine satisfaction with complementary therapy among patients receiving treatment funded within the National Health Service (NHS). DESIGN: Semi-structured interviews using a critical incident approach (n =49). SETTING: 8 sites across England providing complementary therapy services within primary care. RESULTS: Complementary therapies are experienced as ameliorating and curing conditions, including chronic problems. Patients also perceive complementary practitioners as being caring and value the development of a therapeutic relationship within which they are encouraged to take an active part in looking after their health. Positive experiences of complementary therapy use were contrasted with either a failure of orthodox medicine or a dislike of the orthodox treatments available to them. Very few negative aspects were reported. CONCLUSIONS: Patient satisfaction was consistent across settings and type of therapy received. The findings reinforce messages from studies of users in the private sector, but also suggest that for NHS users commitment to treatment develops largely as a result of positive experience rather than prior beliefs. Implications of the findings for research and policy are considered.

Adult↗

[Integration through university studies--experiences and prospects for the future (author's transl)].

The experiences gained over a twelve year period with wheelchair-users attending Marburg university are reviewed. The technical pre-requisites gradually developed at the university and the Konrad-Biesalski-Haus, a residential home providing accommodation for both, disabled and non-disabled students, have proven good and served as a model for similar facilities in Regensburg, Darmstadt, Hannover, Bonn, Bochum and Bielefeld. Up to 1977, 25 severely handicapped students had successfully completed their studies at Marburg university. Of these, 19 are employed according to their qualification or are taking post-graduate courses. According to the graduates' experiences, personal contacts with the appropriate authorities and private employers were very important for their vocational integration. The general public's understanding of the disabled has improved. What remains to be done is the amelioration of vocational and study counselling services for physically disabled secondary school pupils. Preparatory measures for job placement following study completion should be initiated early on.

Persons with Disabilities↗

Effect of chewing betel nut on measurements of salivary progesterone and estradiol.

The measurement of steroids in saliva is both simple and non-invasive and has been widely used in field and clinical-based research. The observance of particular cultural practices by some populations, however, may hamper accurate hormonal analyses. The present study evaluated the effects of one such practice-the chewing of betel nut-on the accurate measurement of salivary progesterone and estradiol. A time series experiment was conducted among Bangladeshi women who are regular users of betel nut. Salivary steroids were analyzed by radioimmunoassay in samples collected prior to and then 30, 60, 120, and 240 min following betel quid use. Results show no significant difference between basal steroid levels and those obtained 60, 120, and 240 min after chewing betel nut. We conclude that with specific collection protocols that take into account time since chewing, salivary steroid analyses can be undertaken in populations among whom the practice of chewing betel nut is endemic.

Adolescent↗

Eigenmobilities in background electrolytes for capillary zone electrophoresis: IV. Computer program PeakMaster.

We are introducing a computer implementation of the mathematical model of zone electrophoresis (CZE) described in Stedry, M., Jaros, M., Hruska, V., Gas, B., Electrophoresis 2004, 25, 3071-3079 program PeakMaster. The computer model calculates eigenmobilities, which are the eigenvalues of the matrix tied to the linearized continuity equations, and which are responsible for the presence of system eigenzones (system zones, system peaks). The model also calculates other parameters of the background electrolyte (BGE)-pH, conductivity, buffer capacity, ionic strength, etc., and parameters of the separated analytes--effective mobility, transfer ratio, molar conductivity detection response, and relative velocity slope. This allows the assessment of the indirect detection, conductivity detection and peak broadening (peak distortion) due to electromigration dispersion. The computer model requires the input of the BGE composition, the list of analytes to be separated, and the system instrumental configuration. The output parameters of the model are directly comparable with experiments; the model also simulates electropherograms in a user-friendly way. We demonstrate a successful application of PeakMaster for inspection of BGEs having no stationary injection zone.

Computer Simulation↗

Evaluation of the home help service and its impact on the informal caregiver's burden of dependent elders.

AIM: This study looks at the objective and subjective characteristics of home respite service provision and its impact on the informal care burden of dependent elders. METHOD: A sample of 296 dependent people and their informal caregivers was randomly selected among users and non-users of the Home Help Service (HHS) in an autonomous Spanish region (Comunidad Valenciana). An experimental design was used and a field study was carrying out that collected information on sociodemographic variables of the dependent person and his/her caregiver, HHS characteristics and the assessment of the services delivered by this resource as well as the informal caregivers'burden. RESULTS: The results show that the services of this resource are very limited, with low cover and frequency, and they do not address the real dependency needs in specific activities of daily living. However, users and caregivers are satisfied with this care and experience a higher quality of life since it was implemented, although the HHS does not alleviate informal caregivers' stress. CONCLUSION: These data show the need to extend the services delivered by the HHS and the duration of care, address the caregiver's need for psychological care, and look at potentially modifiable variables in the care context when designing prevention and psychosocial intervention programmes to lessen the informal caregiver's burden.

Activities of Daily Living↗

Fractal analysis: an objective method for identifying atypical nuclei in dysplastic lesions of the cervix uteri.

OBJECTIVES: Fractal geometry is a tool used to characterize irregularly shaped and complex figures. It can be used not only to generate biological structures (e.g., the human renal artery tree), but also to derive parameters such as the fractal dimension in order to quantify the shapes of structures. As such, it allows user-independent evaluation and does not rely on the experience level of the examiner. METHODS: We applied a box-counting algorithm to determine the fractal dimension of atypical nuclei in dysplastic cervical epithelium. An automatic algorithm was used to determine the fractal dimension of nuclei in order to prevent errors from manual segmentation. Four groups of patients (CIN 1-3 and control) with 10 subjects each were examined. In total, the fractal dimensions of 1200 nuclei were calculated. RESULTS: We found that the fractal dimensions of the nuclei increased as the degree of dysplasia increased. There were significant differences between control and atypical nuclei found by an analysis of variance. Atypical nuclei associated with CIN 1, CIN 2, and CIN 3 also differed significantly among these groups. CONCLUSION: We conclude that the fractal dimension is a valuable tool for detecting irregularities in atypical nuclei of the cervix uteri and thus allows objective nuclear grading.

Cell Nucleus↗

Social users of alcohol and cannabis who detect substance-related changes in a change blindness paradigm report higher levels of use than those detecting substance-neutral changes.

RATIONALE: Understanding the cognitions underpinning substance use has stalled using the Stroop paradigm. OBJECTIVE: To employ a novel version of the flicker paradigm for induced change blindness to independently compare information processing biases in social users of alcohol and cannabis. METHOD: Alcohol and cannabis experiments were independently run. In both, participants were asked to view successively and repeatedly on a monitor two versions of a visual scene (an original and a slightly changed version) until the change was detected. In fact, in both experiments two simultaneous changes competed for detection: a substance-neutral and a substance-related change. RESULTS: In both the alcohol and the cannabis experiments, participants detecting the substance-related change reported higher levels of use than those detecting the substance-neutral change. CONCLUSION: A substance-related processing bias was independently revealed for both substances. The utility of the flicker paradigm for substance use research is demonstrated as sensitive and quick to administer (taking only 1 min).

Alcohol Drinking↗

Norplant implants acceptability and user satisfaction among women in two African countries.

An analysis of 350 users of Norplant contraceptive subdermal implants from six centers in two African countries (Ghana and Nigeria) indicates that method acceptability remained high among the women who used the method for five years. Overall, 90.1% of the 155 five-year users in these countries reported having a very favorable experience and 9.9% a favorable experience with Norplant implants. Ease of use was cited by 56.1% and duration of use by 13.6% of the women as the most liked characteristics of the method at study completion after five years. Menstrual disturbance was the least liked aspect, by 41.9% of the women. On average, women who discontinued early from the study had fewer living children and were more likely to desire additional children at method adoption than those who completed five years of use; the differences were statistically significant. Differences in level of education and previous use of contraception were not found to be statistically significant between completers and non-completers. Differences in age were not significant in Nigeria, but were marginally significant in Ghana, with completers being older than non-completers. Of the clients who completed this study, 79.2% indicated a desire to continue with contraception and 43.9% planned to have a second set of implants inserted. These findings have important implications for counseling, method access and service sustainability in African countries.

Adult↗

Särimner: a computer model of diabetes physiology for education of physicians and patients.

Often diabetic patients have developed their skills by some trial-and-error-like training over a long period of time. To minimize this inconvenience we have made a mathematical model to facilitate diabetes education. The model consists of a number of blocks involved in diabetes physiology: digestion, blood (transport), pancreas, injected insulin absorption, liver, muscles, kidneys, metabolism and insulin sensitivity. The model serves as a demonstration object and the user can change meals, exercise and injections and see the resulting blood glucose level. A more experienced user can search for further explanations of different phenomena deeper in the physiology of the model. The model does not solve any problem for the user, but creates a learning situation in which the user, led by his own curiosity, successively increases his experience of diabetes physiology. Särimner is implemented as an easy-to-use menu driven computer program for IBM PC-clones with Hercules, EGA or VGA graphics.

Adolescent↗

Automatic selection of the optimal cardiac phase for gated three-dimensional coronary x-ray angiography.

RATIONALE AND OBJECTIVES: For the reconstruction of the coronary arteries from rotational angiography data, a crucial point is the selection of the optimal cardiac phase for data reconstruction. To avoid time-consuming interactive selection of the optimal cardiac phase by visual inspection of multiple high-resolution data sets reconstructed at different cardiac phases, an automatic approach for deriving optimal reconstruction windows is attractive. MATERIALS AND METHODS: This paper presents a new approach to fully automatic selection of the optimal cardiac phase for image reconstruction. It is based on the analysis of a four-dimensional data set of the region of interest reconstructed at low-spatial resolution utilizing an image quality index, which quantifies the image quality of a single three-dimensional reconstructed volume. The derived image quality index utilizes the histogram information of a single temporal snapshot as a quality measure for the vessel reconstruction. The proposed technique was applied to 16 projection data sets obtained in eight pigs. RESULTS: Experiments to evaluate the proposed method based on user-defined image quality parameters serving as ground truth, showed a relatively high correlation (>84%) for high-quality (c(phi) > 0.95) images. CONCLUSION: An image-based technique is introduced, which is able to determine the optimal cardiac phase for 3D-RCA fully automatically. The proposed method was successfully applied to 16 data sets obtained in a total of 8 porcine models.

Algorithms↗