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PubMed2005

Use of a Bayesian approach to decide when to stop a therapeutic trial: the case of a chemoprophylaxis trial in human immunodeficiency virus infection.

From 1996 to 1998, a phase III, placebo-controlled, therapeutic trial was conducted in Abidjan, Ivory Coast, to assess the efficacy of cotrimoxazole prophylaxis in reducing severe morbidity in adults at early stages of human immunodeficiency virus infection. The authors used the real data from this trial to simulate three Bayesian interim analyses. Three prior distributions were considered: a noninformative one, a skeptical one, and one based on external information. The posterior distribution was calculated by using directed acyclic graphs and Gibbs sampling. This Bayesian approach showed different results according to the prior distribution chosen. Although use of the noninformative prior would have led to stopping the trial at the same time that the frequentist approach would have, the skeptical prior would have led to continuing it, and the prior based on external data would have led to stopping it 1 year earlier.

Anti-Infective Agents↗

PubMed1997

Retrospective estimation of exposure to benzene in a leukaemia case-control study of petroleum marketing and distribution workers in the United Kingdom.

OBJECTIVE: To provide quantitative estimates of exposure to benzene for cases and controls in an epidemiology study to investigate the risk of leukaemia in petroleum distribution workers. METHODS: Work histories were obtained for cases and controls together with detailed information on the distribution sites. For each job in the work history, an estimate of exposure (parts per million (ppm)) was obtained by multiplying a measure derived from exposure data by modifying factors to reflect the differences between the conditions that existed at the time of measurement and those at the time of interest. The modifying factors used related to job activity, the number of road tankers loaded, the benzene content of the gasoline, the mixture of products handled, temperature, and loading technology. Cumulative exposures for each case and control were obtained by multiplying the exposure estimates for each job by the duration of time in the respective jobs, and summing these over all jobs in the work history. Peak exposure and exposure through dermal contact were quantitatively classified for each job. RESULTS: Measured exposures were obtained for 30 job categories, and ranged from 0.003 to 8.20 ppm. 40% of work histories were assigned background exposures, with a further 34% assigned the exposure estimate for a driver carrying out top submerged loading of motor fuel into road tankers. Cumulative exposures ranged from < 1 to > 200 ppm-years, although 81% were < 5 ppm-years. Comparison of the exposure estimates for selected jobs with data from sources not used in the study showed similar results. CONCLUSION: The estimates of exposure to benzene in this study provide a sound basis for the epidemiological analyses.

Benzene↗

PubMed1996

Benzene exposure in the petroleum distribution industry associated with leukemia in the United Kingdom: overview of the methodology of a case-control study.

This paper describes basic principles underlying the methodology for obtaining quantitative estimates of benzene exposure in the petroleum marketing and distribution industry. Work histories for 91 cases of leukemia and 364 matched controls (4 per case) identified for a cohort of oil distribution workers up to the end of 1992 were obtained, primarily from personnel records. Information on the distribution sites, more than 90% of which were closed at the time of data collection, was obtained from site visits and archive material. Industrial hygiene measurements measured under known conditions were assembled for different tasks. These were adjusted for conditions where measured data were not available using variables known to influence exposure, such as temperature, technology, percentage of benzene in fuel handled, products handled, number of loads, and job activity. A quantitative estimate of dermal contact and peak exposure was also made.

Benzene↗

PubMed1998

Web based 3-D medical image visualization on the PC.

With the recent advance of Web and its associated technologies, information sharing on distribute computing environments has gained a great amount of attention from many researchers in many application areas, such as medicine, engineering, and business. One basic requirement of distributed medical consultation systems is that geographically dispersed, disparate participants are allowed to exchange information readily with each other. Such software also needs to be supported on a broad range of computer platforms to increase the softwares accessibility. In this paper, the development of world-wide-web based medical consultation system for radiology imaging is addressed to provide platform independence and greater accessibility. The system supports sharing of 3-dimensional objects. We use VRML (Virtual Reality Modeling Language), which is the defacto standard in 3-D modeling on the Web. 3-D objects are reconstructed from CT or MRI volume data using a VRML format, which can be viewed and manipulated easily in Web-browsers with a VRML plug-in. A Marching cubes method is used in the transformation of scanned volume data sets to polygonal surfaces of VRML. A decimation algorithm is adopted to reduce the number of meshes in the resulting VRML file. 3-D volume data are often very large in size, hence loading the data on PC level computers requires a significant reduction of the size of the data, while minimizing the loss of the original shape information. This is also important to decrease network delays. A prototype system has been implemented (http://cybernet5.snu.ac.kr/-cyber/mrivrml .html), and several sessions of experiments are carried out.

Algorithms↗

PubMed2000

Net ergonomics: information retrieval in health care domains.

The explosion of Internet-based socio-cultural subcontexts and the possibility, horizontally distributed, of handling information on the Net, are transforming information retrieval in a key topic for psychosocial research. However, describing and analyzing how a huge and complex topic can be discussed in the Net and how people's behaviors and attitudes can be influenced by this discussion, is a very complicated task. The aim of this chapter, is both to point out the limits of traditional approaches to the analysis of information retrieval in complex Internet-based domains, and to propose some advice for a cultural approach to the Net. In particular, starting from the analysis of a specific health care domain--drug abuse--the chapter will try to identify some guidelines for the study of these issues.

Drug Information Services↗

PubMed2005

Data classification with radial basis function networks based on a novel kernel density estimation algorithm.

This paper presents a novel learning algorithm for efficient construction of the radial basis function (RBF) networks that can deliver the same level of accuracy as the support vector machines (SVMs) in data classification applications. The proposed learning algorithm works by constructing one RBF subnetwork to approximate the probability density function of each class of objects in the training data set. With respect to algorithm design, the main distinction of the proposed learning algorithm is the novel kernel density estimation algorithm that features an average time complexity of O(n log n), where n is the number of samples in the training data set. One important advantage of the proposed learning algorithm, in comparison with the SVM, is that the proposed learning algorithm generally takes far less time to construct a data classifier with an optimized parameter setting. This feature is of significance for many contemporary applications, in particular, for those applications in which new objects are continuously added into an already large database. Another desirable feature of the proposed learning algorithm is that the RBF networks constructed are capable of carrying out data classification with more than two classes of objects in one single run. In other words, unlike with the SVM, there is no need to resort to mechanisms such as one-against-one or one-against-all for handling datasets with more than two classes of objects. The comparison with SVM is of particular interest, because it has been shown in a number of recent studies that SVM generally are able to deliver higher classification accuracy than the other existing data classification algorithms. As the proposed learning algorithm is instance-based, the data reduction issue is also addressed in this paper. One interesting observation in this regard is that, for all three data sets used in data reduction experiments, the number of training samples remaining after a naive data reduction mechanism is applied is quite close to the number of support vectors identified by the SVM software. This paper also compares the performance of the RBF networks constructed with the proposed learning algorithm and those constructed with a conventional cluster-based learning algorithm. The most interesting observation learned is that, with respect to data classification, the distributions of training samples near the boundaries between different classes of objects carry more crucial information than the distributions of samples in the inner parts of the clusters.

Algorithms↗

PubMed2004

Use of remote sensing and geographical information systems to identify environmental features that influence the distribution of paramphistomosis in sheep from the southern Italian Apennines.

A geographic information system (GIS) was constructed using remote sensing (RS) and landscape feature data together with Calicophoron daubneyi positive survey records from 197 georeferenced ovine farms with animals pasturing in a 3971 km(2) area of the southern Italian Apennines. The objective was to study the spatial distribution of this rumen fluke, identify environmental features that influence its distribution, and develop a preliminary risk assessment model. The GIS for the study area was constructed utilizing the following environmental variables: normalized difference vegetation index (NDVI), land cover, elevation, slope, aspect, and total length of rivers. These variables were then calculated for "buffer zones" consisting of the areas included in a circle of 3 km diameter centered on 197 farms. The environmental data obtained from GIS and RS and from data taken by the veterinarians on the field (stocking rate and presence of streams, springs and brooks on pasture) were analyzed by univariate (Spearman and ANOVA) and multivariate (discriminant) statistical analyses using the farm coprological status (positive/negative) as the dependent variable. Sheep on 32 of the 197 (16.2%) farms, were positive for C. daubneyi, with an average intensity of 52 epg. A multivariate stepwise discriminant analysis model was developed that included moors and heathland, sclerophyllous and coniferous forest vegetation, autumn-winter NDVI and presence of streams, springs and brooks on pasture. The variables entered in the model were also correlated with C. daubneyi positive farms in the univariate tests and are consistent with the environmental requirements of C. daubneyi and its snail intermediate host.

Animals↗

PubMed1978

Distributed processing techniques: interface design for interactive information sharing.

The Information Systems Division of the University of Iowa Hospitals and Clinics has successfully designed and implemented a set of generalized interface data-handling routines that control message traffic between a satellite minicomputer in a clinical laboratory and a large main-frame computer. A special queue status inquiry transaction has also been developed that displays the current message-processing backlog and other system performance information. The design and operation of these programs are discussed in detail, with special emphasis on the message-queuing and verification techniques required in a distributed processing environment.

Computers↗

PubMed2003

Hyperpolarization-activated current (Ih) in the inferior colliculus: distribution and contribution to temporal processing.

Neurons in the inferior colliculus (IC) process acoustic information converging from inputs from almost all nuclei of the auditory brain stem. Despite its importance in auditory processing, little is known about the distribution of ion currents in IC neurons, namely the hyperpolarization-activated current Ih. This current, as shown in neurons of the auditory brain stem, contributes to the precise analysis of temporal information. Distribution and properties of the Ih current and its contribution to membrane properties and synaptic integration were examined by current- and voltage-clamp recordings obtained from IC neurons in acute slices of rats (P17-P19). Based on firing patterns to positive current injection, three basic response types were distinguished: onset, adapting, and sustained firing neurons. Onset and adapting cells showed an Ih-dependent depolarizing sag and had a more depolarized resting membrane potential and lower input resistance than sustained neurons. Ih amplitudes were largest in onset, medium in adapting, and small in sustained neurons. Ih activation kinetics was voltage dependent in all neurons and faster in onset and adapting compared with sustained neurons. Injecting trains of simulated synaptic currents into the neurons or evoking inhibitory postsynaptic potentials (IPSPs) by stimulating the lemniscal tract showed that Ih reduced temporal summation of excitatory and inhibitory potentials in onset but not in sustained neurons. Blocking Ih also abolished afterhyperpolarization and rebound spiking. These results suggest that, in a large proportion of IC cells, namely the onset and adapting neurons, Ih improves precise temporal processing and contributes to the temporal analysis of input patterns.

Animals↗

PubMed1988

[Occupational information in occupational medicine].

The International Classification of Diseases popularly referred to as 'ICD' has significantly improved accessibility to and promoted distribution of medical information. In the field of occupational health, the use of a standardized occupational classification system is also necessary for similar reasons. Recording occupational information in a standard format, when routinized, will certainly result in the combining of such information with other health relevant data. However, the innumerable occupational categories prevalent in modern industrialized society cannot be encompassed by a single occupational health staff. The tendency of Japanese people to answer in an indirect manner to questions regarding their present occupation or job history complicates the situation. Because of these circumstances, the need to construct an aiding system to compile bits of vague information into a definite standardized job category was recognized. The computerized system under development focuses especially on a person-to-person interview where the interviewer is required to gather information on the respondent's job history. The system is designed to supplement the insufficient understanding of the entire occupation system, thus aiding in occupational health interviews. A description of a prototype is also given.

Computers↗

PubMed2006

Decoding stimulus variance from a distributional neural code of interspike intervals.

The spiking output of an individual neuron can represent information about the stimulus via mean rate, absolute spike time, and the time intervals between spikes. Here we discuss a distinct form of information representation, the local distribution of spike intervals, and show that the time-varying distribution of interspike intervals (ISIs) can represent parameters of the statistical context of stimuli. For many sensory neural systems the mapping between the stimulus input and spiking output is not fixed but, rather, depends on the statistical properties of the stimulus, potentially leading to ambiguity. We have shown previously that for the adaptive neural code of the fly H1, a motion-sensitive neuron in the fly visual system, information about the overall variance of the signal is obtainable from the ISI distribution. We now demonstrate the decoding of information about variance and show that a distributional code of ISIs can resolve ambiguities introduced by slow spike frequency adaptation. We examine the precision of this distributional code for the representation of stimulus variance in the H1 neuron as well as in the Hodgkin-Huxley model neuron. We find that the accuracy of the decoding depends on the shapes of the ISI distributions and the speed with which they adapt to new stimulus variances.

Action Potentials↗

PubMed1997

RNA secondary structure as a reusable interface to biological information resources.

The dissemination of biological information has become critically dependent on the Internet and World Wide Web (WWW), which enable distributed access to information in a platform independent manner. The mode of interaction between biologists and on-line information resources, however, has been mostly limited to simple interface technologies such has hypertext links, tables and forms. The introduction of platform-independent runtime environments facilitates the development of more sophisticated WWW-based user interfaces. Until recently, most such interfaces have been tightly coupled to the underlying computation engines, and not separated as reusable components. We believe that many subdisciplines of biology have intuitive and familiar graphical representations of knowledge that can serve as multipurpose user interface elements. We call such graphical idioms "domain graphics". In order to illustrate the power of such graphics, we have built a reusable interface based on the standard two dimensional (2D) layout of RNA secondary structure. The interface can be used to represent any pre-computed layout of RNA, and takes as a parameters the sets of actions to be performed as a user interacts with the interface. It can provide to any associated application program information about the base, helix, or subsequence selected by the user. We show the versatility of this interface by using it as a special purpose interface to BLAST, Medline and the RNA MFOLD search/compute engines. These demonstrations are available at: http://www-smi.stanford.edu/projects/helix/pubs/ gene-combis-96/

Base Sequence↗

PubMed2006

Human development VI: supracellular morphogenesis. The origin of biological and cellular order.

Uninterrupted morphogenesis shows the informational potentials of biological organisms. Experimentally disturbed morphogenesis shows the compensational dynamics of the biological informational system, which is the rich informational redundancy. In this paper, we use these data to describe morphogenesis in terms of the development of supracellular levels of the organism, and we define complex epigenesis and supracellular differentiation. We review the phenomena of regeneration and induction of Hydra and amphibians, and the higher animal's informational needs for developing their complex nervous systems. We argue, also building on the NO-GO theorem for ontogenesis as chemistry, that the traditional chemical explanations of high-level informational events in ontogenesis, such as transmutation, regeneration, and induction, are insufficient. We analyze the informational dynamics of three embryonic compensatory reactions to different types of disturbances: (1) transmutations of the imaginal discs of insects, (2) regeneration after removal of embryonic tissue, and (3) embryonic induction, where two tissues that normally are separated experimentally are made to influence each other. We describe morphogenesis as a complex bifurcation, and the resulting morphological levels of the organism as organized in a fractal manner and supported by positional information. We suggest that some kind of real nonchemical phenomenon must be taking form in living organisms as an information-carrying dynamic fractal field, causing morhogenesis and supporting the organism's morphology through time. We argue that only such a phenomenon that provides information-directed self-organization to the organism is able to explain the observed dynamic distribution of biological information through morphogenesis and the organism's ability to rejuvenate and heal.

Cell Physiological Phenomena↗

PubMed2000

Baseline STD prevalence in a community intervention trial of the female condom in Kenya.

OBJECTIVE: We present baseline sexually transmitted disease (STD) prevalence rates from an ongoing intervention trial at Kenyan agricultural sites. METHODS: After gaining the cooperation of management, we identified six matched pairs of tea, coffee, and flower plantations and enrolled approximately 160 women at each site. Six intervention sites received an information programme and distributed female and male condoms, while six control sites received male condoms only and similar information about them. At clinic visits, we tested participants for cervical gonorrhoea (GC) and Chlamydia trachomatis (CT) by ligase chain reaction on urine specimens, and Trichomonas vaginalis (TV) by culture. The study has 80% power to detect a 10% prevalence difference during follow up, assuming a combined STD prevalence of 20%, 25% loss to follow up and intracluster correlation coefficient (ICC) of 0.03. RESULTS: Participants at intervention and control sites (total 1929) were similar at baseline. Mean age was 33 years, the majority were married, more than half currently used family planning, 78% had never used male condoms, and 9% reported more than one sexual partner in the 3 months before the study. Prevalences of GC, CT, and TV were 2.6%, 3.2%, and 20.4% respectively (23.9% overall), and were similar at intervention and control sites. The ICC for STD prevalence was 0.0011. Baseline STD was associated with unmarried status, non-use of family planning, alcohol use, and more than one recent sexual partner, but the highest odds ratio was 1.5. CONCLUSIONS: Baseline results confirm a high prevalence of trichomoniasis and bacterial STD at these Kenyan rural sites. Improved STD management is urgently needed there. Our ongoing female condom intervention trial is feasible as designed.

Adolescent↗

PubMed1999

The effect of frequency allocation on phoneme recognition with the nucleus 22 cochlear implant.

HYPOTHESIS: Phoneme recognition performance in patients implanted with the Nucleus 22 cochlear implant is affected by the frequency-to-electrode assignment. BACKGROUND: Multiple electrodes in modern cochlear implants are intended to deliver frequency-specific information to different tonotopic locations along the cochlea. However, the relation between the electrode locations, distribution of frequency information, and performance has not been explored thoroughly. METHODS: Ten listeners were tested on vowel and consonant identification tasks immediately after receiving each of the 15 speech processors. Experimental processors were created with 4, 7, and 20 activated electrodes. Five different frequency allocations were tested with all electrode conditions. RESULTS: For 7- and 20-electrode maps, best vowel recognition performance was obtained with frequency tables 7 and 9, with subjects showing best performance with the table with which they were most familiar. With 4-electrode maps, no change in vowel recognition performance was observed as a function of the frequency allocation. Consonant scores showed only a small effect of frequency allocation across all processors. Results were similar across listeners with different electrode insertion depths. CONCLUSION: The allocation of frequency ranges to electrodes in the Nucleus-22 cochlear implant can affect vowel recognition, when more than four electrodes are used, but is less important for consonant recognition. The allocation of frequency ranges to electrodes is an important factor in multichannel implants with more than four electrodes. The similarity of results across implant listeners with different electrode insertion depths implies that the optimal frequency allocation is one that best matches the allocation to which they've become accustomed, rather than one that matches the original tonotopic location of the electrodes.

Adult↗

PubMedDate not supplied

Importance of format and design in print patient information.

PURPOSE: The purposes of this descriptive study were to: identify characteristics of print education materials that healthcare providers report as important to patients; compare whether Physician Data Query (PDQ) information that was provided in its original form, or was redesigned in color and black and white, influenced the distribution of this information; and explore whether providing PDQ information via patient information racks would increase patients' awareness of and use of PDQ information. DESCRIPTION OF STUDY: Forty-four oncology healthcare professionals were asked to complete a survey identifying characteristics that they believed important for effective print educational materials. PDQ statements were reformatted and placed in brochure racks for a 6-month period. The number of statements distributed before and after this time period were compared. Subsequently, PDQ statements were placed sequentially for a 3-week period in brochure racks in the following formats: original form as printed from the computer, redesigned with color print; and redesigned with black ink only. RESULTS: The following characteristics were rated "very important" aspects of print educational materials by oncology healthcare professionals: appropriate reading level; clarity; credibility of the information; whether information is current/up-to-date; and patient acceptance of material. The characteristic receiving the fewest "very important" marks was attractiveness/eye appeal. The reported low marks on attractiveness/eye appeal contradict the concurrent findings that, after the redesign of PDQ statements (change in booklet size, use of color, increase in foot size for text and headings, and inclusion of a vertical bar to separate columns), there was a ninefold increase in the number PDQ statements distributed. Eighty-nine percent of the statements distributed were the redesigned version. The use of color, however, did not appear to make a difference in the number of PDQ statements disseminated after the redesign. CLINICAL IMPLICATIONS: In developing print education materials for cancer patients, the format, design, and placement of materials for patient access need to be considered. There are many valuable educational materials available on computer databases. Downloading the information and placing it in a brochure format may be an ideal approach for providing access to this information. Furthermore, because physicians and nurses have different priorities for printed patient education materials, it is important to involve both groups in the developments of the brochures.

Ambulatory Care Facilities↗

PubMed2003

Estimating the distribution of lag in the effect of short-term exposures and interventions: adaptation of a non-parametric regression spline model.

Information on the distribution of lag duration between exposure or intervention and the subsequent changes in risk can help in assessing the impact of exposure, predicting cost-effectiveness of intervention, and understanding the underlying biological mechanisms. Previous approaches focused more on optimizing the strength of the exposure-disease association than on directly estimating lag duration. We propose an alternative approach applicable to the analysis of the lagged effects of binary exposure variables. The density function of the distribution of lags is estimated based on flexible modelling of changes in hazard ratio of exposed versus unexposed subjects. The methodology is evaluated in a simulation study and is applied to the Framingham data to investigate the lagged effect of smoking cessation on coronary heart disease risk.

Biometry↗

PubMed1991

Calcium and phosphorus deficiencies affect mineral distribution in neonatal miniature piglets.

Current efforts to monitor the mineral status of preterm infants fed human milk may not provide sufficient information on the distribution of body minerals. To investigate the body distribution of calcium and phosphorus during various degrees of mineral deficiency, neonatal miniature piglets were raised for 2 wk on diets differing only in calcium and phosphorus. Groups A, B, and C were fed 100%, 60%, and 20%, respectively, of the recommended amounts of calcium and phosphorus that, when adjusted for rates of growth, approximated the range of dietary intakes of preterm infants. Group C manifested biochemical and body-composition evidence of mineral deficiency when compared with group A: lower serum phosphorus; higher serum alkaline phosphatase activity; less fat-free tissue, calcium, and phosphorus in tibiae, vertebrae, and whole carcasses. Neonatal miniature piglets are useful for studying mineral deposition during mineral deficiency in preterm infants.

Alkaline Phosphatase↗