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Proceedings of the workshop on food-consumption surveys in developing countries: general approaches to estimation of dietary exposure to contaminants.

The initial steps in estimating dietary exposure to contaminants include gathering the necessary expertise, clarifying the intent and purpose of the work, selecting a dietary exposure model, and gathering available pertinent information. Expertise is generally needed in chemistry, agriculture, toxicology, statistics, nutritional epidemiology, and computer software development. The goal might be to determine the average exposure of a population to contaminants, to identify demographic groups within a population that are especially vulnerable to a contaminant, to evaluate the regulation of agricultural and food-manufacturing practices, or to determine compliance with standards for local and/or imported foods. Examples of dietary exposure models include the core food model, directed core food model, large database model, raw agricultural commodity (RAC) model, regional diet model, duplicate diet model, and total diet composite model. Each model has advantages and disadvantages and different costs and resource requirements. Consideration of the sources and flow of selected contaminants though the food supply may help identify the best exposure model to use. Pertinent information that may already be available includes analytical data on contaminants in foods or commodities, government regulations pertaining to the levels of contaminants in foods, food-consumption data, data on the average body weights of age-gender groups (to express exposure on a body weight basis), and biochemical measures of contaminants or their residues/metabolites. Collecting available information helps to clearly define what critical information is missing so that the planned research can be most effective. Careful documentation of decisions and assumptions allows for recalculating exposure estimates with the same model using different decisions and assumptions; documentation also allows others to understand what was done and how to use the resulting intake estimates properly. Clearly identifying the limitations of the exposure model may provide justification for additional resources to further refine and improve the model.

Developing Countries↗

CASE tools and UML: state of the ART.

With increasing need for automated tools to assist complex systems development, software design methods are becoming popular. This article analyzes the state of art in computer-aided software engineering (CASE) tools and unified modeling language (UML), focusing on their evolution, merits, and industry usage. It identifies managerial issues for the tools' adoption and recommends an action plan to select and implement them. While CASE and UML offer inherent advantages like cheaper, shorter, and efficient development cycles, they suffer from poor user satisfaction. The critical success factors for their implementation include, among others, management and staff commitment, proper corporate infrastructure, and user training.

Computer-Aided Design↗

Use of project ontologies and terminology servers to support software engineering.

Complex medical software imposes new requirements on the methods and tools used for maintenance. Appropriate maintenance tools can increase software reliability and quality by providing means to trace dependencies among software artifacts for reducing unexpected impacts in software caused by software changes. We have used the GRAIL concept-representation language for medical terminologies to build a project ontology that models relationships among software artifacts. Our approach involves modeling of the terminology used in software projects, which enables us to describe, classify and relate individual software artifacts. A networked repository accessible to the entire software development staff stores the conceptual model, source code and associated documents. We present an architecture for a maintenance tool, and show how developers can use GRAIL to build a project ontology.

Databases as Topic↗

Depositing electron microscopy maps.

A meeting was held at the European Bioinformatics Institute (EBI) in Hinxton, United Kingdom to discuss recent progress in the development of EMD, a database for maps determined by electron microscopy that is now integrated with MSD, the macromolecular structure database at EBI. This meeting of representatives of many of the major image processing groups in electron microscopy also discussed possible software developments that would ease the documentation and deposition of such datasets. The meeting concluded with a strong endorsement of map deposition in electron microscopy and its linkage with the family of archival databases in biomedical research.

Computational Biology↗

Gemvid, an open source, modular, automated activity recording system for rats using digital video.

BACKGROUND: Measurement of locomotor activity is a valuable tool for analysing factors influencing behaviour and for investigating brain function. Several methods have been described in the literature for measuring the amount of animal movement but most are flawed or expensive. Here, we describe an open source, modular, low-cost, user-friendly, highly sensitive, non-invasive system that records all the movements of a rat in its cage. METHODS: Our activity monitoring system quantifies overall free movements of rodents without any markers, using a commercially available CCTV and a newly designed motion detection software developed on a GNU/Linux-operating computer. The operating principle is that the amount of overall movement of an object can be expressed by the difference in total area occupied by the object in two consecutive picture frames. The application is based on software modules that allow the system to be used in a high-throughput workflow. Documentation, example files, source code and binary files can be freely downloaded from the project website at http://bioinformatics.org/gemvid/. RESULTS: In a series of experiments with objects of pre-defined oscillation frequencies and movements, we documented the sensitivity, reproducibility and stability of our system. We also compared data obtained with our system and data obtained with an Actiwatch device. Finally, to validate the system, results obtained from the automated observation of 6 rats during 7 days in a regular light cycle are presented and are accompanied by a stability test. The validity of this system is further demonstrated through the observation of 2 rats in constant dark conditions that displayed the expected free running of their circadian rhythm. CONCLUSION: The present study describes a system that relies on video frame differences to automatically quantify overall free movements of a rodent without any markers. It allows the monitoring of rats in their own environment for an extended period of time. By using a low-cost, open source hardware/software solution, laboratories can greatly simplify their data acquisition and analysis pipelines and improve their workload.

Journal Article↗

Measuring energy expenditure in cardiac patients using the Body Media Armband versus indirect calorimetry. A validation study.

AIM: The purpose of this study was to compare differences in energy expenditure using the newly developed SenseWear Armband body monitor to indirect calorimetry in cardiac rehabilitation patients. METHODS: Twenty-four (62+/-8.1 years) patients completed steady state exercise for 8 minutes on 4 modes of exercise (arm ergometry, treadmill walking, recumbent stepping and rowing ergometry). Total cumulative kilojoules were recorded simultaneously by indirect calorimetry and the SenseWear Armband. Statistical analyses assessed the degree of agreement between the 2 measurement methods and 3 different versions of the SenseWear software. RESULTS: The correlations between indirect calorimetry and version 2.2 of the SenseWear armband for arm and rowing ergometry, the treadmill and recumbent stepper were r=0.90, r=0.67, r=0 .80 and r=0.74, respectively. There were no between method differences during arm ergometry (p<1.000) and the recumbent stepper (p<0.102). Bland and Altman plots revealed the greatest spread of scores for the rower and the treadmill. Between method differences were minimal when using the preliminary cardiac software. The correlations for arm and rowing ergometry, the treadmill and recumbent stepper were r=0.90, r=0.84, r=0.78 and r=0.82, respectively. CONCLUSIONS: The accuracy of the BodyMedia SenseWear Armband appears to be exercise modality dependent in those with heart disease when using software developed for the general population. Therefore, the information should be interpreted cautiously, particularly during treadmill walking and rowing. Initial experiments with cardiac-focused software are promising, but preliminary.

Calorimetry, Indirect↗

Just-in-time database-driven Web applications.

"Just-in-time" database-driven Web applications are inexpensive, quickly-developed software that can be put to many uses within a health care organization. Database-driven Web applications garnered 73873 hits on our system-wide intranet in 2002. They enabled collaboration and communication via user-friendly Web browser-based interfaces for both mission-critical and patient-care-critical functions. Nineteen database-driven Web applications were developed. The application categories that comprised 80% of the hits were results reporting (27%), graduate medical education (26%), research (20%), and bed availability (8%). The mean number of hits per application was 3888 (SD = 5598; range, 14-19879). A model is described for just-in-time database-driven Web application development and an example given with a popular HTML editor and database program.

Database Management Systems↗

Development of a three-dimensional treatment planning system based on computed tomographic data.

Current surgical treatment planning systems predict three-dimensional (3D) corrections from two-dimensional (2D) data and are inadequate for complex movements. In this paper, we present a 3D planning system based on computed tomographic (CT) data. A three-dimensional CT scan of the craniofacial skeleton forms the database. Software developed in the Harvard Surgical Planning Laboratory was modified for the craniofacial skeleton. Reproducible skeletal landmarks are identified for superimposition. A 'cutting tool' is used to segment the mandible and segments are moved to their predicted positions. A 'collision tool', alerts the operator of skeletal interferences. An analysis of selected scans is used to demonstrate the system. Three-dimensional visualization of the facial skeleton, selection of landmarks, measurement of angles and distances, simulation of osteotomies, repositioning of bones, detection of collisions and super-imposition of scans were accomplished. In an illustrative case of Hemifacial Microsomia, predicted and actual 3D corrective movements of the entire mandible were documented. Analysis of scans indicated that 3D planning can prevent insufficient jaw lengthening or other surgical inaccuracies which occur with standard 2D methods. Software demonstrated here will allow the surgeon to accurately plan treatment and evaluate craniomaxillofacial surgery outcomes. Future applications may include surgical navigation.

Algorithms↗

Automated acquisition and analysis of animal behavior data utilizing an Apple IIe.

A method is described for interfacing an Apple IIe computer to common programming modules which will allow the collection and organization of digitized data into files compatible with readily available statistical packages. The system will thus eliminate the need for manual entry of data for statistical analysis. The required hardware and software developed is discussed in sufficient detail to allow assembly and use by individuals with minimal computer expertise.

Animals↗

Authorship versus "credit" for participation in research: a case study of potential ethical dilemmas created by technical tools used by researchers and claims for authorship by their creators.

The distinction between authorship and other forms of credit for contribution to a publication has been a persisting controversy that has resulted in numerous guidelines outlining the expected contributions of those claiming authorship. While there have been flagrant, well-publicized deviations from widely accepted standards, they are largely outnumbered by cases that are not publicity-worthy, and therefore remain known to only those directly involved with the inappropriate conduct. We discuss the definition and ethical requirements of authorship, offer a case example of the authorship debate created by a technical tool at our institution, and review parallels that support and dispute the authorship claims of our software developers. Ultimately, we conclude that development of a technical tool that enables data collection does not adequately substitute for contributions to study design and manuscript preparation for authorship purposes. Unless the designers of such a technical tool prospectively participate as a part of the project, they would not have an adequate understanding of the publication's genesis to defend it publicly and cannot be listed as authors. Therefore, it is incumbent upon project members to invite tool developers to participate at the beginning of such projects, and for tool developers to contribute to study design and manuscript preparation when they desire authorship listings.

Authorship↗

Workflow analysis and evidence-based medicine: towards integration of knowledge-based functions in hospital information systems.

The large extent and complexity of scientific evidence described in the concept of evidence-based medicine often overwhelms clinicians who want to apply best external evidence. Hospital Information Systems usually do not provide knowledge-based functions to support context-sensitive linking to external information sources. Knowledge-based components need specific data, which must be entered manually and should be well adapted to clinical environment to be accepted by clinicians. This paper describes a workflow-based approach to understand and visualize clinical reality as a preliminary to designing software applications, and possible starting points for further software development.

Artificial Intelligence↗

Mouse oocytes and preimplantation embryos bear the two sub-units of interferon-gamma receptor.

Cytokines and growth factors play important roles in implantation and maintenance of pregnancy, but also during early development. Among them interferon-gamma (IFNgamma) is highly expressed by mammalian trophoblast cells during implantation and seems to be involved in some cases of pregnancy loss. In the present study we investigated the possible presence of IFNgamma receptors (IFNGR) on mouse oocytes and preimplantation embryos. The two receptor chains IFNgammaRalpha (IFNGR-1) and IFNgammaRbeta (IFNGR-2) have been detected by indirect immunofluorescence at the surface of mouse oocytes (in germinal vesicle and metaphase II stages), as well as at all stages of in vitro embryo development from the one-cell to blastocyst stage. IFNGR appeared to colocalize partly with ganglioside GM1 at the cell surface of oocytes and embryos, indicating a possible preferential localization of this receptor in "rafts" microdomains. This was analyzed in more detail using software developed in the laboratory. IFNgamma was found to bind to its receptor at all stages analyzed. RT-PCR and Southern blot experiments confirmed the presence of the transcriptionally regulated IFNGR-2 chain mRNA, in mouse oocytes and preimplantation embryos. These results show, for the first time, that mouse oocytes and preimplantation embryos bear a complete and theoretically functional IFNGR, suggesting that this cytokine could play a role during early development.

Animals↗

The gene identification problem: an overview for developers.

The gene identification problem is the problem of interpreting nucleotide sequences by computer, in order to provide tentative annotation on the location, structure, and functional class of protein-coding genes. This problem is of self-evident importance, and is far from being fully solved, particularly for higher eukaryotes. Thus it is not surprising that the number of algorithm and software developers working in the area is rapidly increasing. The present paper is an overview of the field, with an emphasis on eukaryotes, for such developers.

Base Sequence↗

From digital image processing of colour Doppler M-mode maps to noninvasive evaluation of the left ventricular diastolic function: a dedicated software package.

Noninvasive estimation of diastolic pressure gradients has recently been validated using the space-temporal velocity distribution available from colour Doppler M-mode (CDM). However, the methods currently applied for analysing CDM patterns of left ventricular (LV) filling have limitations, such as lack of automation, subjective variability and limited use of digital velocity map. For this reason, we have developed software able to acquire and process the CDM maps; thus, providing an easily interpretable graphical and numerical display. The pressure field is obtained by approximating the derivatives with centred finite differences via the incompressible Navier-Stokes equations. After digital filtering of the noise and the removal of the colour black spots, the velocity field is utilised to compute the pressure gradient field and the pressure values by spatial integration. It is concluded that automatic quantification of colour CDM patterns is feasible and will be a strategic tool in the investigation of one of the most intriguing topics in cardiology.

Blood Flow Velocity↗

[Technologic developments in radiotherapy and stereotactic radiosurgery].

We present a review of current technological progress enabling improvement in the quality of stereotactic irradiations: imaging fusion; individual adaptation of dosimetric planning to the shape of the target thanks to several collimation systems, spatial modulation of the beam with the use of multileaf microcollimators, beam intensity modulation, robotisation of the materials, owing to hardware and software developments.

Brain Neoplasms↗

Databases for neuroscience.

Databases for neuroscience must handle large volumes of image and graphical data as well as domain knowledge. Several software development efforts are addressing these issues in an attempt to aid the acquisition, analysis and exchange of complex data sets.

Databases, Bibliographic↗

Computational methods for the analysis of differential conservation in groups of similar DNA sequences.

Multiple sequence alignments are a powerful tool for identifying the regions of DNA which have been constrained in evolutionary divergence, presumably due to their functional role. However, such constraints rarely manifest themselves as perfect conservation of a site clearly standing out in its broader environment, as they reflect the species-specific differences in proteins, as well as the ability of some proteins to interact with multiple variants of their binding sequence. In this paper we explore the use of alignment column uncertainty as an aid in locating differential phylogenetic footprints, which refer to the sites in DNA where groups of related species exhibit sequence conservation, but where the pattern may vary between the groups. We use efficient, linear-time algorithms to locate such sites. We have performed a study of the mammalian CAV2-CAV1 gene region using our software, and we conclude with several observations concerning the differential conservation and the use of computational methods for its detection. The software developed for this project is available, free of charge, by contacting the author.

Animals↗

[Use of palm-top computers within the scope of medical data collection and quality assurance].

Computerisation of the medical profession is advancing particularly as the reform of the German medical system is underway and efforts to maintain high quality standards are being made. More and more clinics and private physicians store the data, which they collect in their daily work, in digital form and exchange it via electronic networks. But lacking overall concepts and resistance from monopolistic structures prevent the introduction of innovative technologies, which would allow convenient data collection "on the fly", patterned after proven work routines. This could lead to a real relief from the daily paper work. New approaches using available hard- and software developed abroad demonstrate medical palmtop computing on the Apple Newton.

Data Collection↗