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PubMedDate not supplied

The Maastricht Cerebral Monitor (MCM) for the neonatal intensive care unit.

Although long-term monitoring of cerebral activity can be important in neonatal intensive care, the complexity of multi-channel EEG makes it less suitable for this purpose. In the past, a cerebral function monitor (CFM) was developed that analyses EEG. The output parameter of the CFM is a semi-logarithmic amplitude distribution resulting from the amplification, bandpass filtering, compression, rectification and smoothing of the single-channel EEG. Drawbacks of the CFM include its inflexibility and limited single-channel processing capacity and its lack of functionality for data storage, review or re-analysis. Modern computers are powerful enough that a system can be built which does not have these drawbacks. We have developed such a system: the Maastricht Cerebral Monitor (MCM). The MCM is a flexible system that not only overcomes the CFM drawbacks but also provides advanced signal analysis. It was developed with a software system (Poly) for acquisition, high quality real-time display, on-line analysis and storage of physiological signals. The MCM processes three EEG signals in the amplitude and frequency domains. Other parameters provided by the MCM are asymmetry of absolute frequency powers, percentage suppression, mean and 90% spectral edge frequency. Electrode impedance is recorded as a measure of quality of the recording.

Brain↗
PubMedDate not supplied

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.

Computer Communication Networks↗
PubMed2005

Fusing microarray experiments with multivariate regression.

MOTIVATION: It is widely acknowledged that microarray data are subject to high noise levels and results are often platform dependent. Therefore, microarray experiments should be replicated several times and in several laboratories before the results can be relied upon. To make the best use of such extensive datasets, methods for microarray data fusion are required. Ideally, the fused data should distil important aspects of the data while suppressing unwanted sources of variation and be amenable to further informal and formal methods of analysis. Also, the variability in the quality of experimentation should be taken into account. RESULTS: We present such an approach to data fusion, based on multivariate regression. We apply our methodology to data from a previous study on cell-cycle control in Schizosaccharomyces pombe. AVAILABILITY: The algorithm implemented in R is freely available from the authors on request.

Algorithms↗
PubMed2005

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices.

SUMMARY: We introduce a novel unsupervised approach for the organization and visualization of multidimensional data. At the heart of the method is a presentation of the full pairwise distance matrix of the data points, viewed in pseudocolor. The ordering of points is iteratively permuted in search of a linear ordering, which can be used to study embedded shapes. Several examples indicate how the shapes of certain structures in the data (elongated, circular and compact) manifest themselves visually in our permuted distance matrix. It is important to identify the elongated objects since they are often associated with a set of hidden variables, underlying continuous variation in the data. The problem of determining an optimal linear ordering is shown to be NP-Complete, and therefore an iterative search algorithm with O(n3) step-complexity is suggested. By using sorting points into neighborhoods, i.e. SPIN to analyze colon cancer expression data we were able to address the serious problem of sample heterogeneity, which hinders identification of metastasis related genes in our data. Our methodology brings to light the continuous variation of heterogeneity--starting with homogeneous tumor samples and gradually increasing the amount of another tissue. Ordering the samples according to their degree of contamination by unrelated tissue allows the separation of genes associated with irrelevant contamination from those related to cancer progression. AVAILABILITY: Software package will be available for academic users upon request.

Algorithms↗
PubMed2006

Using GOstats to test gene lists for GO term association.

MOTIVATION: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing. RESULTS: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results. AVAILABILITY: GOstats is available as an R package from the Bioconductor project: http://bioconductor.org

Algorithms↗
PubMed2006

Enrichment or depletion of a GO category within a class of genes: which test?

MOTIVATION: A number of available program packages determine the significant enrichments and/or depletions of GO categories among a class of genes of interest. Whereas a correct formulation of the problem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying P-value computations. SUMMARY: We review the different formulations of the problem and the tests they lead to: the binomial, chi2, equality of two probabilities, Fisher's exact and hypergeometric tests. We clarify the relationships existing between these tests, in particular the equivalence between the hypergeometric test and Fisher's exact test. We recall that the other tests are valid only for large samples, the test of equality of two probabilities and the chi2-test being equivalent. We discuss the appropriateness of one- and two-sided P-values, as well as some discreteness and conservatism issues. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Data Interpretation, Statistical↗
PubMed2003

Reporting quality of nursing home care to consumers: the Maryland experience.

OBJECTIVE: To design and implement a reporting system for quality of long-term care to empower consumers and to create incentives for quality improvement. To identify a model to approach this technically and politically difficult task. APPROACH: Establishment of a credible and transparent decision process using a public forum. Development of the system based on: (1) review of the literature and existing systems, and discussions with stakeholders about strengths and weaknesses; (2) focus on consumer preferences in the design; and (3) responsiveness to industry concerns in the implementation. LESSONS LEARNED: None of the existing systems appeared to be a suitable model. We decided to develop an entirely new system based on three key design principles that allowed us to tailor the system to consumer needs: (1) designing a decision tool rather than a database; (2) summarizing rather than simplifying information; and (3) accounting for the target audience in the creative execution. Industry concerns focused on the burden of the system, the potential for errors, and the possible communication of a negative impression of the industry. As methodological and data limitations prevented us from resolving those concerns, we addressed them by using cautionary language in the presentation and by making a commitment to incorporate improvements in the future. All stakeholders regarded the final design as an acceptable compromise. CONCLUSIONS: Despite its potentially controversial nature and many methodological challenges, the system has been well received by both the public and the industry. We attribute this success to two key factors: a collaborative decision process, in which all critical design and execution choices were laid out explicitly and debated with stakeholders in a public forum, and realism and honesty regarding the limitations of the system.

Aged↗
PubMed2003

WormBase: a cross-species database for comparative genomics.

WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant expansion in the biological scope of WormBase, including the integration of large-scale, genome-wide data sets, the inclusion of genome sequence and gene predictions from related species and active literature curation. This expansion of data has also driven the development and refinement of user interfaces and operability, including a new Genome Browser, new searches and facilities for data access and the inclusion of extensive documentation. These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the context of a powerful genetic system.

Animals↗
PubMedDate not supplied

Using evidence-based practice in providing care.

Case managers are in prime positions that enable them to implement initiatives, which may lead to evidence-based practice. The possibilities abound regardless of the setting; case managers are charged with the delivery of patient care in the most efficient manner. When the best care is given to patients within the shortest time frame, everyone benefits--the patients and their families, case managers and other staff, and the entire organization. The various tools used to coordinate patient care--protocols and pathways--can be readily used to collect data in a standard way; this is a vital step in initiating evidence-based practice. Initiatives leading to evidence-based practice require several phases: obtaining evidence, monitoring the use of evidence, and evaluating the use of evidence in practice. This article will describe the use of evidence-based practice for case managers and demonstrate the steps to ensuring successful implementation in patient care activities.

Benchmarking↗
PubMed1997

A system for digital reconstruction of gypsum dental casts.

A range scanner is developed that can scan a gypsum dental cast and reconstruct the cast digitally for display and storage purposes. The scanner is based on subtractive light and computes the range values using optical triangulation. A fiducial marker is introduced that, when attached to a dental cast at the time of image acquisition, makes it possible to integrate multiview range images of the cast without image registration. A method for calibrating the scanner is described and experimental results showing the accuracy of the scanner are presented.

Algorithms↗
PubMed2004

Tone-dependent error diffusion.

We present an enhanced error diffusion halftoning algorithm for which the filter weights and the quantizer thresholds vary depending on input pixel value. The weights and thresholds are optimized based on a human visual system model. Based on an analysis of the edge behavior, a tone dependent threshold is designed to reduce edge effects and start-up delay. We also propose an error diffusion system with parallel scan that uses variable weight locations to reduce worms.

Algorithms↗
PubMed2004

Image quality assessment: from error visibility to structural similarity.

Objective methods for assessing perceptual image quality traditionally attempted to quantify the visibility of errors (differences) between a distorted image and a reference image using a variety of known properties of the human visual system. Under the assumption that human visual perception is highly adapted for extracting structural information from a scene, we introduce an alternative complementary framework for quality assessment based on the degradation of structural information. As a specific example of this concept, we develop a Structural Similarity Index and demonstrate its promise through a set of intuitive examples, as well as comparison to both subjective ratings and state-of-the-art objective methods on a database of images compressed with JPEG and JPEG2000.

Algorithms↗
PubMed2004

Iterative multimodel subimage binarization for handwritten character segmentation.

Existing binarization methods are categorized as either global or local. In this paper, we present a new category, where the image is considered a collection of subimages. Each subimage provides a statistical model for the handwritten characters that can be used to optimize the binarization of other subimages based on gray-level and stroke-run features. The proposed method uses these multimodels to iteratively arrive at the optimal threshold for each subimage. It can be applied to different types of documents where prior knowledge about the noisiness of the subimages is not available. Experimental results showed significant improvement in the binarization quality in comparison with other well-established algorithms.

Algorithms↗
PubMed2004

Integrating context-aware public displays into a mobile hospital information system.

Hospitals are convenient settings for deployment of ubiquitous computing technology. Not only are they technology-rich environments, but their workers experience a high level of mobility resulting in information infrastructures with artifacts distributed throughout the premises. Hospital information systems (HISs) that provide access to electronic patient records are a step in the direction of providing accurate and timely information to hospital staff in support of adequate decision-making. This has motivated the introduction of mobile computing technology in hospitals based on designs which respond to their particular conditions and demands. Among those conditions is the fact that worker mobility does not exclude the need for having shared information artifacts particular locations. In this paper, we extend a handheld-based mobile HIS with ubiquitous computing technology and describe how public displays are integrated with handheld and the services offered by these devices. Public displays become aware of the presence of physicians and nurses in their vicinity and adapt to provide users with personalized, relevant information. An agent-based architecture allows the integration of proactive components that offer information relevant to the case at hand, either from medical guidelines or previous similar cases.

Artificial Intelligence↗
PubMed2005

Estimating the pen trajectories of static signatures using hidden Markov models.

Static signatures originate as handwritten images on documents and by definition do not contain any dynamic information. This lack of information makes static signature verification systems significantly less reliable than their dynamic counterparts. This study involves extracting dynamic information from static images, specifically the pen trajectory while the signature was created. We assume that a dynamic version of the static image is available (typically obtained during an earlier registration process). We then derive a hidden Markov model from the static image and match it to the dynamic version of the image. This match results in the estimated pen trajectory of the static image.

Algorithms↗
PubMed2007

Online handwritten shape recognition using segmental hidden Markov models.

We investigate a new approach for online handwritten shape recognition. Interesting features of this approach include learning without manual tuning, learning from very few training samples, incremental learning of characters, and adaptation to the user-specific needs. The proposed system can deal with two-dimensional graphical shapes such as Latin and Asian characters, command gestures, symbols, small drawings, and geometric shapes. It can be used as a building block for a series of recognition tasks with many applications.

Algorithms↗