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PubMed2006

Pilot testing of the Starship Infant Neurological Assessment tool.

Neurological assessment can be a challenge in young children because of their physical, behavioral, and cognitive immaturity. The use of an infant neurological assessment tool allows nurses to easily perform a comprehensive neurological assessment. The Starship Infant Neurological Assessment (SINA) tool is a 21-item instrument designed for use with children under 2 years of age. This study tested its reliability. Four children under 2 years old were videotaped as they were assessed using the SINA. Seven nurses viewed the tapes and indicated their assessment on the tool. Interrater analysis using intraclass correlation coefficients demonstrated good reliability for 17 of 21 items. Areas for future development and research include addition of extra items and further testing.

Age Factors↗

PubMed2007

(Paediatric) magnetic resonance urography: just fancy images or a new important diagnostic tool?

PURPOSE OF REVIEW: Magnetic resonance urography has become an established imaging tool in uroradiology. Its potential to assess anatomy and function makes it an ideal tool for evaluation of urinary tract malformations, renal cysts, genito-urinary tract tumours, infections and renal transplants. This review tries to highlight the potential of magnetic resonance urography in the light of new advances, particularly focusing on paediatric applications. RECENT FINDINGS: Technical innovations such as diaphragmatic tracking, parallel or propeller imaging, faster gradients and higher field strength improve applicability in infants and children. Dynamic studies enable assessment of renal functional parameters such as split renal function, glomerular filtration rate or urinary drainage. Recent advances in magnetic resonance spectroscopy, diffusion imaging and perfusion imaging and new contrast agents promise to widen the potential of magnetic resonance urography as a functional imaging tool, not only in paediatrics but also for other magnetic resonance applications in the genito-urinary tract, such as prostate imaging or in the staging of ovarian and endometrial cancer. SUMMARY: Besides ultrasound being used as the initial imaging method, particularly in children (and as computed tomography in adults), magnetic resonance urography can be envisioned as the major imaging modality for almost all (paediatric) uroradiological queries, consequently creating a growing demand for available equipment and procedural expertise.

Child↗

PubMed2006

Genetic tools for highly pathogenic Francisella tularensis subsp. tularensis.

This paper is the first detailed description of the development and use of new genetic tools specifically for the safe manipulation of highly pathogenic Francisella tularensis subsp. tularensis. Most of these tools are also demonstrated to work with other F. tularensis subspecies. Kanamycin and hygromycin resistance determinants that function as genetic markers in F. tularensis subsp. tularensis strain Schu and sets of episomal shuttle vectors that are either unstable or stably maintained in the absence of selection were developed. In addition, the hyg gene, expressed from the F. tularensis groESL promoter, was successfully used as a marker for transposon mutagenesis. This work also includes the development of sacB-based suicide plasmids expressing kanamycin resistance that can be used for electroporation-mediated allelic exchange of unmarked mutations in Schu and the F. tularensis live vaccine strain (LVS). Using these plasmids, the two predicted beta-lactamase genes, blaA and blaB, in Schu and LVS were deleted. Only the Delta blaB1 mutants had increased susceptibility to ampicillin, and this phenotype was complemented by a plasmid expressing blaB+. The results suggest that the beta-lactam antibiotic resistance phenotype of Schu and LVS is likely due to only one of the two beta-lactamase genes present and that ampicillin resistance can be used as an additional selectable marker in beta-lactamase deletion mutants. The collection of tools presented in this report will be helpful for the genetic analyses of F. tularensis subsp. tularensis pathogenesis.

Ampicillin↗

PubMed2004

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs). zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Animals↗

PubMed2005

FPC Web tools for rice, maize, and distribution.

Many clone-based physical maps have been built with the FingerPrinted Contig (FPC) software, which is written in C and runs locally for fast and flexible analysis. If the maps were viewable only from FPC, they would not be as useful to the whole community since FPC must be installed on the user machine and the database downloaded. Hence, we have created a set of Web tools so users can easily view the FPC data and perform salient queries with standard browsers. This set includes the following four programs: WebFPC, a view of the contigs; WebChrom, the location of the contigs and genetic markers along the chromosome; WebBSS, locating user-supplied sequence on the map; and WebFCmp, comparing fingerprints. For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates the data files for input into GBrowse. This provides an alternative to the WebChrom/WebFPC view. These tools are available to download along with documentation. The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links to sites that contain additional information).

Chromosomes, Plant↗

PubMed2005

Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists.

We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with "omics" platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.

Arabidopsis↗

PubMed2004

Coot: model-building tools for molecular graphics.

CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.

Computer Graphics↗

PubMed1998

Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery.

Many critical functionally distinct subcortical structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia and thalamus has been created from the Schaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be automatically deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for preoperative and intraoperative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of a leukotome and other surgical tools with respect to the atlas data, as well as preregistered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intraoperative planning. To date this system has been employed as an adjunct to over 30 functional neurosurgical cases including surgery for movement disorders.

Algorithms↗

PubMed2006

A syntax-preserving error resilience tool for JPEG 2000 based on error correcting arithmetic coding.

JPEG 2000 is the novel ISO standard for image and video coding. Besides its improved coding efficiency, it also provides a few error resilience tools in order to limit the effect of errors in the codestream, which can occur when the compressed image or video data are transmitted over an error-prone channel, as typically occurs in wireless communication scenarios. However, for very harsh channels, these tools often do not provide an adequate degree of error protection. In this paper, we propose a novel error-resilience tool for JPEG 2000, based on the concept of ternary arithmetic coders employing a forbidden symbol. Such coders introduce a controlled degree of redundancy during the encoding process, which can be exploited at the decoder side in order to detect and correct errors. We propose a maximum likelihood and a maximum a posteriori context-based decoder, specifically tailored to the JPEG 2000 arithmetic coder, which are able to carry out both hard and soft decoding of a corrupted code-stream. The proposed decoder extends the JPEG 2000 capabilities in error-prone scenarios, without violating the standard syntax. Extensive simulations on video sequences show that the proposed decoders largely outperform the standard in terms of PSNR and visual quality.

Algorithms↗

PubMed2002

Biological data integration: wrapping data and tools.

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Algorithms↗

PubMed2005

Using key performance indicators as knowledge-management tools at a regional health-care authority level.

The advantages of the introduction of information and communication technologies in the complex health-care sector are already well-known and well-stated in the past. It is, nevertheless, paradoxical that although the medical community has embraced with satisfaction most of the technological discoveries allowing the improvement in patient care, this has not happened when talking about health-care informatics. Taking the above issue of concern, our work proposes an information model for knowledge management (KM) based upon the use of key performance indicators (KPIs) in health-care systems. Based upon the use of the balanced scorecard (BSC) framework (Kaplan/Norton) and quality assurance techniques in health care (Donabedian), this paper is proposing a patient journey centered approach that drives information flow at all levels of the day-to-day process of delivering effective and managed care, toward information assessment and knowledge discovery. In order to persuade health-care decision-makers to assess the added value of KM tools, those should be used to propose new performance measurement and performance management techniques at all levels of a health-care system. The proposed KPIs are forming a complete set of metrics that enable the performance management of a regional health-care system. In addition, the performance framework established is technically applied by the use of state-of-the-art KM tools such as data warehouses and business intelligence information systems. In that sense, the proposed infrastructure is, technologically speaking, an important KM tool that enables knowledge sharing amongst various health-care stakeholders and between different health-care groups. The use of BSC is an enabling framework toward a KM strategy in health care.

Greece↗

PubMed2005

JViz.Rna--a Java tool for RNA secondary structure visualization.

Many tools have been developed for visualization of RNA secondary structures using a variety of techniques and output formats. However, each tool is typically limited to one or two of the visualization models discussed in this paper, supports only a single file format, and is tied to a specific platform. In order for structure prediction researchers to better understand the results of their algorithms and to enable life science researchers to interpret RNA structure easily, it is helpful to provide them with a flexible and powerful tool.jViz.Rna is a multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file formats. The same structure can be viewed using any of the models supported, including linked graph, circle graph, dot plot, and classical structure. Also, the output is dynamic and can easily be further manipulated by the user. In addition, any of the drawings produced can be saved in either the EPS or PNG file formats enabling easy usage in publications and presentations.

Computer Graphics↗

PubMed2004

FINs: lattice theoretic tools for improving prediction of sugar production from populations of measurements.

This paper presents novel mathematical tools developed during a study of an industrial-yield prediction problem. The set F of fuzzy interval numbers, or FINs for short, is studied in the framework of lattice theory. A FIN is defined as a mapping to a metric lattice of generalized intervals, moreover it is shown analytically that the set F of FINs is a metric lattice. A FIN can be interpreted as a convex fuzzy set, moreover a statistical interpretation is proposed here. Algorithm CALFIN is presented for constructing a FIN from a population of samples. An underlying positive valuation function implies both a metric distance and an inclusion measure function in the set F of FINs. Substantial advantages, both theoretical and practical, are shown. Several examples illustrate geometrically on the plane both the utility and the effectiveness of novel tools. It is outlined comparatively how some of the proposed tools have been employed for improving prediction of sugar production from populations of measurements for Hellenic Sugar Industry, Greece.

Journal Article↗

PubMed2003

Working more productively: tools for administrative data.

OBJECTIVE: This paper describes a web-based resource (http://www.umanitoba.ca/centres/mchp/concept/) that contains a series of tools for working with administrative data. This work in knowledge management represents an effort to document, find, and transfer concepts and techniques, both within the local research group and to a more broadly defined user community. Concepts and associated computer programs are made as "modular" as possible to facilitate easy transfer from one project to another. STUDY SETTING/DATA SOURCES: Tools to work with a registry, longitudinal administrative data, and special files (survey and clinical) from the Province of Manitoba, Canada in the 1990-2003 period. DATA COLLECTION: Literature review and analyses of web site utilization were used to generate the findings. PRINCIPAL FINDINGS: The Internet-based Concept Dictionary and SAS macros developed in Manitoba are being used in a growing number of research centers. Nearly 32,000 hits from more than 10,200 hosts in a recent month demonstrate broad interest in the Concept Dictionary. CONCLUSIONS: The tools, taken together, make up a knowledge repository and research production system that aid local work and have great potential internationally. Modular software provides considerable efficiency. The merging of documentation and researcher-to-researcher dissemination keeps costs manageable.

Databases as Topic↗

PubMedDate not supplied

Tumor size and breast cancer detection: what might be the effect of a less sensitive screening tool than mammography?

In some limited-resource areas, a state-of-the-art mammography program is not affordable. In such circumstances, one might consider a less resource-intensive, but also less sensitive screening tool such as clinical breast examination (CBE). We used data from the Swedish Two-County Trial to estimate the shift in tumor size resulting from invitation to mammographic screening. By postulating a lesser benefit of a less sensitive screening tool (CBE), particularly in terms of detecting very small tumors, we predicted its likely effect on tumor size distribution. In addition, using the observed association between tumor size and nodal status, and between tumor size and fatality, we predicted the likely benefit in terms of reductions in node-positive disease and in breast cancer mortality. An invitation to mammographic screening was associated with a 27% reduction in the number of node-positive tumors and a 31% reduction in the number of breast cancer deaths. We estimate that in the trial population, screening with CBE alone would have led to an 11% reduction in node-positive tumors and an 11% reduction in breast cancer deaths (approximately 42 deaths prevented per 1,000 cases). Assuming instead a tumor size distribution typical of a limited-resource setting (70% of tumors are 30 mm at presentation), we estimate that screening with CBE alone would lead to a 13% reduction in node-positive tumors and a 12% reduction in breast cancer deaths (approximately 72 deaths prevented per 1,000 cases). Thus, although the relative benefit of CBE is only slightly greater in the limited-resource setting, the absolute reduction in deaths per case is about 70% higher. Our findings suggest that a less sensitive tool might be expected to confer a breast cancer mortality reduction about half of that observed with mammography.

Breast Neoplasms↗

PubMed1979

An interdisciplinary tool for assessing patients' readiness for discharge in the rehabilitation setting.

This paper describes the setting up of an interdisciplinary tool to assess readiness for discharge of patients from hospital. The rationale behind the tool is discussed and the literature is reviewed for current perspectives of measurement in rehabilitation, the desirability of planning discharges of referrals and the interdisciplinary nature of the health care team. The concept of readiness is also discussed. Finally, the evolution of the tool is described and its use with selected patients in a rehabilitation hospital is demonstrated.

Decision Making↗

PubMed1981

Pain assessment: development of a tool for the nurse and the patient.

The assessment of pain is a difficult and yet vital component of nursing care. Discrepancies in the nursing management of pain can result from inadequate data collection and personal biases about the pain experienced by the patient. For example, how often is the patient with chronic pain consulted about personal remedies used at home to facilitate pain relief? Do nurses have preconceived ideas of how much pain should exist with each disease entity? A tool was developed which incorporated many of the variables affecting the pain response in order to sensitize nurses to the need for careful pain assessment. The information in this tool was conveyed to both graduate and student nurses resulting in improved charting of the patient's pain and improvement in the ability to assess the patient in pain. Description of pain by the patient is often a frustrating experience and yet necessary in helping to determine the cause of the pain and the appropriate interventions. Patients often have difficulty describing their pain to health professionals. A ruler which includes the most frequently utilized terms to describe pain was developed, revised and tested on various patients. The patients interviewed found the tool easy to use and all felt they could communicate their sensation of pain to the nurse.

Adaptation, Physiological↗

PubMed1997

Evaluating the use of a pain assessment tool and care plan: a pilot study.

Pain control in hospital has long been documented as ineffective and problematic. A multi-professional group of clinicians formed to consider how they might continue to improve pain management at a district general hospital. Following a pain audit, in general wards, it became apparent that pain assessment tools were not being used. The group devised a draft pilot assessment tool and care plan which was piloted over a 2-week period on a rehabilitation ward for elderly people. A review of these documents revealed that pain assessment using the body map ascertained considerable detail about the pain location, and the pain ruler elicited pain intensity and associated descriptors. None of the documented goals for pain were measurable, and interventions focused on analgesia and actions to relieve the physical cause of the pain. No psychosocial interventions were mentioned. All care plans were evaluated at least once but 44% of evaluations did not refer to the pain. On this ward, these outcomes suggest the pain assessment tool has the potential to improve communication of pain between the patient and the nurse but there is an urgent need for education to enable this information to be used effectively and develop pain management strategies which reflect the multidimensional nature of pain.

Aged↗