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PubMedDate not supplied

A new assessment tool for neuropsychopharmacologic research: the Computerized Neuropsychological Test Battery.

The Computerized Neuropsychological Test Battery (CNTB), a new assessment tool for neuropsychopharmacologic research, is based on a neuropsychological approach. While it is based on tests previously shown to be sensitive to subtle changes in neuropsychological functioning, it differs from currently available tools for measuring central nervous system effects of new compounds. It has sensitivity to a broader range of cognitive functioning and is more comprehensive than other measurements in its sampling of neuropsychological functions, providing wider application to diverse clinical populations. The CNTB is valid, reliable, and has two alternative forms. Use of the computer as an expert system maximizes standardization and ease of CNTB administration and data analysis. Using this assessment tool, three groups of subjects were compared: young and elderly neurologically normal subjects and elderly subjects with the dementia syndrome of Alzheimer's disease (AD). The AD subjects' summary score on the CNTB correlated significantly with the Blessed Information Memory Concentration Test score. The CNTB summary score was significantly higher in young subjects than in neurologically normal elderly subjects, demonstrating sensitivity to the effects of aging. The CNTB summary score also was significantly higher in neurologically normal elderly subjects than in elderly subjects with AD dementia.

Adult↗

PubMed2002

Cultural validation of pediatric pain assessment tools: Jordanian perspective.

The purpose of this study was to examine the cultural validity, reliability, and preference of three pain assessment tools among 95 Jordanian children. Pain intensity was assessed using the Poker Chip, the Faces, and the Word Description Scales. The test-retest reliability and the convergent validity were supported for the three scales. Jordanian children preferred the Poker Chip Tool to the Faces Scale and the Word Descriptive Scale. Gender differences in relation to scale preference were evident: female children preferred the Poker Chip Tool and male children preferred the Faces Scale; such differences were contributes of the socialization process within the Arab culture. The three scales are valid, reliable, and can be used with confidence to assess pain among Jordanian children. Findings also showed that children have a subculture of their own regardless of their cultural orientation. Findings have implication to nurses in Jordan as well as to transcultural nursing.

Arabs↗

PubMed2000

The unsolicited diary as a qualitative research tool for advanced research capacity in the field of health and illness.

In this article, the place of diary method is examined in the context of qualitative tools. Although much neglected in qualitative methodology, there is considerable support for its use, and it is argued that unsolicited diary analysis as a qualitative tool has value as a social research method. Although it is commissioned or solicited diaries that are increasingly popular in health research, different kinds of diary usage are examined together with certain possible biases and weaknesses. Although framework analysis was originally developed for analyzing interview data, it is seen as an appropriate qualitative tool for the analysis of unsolicited diaries. The analysis of an unsolicited diary account of a patient suffering from cancer of the larynx is explored as a potential data source.

Attitude to Health↗

PubMedDate not supplied

Evaluation of a behavioral assessment tool for the individual unable to self-report pain.

Assessment of pain intensity using a standard self-reported pain score is standard practice in most institutions. These instruments require the cognitive ability to process the pain intensity into a numeric or descriptive value. Many institutions are considering adopting an assessment tool for cognitive impairment. The purpose of this study is to evaluate a clinician-administered assessment tool, PAINAD, in patients with cognitive impairment. Opioid consumption and frequency of documented unknown pain were collected in 2 cognitive impaired groups. In the control group, a self-reporting pain intensity tool was used, and in a second group, the PAINAD was used. Opioid use was significantly higher (P = .003) and the rates of reported unknown pain were significantly lower (P < .01) in the group using the PAINAD instrument compared to the control group of patients with cognitive impairment. There were no noted differences in opioid-induced adverse reactions in either group.

Aged↗

PubMedDate not supplied

Preliminary assessment: the Pain Inventory and the Pain Coping Tool.

The purpose of this research study was to report the development and preliminary psychometric testing of the Pain Inventory and the Pain Coping Tool. The Pain Inventory was developed to measure cognitive factors believed to impact upon the pain experience. The Pain Coping Tool was developed to measure coping strategies and behaviors believed to be effective in dealing with the pain experience. Forty nursing doctoral students, head nurses, and clinical nurse experts rated the items to establish content validity. Initial testing for reliability found coefficient alphas to be adequate for new scales. Construct validity was established by significant correlations found between these tools and the Pain Intensity and Pain Distress Scales. These findings must be viewed as preliminary based on the small sample of 80 metastatic cancer patients interviewed for this study.

Adaptation, Psychological↗

PubMed1982

Closing the gap in quality assurance: A tool for evaluating group leaders.

A commitment to quality assurance means offering a cycle of feedback to those being evaluated. How to meet that commitment was the question asked by the Health Education Department of a large Health Maintenance Organization whose more than 70 facilitators annually provide instruction for over 3,000 enrollees. As part of the multi-faceted endeavor to develop a systematic quality assurance program for the department's offerings, a reliable participant-scored standardized tool had to be constructed. The staff of the department first identified two concepts as critical for quality instruction: interpersonal skills and technical competence. Based on these criteria a 49-item questionnaire was developed and tested during "pre-pilot" and pilot stages. By computer analysis, 27 items with an alpha-reliability coefficient of .94 remained to form the tool the department uses. The development of the evaluation tool and its use are described.

Consumer Behavior↗

PubMed2003

Towards the development of a paediatric discharge planning screening tool.

This study reports the second phase in the development of a paediatric discharge risk screening tool. It describes evaluation of the reliability and validity of this tool, which is designed to identify children in need of post-discharge care beyond that of routine nursing and physician teaching and follow-up. The first group identified was children who possessed a non-routine or unpredictable pathway of post-hospital treatment. The second group encompassed those with multifaceted, complex post-hospital care needs, requiring extensive internal hospital department coordination and involvement of community-based care providers in the discharge planning process. It was found that discharge risk factors reflecting objective and easily observable illness and treatment criteria were the most reliable predictors of need for social work discharge planning. It is recommended that a discharge risk tool be completed in partnership with unit nursing staff, and that it be subjected to further review in other organizational settings.

Aftercare↗

PubMed2005

Validating the Derbyshire Children's Hospital Pain Tool in children aged 6-12 years.

The Derbyshire Children's Hospital Paediatric Pain Chart (DPC) is the current pain assessment tool used at the Derbyshire Children's Hospital. It was originally devised as a simple pain tool for use in the post-operative clinical area. It is applicable across the spectrum of age groups that present for paediatric surgery. The DPC assesses pain by utilizing three parameters: facial expression, verbal (i.e. self-report) and body movement. This exploratory study was undertaken to determine its reliability and validity in children aged 6-12 years. The research nurse assessed 60 children aged 6-12 years undergoing minor and intermediate surgery and compared the DPC against the validated Oucher Scale. Assessments were performed preoperatively and for four hours post-operatively. Any analgesia administered post-operatively was recorded, and its effects noted. This study supports construct validity and inter-rater reliability of the DPC pain assessment tool for children aged 6-12 undergoing minor and intermediate surgery.

Child↗

PubMed2002

CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes.

BACKGROUND: Improvements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining. RESULTS: CoreGenes is a global JAVA-based interactive data mining tool that identifies and catalogs a "core" set of genes from two to five small whole genomes simultaneously. CoreGenes performs hierarchical and iterative BLASTP analyses using one genome as a reference and another as a query. Subsequent query genomes are compared against each newly generated "consensus." These iterations lead to a matrix comprising related genes from this set of genomes, e. g., viruses, mitochondria and chloroplasts. Currently the software is limited to small genomes on the order of 330 kilobases or less. CONCLUSION: A computational tool CoreGenes has been developed to analyze small whole genomes globally. BLAST score-related and putatively essential "core" gene data are displayed as a table with links to GenBank for further data on the genes of interest. This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes or http://www.bif.atcc.org/CoreGenes.

Algorithms↗

PubMed2004

VisANT: an online visualization and analysis tool for biological interaction data.

BACKGROUND: New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. RESULTS: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. CONCLUSION: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

Animals↗

PubMed2004

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states.

BACKGROUND: Information obtained by DNA microarray technology gives a rough snapshot of the transcriptome state, i.e., the expression level of all the genes expressed in a cell population at any given time. One of the challenging questions raised by the tremendous amount of microarray data is to identify groups of co-regulated genes and to understand their role in cell functions. RESULTS: MiCoViTo (Microarray Comparison Visualization Tool) is a set of biologists' tools for exploring, comparing and visualizing changes in the yeast transcriptome by a gene-centric approach. A relational database includes data linked to genome expression and graphical output makes it easy to visualize clusters of co-expressed genes in the context of available biological information. To this aim, upload of personal data is possible and microarray data from fifty publications dedicated to S. cerevisiae are provided on-line. A web interface guides the biologist during the usage of this tool and is freely accessible at http://www.transcriptome.ens.fr/micovito/. CONCLUSIONS: MiCoViTo offers an easy-to-read picture of local transcriptional changes connected to current biological knowledge. This should help biologists to mine yeast microarray data and better understand the underlying biology. We plan to add functional annotations from other organisms. That would allow inter-species comparison of transcriptomes via orthology tables.

Cluster Analysis↗

PubMed2005

AutoFACT: an automatic functional annotation and classification tool.

BACKGROUND: Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. RESULTS: We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1-2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. CONCLUSION: AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm.

Acanthamoeba castellanii↗

PubMed2005

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.

BACKGROUND: The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular interaction networks has been recognized and applied to the study of model organisms, but its systematic application to the study of human disease has lagged behind due to the lack of tools for performing such integration. RESULTS: We have developed techniques and software tools for simplifying and streamlining the process of integration of diverse experimental data types in molecular networks, as well as for the analysis of these networks. We applied these techniques to extract, from genomic expression data from Hepatitis C virus-infected liver tissue, potentially useful hypotheses related to the onset of this disease. Our integration of the expression data with large-scale molecular interaction networks and subsequent analyses identified molecular pathways that appear to be induced or repressed in the response to Hepatitis C viral infection. CONCLUSION: The methods and tools we have implemented allow for the efficient dynamic integration and analysis of diverse data in a major human disease system. This integrated data set in turn enabled simple analyses to yield hypotheses related to the response to Hepatitis C viral infection.

Computational Biology↗

PubMed2005

DynGO: a tool for visualizing and mining of Gene Ontology and its associations.

BACKGROUND: A large volume of data and information about genes and gene products has been stored in various molecular biology databases. A major challenge for knowledge discovery using these databases is to identify related genes and gene products in disparate databases. The development of Gene Ontology (GO) as a common vocabulary for annotation allows integrated queries across multiple databases and identification of semantically related genes and gene products (i.e., genes and gene products that have similar GO annotations). Meanwhile, dozens of tools have been developed for browsing, mining or editing GO terms, their hierarchical relationships, or their "associated" genes and gene products (i.e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed. RESULTS: We present a standalone package called DynGO, which provides several advanced functionalities in addition to the standard browsing capability of the official GO browsing tool (AmiGO). DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. CONCLUSION: We have presented a standalone package DynGO that provides functionalities to search and browse GO and its association databases as well as several additional functions such as batch retrieval and semantic retrieval. The complete documentation and software are freely available for download from the website http://biocreative.ifsm.umbc.edu/dyngo.

Computer Graphics↗

PubMed2005

T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory.

BACKGROUND: Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. RESULTS: We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. CONCLUSION: We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories without a more sophisticated and expensive system, such as a LIMS.

Clinical Laboratory Information Systems↗

PubMed2005

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

BACKGROUND: maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. RESULTS: maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. CONCLUSION: maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

Data Interpretation, Statistical↗

PubMed2005

ErmineJ: tool for functional analysis of gene expression data sets.

BACKGROUND: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. RESULTS: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. CONCLUSION: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org.

Animals↗

PubMed2005

CGHPRO -- a comprehensive data analysis tool for array CGH.

BACKGROUND: Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. RESULTS: We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the identification of odd clones. CONCLUSION: CGHPRO is a comprehensive and easy-to-use data analysis tool for array CGH. Since all of its features are available offline, CGHPRO may be especially suitable in situations where protection of sensitive patient data is an issue. It is distributed under GNU GPL licence and runs on Linux and Windows.

Algorithms↗