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PubMed1990

Proposed standard for image cytometry data files.

A number of different types of computers running a variety of operating systems are presently used for the collection and analysis of image cytometry data. In order to facilitate the development of sharable data analysis programs, to allow for the transport of image cytometry data from one installation to another, and to provide a uniform and controlled means for including textual information in data files, this document describes a data storage format that is proposed as a standard for use in image cytometry. In this standard, data from an image measurement are stored in a minimum of two files. One file is written in ASCII to include information about the way the image data are written and optionally, information about the sample, experiment, equipment, etc. The image data are written separately into a binary file. This standard is proposed with the intention that it will be used internationally for the storage and handling of biomedical image cytometry data. The method of data storage described in this paper is similar to those methods published in American Association of Physicists in Medicine (AAPM) Report Number 10 and in ACR-NEMA Standards Publication Number 300-1985.

Electronic Data Processing↗
PubMed1996

TongueTwister: an integrated program for analyzing lickometer data.

The analysis of lickometer data is often rendered prohibitively tedious by the large volume of data generated by the typical experiment. TongueTwister is an integrated program for the rapid and automatic analysis, presentation, and summary of long- and medium-access data collected by lickometers or of brief-access data collected by multi-bottle lickometers such as the DiLog Instruments MS80. The program was written in C+2 for Macintosh computers, and analyzes data collected by MS-DOS PCs. It takes advantage of the Macintosh user interface to provide quick and convenient output from all the files of a single experimental session, and to export the data to third-party statistical software or other documents. It can batch-process data files by automatically opening and analyzing all the files in a directory; thus, the user can employ directories as a simple database for organizing experimental groups. When a lickometer data file is opened, a textual summary, a raster plot of the lick pattern, the cumulative licks, the lick rate, a histogram of inter-lick intervals, and a breakdown of the session by fractions are automatically calculated and displayed. When an MS80 brief-access file is opened, the lick pattern for each tube presentation and a textual summary of the mean values derived for each tube are automatically displayed. If a directory of files is opened, the mean values derived across all the individual files are calculated and graphed. Analysis parameters can be tailored to the investigator's liking. Tables or graphs can be saved to disk, or copied and pasted into other Macintosh programs for additional analysis. The program may also be used for general-purpose analysis of periodic event records.

Animals↗
PubMedDate not supplied

Pictorial illustrations enhance memory for sentences in younger and older adults.

In these studies, the authors examined the effects of verbal and pictorial illustrations on younger and older adults' recall of the content of short sentences. During acquisition, base and elaborated sentences were presented under one of three encoding conditions: (a) sentences only; (b) sentences with matching pictures; (c) incomplete sentences with matching pictures. At test, participants recalled the main action of the sentences. Base sentences were recalled more often than elaborated sentences when strict scoring criteria were used. However, older adults showed a recall advantage for elaborated sentences compared to base sentences when lenient scoring criteria were applied. Positive effects of pictorial illustrations occurred for both age groups. Implications for the design of instructional formats to improve older adults' retention of textual material are discussed.

Adult↗
PubMed1997

Use of the QSR.NUD.IST computer program to identify how clinical midwife mentors view their work.

This paper looks at the use of a computer program (QSR.NUD.IST) to analyse qualitative data. The data are derived from interviews with clinical midwife mentors as part of an evaluation of a midwifery educational programme. An account is given of the content analysis of the data with reference to the literature, and then the way the programme was used to analyse the data a second time. A description is given of the way this programme in particular functions using the textual data as an example. The use of computers in general for analysing qualitative data is discussed in terms of their advantages and disadvantages. The results of the study are described briefly showing how the mentors view their role and responsibilities.

Data Interpretation, Statistical↗
PubMed2004

The problem of evidence-based medicine: directions for social science.

Evidence-based medicine (EBM) is arguably the most important contemporary initiative committed to reshaping biomedical reason and practice. The move to establish scientific research as a fundamental ground of medical decision making has met with an enthusiastic reception within academic medicine, but has also generated considerable controversy. EBM and the broader forms of evidence-based decision making it has occasioned raise provocative questions about the relation of scientific knowledge to social action across a variety of domains. Social science inquiry about EBM has not yet reached the scale one might expect, given the breadth and significance of the phenomenon. This paper contributes reflections, critique and analysis aimed at helping to build a more robust social science investigation of EBM. The paper begins with a "diagnostics" of the existing social science literature on EBM, emphasizing the possibilities and limitations of its two central organizing analytic perspectives: political economy and humanism. We further explore emerging trends in the literature including a turn to original empirical investigation and the embrace of "newer" theoretical resources such as postmodern critique. We argue for the need to move the social inquiry of EBM beyond concerns about rationalization and the potential erasure of the patient and, to this end, suggest new avenues of exploration. The latter include analysis of clinical epidemiology and clinical reason as the discursive preconditions of EBM, the role of the patient as a site for the production of evidence, and the textually mediated character of EBM.

Evidence-Based Medicine↗
PubMed1994

Quantitative audit of the content of histopathology reports.

An audit of histopathology reports presents the problem that the output is textual and difficult to quantify. This makes the definition of an adequate report subjective and susceptible to observer variation. A procedure has been developed which allows the quantitative analysis of reports and facilitates the development of local reporting guidelines. A topic is selected; the auditor then lists the possible details that may be included in the report and notes how many reports from a sample include each detail. The results are discussed at a departmental meeting with the aim of agreeing on reporting guidelines. At a later date another sample of reports can be analysed for compliance with the guidelines and compared with the previous reports. Problems with compliance can be discussed further and at the audit meeting the guidelines may be amended appropriately, thus completing the audit cycle. This method of audit has the advantage that the results are quantitative and that the group discussion and re-examination of the guidelines has educational value.

Humans↗
PubMed2005

Evaluation of BioCreAtIvE assessment of task 2.

BACKGROUND: Molecular Biology accumulated substantial amounts of data concerning functions of genes and proteins. Information relating to functional descriptions is generally extracted manually from textual data and stored in biological databases to build up annotations for large collections of gene products. Those annotation databases are crucial for the interpretation of large scale analysis approaches using bioinformatics or experimental techniques. Due to the growing accumulation of functional descriptions in biomedical literature the need for text mining tools to facilitate the extraction of such annotations is urgent. In order to make text mining tools useable in real world scenarios, for instance to assist database curators during annotation of protein function, comparisons and evaluations of different approaches on full text articles are needed. RESULTS: The Critical Assessment for Information Extraction in Biology (BioCreAtIvE) contest consists of a community wide competition aiming to evaluate different strategies for text mining tools, as applied to biomedical literature. We report on task two which addressed the automatic extraction and assignment of Gene Ontology (GO) annotations of human proteins, using full text articles. The predictions of task 2 are based on triplets of protein--GO term--article passage. The annotation-relevant text passages were returned by the participants and evaluated by expert curators of the GO annotation (GOA) team at the European Institute of Bioinformatics (EBI). Each participant could submit up to three results for each sub-task comprising task 2. In total more than 15,000 individual results were provided by the participants. The curators evaluated in addition to the annotation itself, whether the protein and the GO term were correctly predicted and traceable through the submitted text fragment. CONCLUSION: Concepts provided by GO are currently the most extended set of terms used for annotating gene products, thus they were explored to assess how effectively text mining tools are able to extract those annotations automatically. Although the obtained results are promising, they are still far from reaching the required performance demanded by real world applications. Among the principal difficulties encountered to address the proposed task, were the complex nature of the GO terms and protein names (the large range of variants which are used to express proteins and especially GO terms in free text), and the lack of a standard training set. A range of very different strategies were used to tackle this task. The dataset generated in line with the BioCreative challenge is publicly available and will allow new possibilities for training information extraction methods in the domain of molecular biology.

Computational Biology↗
PubMed1995

Effects of inconsistent pictures on remembering text.

An experiment was conducted to examine whether a consistent or an inconsistent picture would facilitate recall of text when recall was tested under two conditions involving a consistent or an inconsistent picture. Analyses indicated that recall in the inconsistent-picture condition was better than that in the consistent-picture condition for missing sentences but not for complete sentences of text. This result suggests that an inconsistent picture may facilitate processing of textual information more elaborately than do consistent pictures.

Adult↗
PubMedDate not supplied

The portrayal of the menstruating woman in menstrual product advertisements.

Because menstrual product advertisements act as mediators of a subset of meanings of femininity linked to menstruation, we performed a comparative conceptual analysis of these advertisements to explicate media-constructed realities of contemporary women. We sought to understand the portrayed women's definition of menstruation and their status as menstruating women. Textual and conceptual analyses led us to conclude that the portrayed women, in an attempt to avoid others' discovery of their menstruation, employed a complex menstrual management system, which often includes feminized menstrual products, to act as an antidote to a tainted state of femininity.

Adaptation, Psychological↗
PubMed2004

Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms.

Web-accessible proteome databases represent indispensable tools for quantitative and comparative proteomics research. The majority of two-dimensional gel electrophoresis (2-DE) databases contains clickable 2-DE gel images and descriptive textual information such as protein name, Mr/pI values, methods of identification, cellular localization and other information on proteins. Although a great part of the work in comparative proteomics consists of the analysis of 2-DE gels using image analysis approaches, most proteome databases lack the ability to present protein abundance data and their alterations within experiments via the web. Now, differentially regulated proteins detected in microbial experiments by quantitative gel image analysis are presented in a web-accessible relational database DIFF (Differentially Regulated Proteins). The DIFF database is a part of the proteome database system for microbial research available at http://www.mpiib-berlin.mpg.de/2D-PAGE.

Bacterial Proteins↗
PubMed1999

George Rupert Palmer--DRG carrier and champion.

Prompted by the retirement of the distinguished health economist, researcher and academic, Professor George Rupert Palmer, the purpose of this paper is to reflect upon and acknowledge one of his many contributions to health services research and development. By employing a conceptual framework devised by Kimberly and de Pouvourville (1993) for analysis of the diffusion of innovations, this paper argues that Palmer played a crucial role in the diffusion into and within Australia of a particular casemix method, diagnosis related groups (DRGs). Textual and interview evidence presented in the paper supports the identification of George Rupert Palmer as the principal carrier of DRGs into Australia, and as one of its key champions within Australia.

Australia↗
PubMed2005

Knowledge discovery and system biology in molecular medicine: an application on neurodegenerative diseases.

The possibility to study an organism in terms of system theory has been proposed in the past, but only the advancement of molecular biology techniques allow us to investigate the dynamical properties of a biological system in a more quantitative and rational way than before . These new techniques can gave only the basic level view of an organisms functionality. The comprehension of its dynamical behaviour depends on the possibility to perform a multiple level analysis. Functional genomics has stimulated the interest in the investigation the dynamical behaviour of an organism as a whole. These activities are commonly known as System Biology, and its interests ranges from molecules to organs. One of the more promising applications is the 'disease modeling'. The use of experimental models is a common procedure in pharmacological and clinical researches; today this approach is supported by 'in silico' predictive methods. This investigation can be improved by a combination of experimental and computational tools. The Machine Learning (ML) tools are able to process different heterogeneous data sources, taking into account this peculiarity, they could be fruitfully applied to support a multilevel data processing (molecular, cellular and morphological) that is the prerequisite for the formal model design; these techniques can allow us to extract the knowledge for mathematical model development. The aim of our work is the development and implementation of a system that combines ML and dynamical models simulations. The program is addressed to the virtual analysis of the pathways involved in neurodegenerative diseases. These pathologies are multifactorial diseases and the relevance of the different factors has not yet been well elucidated. This is a very complex task; in order to test the integrative approach our program has been limited to the analysis of the effects of a specific protein, the Cyclin dependent kinase 5 (CDK5) which relies on the induction of neuronal apoptosis. The system has a modular structure centred on a textual knowledge discovery approach. The text mining is the only way to enhance the capability to extract ,from multiple data sources, the information required for the dynamical simulator. The user may access the publically available modules through the following site: http://biocomp.ge.ismac.cnr.it.

Biomedical Research↗
PubMed2004

Complexity: an internet resource for analysis of DNA sequence complexity.

The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures, as well as by a combination of all these factors. Several numerical measures of textual complexity, including combinatorial and linguistic ones, together with complexity estimation using a modified Lempel-Ziv algorithm, have been implemented in a software tool called 'Complexity' (http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/). The software enables a user to search for low-complexity regions in long sequences, e.g. complete bacterial genomes or eukaryotic chromosomes. In addition, it estimates the complexity of groups of aligned sequences.

Algorithms↗
PubMed2003

Text mining of DNA sequence homology searches.

Primary tasks in analysis and annotation of expressed sequence tag (EST) datasets are to identify similarity among sequences by unsupervised clustering and assign putative function based on BLAST homology searches. We investigated the usefulness of text mining as a simple approach for further higher-level clustering of EST datasets using IBM Intelligent Miner for Text v2.3 tools. Agglomerative and k-means clustering tools were used to cluster BLASTx homology search documents from two onion EST datasets and optimised by pre-processing and pruning. Subjective evaluation confirmed that these tools provided biologically useful and complementary views of the two libraries, provided new insights into their composition and revealed clusters previously identified by human experts. We compared BLASTx textual clusters for two gene families with their DNA sequence-based clusters and confirmed that these shared similar morphology.

Abstracting and Indexing↗
PubMed2005

[Application of virtual instrumentation technique in toxicological studies].

Research investigations require frequently direct connection of measuring equipment to the computer. Virtual instrumentation technique considerably facilitates programming of sophisticated acquisition-and-analysis procedures. In standard approach these two steps are performed subsequently with separate software tools. The acquired data are transfered with export / import procedures of particular program to the another one which executes next step of analysis. The described procedure is cumbersome, time consuming and may be potential source of the errors. In 1987 National Instruments Corporation introduced LabVIEW language based on the concept of graphical programming. Contrary to conventional textual languages it allows the researcher to concentrate on the resolved problem and omit all syntactical rules. Programs developed in LabVIEW are called as virtual instruments (VI) and are portable among different computer platforms as PCs, Macintoshes, Sun SPARCstations, Concurrent PowerMAX stations, HP PA/RISK workstations. This flexibility warrants that the programs prepared for one particular platform would be also appropriate to another one. In presented paper basic principles of connection of research equipment to computer systems were described.

Humans↗
PubMed2005

TV commercials for prescription drugs: a discourse analytic perspective.

BACKGROUND: The US Food and Drug Administration has called for research that may assist in developing standards for risk/benefit messages in the promotion of prescription drugs. Linguistics-based models of meaning and inference, though frequently applied to advertising, have not hitherto been used in this arena. OBJECTIVE: This study was intended to illustrate how discourse analysis, a methodology for microanalysis of texts in context, can elucidate the workings and interplay of promotional, informational, and other functions of direct-to-consumer drug advertising, anticipating threats to "fair balance" and pinpointing textual phenomena and issues suited to empirical study. METHODS: The text and visuals of a small corpus were analyzed along several dimensions, using theoretical insights of linguistic pragmatics and ethnography of speech to ask what the advertisement is seeking to do and what messages a viewer is likely to derive. RESULTS: The linguistic and rhetorical features include an intense switching and fusion of styles and modalities: the traditional advertising distinction between personal and impersonal, "company" and "consumer", was ostentatiously flouted. The role of spokesperson was assigned to characters in a real or virtual narrative. The narrative portion of the text and images often struck an ironic or postmodern note, eg, by mixing science with science fiction. The overall functions of the commercials (promotional, informational, and aesthetic) were themselves frequently blended. The text deployed several linguistic or rhetorical strategies to send a double message for promotional advantage, including syntactic-semantic ambiguity, voice-over risk messages at odds with upbeat visuals, and a vagueness of certain words in particular contexts. CONCLUSIONS: Findings contribute to our understanding of how TV commercials convey meaning with respect to drug benefits and risks, with implications for advertisers, regulators, and patient education. They also suggest new foci for empirical study.

Advertising↗
PubMed1993

The Rancho EMG analyzer: a computerized system for gait analysis.

This paper describes a computer system which accurately defines the EMG patterns of the lower extremities during gait. Footswitches are used to identify the temporal relationships and determine the phases of the gait cycle. Fine wire electrodes, inserted in the desired muscles of the patient being tested, provide EMG signals for comparison with a normal database. The system is also usable with surface electrodes when an appropriate normal database for surface electrodes is incorporated. Descriptive qualifiers (such as 'premature onset', 'delayed cessation', 'no clinically significant EMG', 'continuous activity' etc.) are used to produce a clinically relevant printed (textual) report. The intensity filtered average (IFA) of the EMG is shown graphically with the representative profile of each stride. The IFAs for all muscles tested can be plotted together (up to six on a page) and the graphic representation of the 'raw' EMG can be produced. The methods of generating the normal database by creating time-adjusted mean profiles (TAMP) are enumerated. The clinical use of the system is discussed. A detailed analysis of 31 of the most recent patient tests for which the system was used provides an indication of its accuracy. For 86% of the 428 muscle tests examined, the EMG analyser was considered to have given the correct result as compared with a visual analysis of the raw EMG record by a trained expert. Recommendations for the use and future improvements of the EMG analyser are made.

Adolescent↗
PubMed2006

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package.

BACKGROUND: Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. RESULTS: Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. CONCLUSION: Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de.

Algorithms↗