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PubMed1995

FOLD: integrated analysis and display of protein secondary structure.

FOLD, a computer program for the definition and analysis of protein secondary structure, is described. Algorithms implemented in the software are reviewed. These include methods for the identification of simple features such as hydrogen bonds, alpha helices, beta strands, beta bulges, and beta and psi turns. Techniques are also described for the definition and analysis of higher-order structures, such as beta hairpins, beta sheets and their topology, and beta barrels. In addition to considerable textual output the program supports visualization of protein secondary structure in either an atom-based display style or one reproducing the characteristics of a so-called ribbon drawing.

Computer Graphics↗
PubMed1999

MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.

The trend toward high-throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available information. This problem is particularly severe in the rapidly expanding area of gene expression experiments, for example, those carried out with cDNA microarrays or oligonucleotide chips. We present an Internet-based hypertext program, MedMiner, which filters and organizes large amounts of textual and structured information returned from public search engines like GeneCards and PubMed. We demonstrate the value of the approach for the analysis of gene expression data, but MedMiner can also be extended to other areas involving molecular genetic or pharmacological information. More generally still, MedMiner can be used to organize the information returned from any arbitrary PubMed search.

Databases, Factual↗
PubMed2003

Psychosocial themes in durable employment transitions.

Loss of work capacity through illness or injury may result in loss of employment. The transition to durable employment with those reduced capacities poses many challenges. This paper is based on phenomenological research into the experiences of 13 people who had a disabling injury or chronic illness. These participants lost their capacity for their former employment. After a period of time, extending up to 14 years, the participants successfully changed employment in the open labor market, and retained their current employment for 13 weeks or longer. Data from in excess of 30 hours of in-depth semi-structured individual interviews and a focus group were transcribed and analyzed inductively. Analysis was aided by immersion in the data, reflections on entries in a researcher's log, and a computer program for analyzing textual data. Eleven psychosocial themes emerged. These themes were: pain, intense emotions, determination, financial concerns, role models, concealment, assistance, control, self-concept, satisfaction with employment, and personal change. Each theme is presented with representative text from participants and implications for work rehabilitation professionals. Further research to identify the extent of transferability of the findings is recommended.

Career Mobility↗
PubMed1994

Textual prompts as an antecedent cue self-management strategy for persons with mild disabilities.

Providing learners written task analyses to be used as textual prompts was examined as a self-management strategy for persons with mild disabilities. Initially, modeling, corrective verbal feedback, and contingent descriptive praise were employed to train participants to use the written task analysis to perform one home maintenance task. Subsequently, participants were tested on their use of different task analyses combined with general feedback to perform two novel home maintenance tasks. No training was provided on how to use these new task analyses. Either a multiple baseline or a multiple probe across settings experimental design was used to control extraneous variables. Results indicated that the written task analyses served as self-administered textual prompts and, along with general feedback, provided stimulus control for the second and third tasks. When the self-management task analyses and general feedback were withdrawn, transfer of stimulus control occurred to the natural discriminative stimuli for the majority of tasks. The research suggests that written task analyses, as presented in the present study, may have utility for the self-management of instruction by persons with mild disabilities.

Adult↗
PubMed1994

On-line information sources on chemical substances.

Information technology has brought about changes in the work patterns of researchers and scientists. After some hints on the on-line facilities needed to be connected to the international host computers, an analysis is made of some of the main automated sources available to retrieve information on chemical substances. Special emphasis is given to textual-numeric data banks, first reviewing the main chemical dictionaries, like Registry and Chemline, and then focusing on those sources that offer immediate information in case of emergency. Among the Toxnet files, produced and managed within the US National Library of Medicine Toxicology Information Program, play a very important role in offering publicly available data on toxicology and on hazardous chemicals. Therefore, the Hazardous Substances Data Bank (HSDB) and the Registry of Toxic Effects of Chemical Substances (RTECS) are described for their relevance thereon. Other data banks produced in Europe, like the Environmental Chemicals Data Information Network (ECDIN) and the very specialized Major Hazard Incident Data Service (MHIDAS) are also briefly outlined. To integrate this overview on online information, the attention is then shifted on sources having the characteristic of reference databases: prestigious files covering the international scientific literature, as CA/Chemabs, Toxline/Toxlit, Embase, Medline are introduced. Implications of on-line technology in enhancing information access in the next future are discussed, pointing out the new tools created to meet the information needs of end-users.

Databases, Bibliographic↗
PubMed2001

The benefits of Skinner's analysis of verbal behavior for children with autism.

Behavior analysis has already contributed substantially to the treatment of children with autism, and further gains can result from more use of Skinner's analysis of language in Verbal Behavior (1957) and in the resulting conceptual and experimental work. The approach emphasizes a unit of analysis consisting of the relations between behavior, motivative and discriminative variables, and consequences. Skinner identifies seven types of verbal operants--echoic, mand, tact, intraverbal, textual, transcriptive, and copying a text--which function as components of more advanced forms of language. This approach focuses on the development of each verbal operant (rather than on words and their meanings) and on the independent training of speaker and listener repertoires. Five more specific contributions are described that relate to the importance of (a) an effective language assessment, (b) mand training in early intervention, (c) establishing operations, (d) an intraverbal repertoire, and (e) automatic reinforcement.

Autistic Disorder↗
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↗
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↗
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↗
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↗
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↗