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PubMed1985

Managing bibliographic citations using microcomputers.

Programs are now available to construct and retrieve lists of bibliographic citations by microcomputers. Although considerable effort must be expended to learn to use them, once mastered, they can be useful to anyone who must manage large collections of references. There are several ways to use personal computers to store and retrieve bibliographic citations. Word processors can be used to manage relatively small lists of citations. Preprogrammed bibliographic systems are available that are designed specifically for this purpose. A general data base management program can also be adapted for bibliographic purposes and used for other functions as well. This essay has been prepared to provide guidance to those who have a working knowledge of microcomputers and wish to expand this to use a data management system for bibliographic purposes. The dBASE II program is used to illustrate how to set up a bibliographic system. Methods are described on how to prepare citations for storage and retrieval using combinations of key words and Boolean operators, how to prepare selected lists of references and arrange them in alphabetic order or by subject heading, and how to print tailored lists of citations. The system was found to be highly responsive to commands and able to provide rapid retrieval of information.

Bibliography of Medicine↗
PubMed1984

A retrieval account of the long-term modality effect.

When to-be-remembered (TBR) word pairs are separated by distractor activity, recall of the last few audibly presented pairs is greater than recall of the last few visually presented pairs. The effect is found even after a considerably long distractor-filled retention interval. Five experiments disconfirm echoic storage, short-term storage and long-term storage accounts of these effects, as well as demonstrating that the effect is not an artifact of differential use of a recency-first output strategy. The data are generally consistent with the proposition that retrieval is disrupted by modality-specific similarity between to-be-remembered items and distractor information.

Adult↗
PubMed2005

Accurate data collection for head injury monitoring studies: a data validation methodology.

BACKGROUND: BrainIT is a multi centre, European project, to collect high quality continuous data from severely head injured patients using a previously defined [6] core data set. This includes minute-by-minute physiological data and simultaneous treatment and management information. It is crucial that the data is correctly collected and validated. METHODS: Minute-by-minute physiological monitoring data is collected from the bedside monitors. Demographic and clinical information, intensive care management and secondary insult management data, are collected using a handheld computer. Data is transferred from the handheld device to a local computer where it is reviewed and anonymised before being sent electronically, with the physiological data, to the central database in Glasgow. Automated computer tools highlight missing or ambiguous data. A request is then sent to the contributing centre where the data is amended and returned to Glasgow. Of the required data elements 20% are randomly selected for validation against original documentation along with the actual number of specific episodic events during a known period. This will determine accuracy and the percentage of missing data for each record. CONCLUSION: Advances in patient care require an improved evidence base. For accurate, consistent and repeatable data collection, robust mechanisms are required which should enhance the reliability of clinical trials, assessment of management protocols and equipment evaluations.

Brain Injuries↗
PubMed1994

Functional workstation requirements: clinical perspectives.

This white paper details specific requirements for clinical workstations identified by employees in the Department of Veterans Affairs. The requirements can be grouped into the following five categories: general environmental capabilities, input methods, display features, output abilities, and miscellaneous functionality and features. Clinical workstations meeting these functional requirements can offer a significant enhancement over existing hardware interfaces. Use of these workstations by health care providers could improve their willingness to directly enter data into clinical information systems, increasing the benefits of such systems.

Computer Systems↗
PubMed1991

A distributed image-processing system for measurements of intracellular calcium in living cells.

During the last decade, image-processing techniques have been introduced as a valuable tool in biologically oriented research. In combination with novel fluorescent probes, these techniques permit assessment of subcellular distributions of several intracellularly important cations, such as free calcium ions and protons. Typically, systems used for image processing are located centrally around the experimental setup. This configuration has drawbacks, mainly because the laborious extraction and processing of data that generally follow an experimental session limits the access to the system for other investigators. We describe here the principles of a distributed image processing system, based on IBM-compatible personal computers (PCs), that without extra hardware can cope with all the necessary image processing involved in imaging of intracellular cations. The potential of the PC as an image processor, however, reaches beyond this specific application and many image processing tasks can be carried out successfully on a standard PC. Thus, the centrally located dedicated image processor is used only for image acquisition in the experimental situation. This in turn optimizes the utilization of expensive resources and increases efficiency. The mouse-operated software is described in detail, so that interested investigators can extract useful parts for integration into their own applications and experimental environment.

Animals↗
PubMed2004

SignalML from an EDF+ perspective.

Both SignalML and EDF+ offer a solution for the incompatibility between different data storage formats in biomedicine. This article discusses the SignalML approach from an EDF+ point of view.

Data Interpretation, Statistical↗
PubMed2006

Methods for mining HTS data.

Data mining is a fast-growing field that is finding application across a wide range of industries. HTS is a crucial part of the drug discovery process at most large pharmaceutical companies. Accurate analysis of HTS data is, therefore, vital to drug discovery. Given the large quantity of data generated during an HTS, and the importance of analyzing those data effectively, it is unsurprising that data-mining techniques are now increasingly applied to HTS data analysis. Taking a broad view of both the HTS process and the data-mining process, we review recent literature that describes the application of data-mining techniques to HTS data.

Animals↗
PubMed2006

Discovering meaningful information from large amounts of environment and health data to reduce uncertainties in formulating environmental policies.

This study uses knowledge discovery concepts to analyze large amounts of data step by step for the purpose of assisting in the formulation of environmental policy. We performed data cleansing and extracting from existing nation-wide databases, and used regression and classification techniques to analyze the data. The current water hardness in Kaohsiung, Taiwan contributes to the prevention of cardiovascular disease (CVD) but exacerbates the development of renal stones (RS). However, to focus on water hardness alone to control RS would not be cost effective at all, because the existing database parameters do not adequately allow for a clear understanding of RS. Analysis of huge amounts of data can most often turn up the most reliable and convincing results and the use of existing databases can be cost-effective.

Data Interpretation, Statistical↗
PubMed1998

Human factors in technology replacement: a case study in interface design for a public transport monitoring system.

This paper describes ergonomic issues raised during a project to provide a replacement real-time bus route control system to a large public transport company. Task and system analyses highlighted several deficiencies in the original system architecture, the human-machine interfaces and the general approach to system management. The eventual live prototype replaced the existing original system for a trial evaluation period of several weeks. During this period a number of studies was conducted with the system users in order to measure any improvements the new system, with its ergonomic features, produced over the old. Importantly, the results confirmed that (a) general responsiveness and service quality were improved, and (b) users were more comfortable with the new design. We conclude with a number of caveats which we believe will be useful to any group addressing technology impact in a large organisation.

Attitude↗
PubMedDate not supplied

Assessment of commercial compression algorithms, of the lossy DCT and lossless types, applied to diagnostic digital image files.

The need for diagnostic image compression of the lossy or irreversible type has been declining due to the rapid increase in commercially available formatted hard disk capacity. It is estimated that the latter has increased about three orders of magnitude in the past 14 years while the size of diagnostic image files has, of course, remained constant. During the same period, despite claims for significantly improved performance by vendors, it seems that only small progress has been made in commercial lossless and lossy compression algorithms. There is still no consensus for lossy compression to a level acceptable for diagnosis. This is mostly considered to be around a ratio of 10:1. However, acceptable compression ratios depend heavily on the type of images processed and may be compared with the 3:1 ratio produced by lossless algorithms. This last value was shown to increase to more than 5.5:1 for gamma-camera images when corrected for the noise content of individual bit planes and for the display capabilities of computer monitors. Therefore, any possible benefits of lossy over lossless compression become questionable when the currently available hard disk capacity and network transmission speed are considered against the inevitable loss of information in the lossy type of compression.

Algorithms↗
PubMed2005

Storage and transmission of microarray images.

With the recent explosion of interest in microarray technology, massive amounts of microarray images are currently being produced. The storage and transmission of these types of data are becoming increasingly challenging. This article reviews the latest technologies that allow for the compression and storage of microarray images in dedicated database systems.

Data Compression↗
PubMed2002

Paraphrasing for condensation in journal abstracting.

When authors of empirical science articles write abstracts, they employ a wide variety of distinct linguistic operations which interact to condense and rephrase a subset of sentences from the source text. An on-going comparison of biological and biomedical journal articles with their author-written abstracts is providing a basis for a more linguistically detailed model of abstract derivation using syntactic representations of selected source sentences. The description makes use of rich dictionary information to formulate paraphrasing rules of differing degrees of generality, including some which are sublanguage-specific, and others which appear valid in several languages when formulated using "lexical functions" to express important semantic relationships between lexical items. Some paraphrase operations may use both lexical functions and rhetorical relations between sentences to reformulate larger chunks of text in a concise abstract sentence. The descriptive framework is computable and utilizes existing linguistic resources.

Abstracting and Indexing↗
PubMedDate not supplied

Chemical machine vision: automated extraction of chemical metadata from raster images.

We present a novel application of machine vision methods for the identification of chemical composition diagrams from two-dimensional digital raster images. The method is based on the use of Gabor wavelets and an energy function to derive feature vectors from digital images. These are used for training and classification purposes using a Kohonen network for classification with the Euclidean distance norm. We compare this method with previous approaches to transforming such images to a molecular connection table, which are designed to achieve complete atom connection table fidelity but at the expense of requiring human interaction. The present texture-based approach is complementary in attempting to recognize higher order features such as the presence of a chemical representation in the original raster image. This information can be used for providing chemical metadata descriptors of the original image as part of a robot-based Internet resource discovery tool.

Data Display↗
PubMedDate not supplied

Data mining techniques applied to medical information.

Knowledge discovery from the dramatically increased data of an auto-stored medical information system is still in its infancy. The purpose of this study is to use widely available and easily operated techniques that can satisfy general users in extracting specific knowledge to make the medical information system more functional. Data mining techniques, including data visualisation, correlation analysis, discriminant analysis, and neural networks supervised classification, were applied to heart disease databases. These techniques can help to identify high risk patients, define the most important factors (variables) in heart disease, and build a multivariate relationship model to show the relationship between any two variables in a way that such relationships are easy to view. Simple visualization techniques were utilised to construct this model, which corresponds with current medical knowledge. Two nonparametric (distribution assumption free) classification tools were employed to identify high risk heart disease patients. Both the neural networks supervised classification methods and the discriminant analysis method produced reliable classification rates for heart disease patients. However, neural networks yielded a higher percentage of correct classifications (averaging 89%) than discriminant analysis (79%). Data visualisation and correlation analysis resulted in similar conclusions regarding the most important factors in heart disease. These data mining tools provide simple and effective methods of extracting knowledge from general medical information. The treatment of missing data is also discussed.

Computer Graphics↗
PubMed2005

OxfordGrid: a web interface for pairwise comparative map views.

SUMMARY: OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. AVAILABILITY: OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

Algorithms↗
PubMed2002

The Mouse Genome Database (MGD): the model organism database for the laboratory mouse.

The Mouse Genome Database (MGD) is the community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology and disease (http://www.informatics.jax.org). MGD strives to provide a highly curated, highly integrated information resource that not only includes the consensus view of current knowledge about the mouse, but also provides comparative genomic information particularly for human and rat genomes. MGD includes extensive information about mouse genes, supporting all gene attribute assertions with experimental data, statements of evidence and citation. Detailed information about alleles and mouse mutants includes genotype, molecular variant and phenotype descriptions. Extensive collaboration with other data providers such as NCBI, RIKEN and SWISS-PROT provides standardization of gene:sequence associations and robust interconnections between large information systems based on shared sequence curation. Recent integration of large datasets of mouse full-length cDNAs and radiation-hybrid mapped ESTs, the continued development and use of extensive structured vocabularies and the expansion of the representation of phenotypes highlight this year's developments.

Alleles↗
PubMed1997

Neuropsychology and advances in memory function.

Recent developments in the functional and neural bases of several aspects of memory are described including long term cortical memory storage, the transition from immediate to permanent memory mediated by medial temporal structures, working memory, memory retrieval, and implicit memory. These are linked to current data on the nature of anterograde and retrograde amnesia in the degenerative diseases, and also to issues in the clinical diagnosis of memory impairments. Understanding the bases of memory can inform the diagnosis of memory impairments in degenerative diseases, and the patterns of impairment seen in the degenerative diseases can help contribute to knowledge of the mechanisms of normal memory.

Humans↗