Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Textual analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources
PubMed2000

Qualitative analysis of the clinician interview-based impression of change (Plus): methodological issues and implications for clinical research.

The Clinician Interview-Based Impression of Change, plus carer interview (CIBIC-Plus), is widely used in antidementia drug trials. It comprises Likert scales for disease severity and changes, and written accounts summarizing semistructured interviews evaluating behavior, cognition, and function. Studies using the CIBIC-Plus have focused on the numeric scores to the exclusion of the textual data. Our study explored both sets of data to evaluate whether the CIBIC-Plus written data supported (a) the clinicians' global evaluation of patients' changes during treatment, and (b) the emergence of consistent treatment effects. The global (numeric) scales of change were inconsistently supported by the textual data provided in the CIBIC-Plus. No consistent treatment effects were noted. Methodological problems presently limit the retrospective use of the CIBIC-Plus textual data. Improved standardization of note-taking in the CIBIC-Plus textual data may allow for a better understanding of the typical profiles and clinical importance of changes seen in the course of dementia treatment.

Aged↗
PubMed2005

WinPop 2.5: software for representing population genetics phenomena.

The curriculum for genetics courses is shifting from a classical to a more molecular genetics focus, increasing the importance of subjects such as population genetics. Population genetics is a computational and statistical field that requires a good understanding of the nature of stochastic events. It is a difficult field for biology students with a limited mathematical background and there is a need for visualisation tools to facilitate understanding by the use of practical examples. WinPop provides students and researchers with a visual tool to allow the simulation and representation of population genetics phenomena. WinPop is a user-friendly software meant for use in population genetics courses and basic research. WinPop 2.5 contains six different modules that represent and simulate population genetics models. Genotype and allele frequencies are calculated under the different models: panmixia, genetic drift, assortative matings, selection, gene flow and mutation. The program's interface presents information in Cartesian graphics and isosceles triangular coordinate systems, allowing the user to save graphical and textual data output from the simulations. WinPop is developed in Visual Basic 6.0 and uses Windows 95 and higher. WinPop 2.5 can be downloaded from http://www.genedrift.org/winpop.php.

Algorithms↗
PubMed2004

Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations.

BACKGROUND: Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatially similar and to ultimately infer potential gene interactions. However, the rapid accumulation of gene expression pattern data over the last two decades, facilitated by high-throughput techniques, has produced a need for the development of efficient approaches for direct comparison of images, rather than their textual descriptions, to identify spatially similar expression patterns. RESULTS: The effectiveness of the Binary Feature Vector (BFV) and Invariant Moment Vector (IMV) based digital representations of the gene expression patterns in finding biologically meaningful patterns was compared for a small (226 images) and a large (1819 images) dataset. For each dataset, an ordered list of images, with respect to a query image, was generated to identify overlapping and similar gene expression patterns, in a manner comparable to what a developmental biologist might do. The results showed that the BFV representation consistently outperforms the IMV representation in finding biologically meaningful matches when spatial overlap of the gene expression pattern and the genes involved are considered. Furthermore, we explored the value of conducting image-content based searches in a dataset where individual expression components (or domains) of multi-domain expression patterns were also included separately. We found that this technique improves performance of both IMV and BFV based searches. CONCLUSIONS: We conclude that the BFV representation consistently produces a more extensive and better list of biologically useful patterns than the IMV representation. The high quality of results obtained scales well as the search database becomes larger, which encourages efforts to build automated image query and retrieval systems for spatial gene expression patterns.

Algorithms↗
PubMed2006

Methodological aspects of telephone scatologia: a case study.

The present paper focuses on the sexual paraphilia of telephone scatologia. Some psychological concepts of scatologia are reviewed; their methodological aspects are examined. It is argued that telephone scatologia is only one of the forms of audio scatologia (akophilia), which together with visual and textual scatologias present interactive but remote--intermediary--forms of sexual excitation, when the function of tactile contact is delegated to the sensory specific communication device, and where the perpetrator can be safe and sexually aggressive at the same time. The main objective of this paper is to present a case of prolific telephone scatologist, with the analysis of which the author was closely affiliated. The present paper does not pretend to cover all of the issues associated with etiology and psychogenesis of scatologia, but intends to offer rarely addressed material that could be useful in the fields of psychology, psychiatry, sexology, criminology and interpersonal violence.

Adult↗
PubMed2003

MolMovDB: analysis and visualization of conformational change and structural flexibility.

The Database of Macromolecular Movements (http://MolMovDB.org) is a collection of data and software pertaining to flexibility in protein and RNA structures. The database is organized into two parts. Firstly, a collection of 'morphs' of solved structures representing different states of a molecule provides quantitative data for flexibility and a number of graphical representations. Secondly, a classification of known motions according to type of conformational change (e.g. 'hinged domain' or 'allosteric') incorporates textual annotation and information from the literature relating to the motion, linking together many of the morphs. A variety of subsets of the morphs are being developed for use in statistical analyses. In particular, for each subset it is possible to derive distributions of various motional quantities (e.g. maximum rotation) that can be used to place a specific motion in context as being typical or atypical for a given population. Over the past year, the database has been greatly expanded and enhanced to incorporate new structures and to improve the quality of data. The 'morph server', which enables users of the database to add new morphs either from their own research or the PDB, has also been enhanced to handle nucleic acid structures and multi-chain complexes.

Computer Graphics↗
PubMed1998

Medieval descriptions and doctrines of stroke: preliminary analysis of select sources. Part III: multiplying speculation - the high and late Middle Ages (1000-1450).

By analyzing a body of texts compiled by various medical authors from the 11th to the 15th century, four basic developments can be noted: (1) From the beginning of the eleventh century the reception, translation and assimilation of Arabian and arabicized ancient texts became the ultimate goal of Western medicine (Constantine the African, Arnad of Villanova, et al.). Concepts of stroke were consequently guided by textual tradition, not by observation. (2) Scholastic speculations about different aspects of apoplexy, especially those concerning its origins, were numerous (Johannes Platearius, Batholomaeus Salernitanus, Pietro d'Abano, Giacomo da Forli). Although most medieval physicians used the ancient doctrine of the four humors as model and explanation, opinions differed in many ways. (3) Attempts developed to present a simple outline of the etiology, the prognosis, and the treatment of the disease (Gilbertus Anglicus, Bernard of Gordon, John of Gaddesden). (4) Although lacking in originality, many of these writers nevertheless achieved a certain uniformity in presenting main topics, thus setting the standard for later practitioners.

Arab World↗
PubMedDate not supplied

Rating of textual associations in organized and nonorganized sentences for the assessment of semantic networks in schizophrenia.

BACKGROUND: Collins and Quillian ( Acta Psychol 1970;33:304-314) proposed that semantic representations in the human brain could have a "networklike" theoretical construct. Thought disorders in schizophrenia have been described as disturbances in the spread of activation within semantic networks. Semantic networks are typically evaluated indirectly via reaction times of priming tasks. Medications may interfere with the reaction time of patients, thus, we sought to investigate semantic networks, independent of time, by having patients and controls rate textual associations in sentences organized to various degrees. METHODS: Twenty-eight schizophrenic patients (17 non-thought-disordered and 11 thought-disordered) and 27 healthy controls performed a rating of textual associations task in which they were asked to rate the associative relationship between concepts in sentences on a scale from 1 (totally dissociated) to 10 (completely associated). The task contained 3 sets of sentences; organized meaningful sentences, vague sentences (intermediately disorganized), and completely disorganized sentences. To avoid order effects, sentences were randomly mixed at presentation. RESULTS: Analysis of variance calculations indicated significant differences among the 3 groups (controls, thought-disordered, and non-thought-disordered). The differences were greater for the vague sentences. Compared with controls, schizophrenic patients demonstrated increased SDs in rating associative values between concepts in the sentences, which is higher in disorganized sentences. Inadequate ability to identify and rate associations in disorganized sentences is discussed in the context of disordered semantic networks of schizophrenic patients.

Adult↗
PubMed1998

Why discourse structures in medical reports matter for the validity of automatically generated text knowledge bases.

The automatic analysis of medical full-texts currently suffers from neglecting text coherence phenomena such as reference relations between discourse units. This has unwarranted effects on the description adequacy of medical knowledge bases automatically generated from texts. The resulting representation bias can be characterized in terms of artificially fragmented, incomplete and invalid knowledge structures. We discuss three types of textual phenomena (pronominal and nominal anaphora, as well as textual ellipsis) and outline basic methodologies how to deal with them.

Artificial Intelligence↗
PubMed1989

[The use of personal computers in the angiocardiometric evaluation of the pulmonary artery in complex congenital heart defects].

Application of personal computers in angiocardiometric assessment of the pulmonary artery in such congenital heart diseases as Fallot's tetralogy and total transposition of great vessels made it possible to set up a convenient data bank allowing one to store numerical and textual information, conventionalized drawings of pulmonary arteries showing the degree and location of stenosing lesions and color-marked data on surgically significant constrictions. The system has a rich visual presentation of data and allows for convenient and quick search and processing of information (including the use of standard statistic, graphic, and other present-day packages of analysis and presentation of medical information).

Adolescent↗
PubMed2003

Context-based ontology building support in clinical domains using formal concept analysis.

OBJECTIVE: Ontology in clinical domains is becoming a core research field in the realm of medical informatics. The objective of this study is to explore the potential role of formal concept analysis (FCA) in a context-based ontology building support in a clinical domain (e.g. cardiovascular medicine here). METHODOLOGY: We developed an ontology building support system that integrated an FCA module with a natural language processing (NLP) module. The user interface of the system was developed as a Protégé-2000 JAVA tab plug-in. A collection of 368 textual discharge summaries and a standard dictionary of Japanese diagnostic terms (MEDIS ver2.0) were used as the main knowledge sources. A preliminary evaluation was taken to show the usefulness of the system. RESULTS: Stability was shown on the MEDIS-based medical concept extraction with high precision. 73+/-14% (mean+/-S.D.) of the compound medical phrases extracted were sufficiently meaningful to form a medical concept from a clinical perspective. Also, 57.7% of attribute implication pairs (i.e. medical concept pairs) extracted were identified as positive from a clinical perspective. CONCLUSION: Under the framework of our ontology building support system using FCA, the clinical experts could reach a mass of both linguistic information and context-based knowledge that was demonstrated as useful to support their ontology building tasks.

Decision Support Systems, Clinical↗
PubMed2001

The potential use of SUISEKI as a protein interaction discovery tool.

Relevant information about protein interactions is stored in textual sources. This sources are commonly used not only as archives of what is already known but also as information for generating new knowledge, particularly to pose hypothesis about new possible interactions that can be inferred from the existing ones. This task is the more creative part of scientific work in experimental systems. We present a large-scale analysis for the prediction of new interactions based on the interaction network for the ones already known and detected automatically in the literature. During the last few years it has became clear that part of the information about protein interactions could be extracted with automatic tools, even if these tools are still far from perfect and key problems such as detection of protein names are not completely solved. We have developed a integrated automatic approach, called SUISEKI (System for Information Extraction on Interactions), able to extract protein interactions from collections of Medline abstracts. Previous experiments with the system have shown that it is able to extract almost 70% of the interactions present in relatively large text corpus, with an accuracy of approximately 80% (for the best defined interactions) that makes the system usable in real scenarios, both at the level of extraction of protein names and at the level of extracting interaction between them. With the analysis of the interaction map of Saccharomyces cerevisiae we show that interactions published in the years 2000/2001 frequently correspond to proteins or genes that were already very close in the interaction network deduced from the literature published before these years and that they are often connected to the same proteins. That is, discoveries are commonly done among highly connected entities. Some biologically relevant examples illustrate how interactions described in the year 2000 could have been proposed as reasonable working hypothesis with the information previously available in the automatically extracted network of interactions.

Cell Cycle↗
PubMed1996

Experiences with a distributed virtual patient record system.

TeleMed is a distributed diagnosis and analysis system, which permits physicians who are not collocated to consult on the status of a patient. The patient's record is dynamically constructed from data that may reside at several sites but which can be quickly assembled for viewing by pointing to the patient's name. Then, a graphical patient record appears, through which consulting physicians can retrieve textual and radiographic data with a single mouse click. TeleMed uses modern distributed object technology and emerging telecollaboration tools.

Computer Communication Networks↗
PubMed1986

[Some linguistic aspects of thought disorder in non-acute schizophrenia].

Seventy texts, which had been produced spontaneously but in standardized contexts by (non-acute) schizophrenic patients and by non-schizophrenic subjects, were analysed linguistically in order to investigate the various strategies that speakers may use to join different sentences together to form a unified structure by semantic and lexicogrammatical ties. For this purpose we used Halliday's and Hasan's classification of so-called "cohesive ties". This theoretical framework makes it possible to describe the inner coherence of linguistic texts in a quantitative way. In the "schizophrenic texts" the sentences contained significantly fewer such cohesive ties than in those texts produced by normal speakers. An additional longitudinal analysis revealed an increase in the number of cohesive ties per sentence, when the same schizophrenic speakers were asked to produce a second text (in a similar context) after participating in a 3-month psychotherapy programme. The central goal of psychotherapy was to improve the patients' cognitive ability to face and cope with social stress situations. The results of several textual and statistical procedures are discussed, mainly under the aspect of cognitive dysfunctions during periods of non-acute schizophrenia.

Adult↗
PubMed1999

Discourse structures in medical reports--watch out! The generation of referentially coherent and valid text knowledge bases in the MEDSYNDIKATE system.

The automatic analysis of medical narratives currently suffers from neglecting text structure phenomena such as referential relations between discourse units. This has unwarranted effects on the descriptional adequacy of medical knowledge bases automatically generated from texts. The resulting representation bias can be characterized in terms of incomplete, artificially fragmented and referentially invalid knowledge structures. We focus here on four basic types of textual reference relations, viz. pronominal and nominal anaphora, textual ellipsis and metonymy and show how to deal with them in an adequate text parsing device. Since the types of reference relations we discuss show an increasing dependence on conceptual background knowledge, we stress the need for formally grounded, expressive conceptual representation systems for medical knowledge. Our suggestions are based on experience with MEDSYNDIKATE, a medical text knowledge acquisition system designed to properly deal with various sorts of discourse structure phenomena.

Artificial Intelligence↗
PubMed1993

Use of analogy in learning scientific concepts.

Four experiments compared learning of scientific concepts as expressed in either traditional literal form or through an analogy. Comprehension of basic-level details and inferential implications was measured through multiple-choice testing. In Experiment 1, literal or analogical renditions were presented in textual form only. In Experiment 2, text was accompanied by a dynamic video. In Experiment 3, the video and text literal rendition was compared with a text-only analogical rendition. In Experiment 4, subjects read only about a familiar domain. Subjects consistently answered basic-level questions most accurately when concepts were expressed literally, but answered inferential questions most accurately when concepts were expressed analogically. Analysis of individual differences (Experiment 2) indicated that this interaction strongly characterized the conceptual learning of science novices. The results are discussed within the framework of schema induction.

Adult↗
PubMed2005

An extensible automated protein annotation tool: standardizing input and output using validated XML.

MOTIVATION: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. RESULTS: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Amino Acid Sequence↗
PubMedDate not supplied

A method of evaluating VDT screen layout by eye movement analysis.

The method for evaluating VDT screen layout by eye movements is studied. When the subjects read from the VDT screen, the change in their line of sight was measured by their eye movements. The measured eye movement patterns were divided into the sequential and rereading processes. When related to these characteristics, the performance of subjects was found to be good when the sequential process predominated over the rereading process. The eye movement pattern was shown to change with screen layout. The eye movement pattern proved effective in determining that tabular format is more legible than textual format. This confirmed the usefulness of the method of evaluating VDT screen layout by the eye movement pattern.

Attention↗
PubMed2006

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap, to store the known miRNA genes, the putative miRNA genes, the known miRNA targets and the putative miRNA targets. The known miRNA genes in four mammalian genomes such as human, mouse, rat and dog are obtained from miRBase, and experimentally validated miRNA targets are identified in a survey of the literature. Putative miRNA precursors were identified by RNAz, which is a non-coding RNA prediction tool based on comparative sequence analysis. The mature miRNA of the putative miRNA genes is accurately determined using a machine learning approach, mmiRNA. Then, miRanda was applied to predict the miRNA targets within the conserved regions in 3'-UTR of the genes in the four mammalian genomes. The miRNAMap also provides the expression profiles of the known miRNAs, cross-species comparisons, gene annotations and cross-links to other biological databases. Both textual and graphical web interface are provided to facilitate the retrieval of data from the miRNAMap. The database is freely available at http://mirnamap.mbc.nctu.edu.tw/.

Animals↗