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Results for “knowledge graph”

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At least 73 records · Page 4Linked to original sources

PubMed2002

Not another questionnaire! Maximizing the response rate, predicting non-response and assessing non-response bias in postal questionnaire studies of GPs.

BACKGROUND: Non-response is an important potential source of bias in survey research. With evidence of falling response rates from GPs, it is of increasing importance when undertaking postal questionnaire surveys of GPs to seek to maximize response rates and evaluate the potential for non-response bias. OBJECTIVES: Our aim was to investigate the effectiveness of follow-up procedures when undertaking a postal questionnaire study of GPs, the use of publicly available data in assessing non-response bias and the development of regression models predicting responder behaviour. METHOD: A postal questionnaire study was carried out of a random sample of 600 GPs in Wales concerning their training and knowledge in palliative care. RESULTS: A cumulative response rate graph permitted optimal timing of follow-up mailings: a final response rate of 67.6% was achieved. Differences were found between responders and non-responders on several parameters and between sample and population on some parameters: some of these may bias the sample data. Logistic regression analysis indicated medical school of qualification and current membership of the Royal College of General Practitioners to be the only significant predictors of responders. Late responders were significantly more likely to have been qualified for longer. CONCLUSIONS: This study has several implications for future postal questionnaire studies of GPs. The optimal timing of reminders may be judged from plotting the cumulative response rate: it is worth sending at least three reminders. There are few parameters that significantly predict GPs who are unlikely to respond; more of these may be included in the sample, or they may be targeted for special attention. Publicly available data may be used readily in the analysis of non-response bias and generalizability.

Adult↗

PubMedDate not supplied

An introduction to the reading of electrocardiograms.

This article introduces the basic principles of reading electrocardiograms (ECGs) for nurses who are unfamiliar with reading them. For more experienced practitioners there are a number of useful articles and books (e.g. Hampton, 1992a, b) that will help further their knowledge. The ECG records cardiac electrical activity as a graph; interpretation is illustrated here by sinus rhythm. A single ECG lead (lead II) is used throughout this article. Atrial fibrillation is described to show a contrasting dysrhythmia. Specific nursing care is suggested for patients being monitored or having ECGs taken.

Atrial Fibrillation↗

PubMedDate not supplied

A learning tool in medical imaging: using procedure graphs in radiographic process simulation.

Teaching the procedural elements of imaging protocols and understanding the interrelationships and interdependencies of diagnostic X-ray system parameters and their effects on image quality, are among the main objectives of medical imaging training programs. A teaching tool is designed and implemented to support these goals. Tool design is influenced by hybrid learning system architectures and it is based on a graph approach, which is described. Implementation is carried out using a hypermedia development environment (Toolbook) coupled with a database (Paradox). The core of the system is an attributed priority graph, capable of supporting the organization of the domain knowledge, monitoring of user-machine interaction and managing the user-system dialogue. Use of this approach resulted in an interactive simulation tool, which provides computer aided learning support, to radiology related personnel, such as radiologists and radiographers. The potential value of the tool is not restricted only to didactic tasks, but may include trouble-shooting and documentation.

Computer Simulation↗

PubMedDate not supplied

UMLS-based conceptual queries to biomedical information databases: an overview of the project ARIANE. Unified Medical Language System.

OBJECTIVE: The aim of the project ARIANE is to model and implement seamless, natural, and easy-to-use interfaces with various kinds of heterogeneous biomedical information databases. DESIGN: A conceptual model of some of the Unified Medical Language System (UMLS) knowledge sources has been developed to help end users to query information databases. A query is represented by a conceptual graph that translates the deep structure of an end-user's interest in a topic. A computational model exploits this conceptual model to build a query interactively represented as query graph. A query graph is then matched to the data graph built with data issued from each record of a database by means of a pattern-matching (projection) rule that applies to conceptual graphs. RESULTS: Prototypes have been implemented to test the feasibility of the model with different kinds of information databases. Three cases are studied: 1) information in records is structured according to the UMLS knowledge sources; 2) information is able to be structured without error in the frame of the UMLS knowledge; 3) information cannot be structured. In each case the pattern-matching is processed by the projection rule according to the structure of information that has been implemented in the databases. CONCLUSION: The conceptual graphs theory provides with a homogeneous and powerful formalism able to represent both concepts, instances of concepts in medical contexts, and associations by means of relationships, and to represent data at different levels of details. The conceptual-graphs formalism allows powerful capabilities to operate a semantic integration of information databases using the UMLS knowledge sources.

Databases as Topic↗

PubMed1978

A fast evaluation of diffusion effects on bound enzyme activity.

As the kinetic behavior of bound enzymes is frequently affected by substrate diffusion between the bulk solution and the catalytic sites, a fast and simple method is proposed to detect and, subsequently, to remove diffusion effects on measured enzymic activities. The procedure makes use of the effectiveness factor concept and essentially involves the direct determination on two diagrams of the magnitude of both external and internal diffusion limitations. It requires a prior estimation of the volume and external surface area of the matrix, of the substrate external transport coefficient and internal diffusivity, and of the intrinsic Michaelis constant of the bound enzyme. However, it does not necessitate the knowledge of the quantity of bound enzyme. The two basic graphs have been calculated for Michaelis-Menten kinetics. They can also be used to evaluate diffusional effects on two-substrate reactions, as illustrated with previously published data.

Diffusion↗

PubMed2026

Knowledge-driven interpretable neural networks provide mechanistic insight.

Analyzing omics data in the context of pathway knowledge is critical for understanding the molecular mechanisms underlying pathological changes. However, current pathway analysis methods do not model the detailed mechanistic nature of biological interactions, limiting the understanding of pathway behavior to a relatively shallow level. To address this issue, we present a knowledge-driven machine learning framework that embeds features into pathway graphs and models reactions analytically, producing interpretable feature hierarchies and subnetworks in which functional associations are estimated to model biological interactions. The approach is agnostic to feature selection, enabling the use of full omics data sets without discarding weak signals. Applications to breast cancer microRNA-gene regulation data and COVID-19 metabolomic data highlight immune and metabolic pathways relevant to disease progression. This framework bridges predictive modeling with mechanistic interpretation and offers a foundation for integrative pathway analysis.

Humans↗

PubMed2004

A surgeon can operate or approach a complicated integral calculus instead of a renal one: implications for conceptual and lexical semantic disambiguation.

This paper approaches lexical semantic disambiguation and polysemy in the context of medical language understanding. These issues have been addressed as linguistic and cognitive requirements to build a knowledge extraction tool that turns natural language input into conceptual graphs. Previous results obtained with semantic analysis of medical terms in the domain of transplantation and organ failure prompt us to check the capabilities of our prototype to deal with ambiguities and polysemy. Starting from linguistic observation, we attempt to demonstrate how the respect of ambiguities when the co-text is not sufficient for disambiguation implies to introduce a void type in the concept type lattice. Then we show how the "creative use of words" (i.e. new senses in novel context) imposes to dynamically allocate type, categories and roles with the co-text.

Linguistics↗

PubMed2006

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.

BACKGROUND: The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both. RESULTS: To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at http://function.princeton.edu/GOLEM.

Computer Graphics↗

PubMed2005

High-resolution protein folding with a transferable potential.

A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximately 3 A without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that an accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential and hydrogen bonding are essential features for a realistic protein model.

Animals↗

PubMed2005

An intelligent tutoring system for visual classification problem solving.

OBJECTIVE: This manuscript describes the development of a general intelligent tutoring system for teaching visual classification problem solving. MATERIALS AND METHODS: The approach is informed by cognitive theory, previous empirical work on expertise in diagnostic problem-solving, and our own prior work describing the development of expertise in pathology. The architecture incorporates aspects of cognitive tutoring system and knowledge-based system design within the framework of the unified problem-solving method description language component model. Based on the domain ontology, domain task ontology and case data, the abstract problem-solving methods of the expert model create a dynamic solution graph. Student interaction with the solution graph is filtered through an instructional layer, which is created by a second set of abstract problem-solving methods and pedagogic ontologies, in response to the current state of the student model. RESULTS: In this paper, we outline the empirically derived requirements and design principles, describe the knowledge representation and dynamic solution graph, detail the functioning of the instructional layer, and demonstrate two implemented interfaces to the system. CONCLUSION: Using the general visual classification tutor, we have created SlideTutor, a tutoring system for microscopic diagnosis of inflammatory diseases of skin.

Artificial Intelligence↗

PubMed2000

Graphical tool for navigation within the semantic network of the UMLS metathesaurus on a locally installed database.

Knowledge in the environment of information technologies is bound to structured vocabularies. Medical data dictionaries are necessary for uniquely describing findings like diagnoses, procedures or functions. Therefore we decided to locally install a version of the Unified Medical Language System (UMLS) of the U.S. National Library of Medicine as a repository for defining entries of a medical multimedia database. Because of the requirement to extend the vocabulary in concepts and relations between existing concepts a graphical tool for appending new items to the database has been developed: Although the database is an instance of a semantic network the focus on single entries offers the opportunity of reducing the net to a tree within this detail. Based on the graph theorem, there are definitions of nodes of concepts and nodes of knowledge. The UMLS additionally offers the specification of sub-relations, which can be represented, too. Using this view it is possible to manage these 1:n-Relations in a simple tree view. On this background an explorer like graphical user interface has been realised to add new concepts and define new relationships between those and existing entries for adapting the UMLS for specific purposes such as describing medical multimedia objects.

Computer Graphics↗

PubMed2005

Sonographic assessment of the normal limits and percentile curves of liver, spleen, and kidney dimensions in healthy school-aged children.

OBJECTIVE: The purpose of this study was to determine the normal standards of liver, spleen, and kidney dimensions and the relationship of each with sex, age, body weight, height, body mass index, and body surface area in healthy school-aged children. METHODS: Seven hundred twelve healthy school-aged children (7-15 years) in 2 neighboring cities, including rural areas and city centers, were evaluated prospectively. Sex, age, weight, height, body mass index, and body surface area were determined for each case. Organ dimensions were measured 3 times, and the mean values were recorded. All measured organs had a normal position, shape, and echo texture. The children were separated into 5 groups according to body weight. RESULTS: There were no significant differences in organ dimensions with respect to sex (P > .05). The mean right kidney length was shorter than the left kidney length, and the difference was significant (P = .009). Body weight showed the best correlation with liver, spleen, and kidney dimensions. The results were also supported by the variance and covariance of the correlation coefficients. CONCLUSIONS: The normal limits of the liver, spleen, and kidneys are important parameters during a sonographic examination. This study revealed that organ dimensions showed the best correlation with body weight. To our knowledge, in clinical practice there are no pediatric organ dimension percentile graphs for interpretation of sonographic examinations. We hope this study contributes to daily practice in radiology clinics.

Adolescent↗

PubMed2001

Knowledge representation of signal transduction pathways.

MOTIVATIONS: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans. RESULTS: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.

Amino Acid Motifs↗

PubMed1997

Single bone straight line graphs for the lower extremity.

Valuable information about growth and growth prediction in the lower extremity has been provided in the past by Anderson and Green, Moseley, and Menelans. Greater patient expectations and advanced techniques for lower extremity lengthening require more precise information regarding the growth characteristics of each long bone. A simple method for predicting growth is presented for the femur and tibia. Straight line graphs similar to one described previously by Moseley for the entire lower extremity have been drawn separately for the femur and tibia. Information from a contemporary population and new knowledge about growth plate activity have been included to provide more accurate predictions. By superimposing identically scaled growth remaining graphs on these single bone straight line graphs, a simple and accurate estimate is obtained for the timing and effect of epiphysiodeses or lengthening procedures.

Adolescent↗

PubMed2005

Flexible information storage in MUDR(II) EHR.

An important research task of the EuroMISE Centre is the applied research in the field of electronic health record (EHR) design including electronic medical guidelines and intelligent systems for data mining and decision support. The research in this field was inspired by several European projects. We have proposed a mathematical meta-description of a flexible information storage model based on the experience gathered in cooperation in those projects. In this model, we use two basic structures called a knowledge base and data files. We describe those two structures using the graph theory concepts. Furthermore, we use logical formulas to express conditions that should be valid. Additionally, we present a description of a global system architecture of a 3-tier EHR application with interfaces based on the latest technologies; predominately on Web Services, SOAP, XML, HTTP, CORBA, etc. According to our experience and test results gained from the MUDR EHR usage, we describe an open universal solution, which can be applied as the EHR kernel of hospital information systems. To realize this approach in a daily practice for health professionals we have started a co-operative project with clinical information systems developers. Within that project we are developing a new system for continual shared health care.

Biomedical Research↗

PubMed2026

Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.

MOTIVATION: Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e. without basecalling). However, existing solutions cannot interpret raw signals directly if a reference genome is unknown due to a lack of accurate mechanisms to handle increased noise in pairwise raw signal comparison. Our goal is to enable the direct analysis of raw signals without a reference genome. To this end, we propose Rawsamble, the first mechanism that can identify regions of similarity between all raw signal pairs, known as all-vs-all overlapping, using a hash-based search mechanism. RESULTS: We use these overlaps to construct de novo assembly graphs with an existing assembler, miniasm, off-the-shelf. To our knowledge, these are the first de novo assemblies ever constructed directly from raw signals without basecalling. Our extensive evaluations across multiple genomes of varying sizes show that Rawsamble provides a significant speedup (on average by 5.01× and up to 23.10×) and reduces peak memory usage (on average by 5.74× and up to by 22.00×) compared to a conventional genome assembly pipeline using the state-of-the-art tools for basecalling (Dorado's fastest mode) and overlapping (minimap2) on a CPU. We find that around one-third of Rawsamble's overlapping pairs are also found by minimap2. We find that when we use overlapping reads from Rawsamble, we can construct unitigs that are (i) as accurate as those built from minimap2's overlaps and (ii) up to half a chromosome in length (e.g. 2.3 million bases for E. coli). AVAILABILITY AND IMPLEMENTATION: Rawsamble is available at https://github.com/CMU-SAFARI/RawHash. We also provide the scripts to fully reproduce our results on our GitHub page.

Nanopores↗

PubMed2001

Observation of single transits in supercooled monatomic liquids.

A transit is the motion of a system from one many-particle potential energy valley to another. We report the observation of transits in molecular dynamics calculations of supercooled liquid argon and sodium. Each transit is a correlated simultaneous shift in the equilibrium positions of a small local group of particles, as revealed in the fluctuating graphs of the particle coordinates versus time. To the best of our knowledge, this is the first reported direct observation of transit motion in a monatomic liquid in thermal equilibrium. We found transits involving 2-11 particles, having mean shift in equilibrium position on the order of 0.4R(1) in argon and 0.25R(1) in sodium, where R1 is the nearest neighbor distance. The time it takes for a transit to occur is approximately one mean vibrational period, confirming that transits are fast.

Journal Article↗

PubMed1992

A review of pressure reduction device studies.

When considering patient morbidity, mortality and costs, pressure sore formation is a major health care concern. An adjunct to the nursing care plan for prevention and treatment is the selection of a pressure reduction/relief device. This review of four pressure reduction device studies is intended to increase the vascular nurse's knowledge base concerning pressure reduction device efficacy. Each study is reviewed and graphed to identify like patterns within each study. Foam is judged to be least effective. Air cell and air mattress overlays are found to be intermediate devices and the low air loss beds appear to be the most effective. Few of the tested devices reduced pressure below 32mmHg at the heel site, leaving the heel at risk for breakdown.

Bedding and Linens↗