Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “knowledge graphs”

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 235 records · Page 13Linked to original sources
PubMed1976

Lateralization in stroke syndromes as a factor in ambulation.

Lateralization should not be ignored in any rehabilitation program for patients with stroke syndromes. Despite the known differences resulting from the localization in the dominant versus the nondominant hemisphere (spatial perception, speech, etc.), practical application of this knowledge in gait training is sparse. The authors looked into different stages of ambulation and the time sequence between these stages and the onset of disease. Standing and walking in parallel bars and outside, as well as elevation activities were given numerical values in an effort to assess abilities quantitatively. The assessment of each patient was recorded graphically (stage of gait against time) and then the different graphs were summated in order to form a common right hemiparetic versus left hemiparetic curve. This study of 236 out of 298 patients (129 left hemiparetics and 107 right ones) showed the following: (1) The right hemiparetics progressed more rapidly in all stages of ambulation, statistically significant figures being obtained for the first two stages; (2) a greater percentage of right versus left hemiparetics reached the assigned levels of ambulation: and (3) 89% out of the 236 patients included in our study were able to ambulate in parallel bars, 81% outside the bars and 38.5% were proficient in stair climbing. Out of the original total number of patients (298), 64% were able able to ambulate outside the bars.

Adolescent↗
PubMed2005

Correlation between 2 interstitial cystitis symptom instruments.

PURPOSE: Two statistically validated interstitial cystitis (IC) symptom instruments have been used in clinical research. In this study we report what is to our knowledge the first direct comparison of the University of Wisconsin Symptom Instrument (UWI) with the O'Leary-Sant instruments, that is the IC Symptom Index (ICSI) and IC Problem Index (ICPI). MATERIALS AND METHODS: A convenience sampling of 107 patients with IC evaluated at the urology clinic at our institution from March through August 2000 were asked to complete ICSI, ICPI and UWI. The scores were analyzed and graphed. RESULTS: Mean ICSI, ICPI and UWI scores +/- SD were 12.6 +/- 4.3, 10.5 +/- 3.8 and 25.5 +/- 10.8, respectively. UWI and ICSI scores correlated at r = 0.80 (p <0.01) and ICSI/ICPI scores correlated at r = 0.83 (p <0.01). ICSI and ICPI contain 4 symptom-problem pairs. There are relevant differences in the correlation of symptom severity (ICSI question) and its associated problem (ICPI question). The symptom of urgency correlated best with the associated problem (r = 0.84), followed by nocturia (r = 0.82), pain (r = 0.70) and frequency (r = 0.68). CONCLUSIONS: The ICSI and UWI symptom instruments correlate strongly in a large population of patients with IC. The data presented will aid in interpreting the literature. A relatively poor correlation between pain symptom-problem pairs in the O'Leary-Sant instruments is probably an artifact of wording. The word pressure appears in ICPI but not in ICSI. We suggest using parallel wording of the pain symptom-problem pair containing the identical phrase, burning, pain, discomfort or pressure, to improve the ICSI/ICPI correlation and more accurately reflect the clinical condition.

Adult↗
PubMed2001

Evaluation of dental radiographic identification: an experimental study.

The object of this study was to assess the value of dental radiographs for the purposes of personal identification in the absence of tooth restorations. 198 periapical and bitewing radio graphs were taken of teeth contained in 22 dry skulls obtained from the skull collection of the Royal College of Surgeons of Edinburgh. Each selected view was taken three times: by a scientist, a dentist and a dental radiographer. Each operator independently positioned the films, selected the exposure times and positioned the cone of the X-ray machine. Three groups comprising forensic odontologists, dental vocational trainees and dental trainee hygienists attempted to match the randomly mixed radiographs into sets of three. Success rates for matching radio graphs ranged from 63.6 to 100%. The average for forensic odontologists was 93.3%, vocational trainees 85.2% and hygienists 89.7%. Where forensic odontologists had both formal training and experience, or extensive experience without formal training, the success rate was 100%. Where there was formal training but little experience the success rate was lower. Participants believed that root morphology and alignment had been the greatest aid to matching and not crown morphology. The depth of knowledge of the viewer correlated poorly with the number of correct results, although the forensic odontologists achieved the highest success rate. Formal training, although highly desirable, is no substitute for practical experience. Root morphology and alignment were cited most frequently as facilitating matching.

Clinical Competence↗
PubMedDate not supplied

Web portal to an image database for high-resolution three-dimensional reconstruction.

The exponential increase of image data in high-resolution reconstructions by electron cryomicroscopy (cryoEM) has posed a need for efficient data management solutions in addition to powerful data processing procedures. Although relational databases and web portals are commonly used to manage sequences and structures in biological research, their application in cryoEM has been limited due to the complexity in accomplishing the dual tasks of interacting with proprietary software and simultaneously providing data access to users without database knowledge. Here, we report our results in developing web portal to SQL image databases used by the Image Management and Icosahedral Reconstruction System (IMIRS) to manage cryoEM images for subnanometer-resolution reconstructions. Fundamental issues related to the design and deployment of web portals to image databases are described. A web browser-based user interface was designed to accomplish data reporting and other database-related services, including user authentication, data entry, graph-based data mining, and various query and reporting tasks with interactive image manipulation capabilities. With an integrated web portal, IMIRS represents the first cryoEM application that incorporates both web-based data reporting tools and a complete set of data processing modules. Our examples should thus provide general guidelines applicable to other cryoEM technology development efforts.

Cryoelectron Microscopy↗
PubMed1999

Quality through metrics.

The Quality Assurance Unit analyzed 18 months of departmental data regarding the report-audit cycle. Process mapping was utilized to identify milestones in the cycle for measurement. Five milestones were identified in the audit cycle, as follows: (1) time from report receipt in quality assurance to start of audit, (2) total calendar days to audit a report, (3) actual person-hours to perform a report audit, (4) time from completion of audit to issuance of report, and (5) total time a report is in quality assurance. An interrelationship diagraph is a quality tool that is used to identify what activities impact the overall report-auditing process. Once the data collection procedure is defined, a spreadsheet is constructed that captures the data. The resulting information is presented in time charts and bar graphs to visually aid in interpretation and analysis. Using these quality tools and statistical analyses, the Quality Assurance Unit identified areas needing improvement and confirmed or dispelled previous assumptions regarding the report-auditing process. By mapping, measuring, analyzing, and displaying the data, the overall process was examined critically. This resulted in the identification of areas needing improvement and a greater understanding of the report-audit cycle. A further benefit from our increased knowledge was the ability to explain our findings objectively to our client groups. This sharing of information gave impetus to our clients to examine their report-generation process and to make improvements.

Data Collection↗
PubMed2003

Simultaneous determination of hydroxycinnamates and catechins in human urine samples by column switching liquid chromatography coupled to atmospheric pressure chemical ionization mass spectrometry.

A quantitative liquid chromatography mass spectrometry (LC-MS) methodology with online sample clean up by column switching is described for the simultaneous determination of the hydroxycinnamates, caffeic acid and chlorogenic acid, and of the catechins, epicatechin and catechin in human urine samples. Enzymatically treated urine samples were directly injected onto the LC-MS system, where sample clean up was performed by a reversed-phase Zorbax 300SB C(3) column and selective elution of the target compounds onto a Zorbax SB C(18) column resulted in final separation prior to detection by atmospheric pressure chemical ionization (APCI) MS using single ion monitoring (SIM) in negative mode. Linear calibration graphs were achieved in the dynamic range of 10-1000 ng/ml urine. The inter- and intraassay coefficients of variation (C.V.%) for the analysis of the four compounds in quality control urine samples were between 7.8 and 10.9, n=17 (reproducibility), and the repeatability of the assay was between 2.5 and 5.0% (n=12). Analyses of urine samples from a human dietary intervention study with intake of 600 g of fruits and vegetables were demonstrated. To our knowledge, this is the first method described that allows simultaneous determination of both hydroxycinnamates and catechins in biological samples.

Atmospheric Pressure↗
PubMed2006

Extraction and analysis of traffic and topologies of transportation networks.

The knowledge of real-life traffic patterns is crucial for a good understanding and analysis of transportation systems. These data are quite rare. In this paper we propose an algorithm for extracting both the real physical topology and the network of traffic flows from timetables of public mass transportation systems. We apply this algorithm to timetables of three large transportation networks. This enables us to make a systematic comparison between three different approaches to construct a graph representation of a transportation network; the resulting graphs are fundamentally different. We also find that the real-life traffic pattern is very heterogenous, in both space and traffic flow intensities, which makes it very difficult to approximate the node load with a number of topological estimators.

Journal Article↗
PubMed1996

Should Common Optimal Movement Patterns Be Identified as the Criterion to Be Achieved?

Recently, a new paradigm has been proposed for the study of knowledge of performance (Schmidt & Young, 1991). In this paradigm, the experimenters identified an optimal kinematic movement pattern, based on the performance of a best subject, which was imposed on all subjects as the criterion to achieve. This approach, which assumes that this pattern is the best way for all subjects to do the task, was tested in the present experiment. In Experiment 1, a common optimal movement pattern could not be identified by an analysis of scatterplot graphs of the scores plotted as a function of various kinematic vanables or by correlating (within and across subjects [N = 14]) each kinematic variable with the score. In Experiment 2, subjects (N = 12) were retrained in 2 separate sessions, during which they tried to reproduce either a personal best or the best subject's template. Results indicated that scores were similar regardless of the template pattern being used. During training, however, subjects who used their personal template had a lower incidence of zero scores and were more consistent than those who used the template of the best subject. This provided a second line of evidence against the assumption that a common optimal movement pattern exists for this type of task.

Journal Article↗
PubMed1991

A laser densitometer for selective spot analysis on dot blots and two-dimensional gel autoradiograms.

We describe an inexpensive densitometer, employing a small HeNe laser and an IBM-compatible personal computer that performs accurate measurements of selected spots on two-dimensional gel autoradiograms or chromatograms with an accuracy and a sensitivity equal or superior to those of many commercial instruments. Our open-table design allows the operator to visually monitor the scanning process in room lighting, and provides great flexibility in both the size and the nature of items to be scanned. The instrument has two moving parts (a prism and a small motor). A commercially available software package (ASYST) acquires digital data, graphs the data on the TV monitor, converts the data to optical density or to radioactive incorporation (cpm), subtracts background, integrates peak areas, and stores data on disk. The total time for these operations is 20-30 s per spot. The instrument has a dynamic range of 0.25 to 3.0 OD units and can measure a 10,000-fold range of 14C or 35S isotope concentrations on autoradiograms. The complete device can be assembled with a hobbyist's knowledge of electronics, moderate programming abilities (no machine language required), and a cost of less than $3000, not including the IBM PC.

Costs and Cost Analysis↗
PubMed2005

Assessment of the repeatability of a milk Ostertagia ostertagi ELISA and effects of sample preparation.

An indirect Ostertagia ostertagi ELISA on milk is a promising diagnostic tool in bovine parasitology. Interpretation of the test results requires a good knowledge of the test characteristics. In this study, border effects, the repeatability of the ELISA and the effect of different factors such as storage, skimming and freeze-thaw cycles of the milk samples were investigated. The border effects trial showed that significant border effects can occur. The repeatability trial was conducted over 3 days. An alternative graphical technique to assess the repeatability over a large number of ELISA plates measured over different days was developed. From these graphs, it was obvious that the ODR values obtained on the third day were deviating from the values on the first and second day. On the third day, also abnormal control values were observed. When the control values were normal, 94% of the variability was explained by the milk sample and 6% by assay variability. The expected 95% range of the difference of 2 ODR readings of the same sample on the same plate and the same sample on different plates was -0.14 to 0.14 and -0.16 to 0.16. No extra variability was observed when samples were tested on a different day, however these results are based on the measurement of 2 days. Storage for 2-4 days at 4 degrees C, using whole milk instead of skimmed milk and up to 2 extra freeze-thaw cycles of the milk samples did not significantly affect the test results.

Animals↗
PubMed2005

Providing visualisation support for the analysis of anatomy ontology data.

BACKGROUND: Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that promote data exchange and re-use, improving analysis. The Edinburgh Mouse Atlas Project stores the developmental stages of the mouse embryo in anatomy ontologies. This project is looking at the use of visual data overviews for intuitive analysis of the ontology data. RESULTS: A prototype has been developed that visualises the ontologies using directed acyclic graphs in two dimensions, with the ability to study detail in regions of interest in isolation or within the context of the overview. This is followed by the development of a technique that layers individual anatomy ontologies in three-dimensional space, so that relationships across multiple data sets may be mapped using physical links drawn along the third axis. CONCLUSION: Usability evaluations of the applications confirmed advantages in visual analysis of complex data. This project will look next at data input from multiple sources, and continue to develop the techniques presented to provide intuitive identification of relationships that span multiple ontologies.

Anatomy↗
PubMed2003

A general architecture for intelligent tutoring of diagnostic classification problem solving.

We report on a general architecture for creating knowledge-based medical training systems to teach diagnostic classification problem solving. The approach is informed by our previous work describing the development of expertise in classification problem solving in Pathology. The architecture envelops the traditional Intelligent Tutoring System design within the Unified Problem-solving Method description Language (UPML) architecture, supporting component modularity and reuse. 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. We outline the advantages and limitations of this general approach, and describe it's implementation in SlideTutor - a developing Intelligent Tutoring System in Dermatopathology.

Artificial Intelligence↗
PubMed1995

Mathematical model of oxygen transport: a teaching aid for normal physiology adaptable to extracorporeal oxygenation circuits.

The ultimate aim of most intensive care therapies is to improve tissue oxygen delivery; consequently, a detailed knowledge of this area of physiology is important to a wide range of Critical Care Staff. We describe a simple mathematical model of oxygen transport that was initially written as a training aid for extracorporeal oxygenation training. The model has subsequently proved useful for explaining the determinants of oxygen transport to a broader audience. It is based on simple linear equations and is easily displayed with a standard computer spreadsheet. Apart from its teaching value, the model can also generate a graph of oxygen saturation vs. inspired oxygen fraction for different degrees of pulmonary shunt. This provides a noninvasive method for determining the magnitude of pulmonary venous admixture and may also prove to have some clinical value.

Biological Transport, Active↗
PubMedDate not supplied

A formal model of family medicine.

BACKGROUND: The American Board of Family Practice is developing a computer-based recertification process. An optimal implementation requires a formal model of family medicine, which will become the basis for a knowledge base. DESIGN: The proposed model of family medicine contains six entities: Population, Record, Agents of Change, Health States, Findings, and Courses of Action. The model illustrates 15 important relations between entities. For instance: Health States Lead to Health States, and Findings Associate with Health States. These two relations describe natural history, manifestations of disease, and the effects of medical interventions and risk factors. Because time is such an important aspect of primary care, nearly all numeric data are represented as graphs of possible values over time, called Patterns, which include details about periodicity. Patterns and other aspects of the model provide a means of describing covariance between observations, such as the influence of height on weight. RESULTS: The model reflects many family practice activities and suggests some formal descriptions of family practice. For instance, diagnostic activities focus largely on classifying early or short segments of Patterns in Findings. Most medical interventions attempt to alter either the probability distributions in a Lead-to relation or the impact of a Finding. CONCLUSION: The proposed model of family medicine could find uses in many applications, including computer-based tests, medical records, reference systems, and decision support tools.

Family Practice↗
PubMed2003

Statistical shape analysis of neuroanatomical structures based on medial models.

Knowledge about the biological variability of anatomical objects is essential for statistical shape analysis and discrimination between healthy and pathological structures. This paper describes a novel approach that incorporates the variability of an object population into the generation of a characteristic 3D shape model. The proposed shape representation is a coarse-scale sampled medial description derived from a fine-scale spherical harmonics (SPHARM) boundary description. This medial description is composed of a net of medial samples (m-rep) with fixed graph properties. The medial model is computed automatically from a predefined shape space using pruned 3D Voronoi skeletons. A new method determines the stable medial branching topology from the shape space. An intrinsic coordinate system and an implicit correspondence between shapes is defined on the medial manifold. Several studies of biological structures clearly demonstrate that the novel representation has the promise to describe shape changes in a natural and intuitive way. A new medial shape similarity study of group differences between monozygotic and dizygotic twins in lateral ventricle shape demonstrates the meaningful and powerful representation of local and global form.

Algorithms↗
PubMed2006

A model diagram layout extension for SBML.

MOTIVATION: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model. RESULTS: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation. AVAILABILITY: The complete specification can be found on (http://projects.villa-bosch.de/bcb/sbml/ (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, http://www.sbml.org/software/libsbml/).

Cell Physiological Phenomena↗
PubMed1992

Mathematical assessment of the spatial distribution of Langerhans cells in guinea pig epidermis.

Two mathematical indexes, Hopkins-Skellam index (HSI) and Morisita index (MI), were applied to assess the distribution of ATPase-stained epidermal Langerhans cells (ELC) in the guinea pig skin. To our knowledge, this is the first report in which the degree of regularity has been expressed numerically by computation based on theoretical equations. The regularity of ELC in the normal skin was confirmed by the value of HSI (P < 0.0001). In the topical steroid applied skin, the number of ELC decreased significantly but the value of HSI was similar to that of the normal skin; while in the ultraviolet B (UVB) exposed skin, both number of ELC and regularity of ELC distribution decreased significantly. The graph of MI for the UVB exposed skin clearly showed that the distribution of ELC had local clumps. The two indexes, HSI and MI have been quite useful for determining the regularity of ELC. These indexes may have a wide application to other cells.

Animals↗
PubMed1988

Biological applications of the SAS system: an overview.

The SAS system provides biologists with a flexible, easy to use software package for data analysis. Through a combination of data management tools, a wide variety of pre-programmed procedures for sorting, graphing, and statistical analysis and a sophisticated programming language, SAS software can perform all analytical needs for most problems. The recent availability of SAS software on mainframes other than IBM, and more recently on the microcomputer, means that most scientists can have access to the software. In this review we discuss the structure of the SAS language and demonstrate its power in the analysis of biological problems. Although to a lesser extent now than originally, the SAS system is statistically oriented and a working knowledge of statistics is recommended before using its statistical capabilities. However, all biologists will find its data management and summarization capabilities very useful.

Biology↗