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At least 199 records · Page 11Linked to original sources
PubMed2000

A pattern catalogue of surgical interventions for computer-supported operation planning.

In this paper we present a new operation planning system which was evaluated in the clinic for Cranio-Maxillo-Facial-Surgery at the University of Heidelberg. In opposite to commercial systems our goal was, that the system considers the complete surgical intervention and not only a single procedure of it. A second goal was, that the system enables managing of complex operations, independent of which way the intervention will be intraoperatively performed (without technical support, with passive navigation support or active support by robots). Our system supports the surgeon during the preoperative planning as well as during the intraoperative execution phase. Therefore we developed a course model by which the managing of surgical interventions is possible. The focus of this paper is on this course model. At first we introduce instruction graphs and describe the structure of each activity observing its attributes and their context. Additionally, various surgical scopes will be presented which enable the surgeon to select one view among different ones of the individual operation procedures in accordance to medical and technical knowledge as well as in accordance to different degrees of abstraction. At last we demonstrate operation patterns, used as expert knowledge.

Computer Simulation↗
PubMed2002

Computational approaches to the prediction of the blood-brain distribution.

This review attempts to summarise present knowledge related to the theoretical modelling of drug transport across the blood-brain barrier. Several computational protocols are described ranging from quantum mechanics-based approaches through molecular mechanics-related techniques to simple and fast procedures based on only the 2-D graph of the investigated structures. Amazingly, few descriptors have been shown to influence the derived relationships in a significant manner and a cornerstone in most of the described models are terms describing hydrogen bonding. A very quick quantitative assessment of the brain partitioning of a compound has also been devised using the following two rules: If N+O (the number of nitrogen and oxygen atoms) in a molecule is less than or equal to five, it has a high chance of entering the brain. The second rule predicts that if log P-(N+O) is positive then log BB is positive.

Algorithms↗
PubMed2004

Disulfide connectivity prediction using recursive neural networks and evolutionary information.

MOTIVATION: We focus on the prediction of disulfide bridges in proteins starting from their amino acid sequence and from the knowledge of the disulfide bonding state of each cysteine. The location of disulfide bridges is a structural feature that conveys important information about the protein main chain conformation and can therefore help towards the solution of the folding problem. Existing approaches based on weighted graph matching algorithms do not take advantage of evolutionary information. Recursive neural networks (RNN), on the other hand, can handle in a natural way complex data structures such as graphs whose vertices are labeled by real vectors, allowing us to incorporate multiple alignment profiles in the graphical representation of disulfide connectivity patterns. RESULTS: The core of the method is the use of machine learning tools to rank alternative disulfide connectivity patterns. We develop an ad-hoc RNN architecture for scoring labeled undirected graphs that represent connectivity patterns. In order to compare our algorithm with previous methods, we report experimental results on the SWISS-PROT 39 dataset. We find that using multiple alignment profiles allows us to obtain significant prediction accuracy improvements, clearly demonstrating the important role played by evolutionary information. AVAILABILITY: The Web interface of the predictor is available at http://neural.dsi.unifi.it/cysteines

Algorithms↗
PubMed2006

[Contribution of medical technologists in team medical care of diabetics].

For the effective treatment of diabetic mellitus (DM), patients are encouraged to self-manage their disease according to the doctor's instructions and advice from certified diabetes educators (CDE) and other comedical staff. Therefore, the cooperation of medical staff consisting of a doctor, CDE, nurse, pharmacist, dietitian, and medical technologist is important for DM education. Medical technologists licensed for CDE (MT-CDE) have been participating in the DM education team in Kobe University Hospital since 2000. MT-CDE are in charge of classes for medical tests, guidance for self-monitoring of blood glucose and teaching how to read the fluctuation graph of the blood glucose level in the education program for hospitalized DM patients. MT-CDEs teach at the bedside how to read the results of medical tests during the first few days of hospitalization using pamphlets for medical tests. The pamphlets are made comprehensible for patients by using graphics and photographs as much as possible. It is important to create a friendly atmosphere and answer frank questions from patients, since they often feel stress when having medical tests at the early stage of hospitalization. This process of questions and answers promotes their understanding of medical tests, and seems to reduce their anxiety about having tests. We repeatedly evaluate their level of understanding during hospitalization. By showing them the fluctuation graph of the glucose level, patients can easily understand the status of their DM. When prescriptions are written on the graph, their therapeutic effects are more comprehensible for the patients. The items written on the graph are chosen to meet the level of understanding of each patient to promote their motivation. In summary, the introduction of MT-CDE has been successful in the education program for DM patients in our hospital. We plan to utilize the skills and knowledge of MT-CDE more in our program so that our DM education program will help patients cope with life with DM.

Blood Glucose Self-Monitoring↗
PubMed2002

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations.

In the framework of genome annotation, scientific literature is obviously the major source of biological knowledge. The aim of the work described in this paper is to exploit this source of data for the model plant Arabidopsis thaliana. The first step has consisted in constituting a relevant bibliographic references dataset for plant genomic research. Genes co-citations have then been systematically annotated in this reference dataset, starting from the simple idea that if genes are cited in the same publication, they must probably share some related functional properties. In order to deal with the synonymous gene name problem, a gene name reference list has been constituted starting from A. thaliana SwissProt entries. This list was used to build clusters of co-cited genes by a single linkage procedure such that any gene in a given cluster possesses at least one co-cited partner in the same cluster. Analysis of the clusters demonstrate the biological consistency of this approach, with only very few fortuitous links. As an example, a cluster including genes related to flowering time is more deeply described in the paper. Finally, a graphical representation of each cluster was performed, which provides a convenient way to retrieve the genes (the nodes of the graphs) and the references in which they were co-cited (the edges of the graphs). All the results can be accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/.

Arabidopsis↗
PubMed2004

Mapping topics and topic bursts in PNAS.

Scientific research is highly dynamic. New areas of science continually evolve; others gain or lose importance, merge, or split. Due to the steady increase in the number of scientific publications, it is hard to keep an overview of the structure and dynamic development of one's own field of science, much less all scientific domains. However, knowledge of "hot" topics, emergent research frontiers, or change of focus in certain areas is a critical component of resource allocation decisions in research laboratories, governmental institutions, and corporations. This paper demonstrates the utilization of Kleinberg's burst detection algorithm, co-word occurrence analysis, and graph layout techniques to generate maps that support the identification of major research topics and trends. The approach was applied to analyze and map the complete set of papers published in PNAS in the years 1982-2001. Six domain experts examined and commented on the resulting maps in an attempt to reconstruct the evolution of major research areas covered by PNAS.

Algorithms↗
PubMedDate not supplied

The application of the Transtheoretical Model of Change to adolescent sexual decision-making.

The Transtheoretical Model of Change (TTM) was examined for its applicability to the study of adolescent sexual abstinence behaviors. This investigation involved a cross-sectional secondary analysis of 7th grade students (N = 694) participating is a school-based program funded by the Virginia State Abstinence Initiative. The purpose was to explore the relationships among the concepts and variables of the TTM in an adolescent population with regard to sexual decision-making in abstinence behaviors. The relationship of the different stages of change among virgins and nonvirgins to the decisional balance variable was examined. Results demonstrated significant difference in the decisional balance variable among virgin adolescents in the precontemplation, contemplation, preparation, and action stages of sexual abstinence using ANOVA testing. However, these differences were not seen in the nonvirgin subjects. The virgins followed a highly predictable pattern of sexual decision-making following the graphing of T scores, but this decision-making pattern was not apparent in the nonvirgin subjects. These results support the applicability of the TTM to the behavior of sexual abstinence. Nurses must be aware of the differences in adolescent decision-making processes and incorporate a knowledge of these differences into intervention strategies. Future research will focus on the replication of results in older adolescents and the development of stage-matched interventions to promote healthy sexual behaviors.

Adolescent↗
PubMed2006

Rules for modeling signal-transduction systems.

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic interaction map, but unlike most such maps, rules have precise interpretations. Rules can be processed to automatically generate a mathematical or computational model for a system, which enables explanatory and predictive insights into the system's behavior. Rules are independent units of a model specification that facilitate model revision. Instead of changing a large number of equations or lines of code, as may be required in the case of a conventional mathematical model, a protein interaction can be introduced or modified simply by adding or changing a single rule that represents the interaction of interest. Rules can be defined and visualized by using graphs, so no specialized training in mathematics or computer science is necessary to create models or to take advantage of the representational precision of rules. Rules can be encoded in a machine-readable format to enable electronic storage and exchange of models, as well as basic knowledge about protein-protein interactions. Here, we review the motivation for rule-based modeling; applications of the approach; and issues that arise in model specification, simulation, and testing. We also discuss rule visualization and exchange and the software available for rule-based modeling.

Computer Simulation↗
PubMed2026

Evolution of maize recombination landscape during domestication.

Despite the plethora of knowledge about the benefits of meiotic recombination and numerous theoretical studies examining how recombination rates evolve, there is a general lack of empirical support and consensus across species. To fill this knowledge gap, we characterized the evolution of recombination landscape in maize during its domestication from teosinte and related the observed changes to established theoretical frameworks. Through examining recombination in experimental populations of maize and teosinte and the population genomics approach of identifying historical recombination events using ancestral recombination graph inference to generate saturated maize and teosinte recombination maps, we found that during domestication, maize experienced a 12% increase in its genome-wide recombination rate. Furthermore, maize evolved higher recombination rates on the long arms of chromosomes in regions closer to centromeres, where recombination is generally very low. The repatterning of crossover events came from changes in global crossover positioning rather than alterations in cis-acting chromatin factors. Consequently, we found evidence of selection acting on trans-acting recombination modifiers affecting crossover interference and controlling the interference-dependent class I crossover pathway. We show that CO repatterning was likely beneficial for maize fitness, as significant recombination rate increases were predominantly in gene-rich regions, which harbor domestication-related variation. This work suggests genomic and mechanistic processes leading to the evolution of meiotic recombination landscape in response to directional selection pressure and provides evidence for the evolutionary advantage of recombination.

Zea mays↗
PubMed1986

A graphical method for forecasting radiation exposure from multi-aged fallout from nuclear weapons.

After a nuclear attack it may be necessary for emergency workers, such as firemen, utility workers and medical personnel, to perform urgent tasks in areas highly contaminated by radioactive fallout. To assist the control of radiation exposure of these workers, it will be useful to provide means to forecast radiation exposures both inside and outside the fallout shelter. The method described in this paper is intended for use during the first few days to weeks after the attack, after which time more sophisticated methods may become available. This method requires only a radiation-rate meter, special graph paper, and a timepiece. Communications with Emergency Operating Centers or other sources of information are not necessary. The method permits the determination of the age of fallout and future exposure rates for a location that might be subjected to a number of different fallout clouds, without requiring knowledge of the weapon yields or times of detonation. This method will provide results with less accuracy if different-aged fallout clouds arrive simultaneously. The method is self-correcting so that if the actual decay rate is different than that which is assumed, the forecasted rates will have less error than results obtained by previous methods.

Nuclear Warfare↗
PubMedDate not supplied

Symbolic anatomic knowledge representation in the Read Codes version 3: structure and application.

The Read Thesaurus (Version 3 of the Read Codes) is a controlled medical vocabulary produced during the Clinical Terms Projects with the involvement of over 2,000 health care professionals from all United Kingdom specialties. In addition to allowing the transfer of clinical information in a meaningful way, it supports analysis of this information and provides a basis for the development of shareable medical knowledge bases. The thesaurus includes a comprehensive, dynamic set of over 7,000 gross anatomic concepts richly linked in a network with over 16,000 operative procedures and 40,000 disorders. The representation of anatomic concepts aims to balance the requirements for expressivity, clearness, and simplicity. The underlying directed acyclic graph hierarchy is independent of the alphanumeric code and enables continued refinement and expansion. A template table allows semantic definition, qualification, and linkage of concepts.

Anatomy↗
PubMed1990

A computer system for contact dermatitis: graphical representation of data.

An overview is given of the computer applications we have developed over the last twelve years in the field of contact dermatitis. The dissemination of exposure lists to sensitised individuals and the development of a knowledge-based system are mentioned only briefly. Priority here is given to the explanation of the graphical representation of the patient data collected since 1978 on 12,000 patients referred to three contact dermatitis units. More than a hundred parameters of each patient have been collected in a database. Several graphs are given of these data and are discussed in detail.

Adolescent↗
PubMed1992

Dynamics for communications data.

To create a complex dynamical model for a complex system, it is normally necessary to have a directed graph of the network, a dynamical model for each node, and a coupling function for each directed edge. But in many applications, the only observable data consists of communications from one node to another. In this situation, the modeler may infer a complex dynamical model for the network without any explicit knowledge of the independent dynamical behavior of the component systems (nodes). Here we present one procedure for this type of modeling problem, inspired by the attractor reconstruction procedure of chaos theory. Part of this proposal consists of a strategy for computer graphic presentation of the interactive dynamics of the complex system (or social network of dynamical schemes) called a netscope. We can imagine applications to diverse situations, such as decision groups, management, forecasting, international relations, classroom monitoring, therapy (personal, family, group, etc.) and distributed processors, to name a few.

Communication↗
PubMed1983

The case report. I. Guidelines for preparation.

A case report, if prepared properly, is a valuable educational device to describe an unusual clinical syndrome, association, reaction, or treatment. If a case advances basic understanding of a disorder, increases clinical skill, or suggests useful research, it is worthy of publication. Conciseness is paramount. The description of the case should contain only pertinent positive and negative findings. Irrelevant material or excessive detail can obscure the essence of a report and repel editors and readers. The discussion should emphasize the salient features of the case, show their relation to previous knowledge, interpret their significance, draw conclusions or generalizations about future cases when warranted by the evidence presented, or suggest further possible studies. Information withheld by the patient and unjustified speculation can nullify the value of a case report. Illustrations add visual appeal and enhance the educational value of a report. Tables and graphs should reduce any statistical data to readily interpretable form. All visual supplements should be simple, compact, and self-contained. Appropriate documentation is desirable, but only essential citations need be included, and the author should have carefully reviewed and verified all references used. Begin with a clear title and end with an informative Summary. A useful case report is factual, concise, logically organized, clearly presented, and readable. The three primary principles to remember: (1) Make sure the case warrants publication. (2) Include only pertinent information. (3) Be concise.

Humans↗
PubMed2004

Modelling bound ligands in protein crystal structures.

Methods for automated identification and building of protein-bound ligands in electron-density maps are described. An error model of the geometrical features of the molecular structure of a ligand based on a lattice distribution of positional parameters is obtained via simulation and is used for the construction of an approximate likelihood scoring function. This scoring function combined with a graph-based search technique provides a flexible model-building scheme and its application shows promising initial results. Several ligands with sizes ranging from 9 to 44 non-H atoms have been identified in various X-ray structures and built in an automatic way using a minimal amount of prior stereochemical knowledge.

Adenosine Monophosphate↗
PubMed2004

Graphical models for causation, and the identification problem.

This article (which is mainly expository) sets up graphical models for causation, having a bit less than the usual complement of hypothetical counterfactuals. Assuming the invariance of error distributions may be essential for causal inference, but the errors themselves need not be invariant. Graphs can be interpreted using conditional distributions, so that we can better address connections between the mathematical framework and causality in the world. The identification problem is posed in terms of conditionals. As will be seen, causal relationships cannot be inferred from a data set by running regressions unless there is substantial prior knowledge about the mechanisms that generated the data. There are few successful applications of graphical models, mainly because few causal pathways can be excluded on a priori grounds. The invariance conditions themselves remain to be assessed.

Bayes Theorem↗
PubMed2006

How do experts recognize schizophrenia: the role of the disorganization symptom.

OBJECTIVE: Research on clinical reasoning has been useful in developing expert systems. These tools are based on Artificial Intelligence techniques which assist the physician in the diagnosis of complex diseases. The development of these systems is based on a cognitive model extracted through the identification of the clinical reasoning patterns applied by experts within the clinical decision-making context. This study describes the method of knowledge acquisition for the identification of the triggering symptoms used in the reasoning of three experts for the diagnosis of schizophrenia. METHOD: Three experts on schizophrenia, from two University centers in Sao Paulo, were interviewed and asked to identify and to represent the triggering symptoms for the diagnosis of schizophrenia according to the graph methodology. RESULTS: Graph methodology showed a remarkable disagreement on how the three experts established their diagnosis of schizophrenia. They differed in their choice of triggering-symptoms for the diagnosis of schizophrenia: disorganization, blunted affect and thought disturbances. CONCLUSIONS: The results indicate substantial differences between the experts as to their diagnostic reasoning patterns, probably under the influence of different theoretical tendencies. The disorganization symptom was considered to be the more appropriate to represent the heterogeneity of schizophrenia and also, to further develop an expert system for the diagnosis of schizophrenia.

Decision Support Systems, Clinical↗
PubMed2003

A prototype natural language interface to a large complex knowledge base, the Foundational Model of Anatomy.

We describe a constrained natural language interface to a large knowledge base, the Foundational Model of Anatomy (FMA). The interface, called GAPP, handles simple or nested questions that can be parsed to the form, subject-relation-object, where subject or object is unknown. With the aid of domain-specific dictionaries the parsed sentence is converted to queries in the StruQL graph-searching query language, then sent to a server we developed, called OQAFMA, that queries the FMA and returns output as XML. Preliminary evaluation shows that GAPP has the potential to be used in the evaluation of the FMA by domain experts in anatomy.

Anatomy↗