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At least 847 records · Page 47Linked to original sources
PubMed2006

Assessing self organizing maps via contiguity analysis.

Contiguity analysis is a straightforward generalization of linear discriminant analysis in which the partition of elements is replaced by a more general graph structure. Applied to the graph induced by a Self Organizing Map (SOM), contiguity analysis provides a set of linear projectors leading to a planar representation as close as possible to the SOM. As expected, such projectors may only concern local parts of the SOMs. They allow us to visualize the shapes of the clusters (convex hulls of the projections of the elements belonging to a cluster) and the pattern of the elements within each cluster. In some contexts, it is possible to project the bootstrap replicates of the elements, and therefore to produce confidence areas for elements via a standard partial bootstrap procedure.

Algorithms↗
PubMed2000

Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies.

Mutually catalytic sets of simple organic molecules have been suggested to be capable of self-replication and rudimentary chemical evolution. Previous models for the behavior of such sets have analyzed the global properties of short biopolymer ensembles by using graph theory and a mean field approach. In parallel, experimental studies with the autocatalytic formation of amphiphilic assemblies (e.g., lipid vesicles or micelles) demonstrated self-replication properties resembling those of living cells. Combining these approaches, we analyze here the kinetic behavior of small heterogeneous assemblies of spontaneously aggregating molecules, of the type that could form readily under prebiotic conditions. A statistical formalism for mutual rate enhancement is used to numerically simulate the detailed chemical kinetics within such assemblies. We demonstrate that a straightforward set of assumptions about kinetically enhanced recruitment of simple amphiphilic molecules, as well as about the spontaneous growth and splitting of assemblies, results in a complex population behavior. The assemblies manifest a significant degree of homeostasis, resembling the previously predicted quasi-stationary states of biopolymer ensembles (Dyson, F. J. (1982) J. Mol. Evol. 18, 344-350). Such emergent catalysis-driven, compositionally biased entities may be viewed as having rudimentary "compositional genomes." Our analysis addresses the question of how mutually catalytic metabolic networks, devoid of sequence-based biopolymers, could exhibit transfer of chemical information and might undergo selection and evolution. This computed behavior may constitute a demonstration of natural selection in populations of molecules without genetic apparatus, suggesting a pathway from random molecular assemblies to a minimal protocell.

Catalysis↗
PubMed2006

Population structure inferred by local spatial autocorrelation: an example from an Amerindian tribal population.

Spatial autocorrelation (SA) methods were recently extended to detect local spatial autocorrelation (LSA) at individual localities. LSA statistics serve as useful indicators of local genetic population structure. We applied this method to 15 allele frequencies from 43 villages of a South American tribe, the Yanomama. Based on a network of links <or=51 km between neighboring villages, we calculated LSA statistics for Moran, Geary, and Getis-Ord coefficients. We also developed two new, rescaled indices of local SA. Local indicators of positive SA highlight villages surrounded by genetically similar near neighbors. Negative LSA statistics indicate sharp genetic differences from near neighbors. Markedly positive LSA was found for all 11 outlier villages. The most negatively LSA villages are in the central, densely connected cluster. The Getis-Ord coefficients of suitably transformed allele frequencies point to clusters of villages with unusually high or low allelic polymorphisms. The most homozygous villages are all in the four geographically isolated village clusters. The most polymorphic villages are all in the large, densely settled Yanomame dialect group. An ad hoc linguistic isolation index between neighboring villages showed that villages in isolated pairs and triplets have linguistically similar neighbors, whereas nine villages with notably negative LSA are all near dialect and kinship boundaries. The location of a village with respect to the graph structure of its neighborhood affects its LSA and genetic polymorphism. The implications of these findings for the population structure of the Yanomama are compatible with those from an earlier study of global SA in these villages.

Demography↗
PubMed2003

A model to predict survival at one month, one year, and five years after liver transplantation based on pretransplant clinical characteristics.

Reliable models that could predict outcome of liver transplantation (LT) may guide physicians to advise their patients of immediate and late survival chances and may help them to optimize organ use. The objective of this study was to develop user-friendly models to predict short and long-term mortality after LT in adults based on pre-LT recipient characteristics. The United Network for Organ Sharing (UNOS) transplant registry (n = 38,876) from 1987 to 2001 was used to develop and validate the model. Two thirds of patients were randomized to develop the model (the modeling group), and the remaining third was randomized to cross-validate (the cross-validation group) it. Three separate models, using multivariate logistic regression analysis, were created and validated to predict survival at 1 month, 1 year, and 5 years. Using the total severity scores of patients in the modeling group, a predictive model then was created, and the predicted probability of death as a function of total score then was compared in the cross-validation group. The independent variables that were found to be very significant for 1 month and 1 year survival were age, body mass index (BMI), UNOS status 1, etiology, serum bilirubin (for 1 month and 1 year only), creatinine, and race (only for 5 years). The actual deaths in the cross-validation group followed very closely the predicted survival graph. The chi-squared goodness-of-fit test confirmed that the model could predict mortality reliably at 1 month, 1 year, and 5 years. We have developed and validated user-friendly models that could reliably predict short-term and long-term survival after LT.

Adult↗
PubMed1999

Graph-theoretic description of the interplay between non-linearity and connectivity in biological systems.

The purpose of this article is to stress the implications that the consideration of nonlinearity has upon the extension and strength of connectivity, if this is understood as a characterization of the degree of interrelation between parts of the system. This objective is reached within the QP formalism for non-linear ODEs. The formalism is developed in a graph-theoretic setting, with the help of which the connectionist aspect of non-linearity becomes apparent. Topology-preserving transformations involve an exchange between the degree of non-linearity and the strengths of interactions, thus assembling systems of apparently different nature into classes of equivalence. We argue that, if we have in mind a classification of systems according to behavior, these classes of equivalence should be given their proper singularity. We characterize globally the connectivity of a class with an index, although we point out during the discussion that the mathematical conception of the complex idea of connectivity is still incomplete.

Linear Models↗
PubMed2002

Science's signal transduction knowledge environment: the connections maps database.

Knowledge environment (KE) describes the collection of electronic networking tools that have been and continue to be developed by AAAS and Stanford University libraries. Knowledge environments use practical, production-quality tools to systematize the consensus knowledge within a scientific domain and facilitate users' access to that knowledge. Science's Signal Transduction Knowledge Environment (STKE) is the first in this new concept in electronic publishing that combines the traditional, albeit electronic, publishing of articles, such as reviews, perspectives, and protocols, with tools for organizing and collating information in the cross-disciplinary field of signal transduction. One of the major tools developed for the STKE is the Connections Map database and the software (called CMADES [Connections Maps Authority Data Entry Software]) created to facilitate data entry by Pathway Authorities. The Connections Maps are a graphical representation of a database of information about the molecules involved in cellular signaling cascades. CMADES automates many of the functions involved in adding data into the Connections Maps database, such as references and descriptors, as well as allowing the Authorities to indicate the relationships between the components in the pathway through the use of a graphing tool. CMADES and the Connections Maps represent evolving tools that assist the Authorities in systemizing information regarding a particular system at the organism- and cell-specific level and the canonical level, as well as provide the STKE user with organized and expert-supplied information about signal transduction pathways.

Biology↗
PubMed1995

Seven years experience with a computerized diabetes clinic database.

With the emergence of information technology applications in medicine, a computerized medical record system that could be used to : (1) maintain patients' clinical records over time, (2) communicate with referring practitioners, and (3) form the basis of a potential research database of information, was sought. In 1987, we developed such a clinical database to register patients attending our busy Diabetes Clinic, now seeing in excess of 300 new referrals and, on average, 3,000 clinic visits per year. Baseline demographic data, clinical history, and examination and investigation results are recorded. We also record diabetes therapy and other medication dosage and changes, monitor follow-up, assess health outcome information (such as stroke or amputation), and generate results, summaries, and reports to referring practitioners and other health professionals. We now have almost seven years of experience using the system. Initially established on a single PC with paper-based data collection and subsequent data entry (running as a DOS application), it is now established on a PC Local Area Network [LAN] with terminals in the clinic consultation rooms enabling direct data entry and allowing patients to view their results in graphic form on screen. From its inception, the Diabetes Clinic Database System has maintained patient demographic and clinical data (which facilitates efficient clinic management) with patient clinic lists and adhesive address labels generated from appropriate menus. Batch mode processing produces daily work sheets which facilitate the running of clinics as well as ad hoc, daily, and weekly reports for all patients (as required). This expedites correspondence with referring doctors. A quality assurance report to the clinic doctor highlights missing clinical information which must be obtained in order to ensure data completeness. The initial system was relatively inefficient in that it required data entry following patient consultation and provided no immediate feedback to patients themselves. In January 1994, to address these deficiencies, the system was established on a PC LAN (running under Novell); it provided on-line data entry within the clinic setting and enabled patients to participate in the recording of their information, observe their own progress by way of on-screen graphs (e.g., blood sugar control, weight, cholesterol), and receive hand-held summaries generated immediately following the clinic visit. Batch programs generate hard copies of this data to be filed in medical records. Two major assessments of the system have been undertaken. In February 1990, we undertook a survey of Local Doctors with 5 or more patient referrals on the system; this resulted in a pleasing 66% response rate. There was an almost universal acceptance and indeed a significant preference for this system over 'traditional' letters. In January 1994, following the introduction of the system onto the PC LAN for direct data entry in the clinic setting, we assessed (by anonymous questionnaire at the end of the consultation) patient attitudes towards these changes. The development of the CRS Diabetes Clinic Database System has improved our approach to diabetes outpatient care and our communication with other health professionals. It has the added benefit of providing a database of information that is suitable to address critical clinical research issues in diabetes management. This system provides an acceptable blend of information technology and clinical medicine, redesigning and enhancing the way we deliver medical care to patients with diabetes. Involving the patient in the collection and interpretation of their clinical data via a computer system (as utilized within our clinical unit), is both acceptable to the patient and her referring doctor. Ongoing system refinement and assessment remains integral to our use of information technology.

Australia↗
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↗
PubMed2025

CaXML: Chemistry-informed machine learning explains mutual changes between protein conformations and calcium ions in calcium-binding proteins using structural and topological features.

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of CaXML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

Machine Learning↗
PubMedDate not supplied

From multimodality digital imaging to multimedia patient record.

The constant improvement in computer power and performance nowadays offers convenient and efficient means of manipulating images, graphics, and movies on off-the-shelf workstations. With this improvement the trend toward integration of multimodality clinical documents from patient records comes naturally. Images and graphs are certainly the most important part of the complementary information that must accompany the text and numerical data. It is, however, possible to include sounds and voice messages together with all the other modalities. In medicine that could certainly help conveying hart murmur or sounds, but could also offer a convenient way of including vocal messages and comments. These new possibilities will certainly change the way physicians use workstations for direct communication. The computer industry will soon offer means of interactive communication between remote users through computer workstations. That alone will open a completely new era in cooperative computing and remote consultation scenarios in medicine. More than the technology itself, a complete change in behavior and work habits can be expected in the medical community.

Computer Communication Networks↗
PubMed2006

Switching mechanism for branched biochemical fluxes: graph-theoretical analysis.

A graph-theoretical method is applied to characterize the structure of a simplest switching mechanism of common biochemical importance. This mechanism is based on competition of two coupled substrate-binding pathways for a single substrate. No other regulatory interactions are shown to be needed for the switching phenomenon to be observed. It is shown that switch in branch effluxes is observed as bistability or reciprocal oscillations, depending on the value of steady influx. Frequency of reciprocal efflux oscillations in branches is regulated by steady influx. Therefore, the switching mechanism can function as the coding mechanism in the manner of "influx steady level-efflux frequency". The calculated kinetic equations for the switching mechanism demonstrate very steep transitions in the branch fluxes without using high non-linearity of these equations.

Enzymes↗
PubMed1997

Efficient discovery of conserved patterns using a pattern graph.

MOTIVATION: We have previously reported an algorithm for discovering patterns conserved in sets of related unaligned protein sequences. The algorithm was implemented in a program called Pratt. Pratt allows the user to define a class of patterns (e.g. the degree of ambiguity allowed and the length and number of gaps), and is then guaranteed to find the conserved patterns in this class scoring highest according to a defined fitness measure. In many cases, this version of Pratt was very efficient, but in other cases it was too time consuming to be applied. Hence, a more efficient algorithm was needed. RESULTS: In this paper, we describe a new and improved searching strategy that has two main advantages over the old strategy. First, it allows for easier integration with programs for multiple sequence alignment and data base search. Secondly, it makes it possible to use branch-and-bound search, and heuristics, to speed up the search. The new search strategy has been implemented in a new version of the Pratt program.

Algorithms↗
PubMed1998

Periodically-modulated inhibition of living pacemaker neurons--III. The heterogeneity of the postsynaptic spike trains, and how control parameters affect it.

Codings involving spike trains at synapses with inhibitory postsynaptic potentials on pacemakers were examined in crayfish stretch receptor organs by modulating presynaptic instantaneous rates periodically (triangles or sines; frequencies, slopes and depths under, respectively, 5.0 Hz, 40.0/s/s and 25.0/s). Timings were described by interspike and cross-intervals ("phases"); patterns (dispersions, sequences) and forms (timing classes) were identified using pooled graphs (instant along the cycle when a spike occurs vs preceding interval) and return maps (plots of successive intervals). A remarkable heterogeneity of postsynaptic intervals and phases characterizes each modulation. All cycles separate into the same portions: each contains a particular form and switches abruptly to the next. Forms differ in irregularity and predictability: they are (see text) "p:q alternations", "intermittent", "phase walk-throughs", "messy erratic" and "messy stammering". Postsynaptic cycles are asymmetric (hysteresis). This contrasts with the presynaptic homogeneity, smoothness and symmetry. All control parameters are, individually and jointly, strongly influential. Presynaptic slopes, say, act through a postsynaptic sensitivity to their magnitude and sign; when increasing, hysteresis augments and forms change or disappear. Appropriate noise attenuates between-train contrasts, providing modulations are under 0.5 Hz. Postsynaptic natural intervals impose critical time bases, separating presynaptic intervals (around, above or below them) with dissimilar consequences. Coding rules are numerous and have restricted domains; generalizations are misleading. Modulation-driven forms are trendy pacemaker-driven forms. However, dissimilarities, slight when patterns are almost pacemaker, increase as inhibition departs from pacemaker and incorporate unpredictable features. Physiological significance-(1) Pacemaker-driven forms, simple and ubiquitous, appear to be elementary building blocks of synaptic codings, present always but in each case distorted typically. (2) Synapses are prototype: similar behaviours should be widespread, and networks simulations benefit by nonlinear units generating all forms. (3) Relevant to periodic functions are that few variables need be involved in form selection, that distortions are susceptible to noise levels and, if periods are heterogeneous, that simple input cycles impose heterogeneous outputs. (4) Slow Na inactivations are necessary for obtaining complex forms and hysteresis. Formal significance--(1) Pacemaker-driven forms and presumably their modulation-driven counterparts, pertain to universal periodic, intermittent, quasiperiodic and chaotic categories whose formal properties carry physiological connotations. (2) Only relatively elaborate, nonlinear geometric models show all forms; simpler ones, show only alternations and walk-throughs. (3) Bifurcations resemble those of simple maps that can provide useful guidelines. (4) Heterogeneity poses the unanswered question of whether or not the entire cycle and all portions have the same behaviours: therefore, whether trajectories are continuous or have discontinuities and/or singular points.

Action Potentials↗
PubMedDate not supplied

Synaptic weight normalization effects for topographic mapping formation.

We propose a simple topographic mapping formation model between cell layers with weight normalization. In our model, each cell layer can have an arbitrary neighborhood relation between the cells represented by an undirected graph. Thus, a topographic mapping described in this model is a map which preserves the adjacency relation. We define several learning rules, input and output type weight normalization methods. Then, we not only concentrate on a Hebbean weight modification but also investigate the effects of normalization under a non-Hebbean weight modification. We first show that when an input type normalization is adopted or without normalization, a topographic mapping is stable under the correlational type learning rule, but when an output type normalization is adopted a topographic mapping is stable under not only the correlational type learning rule but also the non-correlational one. Next, we show by computer simulations that when an output type normalization is considered we have more learning rules which yield topographic mappings than the cases when an input type normalization is adopted or without normalization.

Algorithms↗
PubMed2000

[Prediction and estimation on molar response values of alkanes by using molecular path vector].

A new method based on a novel molecular topological index vector, called the molecular path vector (MPV), of alkane molecules is proposed and employed for estimation and prediction of the molar response values of various alkanes. The novel MPV, p = (P1, P2, P3, P4, P5, P6, P7, P8, P9, P10)', which derived directly from the interaction terms of molecular graph, is used to characterize well molecular structures of all alkanes from one through ten or eleven carbon atoms. It showed that there exists very good correlation between the MPV elements and molar response values on both FID and TCD detectors in classical gas chromatography. Based on the given calibration set with different sample numbers and by using the practical multiple linear regression, the quantitative structure-response relationship (QSRR) equations, for the molar response values (SM) on both FID and TCD, are respectively given as follows: SM(FID) = 15.4004881 + 17.9905995 X1 - 0.1652116 X2 - 0.6974103 X3 - 0.8452390 X4 - 0.2671000 X5 - 1.5657273 X6 + 0.0944440 X7, n = 50, m = 7, r = 0.9976, ST = 26.132, SR = 1.965 1, Ev = 99.72%, RMS = 1.801, F = 1231.71 SM(TCD) = 11.9946996 + 29.1490916 X1 - 4.7451669 X2 - 3.7673385 X3 - 1.4948330 X4 - 1.6278831 X5 - 0.7934611 X6 - 3.0566093 X7, n = 32, m = 7, r = 0.9968, ST = 15.72, SR = 1.4310, Ev = 99.59%, RMS = 1.239, F = 531.227 where the independent descriptor variables, X1-X7, refer to the elements, P1, P2, P3, P4, P5, P6, P7 in the molecular path vector for all samples in both FID and TCD training sets; n, r, ST, SR, Ev, RMS and F are the sample number, regression coefficient, total standard deviation, standard residual deviation, explained variance, rooted mean squared error and F-statistic value, respectively. To test both models by using back-propagation neural network (BPNN) with the topological structure NN(7-4-2) and the cross validation through leave-one-out (LOO) procedure, the correlation coefficient of cross validation is over 0.96. Because there exists a quite good linear relationship between the molar responses and molecular path parameters, BPNN (r = 0.989 and 0.968) does not show its nonlinear advantage over multiple linear regression(MLR) (r = 0.9976 and 0.9968) in both presently examined cases, FID and TCD in the GC technique, for molecular modelling and quantitative prediction.

Alkanes↗
PubMed2006

Evaluation of the GTRACT diffusion tensor tractography algorithm: a validation and reliability study.

Fiber tracking, based on diffusion tensor imaging (DTI), is the only approach available to non-invasively study the three-dimensional structure of white matter tracts. Two major obstacles to this technique are partial volume artifacts and tracking errors caused by image noise. In this paper, a novel fiber tracking algorithm called Guided Tensor Restore Anatomical Connectivity Tractography (GTRACT) is presented. This algorithm utilizes a multi-pass approach to fiber tracking. In the first pass, a 3D graph search algorithm is utilized. The second pass incorporates anatomical connectivity information generated in the first pass to guide the tracking in this stage. This approach improves the ability to reconstruct complex fiber paths as well as the tracking accuracy. Validation and reliability studies using this algorithm were performed on both synthetic phantom data and clinical human brain data. A method is also proposed for the evaluating reliability of fiber tract generation based both on the position of the fiber tracts, as well the anisotropy values along the path. The results demonstrate that the GTRACT algorithm is less sensitive to image noise and more capable of handling areas of complex fiber crossing, compared to conventional streamline methods.

Algorithms↗
PubMed1997

Horizontal wires replace the vertical files.

Traditionally, clippings of newspaper articles, pictures from magazines, pamphlets, charts, graphs, posters, proceedings, or copies thereof, and other miscellaneous information sources have been stored in vertical files in libraries. The practice of creating and maintaining vertical files is extremely time consuming. In a medical library, in particular, old information about diagnosis, treatment, and prognosis can quickly become incorrect, misleading, and possibly harmful. Adequately tending to the vertical files can require a librarian to create a balancing act between properly maintaining vertical files and meeting the needs of the users in other areas of the library. The maintenance of vertical files is, by nature, highly consumptive of paper and space consuming. A reasonable alternative to the traditional vertical files is the World-Wide Web. Search engines exist for locating specific information, and bookmarks and/or links which point users to particularly useful sites can be set in search software. Some methods for searching are discussed, and a variety of World-Wide Web information sources are offered.

Computer Communication Networks↗
PubMed1994

Data utilization and analytical skills among mid-level health programme managers in a developing country.

Mid-level health managers in a developing country were studied to examine the extent to which they are able to use and analyse data they receive from a new health information system. Among 168 managers filling out a self-administered questionnaire, 52% could compute a simple cost-effectiveness ratio and 27% were able to calculate proportions. Only 43% of the managers were able to construct a cumulative graph similar to the one recommended by WHO. Facility with these tasks was not related to levels of training or age. Twelve out of 25 programme managers interviewed in depth did not know how well their particular programme had performed in the previous year. Similarly, only six of these managers knew their best and poorest performing districts. The results of this study suggest; 1) Training managers in data analysis and use is critical if health information systems are to actually improve health care delivery. 2) Data intended for the use of programme managers need to be presented in simple ways. 3) Further social research is required to understand how managers perceive and use data. 4) Efforts to ensure the use of data should not be seen as something to be 'added on' after information systems are in place.

Data Interpretation, Statistical↗