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At least 253 records · Page 14Linked to original sources

Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae.

As we are moving into the post genome-sequencing era, various high-throughput experimental techniques have been developed to characterize biological systems on the genomic scale. Discovering new biological knowledge from the high-throughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a Bayesian statistical method together with Boltzmann machine and simulated annealing for protein functional annotation in the yeast Saccharomyces cerevisiae through integrating various high-throughput biological data, including yeast two-hybrid data, protein complexes and microarray gene expression profiles. In our approach, we quantified the relationship between functional similarity and high-throughput data, and coded the relationship into 'functional linkage graph', where each node represents one protein and the weight of each edge is characterized by the Bayesian probability of function similarity between two proteins. We also integrated the evolution information and protein subcellular localization information into the prediction. Based on our method, 1802 out of 2280 unannotated proteins in yeast were assigned functions systematically.

Bayes Theorem↗

Feature subset selection for splice site prediction.

MOTIVATION: The large amount of available annotated Arabidopsis thaliana sequences allows the induction of splice site prediction models with supervised learning algorithms (see Haussler (1998) for a review and references). These algorithms need information sources or features from which the models can be computed. For splice site prediction, the features we consider in this study are the presence or absence of certain nucleotides in close proximity to the splice site. Since it is not known how many and which nucleotides are relevant for splice site prediction, the set of features is chosen large enough such that the probability that all relevant information sources are in the set is very high. Using only those features that are relevant for constructing a splice site prediction system might improve the system and might also provide us with useful biological knowledge. Using fewer features will of course also improve the prediction speed of the system. RESULTS: A wrapper-based feature subset selection algorithm using a support vector machine or a naive Bayes prediction method was evaluated against the traditional method for selecting features relevant for splice site prediction. Our results show that this wrapper approach selects features that improve the performance against the use of all features and against the use of the features selected by the traditional method. AVAILABILITY: The data and additional interactive graphs on the selected feature subsets are available at http://www.psb.rug.ac.be/gps

Arabidopsis↗

Networks and epidemic models.

Networks and the epidemiology of directly transmitted infectious diseases are fundamentally linked. The foundations of epidemiology and early epidemiological models were based on population wide random-mixing, but in practice each individual has a finite set of contacts to whom they can pass infection; the ensemble of all such contacts forms a 'mixing network'. Knowledge of the structure of the network allows models to compute the epidemic dynamics at the population scale from the individual-level behaviour of infections. Therefore, characteristics of mixing networks-and how these deviate from the random-mixing norm-have become important applied concerns that may enhance the understanding and prediction of epidemic patterns and intervention measures. Here, we review the basis of epidemiological theory (based on random-mixing models) and network theory (based on work from the social sciences and graph theory). We then describe a variety of methods that allow the mixing network, or an approximation to the network, to be ascertained. It is often the case that time and resources limit our ability to accurately find all connections within a network, and hence a generic understanding of the relationship between network structure and disease dynamics is needed. Therefore, we review some of the variety of idealized network types and approximation techniques that have been utilized to elucidate this link. Finally, we look to the future to suggest how the two fields of network theory and epidemiological modelling can deliver an improved understanding of disease dynamics and better public health through effective disease control.

Animals↗

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms.

BACKGROUND: Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be extracted in a reasonable way and funneled into manageable and functionally meaningful patterns. Genes may be reasonably combined using knowledge about their interaction behaviour. On a proteomic level, biochemical research has elucidated an increasingly complete image of the metabolic architecture, especially for less complex organisms like the well studied bacterium Escherichia coli. RESULTS: We sought to discover central components of the metabolic network, regulated by the expression of associated genes under changing conditions. We mapped gene expression data from E. coli under aerobic and anaerobic conditions onto the enzymatic reaction nodes of its metabolic network. An adjacency matrix of the metabolites was created from this graph. A consecutive ones clustering method was used to obtain network clusters in the matrix. The wavelet method was applied on the adjacency matrices of these clusters to collect features for the classifier. With a feature extraction method the most discriminating features were selected. We yielded network sub-graphs from these top ranking features representing formate fermentation, in good agreement with the anaerobic response of hetero-fermentative bacteria. Furthermore, we found a switch in the starting point for NAD biosynthesis, and an adaptation of the l-aspartate metabolism, in accordance with its higher abundance under anaerobic conditions. CONCLUSION: We developed and tested a novel method, based on a combination of rationally chosen machine learning methods, to analyse gene expression data on the basis of interaction data, using a metabolic network of enzymes. As a case study, we applied our method to E. coli under oxygen deprived conditions and extracted physiologically relevant patterns that represent an adaptation of the cells to changing environmental conditions. In general, our concept may be transferred to network analyses on biological interaction data, when data for two comparable states of the associated nodes are made available.

Algorithms↗

Clinical trials in surgery.

Scientific knowledge is reliable because it has been built on accurate measurements. Clinical knowledge is not. The science of biometry was started in 1835 by the Belgian astronomer Adolphe Quetelet. In the last fifty years a precise set of rules have been invented for this science. The method is suitable for a wide range of problems in clinical medicine and as the result of its application in recent years a firm foundation has been laid upon which scientific clinical knowledge can be built. Surge-ns, particularly, have been slow to apply biometrical methods to their clinical problems; but a start has now been made. The outcome of a particular type of treatment is determined by a complex set of inter-acting factors. The basis of the appropriate biometrical method is the elimination of all bias in favour of one of the rival techniques being compared. If this precaution is taken the observed results of the trial can be fitted onto Quetelet's distribution graph, and the probability of the observed difference in the results being due to chance, and nothing else, can be measured mathematically. The accuracy of this measurement deteriorates the greater are the number of the patients who can not be found and examined at the end of the trial. To make this point two trials conducted by the author are used. In the trial designed to discover if postoperative deep vein thrombosis and pulmonary embolism could be prevented by electrically stimulating the patients legs during the operation there was no difficulty. All the patients were examined at the end of the trial, because it ended before any of the patients left the hospital. The trial to discover if the primary treatment of varicose veins ought to be by Fegan's sclerotherapy or by operation was the exact opposite. At the end of the first year of the two year trial 15% of the patients could not be traced. The results in these patients, therefore, was unknown. Because of this, elaborate mathematical calculations had to be made to try and reach a reliable conclusion to the trial. The loss of patients before the end of the trial is a very serious practical difficulty which besets all long-term clinical trials.

Clinical Trials as Topic↗

A hybrid system for diagnosing multiple disorders.

This paper investigates the advantages of introducing feedback between the processes of automated medical diagnosis and automated diagnostic-knowledge acquisition. Experimental results show that a diagnostic system with such feedback is capable of an efficiency/accuracy trade-off when applied to the problem of diagnosing multiple disorders. A primary feature of this work is a new mechanism, called the "diagnostic-unit" representation, for remembering results of previous diagnoses. The diagnostic-unit representation is explicitly tailored to capture the most likely relationships between disorders and clusters of findings. Unlike typical bipartite "If-Then" representations, the diagnostic-unit representation uses a general graph representation to efficiently represent complex causal relationships between disorders and clusters of findings. In addition to the basic diagnostic-unit concept, this paper presents experience-based strategies for incrementally deriving and updating diagnostic units and the various relationships between them. Techniques for selecting diagnostic units relevant to a given problem and then combining them to generate solutions are also described.

Artificial Intelligence↗

FlexProt: alignment of flexible protein structures without a predefinition of hinge regions.

FlexProt is a novel technique for the alignment of flexible proteins. Unlike all previous algorithms designed to solve the problem of structural comparisons allowing hinge-bending motions, FlexProt does not require an a priori knowledge of the location of the hinge(s). FlexProt carries out the flexible alignment, superimposing the matching rigid subpart pairs, and detects the flexible hinge regions simultaneously. A large number of methods are available to handle rigid structural alignment. However, proteins are flexible molecules, which may appear in different conformations. Hence, protein structural analysis requires algorithms that can deal with molecular flexibility. Here, we present a method addressing specifically a flexible protein alignment task. First, the method efficiently detects maximal congruent rigid fragments in both molecules. Transforming the task into a graph theoretic problem, our method proceeds to calculate the optimal arrangement of previously detected maximal congruent rigid fragments. The fragment arrangement does not violate the protein sequence order. A clustering procedure is performed on fragment-pairs which have the same 3-D rigid transformation regardless of insertions and deletions (such as loops and turns) which separate them. Although the theoretical worst case complexity of the algorithm is O(n(6)), in practice FlexProt is highly efficient. It performs a structural comparison of a pair of proteins 300 amino acids long in about seven seconds on a standard desktop PC (400 MHz Pentium II processor with 256MB internal memory). We have performed extensive experiments with the algorithm. An assortment of these results is presented here. FlexProt can be accessed via WWW at bioinfo3d.cs.tau.ac.il/FlexProt/.

Computational Biology↗

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

BACKGROUND: To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. RESULTS: To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. CONCLUSION: By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.

Archaeal Proteins↗

Simplified representation of concepts and relations on screen.

The fully automated generation of diagnostic codes requires a knowledge-based system which is capable of interpreting noun phrases. The sense content of the words must be analysed and represented for this purpose. The codes are then generated based on this representation.In comparison with other knowledge-based systems, a system of this kind places the emphasis on the data structures and not on the calculus; coding itself is a simple matter compared to the much more difficult task of incorporating the complex information contained in the words used in natural language in a systematic data model. Initial attempts were based on the assumption that each word was linked to one conceptual meaning, whereas such a naive viewpoint certainly no longer applies today. The notation of concepts and their relations is the task at hand.Existing notation methods include predicate logic, conceptual graphs (CGs) as proposed by J. F. Sowa [2], GRAIL as used by the GALEN Project [1] and methods developed as part of the WWW consortium, e.g. RDF's (Resource Description Frameworks). For the purpose of coding, we developed a notation system using "concept particles" back in 1989 [3]. In 1996, the resulting experience led us to represent "concept molecules" (CM), with which both complex data structures and multi-branched rules can be denoted in a simple manner [4]. In this paper we shall explain the principles behind this notation and compare it with another modern concept representation system, conceptual graphs.

Expert Systems↗

Combinatorial explosion in model gene networks.

The explosive growth in knowledge of the genome of humans and other organisms leaves open the question of how the functioning of genes in interacting networks is coordinated for orderly activity. One approach to this problem is to study mathematical properties of abstract network models that capture the logical structures of gene networks. The principal issue is to understand how particular patterns of activity can result from particular network structures, and what types of behavior are possible. We study idealized models in which the logical structure of the network is explicitly represented by Boolean functions that can be represented by directed graphs on n-cubes, but which are continuous in time and described by differential equations, rather than being updated synchronously via a discrete clock. The equations are piecewise linear, which allows significant analysis and facilitates rapid integration along trajectories. We first give a combinatorial solution to the question of how many distinct logical structures exist for n-dimensional networks, showing that the number increases very rapidly with n. We then outline analytic methods that can be used to establish the existence, stability and periods of periodic orbits corresponding to particular cycles on the n-cube. We use these methods to confirm the existence of limit cycles discovered in a sample of a million randomly generated structures of networks of 4 genes. Even with only 4 genes, at least several hundred different patterns of stable periodic behavior are possible, many of them surprisingly complex. We discuss ways of further classifying these periodic behaviors, showing that small mutations (reversal of one or a few edges on the n-cube) need not destroy the stability of a limit cycle. Although these networks are very simple as models of gene networks, their mathematical transparency reveals relationships between structure and behavior, they suggest that the possibilities for orderly dynamics in such networks are extremely rich and they offer novel ways to think about how mutations can alter dynamics. (c) 2000 American Institute of Physics.

Journal Article↗

Ten years of medical informatics education experience at the Faculty of Medicine in Sarajevo.

INTRODUCTION: The medical informatics as the separate medical discipline very quickly gets developed, both in Bosnia and Herzegovina. In our country, the medical informatics is a separate subject for the last ten years, regarding to the Medical curriculum at the biomedical faculties in Bosnia and Herzegovina is in accordance with the project of the education related to Bologna declaration and the project EURO MEDICINA. This year the Chair of the Medical Informatics of the Medical Faculty in Sarajevo celebrates ten years of its existence. WORK METHOD: By the descriptive method of the research which included the questionnaire of about 400 students of the biomedical faculties, we established the attitudes and we took into consideration opinions of the students of these faculties about the validity of the contents of the subject of the medical informatics, the availability of the adoption of the material by the theoretical and practical performance of the teaching process and the suggestions and recommendations of the students about the contents that have to be throwned out from the curriculum and the teaching material that needs to be included. WORK RESULTS: The research was performed using the separate questionnaire pattern data carriers with the defined characteristics for the quality assessment of the performed course. The total attitude of the assessed students speaks about dominantly expressed satisfaction with the majority of the parameters that are important for assessment of the quality and the tuition contents that was evaluated during the questionnaire. The results are shown in the tables and graphs, and they are describing the program of the tuition and the contents of the methodical units, and the system of the examination for the students using the method of "multiple choice". CONCLUSION: The education in the field of the medical informatics is based at the concept which is used in the developed countries of the world, and according the recommendations of the working groups of the European and world association of the medical informatics. The theoretical and practical teaching and training performance in the wholeness is performed by use of the computer equipment, and the final knowledge check of the students also is performed using the Data Base Management System MSAccess specifically designed to cover full teaching and training material by using questions set in the data base which encircled nearly 1500 questions combinations.

Bosnia and Herzegovina↗

[The effect of knowledge regarding the importance of oral health in pregnancy].

INTRODUCTION: Although in modern dental medicine a pregnant woman and her foetus are completely safe during all dental procedures, the prevention is still the most effective measure for the preservation of oral health in pregnancy. However, pregnant women often visit a stomatologist only when there are already serious disturbances, regardless of the fact that they are referred to a stomatologist even at their first visit to a gynaecologist. The aim of the study was to investigate (possible) changes in pregnant women's attitudes toward oral health during pregnancy according to our educational programme. METHODS: One hundred and sixty pregnant patients were randomly selected for the educational programme and were enrolled in the study. In direct contact (groups of 4 to 14 pregnant patients) they received basic information about the condition for attaining and maintaining their and foetal good health [1]. In order to establish the results, three anonymous questionnaires were conducted. Two of them made the questionnaire A because of identical results obtained before and after the education, and the third questionnaire B was different, and was conducted at the end. The questionnaire B concerned the personal point of view of pregnant women about the obtained information [2]. RESULTS: The results of the first two questionnaires (questionnaire A) are shown in Graph with a quantity of correct answers expressed in percents. The results of the questionnaire B are formulated according to answers to a question with "YES" and "NO", and they are expressed in percentage. The following results were obtained for questionnaire B: A hundred percent of pregnant women stated that they had learned something new about oral health, 67 percent had immediately changed their nutrition for healthy food, 100 percent of them understood well the significant role of fluor prophylaxis, 16 percent did not accept it for unknown reasons, but 100 percent thought that it was very useful to hear lectures about oral health [3]. DISCUSSION: A great interest existed for all preventive stomatologic measures and dental procedures during pregnancy, which formerly, as a rule, were avoided because of ignorance [4]. It is necessary to carry out a proper prevention, and adequately inform and motivate pregnant women, so that we could have a satisfied mother and carefree child in the future.

Attitude to Health↗

[Perception of risk for infection with the human immunodeficiency virus].

Prevention of AIDS is very complex and requires, apart from basic knowledge about modes of transmission and protection, individual awareness of personal risk of infection and modification of one's risky behavior. Perception of risk has been suggested as an important element of sexual behavior change among people who engage in behaviors that place them at risk of HIV infection. This study investigates perceived risk of an HIV infection among inhabitants of municipality of Palilula. The purpose of this study was to determine the relative accuracy of risk assessment, especially for those with high-risk sexual behavior and to assess the factors related to self perception of developing AIDS. The survey was conducted as a household survey in Belgrade municipality "Palilula". The design of the survey was based on a two-stage stratified random sample. The population of Palilula municipality was divided in two stratums and 840 households were selected from each stratum. All members of selected households aged 15-49 years were interviewed. Total of 2659 persons was interviewed. Self administered questionnaire, developed by WHO and described in the Evaluation of National AIDS Programme: A Methods Package 1. Prevention of HIV infection, Geneva, 1994, was translated and adapted for local application. For analysis of findings methods of descriptive statistics, chi square test and logistic regression were used. Statistical analysis was performed using SPSS/PC. The results showed that most of the respondents (1662, 62.5%) do not perceive themselves to be at risk of HIV infection. Interestingly, almost one quarter of the sample couldn't estimate personal chances of being HIV infected. Significantly larger proportion of respondents living in urban area than those living in rural area perceived themselves at risk (17.1% of urban vs. 7.7% from rural area, chi square = 54.06, Ir0.00). Significant differences between age groups were found for perception of personal risk. Respondents up to 19 and those older than 25 in more than 60 percent and only a half of those between 20 and 24 believed that there was no chance they could become HIV infected. Almost 16% of respondents between 20 and 24 believed that they had some chances of contracting HIV, also approximately one third of them couldn't estimate personal risk of contracting HIV infection (chi square = 2.10, p = 0.00)(Graphe 1). Those who engaged in sex with irregular partners were found to perceive themselves in higher risk then those who were engaged in sex only with regular partners in previous 12 months. One fifth of those with irregular partners estimated their chances as good versus only 10% of those with only regular partners. A logistic regression analysis found that those who believed they were personally at risk knew someone with HIV, had more irregular sexual partners in last 12 months, were younger, and lived in urban area (Table 1). People correctly perceived the risk of HIV infection as being minimal as most of them didn't engage in risk behavior. Risk perception was higher among those who had more irregular partners, younger and those from urban area. Most important predictor of risk perception was knowledge of HIV positive individual.

Adolescent↗

Hidden complexity of free energy surfaces for peptide (protein) folding.

An understanding of the thermodynamics and kinetics of protein folding requires a knowledge of the free energy surface governing the motion of the polypeptide chain. Because of the many degrees of freedom involved, surfaces projected on only one or two progress variables are generally used in descriptions of the folding reaction. Such projections result in relatively smooth surfaces, but they could mask the complexity of the unprojected surface. Here we introduce an approach to determine the actual (unprojected) free energy surface and apply it to the second beta-hairpin of protein G, which has been used as a model system for protein folding. The surface is represented by a disconnectivity graph calculated from a long equilibrium folding-unfolding trajectory. The denatured state is found to have multiple low free energy basins. Nevertheless, the peptide shows exponential kinetics in folding to the native basin. Projected surfaces obtained from the present analysis have a simple form in agreement with other studies of the beta-hairpin. The hidden complexity found for the beta-hairpin surface suggests that the standard funnel picture of protein folding should be revisited.

Amino Acid Sequence↗

The biomechanics of the long jump.

The preceding review has been based on over 200 publications in Czech, English, French, German, Japanese, Polish, and Russian. Even a cursory perusal of these materials is sufficient to show that much has been done to try and obtain a scientific understanding of long jump techniques. It is clear, too, that still more remains to be done. Much of the work to date has been focused on just a few aspects of long jump technique. Other important aspects have received relatively little attention. The latter include the accuracy of the approach, the techniques used during the final strides of the approach, the role of elastic energy in the takeoff, the initiation and control of the jumper's angular momentum, and the techniques used in the landing. Future research efforts might well be directed towards resolving major issues concerning these aspects of long jump technique. The methods used to gather data in the studies reviewed have been rather unimaginative. Two-dimensional cinematography has been used in the vast majority of the studies and force platforms in a few. Other data-gathering procedures like three-dimensional cinematography, electromyography and accelerometry have rarely, if ever, been used. In only one or two studies was anything remotely approaching experimental or technological innovation in evidence. The methods used to analyze data have also been very limited. With the notable exception of a study by Ballreich, few papers have involved anything more sophisticated than means, standard deviations, correlation coefficients and an occasional multiple regression equation. Given these facts, it is hard to avoid the conclusion that our knowledge of long jump techniques might be greatly improved if the full range of available and appropriate procedures were turned to the purpose. Finally, no review of the literature on long jump techniques would be complete without reference to the level of scholarship displayed in the works under consideration. With only a few exceptions, the level shown in the scientific papers reviewed here left much to be desired. Time and again, variables were not defined, crucial measurement techniques were not described and major results were not presented or discussed. In addition, much of the data presented in tables and graphs were patently in error. In light of all this, it is clear that unless the level of scholarship improves, future progress in this area of sports biomechanics is likely to be very slow.

Biomechanical Phenomena↗

Transmitting a signal by amplitude modulation in a chaotic network.

We discuss the ability of a model of network with nonlinear units and chaotic dynamics to transmit signals, on the basis of a linear response theory developed by Ruelle [D. Ruelle, J. Stat. Phys. 95, 393 (1999)] for dissipative systems. We discuss in particular how the dynamics may interfere with the graph topology to produce an effective transmission network, whose topology depends on the signal, and cannot be directly read on the "wired" network. Then, we show examples where, with a suitable choice of the carrier frequency (resonance), one can transmit a signal from a node to another one by amplitude modulation, in spite of chaos. Also, we give an example where a signal, transmitted to any node via different paths, can only be recovered by a couple of specific nodes. This opens up the possibility for encoding data in a way such that the recovery of the signal requires the knowledge of the carrier frequency and can be performed only at some specific node.

Journal Article↗

Recursive neural networks for processing graphs with labelled edges: theory and applications.

In this paper, we introduce a new recursive neural network model able to process directed acyclic graphs with labelled edges. The model uses a state transition function which considers the edge labels and is independent both from the number and the order of the children of each node. The computational capabilities of the new recursive architecture are assessed. Moreover, in order to test the proposed architecture on a practical challenging application, the problem of object detection in images is also addressed. In fact, the localization of target objects is a preliminary step in any recognition system. The proposed technique is general and can be applied in different detection systems, since it does not exploit any a priori knowledge on the particular problem. Some experiments on face detection, carried out on scenes acquired by an indoor camera, are reported, showing very promising results.

Computer Simulation↗

Integrated visualization of problemcentric urologic patient records.

The collision of computer-based technologies and the medical environment is resulting in an increasingly electronic multimedia patient record, consisting of not only the traditional types of data (e.g., clinic notes and laboratory reports), but also digital images (e.g., computed tomography and magnetic resonance imaging) and other visual representations of patient data (e.g., pulmonary function graphs and urodynamic charts). Given the increasing amount of data made available to physicians, it is not only critical that the totality of a patient's medical record be accessible to a clinician, but that the diverse data be integrated and presented in a manner conducive to patient management: key information should be easily discovered. This paper describes a problemcentric time-based visualization of urologic conditions, whereby a patient's medical history is automatically organized around a medical problem and presented as a graphic chronology. Urology-related data in the patient medical record is organized in accord with an expert constructed knowledge-base, and plotted on a timeline using iconic representations. The user interface permits the physician to quickly view multimedia data and to visualize relationships between events in the patient's history.

Computer Systems↗