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PubMed2005

Adaptive neuro-fuzzy inference systems for analysis of internal carotid arterial Doppler signals.

In this study, a new approach based on adaptive neuro-fuzzy inference system (ANFIS) was presented for detection of internal carotid artery stenosis and occlusion. The internal carotid arterial Doppler signals were recorded from 130 subjects that 45 of them suffered from internal carotid artery stenosis, 44 of them suffered from internal carotid artery occlusion and the rest of them were healthy subjects. The three ANFIS classifiers were used to detect internal carotid artery conditions (normal, stenosis and occlusion) when two features, resistivity and pulsatility indices, defining changes of internal carotid arterial Doppler waveforms were used as inputs. To improve diagnostic accuracy, the fourth ANFIS classifier (combining ANFIS) was trained using the outputs of the three ANFIS classifiers as input data. The proposed ANFIS model combined the neural network adaptive capabilities and the fuzzy logic qualitative approach. Some conclusions concerning the impacts of features on the detection of internal carotid artery stenosis and occlusion were obtained through analysis of the ANFIS. The performance of the ANFIS model was evaluated in terms of classification accuracies and the results confirmed that the proposed ANFIS classifiers have some potential in detecting the internal carotid artery stenosis and occlusion. The ANFIS model achieved accuracy rates which were higher than that of the stand-alone neural network model.

Adolescent↗

PubMed2004

Spontaneous self-assembly of an unsymmetric trinuclear triangular copper(II) pyrazolate complex, [Cu3(micro3-OH)(micro-pz)3(MeCOO)2(Hpz)] (Hpz = pyrazole). synthesis, experimental and theoretical characterization, reactivity, and catalytic activity.

The almost quantitative formation of the triangular trinuclear copper derivative [Cu3(3-OH)(-pz)3(MeCOO)2(Hpz)] (1) (Hpz = pyrazole), has been simply achieved by adding Hpz to an ethanol solution of Cu(MeCOO)2 x H2O. An X-ray molecular structure determination shows that 1 is completely unsymmetric and that trinuclear units result assembled in an extended bidimensional network formed through acetate bridges and hydrogen bonds. EPR and magnetic measurements are consistent with the presence of a single unpaired electron. Theoretical density functional calculations carried out for S = 1/2 provide a thorough description of the electronic structure of 1, allowing a detailed assignment of its UV-vis absorption spectrum. Compound 1 reacts with MeONa, yielding [Cu3(micro3-OH)(micro-pz)3(MeCOO)(MeO)(Hpz)] (2) and [Cu3(micro3-OH)(micro-pz)3(MeO)2(Hpz)] (3) through the substitution of one and two acetate ions, respectively, with MeO- ion(s). The spontaneous self-assembly of the triangular trinuclear Cu3 moiety seems to occur only with pyrazole as can be inferred by the results obtained in the reactions of copper(II) acetate with some substituted pyrazoles leading to the formation of mononuclear [Cu(MeCOO)2(L)2] (4-8) and dinuclear [Cu(MeCOO)2(L)]2 (9-11) (L = substituted pyrazole) compounds. Also the presence of acetate ions seems to play a leading role in determining the formation of the trinuclear triangular arrangement, as indicated by the formation of a mononuclear derivative, [Cu(CF3COO)2(Hpz)]2 (compound 12), in the reaction of copper(II) trifluoroacetate with pyrazole. Compounds 1-3, as well as some other mono- and dinuclear copper(II)-substituted pyrazole complexes, have been tested as catalyst precursors in cyclopropanation reaction, observing the formation of products in a syn:anti ratio opposite that normally reported.

Journal Article↗

PubMed2006

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.

BACKGROUND: A transcriptional regulatory module (TRM) is a set of genes that is regulated by a common set of transcription factors (TFs). By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation. RESULTS: Integrating gene expression and ChIP-chip data, we develop a method, called MOdule Finding Algorithm (MOFA), for reconstructing TRMs of the yeast cell cycle. MOFA identified 87 TRMs, which together contain 336 distinct genes regulated by 40 TFs. Using various kinds of data, we validated the biological relevance of the identified TRMs. Our analysis shows that different combinations of a fairly small number of TFs are responsible for regulating a large number of genes involved in different cell cycle phases and that there may exist crosstalk between the cell cycle and other cellular processes. MOFA is capable of finding many novel TF-target gene relationships and can determine whether a TF is an activator or/and a repressor. Finally, MOFA refines some clusters proposed by previous studies and provides a better understanding of how the complex expression program of the cell cycle is regulated. CONCLUSION: MOFA was developed to reconstruct TRMs of the yeast cell cycle. Many of these TRMs are in agreement with previous studies. Further, MOFA inferred many interesting modules and novel TF combinations. We believe that computational analysis of multiple types of data will be a powerful approach to studying complex biological systems when more and more genomic resources such as genome-wide protein activity data and protein-protein interaction data become available.

Algorithms↗

PubMed1996

Nonlinear enzyme kinetics can lead to high metabolic flux control coefficients: implications for the evolution of dominance.

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can except high values of control coefficient for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial "default" consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Animals↗

PubMed1994

Finding temporal patterns--a set-based approach.

We created an inference engine and query language for expressing temporal patterns in data. The patterns are represented by using temporally-ordered sets of data objects. Patterns are elaborated by reference to new objects inferred from original data, and by interlocking temporal and other relationships among sets of these objects. We found the tools well-suited to define scenarios of events that are evidence of inappropriate use of prescription drugs, using Medicaid administrative data that describe medical events. The tools' usefulness in research might be considerably more general.

Artificial Intelligence↗

PubMed2006

Representation and timing in theories of the dopamine system.

Although the responses of dopamine neurons in the primate midbrain are well characterized as carrying a temporal difference (TD) error signal for reward prediction, existing theories do not offer a credible account of how the brain keeps track of past sensory events that may be relevant to predicting future reward. Empirically, these shortcomings of previous theories are particularly evident in their account of experiments in which animals were exposed to variation in the timing of events. The original theories mispredicted the results of such experiments due to their use of a representational device called a tapped delay line. Here we propose that a richer understanding of history representation and a better account of these experiments can be given by considering TD algorithms for a formal setting that incorporates two features not originally considered in theories of the dopaminergic response: partial observability (a distinction between the animal's sensory experience and the true underlying state of the world) and semi-Markov dynamics (an explicit account of variation in the intervals between events). The new theory situates the dopaminergic system in a richer functional and anatomical context, since it assumes (in accord with recent computational theories of cortex) that problems of partial observability and stimulus history are solved in sensory cortex using statistical modeling and inference and that the TD system predicts reward using the results of this inference rather than raw sensory data. It also accounts for a range of experimental data, including the experiments involving programmed temporal variability and other previously unmodeled dopaminergic response phenomena, which we suggest are related to subjective noise in animals' interval timing. Finally, it offers new experimental predictions and a rich theoretical framework for designing future experiments.

Algorithms↗

PubMed2004

Bayesian inference for randomized clinical trials with treatment failures.

During the course of a clinical trial, subjects may experience treatment failure. For ethical reasons, it is necessary to administer emergency or rescue medications for such subjects. However, the rescue medications may bias the set of response measurements. This bias is of particular concern if a subject has been randomized to the control group, and the rescue medications improve the subject's condition. The standard approach to analysing data from a clinical trial is to perform an intent-to-treat (ITT) analysis, wherein the data are analysed according to treatment randomization. Supplementary analyses may be performed in addition to the ITT analysis to account for the effect of treatment failures and rescue medications. A Bayesian, counterfactual approach, which uses the data augmentation (DA) algorithm, is proposed for supplemental analysis. A simulation study is conducted to compare the operating characteristics of this procedure with a likelihood-based, counterfactual approach based on the EM algorithm. An example from the Asthma Clinical Research Network (ACRN) is used to illustrate the Bayesian procedure.

Algorithms↗

PubMed2003

Molecular evolution of a plastid tandem repeat locus in an orchid lineage.

The molecular evolution of a chloroplast minisatellite locus in the Anacamptis palustris (Orchidaceae) lineage and haplotype variation in two Italian A. palustris populations were investigated. A phylogenetic analyses of the chloroplast tRNA(LEU) intron, where the minisatellite locus is located, revealed that a deletion in the ancestor of the A. palustris lineage led to the formation of two noncontiguous, complementary sequence motifs. We propose a model to explain the initial formation of the minisatellite repeat motif, starting with the two noncontiguous, complementary sequence motifs. A survey of minisatellite variation in four species of the A. palustris lineage revealed several haplotypes that differed not only in repeat number, but also in repeat organization. A haplotype network suggests that three different minisatellite loci evolved independently at the same position in the tRNA(LEU) intron. A secondary structure model revealed that the A. palustris minisatellite repeat forms a stem region of the tRNA(LEU) intron, which allows its notable expansion without negatively affecting splicing. Minisatellite variation was high in the two examined A. palustris populations where 20 haplotypes were detected, whereas no length variation was detected in a neighboring poly (A) microsatellite locus. We estimated a chloroplast minisatellite mutation rate of 3.2 x 10(-3) mutations per generation. Southern blot analyses did not find evidence for chloroplast heteroplasmy. Based on the analysis of the largest known, extant A. palustris population, a stepwise mutation model (SMM) was inferred.

Evolution, Molecular↗

PubMed2001

Neuronal contact guidance in magnetically aligned fibrin gels: effect of variation in gel mechano-structural properties.

Neurite outgrowth from chick dorsal root ganglia entrapped in isotropic and magnetically aligned fibrin gels was studied, and the dependence on the diameter of the fibrin fibrils was characterized. The fibrin fibril diameter was varied, as inferred from turbidity measurements, by using different Ca2+ concentrations in the fibrin-forming solution, but this variation was accomplished without affecting the degree of magnetic-induced alignment, as directly visualized in fluorescently spiked gels. Magnetically aligned fibrin gels possessing different fibril diameters but similar alignment resulted in drastic changes in the contact guidance response of neurites, with no response in gels formed in 1.2 mM Ca2+ (having smaller fibril diameter, ca. 150 nm), but a strong response in gels formed in 12 and 30 mM Ca2+ (having larger fibril diameter, ca. 510 nm) with an attendant two-fold increase in neurite length. These changes are attributed to variation of the mechano-structural properties of the network of aligned fibrils as the fibril diameter is varied.

Animals↗

PubMed2003

Visualizing how one brain understands another: a PET study of theory of mind.

OBJECTIVE: Theory of mind (TOM), or "mentalizing," refers to the ability to attribute mental states to self and others. Inferring what people are thinking and feeling is an important aspect of human social interaction, and it is also an important aspect of both psychiatric diagnosis and treatment. The authors conducted a positron emission tomography (PET) study to examine the neural substrates of TOM, using a task that mimics real-life social interaction. METHOD: Thirteen healthy volunteers underwent [(15)O]H(2)O PET while performing an experimental task and a control task. During the experimental task they created a "story" about the mental state of a stranger whom they imagined encountering on a park bench. During the control task, they read aloud a story requiring no mental state attribution. RESULTS: The TOM task activated an extensive neural network that included the medial frontal cortex, the superior frontal cortex, the anterior and retrosplenial cingulate, and the anterior temporal pole; most of these activations were limited to the left hemisphere. In addition, the largest activation was in the contralateral right cerebellum, as well as the anterior vermis. CONCLUSIONS: A language-based TOM task activated distributed brain regions that are important for representing mental states of the self and others, retrieving memory of personal experiences, and coordinating and monitoring the overall performance of the task. The activations in the medial frontal cortex replicate findings in previous TOM studies, while the activations in the cerebellum reinforce the growing evidence that the cerebellum performs cognitive functions in the human brain.

Adult↗

PubMed2001

The laminins in the murine inner ear: developmental transitions and expression in cochlear basement membranes.

The laminins are a family of heterotrimeric extracellular matrix molecules that form suprastructural networks in basement membranes and elsewhere. They interact with integrin receptors, playing key roles in modulating programs of cytodifferentiation and maintaining tissue homeostasis in animals. Earlier studies have demonstrated an extensive laminin network in both the developing and adult cochlea, primarily associated with the basement membranes. These studies, however, did not address the laminin chain composition of these networks. In this study, we used antibodies specific for the known laminin chains to examine the composition of laminins in both the developing and adult murine cochlea. The results illustrate a complex and dynamic postnatal developmental regulation pattern for most of these chains, and suggest that an unusually large number of laminin heterotrimers are present in both the developing and adult cochlea. The laminin composition at postnatal day 2 is relatively simple. By postnatal day 7, however, activation of several laminin chains results in a very complex laminin composition. In the basement membrane underlying the region of the basilar membrane under the developing organ of Corti, eight of the 11 known basement membrane laminins are possible by co-localization inference. Dynamic changes in expression continue through day 14, but simplify by adulthood. Thus, the most dynamic period for laminin expression in the mouse cochlea coincides with terminal cytodifferentiation of the cochlear epithelial structures. Considering the well established role of laminins in regulating both embryonic and organ development in other systems, these data suggest a closer look at the role of the laminins in cochlear development and function may be warranted.

Aging↗

PubMedDate not supplied

Database mining using soft computing techniques. An integrated neural network-fuzzy logic-genetic algorithm approach.

Two different soft computing (SC) techniques (a competitive learning neural network and an integrated neural network-fuzzy logic-genetic algorithm approach) are employed in the analysis of a database subset obtained from the Cambridge Structural Database. The chemical problem chosen for study is relevant to the relationship between various metric parameters in transition metal imido (LnMdNZ, Z = carbon-based substituent) complexes and the chemical consequences of such relationships. The SC techniques confirmed and quantified the suspected relationship between the metal-nitrogen bond length and the metal-nitrogen-substituent bond angle for transition metal imidos: increased metal-nitrogen-carbon angles correlate with shortened metal-nitrogen distances. The mining effort also yielded an unexpected correlation between the NC distance and the MNC angle-shorter NC correlate with larger MNC. A fuzzy inference system is used to construct an MNred-NC-MNC hypersurface. This hypersurface suggests a complicated interdependence among NC, MNred, and the angle subtended by these two bonds. Also, major portions of the hypersurface are very flat, in regions where MNC is approaching linearity. The relationships are also seen to be influenced by whether the imido substituent is an alkyl or aryl group. Computationally, the present results are of particular interest in two respects. First, SC classification was able to isolate an "outlier" cluster. Identification of outliers is important as they may correspond to unreported experimental errors in the database or novel chemical entities, both of which warrant further investigation. Second, the SC database mining not only confirmed and quantified a suspected relationship (MNred versus MNC) within the data but also yielded a trend that was not suspected (NC versus MNC).

Journal Article↗

PubMed2006

Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase.

In this work we compare the dynamics and conformational stability of Pseudomonas mendocina lipase enzyme and its F180P/S205G mutant that shows higher activity and stability for use in washing powders. Our NMR analyses indicate virtually identical structures but reveal remarkable differences in local dynamics, with striking correspondence between experimental data (i.e., (15)N relaxation and H/D exchange rates) and data from Molecular Dynamics simulations. While overall the cores of both proteins are very rigid on the pico- to nanosecond timescale and are largely protected from H/D exchange, the two point mutations stabilize helices alpha1, alpha4, and alpha5 and locally destabilize the H-bond network of the beta-sheet (beta7-beta9). In particular, it emerges that helix alpha5, undergoing some fast destabilizing motions (on the pico- to nanosecond timescale) in wild-type lipase, is substantially rigidified by the mutation of Phe180 for a proline at its N terminus. This observation could be explained by the release of some penalizing strain, as proline does not require any "N-capping" hydrogen bond acceptor in the i+3 position. The combined experimental and simulated data thus indicate that reduced molecular flexibility of the F180P/S205G mutant lipase underlies its increased stability, and thus reveals a correlation between microscopic dynamics and macroscopic thermodynamic properties. This could contribute to the observed altered enzyme activity, as may be inferred from recent studies linking enzyme kinetics to their local molecular dynamics.

Amino Acid Sequence↗

PubMed2005

Divergent evolution within protein superfolds inferred from profile-based phylogenetics.

Many dissimilar protein sequences fold into similar structures. A central and persistent challenge facing protein structural analysis is the discrimination between homology and convergence for structurally similar domains that lack significant sequence similarity. Classic examples are the OB-fold and SH3 domains, both small, modular beta-barrel protein superfolds. The similarities among these domains have variously been attributed to common descent or to convergent evolution. Using a sequence profile-based phylogenetic technique, we analyzed all structurally characterized OB-fold, SH3, and PDZ domains with less than 40% mutual sequence identity. An all-against-all, profile-versus-profile analysis of these domains revealed many previously undetectable significant interrelationships. The matrices of scores were used to infer phylogenies based on our derivation of the relationships between sequence similarity E-values and evolutionary distances. The resulting clades of domains correlate remarkably well with biological function, as opposed to structural similarity, indicating that the functionally distinct sub-families within these superfolds are homologous. This method extends phylogenetics into the challenging "twilight zone" of sequence similarity, providing the first objective resolution of deep evolutionary relationships among distant protein families.

Evolution, Molecular↗

PubMed2006

Complete functional characterization of sensory neurons by system identification.

System identification is a growing approach to sensory neurophysiology that facilitates the development of quantitative functional models of sensory processing. This approach provides a clear set of guidelines for combining experimental data with other knowledge about sensory function to obtain a description that optimally predicts the way that neurons process sensory information. This prediction paradigm provides an objective method for evaluating and comparing computational models. In this chapter we review many of the system identification algorithms that have been used in sensory neurophysiology, and we show how they can be viewed as variants of a single statistical inference problem. We then review many of the practical issues that arise when applying these methods to neurophysiological experiments: stimulus selection, behavioral control, model visualization, and validation. Finally we discuss several problems to which system identification has been applied recently, including one important long-term goal of sensory neuroscience: developing models of sensory systems that accurately predict neuronal responses under completely natural conditions.

Animals↗

PubMedDate not supplied

Webifying a patient interview support application.

This paper reports on the software engineering challenges, and resultant benefits experienced, in porting an interactive, knowledge-based system from Microsoft Windows to the World Wide Web for evaluation purposes. The Patients Interview Support Application (PISA) is a program intended for operation by a non-expert clerk to interview an ambulatory primary care patient. The PISA code had to be re-written substantially to address the 'connectionless' nature of Web dialog and to work in terms of dynamically generated HTML forms; however, it was possible to avoid any revision of the central knowledge-base or inference engine. The resultant Web environment attracted thought-provoking and detailed feedback from users, indicating that significant attention can be obtained from the global community by mounting an interactive system on the Web. Specific enhancements to the PISA's artificial intelligence are suggested by user reaction. A future global health informatics 'marketplace' with a multidue of Web-based system components available for composition of health information systems is envisioned.

Artificial Intelligence↗

PubMed1995

Quality assurance in clinical neurophysiology: the ESTEEM project example.

This paper describes the current status of the utilisation of clinical practice guidelines (protocols) in the ESTEEM project as one form of the clinical quality assurance procedures considered in the project. The performance of electrodiagnostic studies, in terms of which types of conclusions need to be inferred during the examination plan, is briefly described. The main focus of the paper is a description of an European multicentre clinical audit in the field of Clinical Neurophysiology, using a common data-entry protocol for prospective EMG case collection and assessment with the ultimate objective of building up a multicentre reference database of EMG cases.

Computer Communication Networks↗

PubMed2006

Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia.

The badger, Meles meles, is a widely distributed mustelid in Eurasia and shows large geographic variability in morphological characters whose evolutionary significance is unclear and needs to be contrasted with molecular data. We sequenced 512 bp of the mitochondrial DNA control region in 115 Eurasian badgers from 21 countries in order to test for the existence of structuring in their phylogeography, to describe the genetic relationships among their populations across its widespread geographic range, and to infer demographic and biogeographic processes. We found that the Eurasian badger is divided into four groups regarding their mitochondrial DNA: Europe, Southwest Asia, North and East Asia, and Japan. This result suggests that the separation of badgers into phylogeographic groups was influenced by cold Pleistocene glacial stages and permafrost boundaries in Eurasia, and by geographic barriers, such as mountains and deserts. Genetic variation within phylogeographic groups based on distances assuming the Tamura-Nei model with rate heterogeneity and invariable sites (d(T-N) range: 3.3-4.2) was much lower than among them (d(T-N) range: 10.7-38.0), and 80% of the variation could be attributed to differences among regions. Spatial analysis of molecular variance (samova), median-joining network, and Mantel test did not detect genetic structuring within any of the phylogeographic groups with the exception of Europe, where 50% of variation was explained by differences among groups of populations. Our data suggest that the European, Southwest Asian, and North and East Asian badgers evolved separately since the end of Pliocene, at the beginnings of glacial ages, whereas Japanese badgers separated from continental Asian badgers during the middle Pleistocene. Endangered badgers from Crete Island, classified as Meles meles arcalus subspecies, were closely related to badgers from Southwest Asia. We also detected sudden demographic growth in European and Southwest Asian badgers that occurred during the Middle Pleistocene.

Animal Migration↗