Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Generative models”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,675 records · Page 93Linked to original sources
PubMed2006

Rapid knot detection and application to protein structure prediction.

MOTIVATION: Knots in polypeptide chains have been found in very few proteins, and consequently should be generally avoided in protein structure prediction methods. Most effective structure prediction methods do not model the protein folding process itself, but rather seek only to correctly obtain the final native state. Consequently, the mechanisms that prevent knots from occurring in native proteins are not relevant to the modeling process, and as a result, knots can occur with significantly higher frequency in protein models. Here we describe Knotfind, a simple algorithm for knot detection that is fast enough for structure prediction, where tens or hundreds of thousands of conformations may be sampled during the course of a prediction. We have used this algorithm to characterize knots in large populations of model structures generated for targets in CASP 5 and CASP 6 using the Rosetta homology-based modeling method. RESULTS: Analysis of CASP5 models suggested several possible avenues for introduction of knots into these models, and these insights were applied to structure prediction in CASP 6, resulting in a significant decrease in the proportion of knotted models generated. Additionally, using the knot detection algorithm on structures in the Protein Data Bank, a previously unreported deep trefoil knot was found in acetylornithine transcarbamylase. AVAILABILITY: The Knotfind algorithm is available in the Rosetta structure prediction program at http://www.rosettacommons.org.

Algorithms↗
PubMed2006

Gray correlation analysis and prediction models of living refuse generation in Shanghai city.

A better understanding of the factors that affect the generation of municipal living refuse (MLF) and the accurate prediction of its generation are crucial for municipal planning projects and city management. Up to now, most of the design efforts have been based on a rough prediction of MLF without any actual support. In this paper, based on published data of socioeconomic variables and MLF generation from 1990 to 2003 in the city of Shanghai, the main factors that affect MLF generation have been quantitatively studied using the method of gray correlation coefficient. Several gray models, such as GM(1,1), GIM(1), GPPM(1) and GLPM(1), have been studied, and predicted results are verified with subsequent residual test. Results show that, among the selected seven factors, consumption of gas, water and electricity are the largest three factors affecting MLF generation, and GLPM(1) is the optimized model to predict MLF generation. Through this model, the predicted MLF generation in 2010 in Shanghai will be 7.65 million tons. The methods and results developed in this paper can provide valuable information for MLF management and related municipal planning projects.

China↗
PubMed2004

Generalization as a behavioral window to the neural mechanisms of learning internal models.

In generating motor commands, the brain seems to rely on internal models that predict physical dynamics of the limb and the external world. How does the brain compute an internal model? Which neural structures are involved? We consider a task where a force field is applied to the hand, altering the physical dynamics of reaching. Behavioral measures suggest that as the brain adapts to the field, it maps desired sensory states of the arm into estimates of force. If this neural computation is performed via a population code, i.e., via a set of bases, then activity fields of the bases dictate a generalization function that uses errors experienced in a given state to influence performance in any other state. The patterns of generalization suggest that the bases have activity fields that are directionally tuned, but directional tuning may be bimodal. Limb positions as well as contextual cues multiplicatively modulate the gain of tuning. These properties are consistent with the activity fields of cells in the motor cortex and the cerebellum. We suggest that activity fields of cells in these motor regions dictate the way we represent internal models of limb dynamics.

Biomechanical Phenomena↗
PubMed1982

Chlorination of taurine by human neutrophils. Evidence for hypochlorous acid generation.

The model hydrogen peroxide-myeloperoxidase-chloride system is capable of generating the powerful oxidant hypochlorous acid, which can be quantitated by trapping the generated species with the beta-amino acid, taurine. The resultant stable product, taurine chloramine, can be quantitated by its ability to oxidize the sulfhydryl compound, 5-thio-2-nitro-benzoic acid to the disulfide, 5,5'-dithiobis(2-nitroben-zoic acid) or to oxidize iodide to iodine. Using this system, purified myeloperoxidase in the presence of chloride and taurine converted stoichiometric quantities of hydrogen peroxide to taurine chloramine. Chloramine generation was absolutely dependent on hydrogen peroxide, myeloperoxidase, and chloride and could be inhibited by catalase, myeloperoxidase inhibitors, or chloride-free conditions. In the presence of taurine, intact human neutrophils stimulated with either phorbol myristate acetate or opsonized zymosan particles generated a stable species capable of oxidizing 5-thio-2-nitrobenzoic acid or iodide. Resting cells did not form this species. The oxidant formed by the stimulated neutrophils was identified as taurine chloramine by both ultraviolet spectrophotometry and electrophoresis. Taurine chloramine formation by the neutrophil was dependent on the taurine concentration, time, and cell number. Neutrophil-dependent chloramine generation was inhibited by catalase, the myeloperoxidase inhibitors, azide, cyanide, or aminotriazole and by chloride-free conditions, but not by superoxide dismutase or hydroxyl radical scavengers. Thus, it appears that stimulated human neutrophils can utilize the hydrogen peroxide-myeloperoxidase-chloride system to generate taurine chloramine. Based on the demonstrated ability of the myeloperoxidase system to generate free hypochlorous acid we conclude that neutrophils chlorinate taurine by producing this powerful oxidant. The biologic reactivity and cytotoxic potential of hypochlorous acid and its chloramine derivatives suggest that these oxidants play an important role in the inflammatory response and host defense.

Cells, Cultured↗
PubMed1992

Motor-pattern-generating networks in invertebrates: modeling our way toward understanding.

Motor-pattern-generating networks in invertebrates have been the objects of intensive study to determine the origin and modulation of rhythmic neural activity. In some pattern generators, intrinsically bursting neurons drive activity throughout the network. In most pattern generators, however, rhythmicity arises from the interplay between intrinsic membrane properties and synaptic interaction. Reciprocal inhibitory synapses between neurons are thought to be crucial for generating oscillation in these networks, but a fundamental understanding of how such network oscillators work remains elusive. Progress towards this goal has come from attempts to combine computational modeling approaches with conventional physiological analysis.

Animals↗
PubMed2005

Quantitative characterization of a mitotic cyclin threshold regulating exit from mitosis.

Regulation of cyclin abundance is central to eukaryotic cell cycle control. Strong overexpression of mitotic cyclins is known to lock the system in mitosis, but the quantitative behavior of the control system as this threshold is approached has only been characterized in the in vitro Xenopus extract system. Here, we quantitate the threshold for mitotic block in budding yeast caused by constitutive overexpression of the mitotic cyclin Clb2. Near this threshold, the system displays marked loss of robustness, in that loss or even heterozygosity for some regulators becomes deleterious or lethal, even though complete loss of these regulators is tolerated at normal cyclin expression levels. Recently, we presented a quantitative kinetic model of the budding yeast cell cycle. Here, we use this model to generate biochemical predictions for Clb2 levels, asynchronous as well as through the cell cycle, as the Clb2 overexpression threshold is approached. The model predictions compare well with biochemical data, even though no data of this type were available during model generation. The loss of robustness of the Clb2 overexpressing system is also predicted by the model. These results provide strong confirmation of the model's predictive ability.

Cell Cycle↗
PubMed2006

Synthesis, anti-tuberculosis activity, and 3D-QSAR study of 4-(adamantan-1-yl)-2-substituted quinolines.

Structural optimization of the previously identified 4-(adamantan-1-yl)-2-quinolinecarbohydrazide (AQCH, MIC=6.25 microg/mL, 99% inhibition, Mycobacterium tuberculosis H37Rv) has led to two series of 4-(adamantan-1-yl)-2-substituted quinolines (Series 1-2). All new derivatives were evaluated in vitro for antimycobacterial activities against drug-sensitive M. tuberculosis H37Rv strain. Several 4-adamantan-1-yl-quinoline-2-carboxylic acid N'-alkylhydrazides (Series 1) described herein showed promising inhibitory activity. In particular, analogs 7, 9, 20, and 21 displayed MIC of 3.125 microg/mL. Further investigation of AQCH by its reaction with various aliphatic, aromatic, and heteroaromatic aldehydes led to the synthesis of 4-adamantan-1-yl-quinoline-2-carboxylic acid alkylidene hydrazides (Series 2). Analogs 42-44 and 48 have produced promising antimycobacterial activities (99% inhibition) at 3.125 microg/mL against drug-sensitive M. tuberculosis H37Rv strain. The most potent analog 35 of the series produced 99% inhibition at 1.00 microg/mL against drug-sensitive strain, and MIC of 3.125 microg/mL against isoniazid-resistant TB strain. To understand the relationship between structure and activity, a 3D-QSAR analysis has been carried out by three methods-comparative molecular field analysis (CoMFA), CoMFA with inclusion of a hydropathy field (HINT), and comparative molecular similarity indices analysis (CoMSIA). Several statistically significant CoMFA, CoMFA with HINT, and CoMSIA models were generated. Prediction of the activity of a test set of molecules was the best for the CoMFA model generated with database alignment. Based on the CoMFA contours, we have tried to explain the structure-activity relationships of the compounds reported herein.

Adamantane↗
PubMed2002

QSAR of HIV-1 integrase inhibitors by genetic function approximation method.

Quantitative structure--activity relationship (QSAR) paradigm, using genetic function approximation (GFA) technique was used to examine the correlations between the calculated physicochemical descriptors and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. Depending on the chemical structure, all molecules were divided into two classes---catechols and noncatechols. Eighty-one molecules were used in the present study and they were divided into training set and test set. The training set in each class consisted of 35 molecules and QSAR models were generated separately for both catechols and noncatechols. Equations were evaluated using internal as well as external test set predictions. Models generated for catechols show that electronic, shape related, and thermodynamic parameters are important whereas for noncatechols, spatial, structural, and thermodynamic properties play an important role for the activity.

Anti-HIV Agents↗
PubMed2005

3D-QSAR study of ring-substituted quinoline class of anti-tuberculosis agents.

A 3D-QSAR analysis of a new class of ring-substituted quinolines with anti-tuberculosis activity has been carried out by three methods-Comparative Molecular Field Analysis (CoMFA), CoMFA with inclusion of a hydropathy field (HINT), and Comparative Molecular Similarity Indices Analysis (CoMSIA). The conformation of the molecules was generated using a simulated annealing protocol and they were superimposed using features common to the set with database alignment (SYBYL) and field fit methods. Several statistically significant CoMFA, CoMFA with HINT, and CoMSIA models were generated. Prediction of the activity of a set of test molecules was the best for the CoMFA model generated with database alignment. Based upon the information contained in the CoMFA model, we have identified some novel features that can be incorporated into the quinoline framework to improve the activity.

Antitubercular Agents↗
PubMed1991

Bifurcating spatially heterogeneous solutions in a chemotaxis model for biological pattern generation.

We consider a simple cell-chemotaxis model for spatial pattern formation on two-dimensional domains proposed by Oster and Murray (1989, J. exp. Zool. 251, 186-202). We determine finite-amplitude, steady-state, spatially heterogeneous solutions and study the effect of domain growth on the resulting patterns. We also investigate in-depth bifurcating solutions as the chemotactic parameter varies. This numerical study shows that this deceptively simple-chemotaxis model can produce a surprisingly rich spectrum of complex spatial patterns.

Animals↗
PubMed1997

Modeling neural mechanisms for genesis of respiratory rhythm and pattern. II. Network models of the central respiratory pattern generator.

The present paper describes several models of the central respiratory pattern generator (CRPG) developed employing experimental data and current hypotheses for respiratory rhythmogenesis. Each CRPG model includes a network of respiratory neuron types (e.g., early inspiratory; ramp inspiratory; late inspiratory; decrementing expiratory; postinspiratory; stage II expiratory; stage II constant firing expiratory; preinspiratory) and simplified models of lung and pulmonary stretch receptors (PSR), which provide feedback to the respiratory network. The used models of single respiratory neurons were developed in the Hodgkin-Huxley style as described in the previous paper. The mechanism for termination of inspiration (the inspiratory off-switch) in all models operates via late-I neuron, which is considered to be the inspiratory off-switching neuron. Several two- and three-phase CRPG models have been developed using different accepted hypotheses of the mechanism for termination of expiration. The key elements in the two-phase models are the early-I and dec-E neurons. The expiratory off-switch mechanism in these models is based on the mutual inhibitory connections between early-I and dec-E and adaptive properties of the dec-E neuron. The difference between the two-phase models concerns the mechanism for ramp firing patterns of E2 neurons resulting either from the intrinsic neuronal properties of the E2 neuron or from disinhibition from the adapting dec-E neuron. The key element of the three-phase models is the pre-I neuron, which acts as the expiratory off-switching neuron. The three-phase models differ by the mechanisms used for termination of expiration and for the ramp firing patterns of E2 neurons. Additional CRPG models were developed employing a dual switching neuron that generates two bursts per respiratory cycle to terminate both inspiration and expiration. Although distinctly different each model generates a stable respiratory rhythm and shows physiologically plausible firing patterns of respiratory neurons with and without PSR feedback. Using our models, we analyze the roles of different respiratory neuron types and their interconnections for the respiratory rhythm and pattern generation. We also investigate the possible roles of intrinsic biophysical properties of different respiratory neurons in controlling the duration of respiratory phases and timing of switching between them. We show that intrinsic membrane properties of respiratory neurons are integrated with network properties of the CRPG at three hierarchical levels: at the cellular level to provide the specific firing patterns of respiratory neurons (e.g., ramp firing patterns); at the network level to provide switching between the respiratory phases; and at the systems level to control the duration of inspiration and expiration under different conditions (e.g., lack of PSR feedback).

Adaptation, Physiological↗
PubMed2002

Can we tell how a community was constructed? A comparison of five evenness indices for their ability to identify theoretical models of community construction.

Evenness indices provide a simple measure of community structure. It might therefore be possible to use them to identify the process by which a community has been assembled. To test whether this is practicable, we constructed simulated community samples using five stochastic models of community construction, proposed by Tokeshi. We then examined the ability of five evenness indices to identify the model under which the community samples were produced. Each model produced samples with a range of evenness values, but mean evenness differed between the models. The dominance decay (DD) model produced community samples with the greatest evenness, followed by MacArthur fraction (MF). Evenness was lowest under the dominance pre-emption (DP) model. The differences between models were quite consistent across indices and consistent between 5-species and 15-species communities. Samples produced under the DD and MF models varied least in evenness between 5-species and 15-species samples, and those produced under the random assortment (RA) model varied most, irrespective of the evenness index used. Evenness varied considerably between replicate samples, as expected with stochastic processes. In 5-species communities, the greatest robustness in evenness across replicates was seen using indices O or E'. In 15-species communities, O and E(Q) were the most robust. The index best able to identify the model which had generated the sample differed between models and with species richness. If the model of interest is not known in advance, the best index for identifying the generating model is E(var) for communities of more than 10 species for RF, RA and DP models and O for other communities. The number of samples required in a data set before it could be effectively identified was, for example, more than 30 for 5-species samples produced under the random fraction (RF) model, and 3 for 15-species RF samples. In contrast, a 5-species DD data set could be effectively identified when it contained 15 or more samples. We conclude that evenness can be used to identify the process by which the community has been constructed, out of the five models considered here. The best evenness index for doing this varies with the species richness and the evenness of the community but we can suggest the use of O without knowing the model because its the more stable one against species richness and the more robust and unbiased against simulated samples and it encompass a good discriminating power between the models in most of the cases studied.

Abstracting and Indexing↗
PubMed2001

Models of central pattern generators for quadruped locomotion. II. Secondary gaits.

We continue the analysis of the network of symmetrically coupled cells modeling central pattern generators (CPG) for quadruped locomotion proposed by Golubitsky, Stewart, Buono and Collins by studying secondary gaits. Secondary gaits are modeled by output signals from the CPG where each cell emits one of two different output signals along with exact phase shifts. Examples of secondary gaits are transverse gallop, rotary gallop, and canter. We classify secondary gaits that bifurcate when the Poincaré map of a primary gait has a real eigenvalue crossing the unit circle. In particular, we show that periodic solutions modeling transverse gallop and rotary gallop bifurcate from primary gaits. Moreover, we find gaits from period-doubling bifurcations and analyze plausible footfall patterns. Numerical simulations are performed using the Morris-Lecar equations as cell dynamics.

Animals↗
PubMed1993

PROGEN: an automated modelling algorithm for the generation of complete protein structures from the alpha-carbon atomic coordinates.

A modelling algorithm (PROGEN) for the generation of complete protein atomic coordinates from only the alpha-carbon coordinates is described. PROGEN utilizes an optimal geometry parameter (OGP) database for the positioning of atoms for each amino acid of the polypeptide model. The OGP database was established by examining the statistical correlations between 23 different intra-peptide and inter-peptide geometric parameters relative to the alpha-carbon distances for each amino acid in a library of 19 known proteins from the Brookhaven Protein Database (BPDB). The OGP files for specific amino acids and peptides were used to generate the atomic positions, with respect to alpha-carbons, for main-chain and side-chain atoms in the modelled structure. Refinement of the initial model was accomplished using energy minimization (EM) and molecular dynamics techniques. PROGEN was tested using 60 known proteins in the BPDB, representing a wide spectrum of primary and secondary structures. Comparison between PROGEN models and BPDB crystal reference structures gave r.m.s.d. values for peptide main-chain atoms between 0.29 and 0.76 A, with a grand average of 0.53 A for all 60 models. The r.m.s.d. for all non-hydrogen atoms ranged between 1.44 and 1.93 A for the 60 polypeptide models. PROGEN was also able to make the correct assignment of cis- or trans-proline configurations in the protein structures examined. PROGEN offers a fully automatic building and refinement procedure and requires no special or specific structural considerations for the protein to be modelled.

Algorithms↗
PubMedDate not supplied

3D modeling of phased array generated ultrasounds in lossy media.

A general algorithm for three-dimensional (3D) modeling of acoustic fields generated by phased array transducers and propagating in uniformly lossy media is introduced and illustrated also with the help of specific examples. Applications of the method are foreseen in the analysis and the design of transducers for echographic applications in order to evaluate and/or optimize their performances.

Acoustics↗
PubMed1998

Determinants of the substrate specificity of human cytochrome P-450 CYP2D6: design and construction of a mutant with testosterone hydroxylase activity.

Cytochrome P-450 CYP2D6, human debrisoquine hydroxylase, metabolizes more than 30 prescribed drugs, the vast majority of which are small molecules containing a basic nitrogen atom. In contrast, the similar mouse protein Cyp2d-9 was first characterized as a testosterone 16alpha-hydroxylase. No common substrates have been reported for the two enzymes. Here we investigate the structural basis of this difference in substrate specificity. We have earlier used a combination of NMR data and homology modelling to generate a three-dimensional model of CYP2D6 [Modi, Paine, Sutcliffe, Lian, Primrose, Wolf, C.R. and Roberts (1996) Biochemistry 35, 4541-4550]. We have now generated a homology model of Cyp2d-9 and compared the two models to identify specific amino acid residues that we believe form the substrate-binding site in each protein and therefore influence catalytic selectivity. Although there are many similarities in active site structure, the most notable difference is a phenylalanine residue (Phe-483) in CYP2D6, which in the model is located such that the bulky phenyl ring is positioned across the channel mouth, thus limiting the size of substrate that can access the active site. In Cyp2d-9, the corresponding position is occupied by an isoleucine residue, which imposes fewer steric restraints on the size of substrate that can access the active site. To investigate whether the amino acid residue at this position does indeed influence the catalytic selectivity of these enzymes, site-directed mutagenesis was used to change Phe-483 in CYP2D6 to isoleucine and also to tryptophan. CYP2D6, Cyp2d-9 and both mutant CYP2D6 proteins were co-expressed with NADPH cytochrome P-450 reductase as a functional mono-oxygenase system in Escherichia coli and their relative catalytic activities towards bufuralol and testosterone were determined. All four proteins exhibited catalytic activity towards bufuralol but only Cyp2d-9 catalysed the formation of 16alpha-hydroxytesterone. Uniquely, the CYP2D6F483I mutant acquired the ability to metabolize testosterone to a novel product, which was identified by MS and proton NMR spectroscopy as 15alpha-hydroxytestosterone. NMR spin relaxation experiments were used to measure distances between the haem iron and protons of testosterone bound to the CYP2D6F483I mutant. These experiments demonstrate that very minor modifications to the active site structure of CYP2D6 can have a profound influence on the substrate specificity of the enzyme.

Amino Acid Sequence↗
PubMed2001

Models of central pattern generators for quadruped locomotion. I. Primary gaits.

In this paper we continue the analysis of a network of symmetrically coupled cells modeling central pattern generators for quadruped locomotion proposed by Golubitsky, Stewart, Buono, and Collins. By a cell we mean a system of ordinary differential equations and by a coupled cell system we mean a network of identical cells with coupling terms. We have three main results in this paper. First, we show that the proposed network is the simplest one modeling the common quadruped gaits of walk, trot, and pace. In doing so we prove a general theorem classifying spatio-temporal symmetries of periodic solutions to equivariant systems of differential equations. We also specialize this theorem to coupled cell systems. Second, this paper focuses on primary gaits; that is, gaits that are modeled by output signals from the central pattern generator where each cell emits the same waveform along with exact phase shifts between cells. Our previous work showed that the network is capable of producing six primary gaits. Here, we show that under mild assumptions on the cells and the coupling of the network, primary gaits can be produced from Hopf bifurcation by varying only coupling strengths of the network. Third, we discuss the stability of primary gaits and exhibit these solutions by performing numerical simulations using the dimensionless Morris-Lecar equations for the cell dynamics.

Animals↗
PubMed2002

A lead-gill binding model to predict acute lead toxicity to rainbow trout (Oncorhynchus mykiss).

Rainbow trout (Oncorhynchus mykiss, approximately 2 g) were exposed to 0.6-1.0 microM Pb (125-200 microgl(-1)) for 3 h in ion-poor water. Complexing ligands (citrate, ethylenediamine, organic matter (OM)) or competing cations (Ca, Mg, Na) were added to the water. After exposure, trout gills were removed and analyzed for accumulated Pb. From these exposures, a conditional equilibrium binding constant (K) for Pb-gill binding was calculated (log K(Pb-gillPb)=6.0), plus conditional binding constants for cationic competition at the Pb binding sites and for Pb binding to OM in the water. These log K values were entered into the MINEQL+ aquatic chemistry equilibrium program, to calculate binding of Pb by trout gills. Two versions of the Pb-gill binding model were generated, one of which took into account OM quality as indicated by a simple measure of OM aromaticity, the specific absorption coefficient. The two model versions were tested against acute Pb toxicity (as the time to reach 50% fish mortality; LT50) during 1-week exposures of trout to 3.9 microM Pb in water collected from across southern Ontario. Both versions of the model generated highly significant correlations between the LT50 values and gill Pb concentrations calculated from measured exposure water chemistry, with the OM quality version correlating slightly better. Water pH also correlated well with the LT50 values, because the Pb exposures were in the pH range (7-8) where there is a nearly linear relationship between water pH and inorganic complexation of Pb. Advantages of the Pb-gill binding model include its completeness and the flexibility inherent in its conceptual framework, for example the inclusion of competition by Ca and H(+) for Pb binding sites on gills, and inclusion of complexation of Pb in the water column by natural OM and by carbonate.

Animals↗