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PubMed2003

Numerical characterization and similarity analysis of DNA sequences based on 2-D graphical representation of the characteristic sequences.

Based on the classifications of the four nucleic acid bases, He and Wang reduced a DNA sequence to three binary sequences, which are called the characteristic sequences (J. Chem. Inf. Comput. Sci. 42 (2002) 1080). In this paper, we associate each characteristic sequence with a (b)L / (b)L matrix by giving a 2-D 'two horizontal lines' graphical representation, and thus obtain a 3-component vector with entries being the sums of the maximal and minimal eigenvalues of the (b)L / (b)L matrices. The introduced vector results in more simple characterizations and comparisons among the coding sequences of exon 1 of beta-globin gene of eleven different species.

Animals↗

PubMed2004

Inference for the proportional hazards model with misclassified discrete-valued covariates.

We consider the Cox proportional hazards model with discrete-valued covariates subject to misclassification. We present a simple estimator of the regression parameter vector for this model. The estimator is based on a weighted least squares analysis of weighted-averaged transformed Kaplan-Meier curves for the different possible configurations of the observed covariate vector. Optimal weighting of the transformed Kaplan-Meier curves is described. The method is designed for the case in which the misclassification rates are known or are estimated from an external validation study. A hybrid estimator for situations with an internal validation study is also described. When there is no misclassification, the regression coefficient vector is small in magnitude, and the censoring distribution does not depend on the covariates, our estimator has the same asymptotic covariance matrix as the Cox partial likelihood estimator. We present results of a finite-sample simulation study under Weibull survival in the setting of a single binary covariate with known misclassification rates. In this simulation study, our estimator performed as well as or, in a few cases, better than the full Weibull maximum likelihood estimator. We illustrate the method on data from a study of the relationship between trans-unsaturated dietary fat consumption and cardiovascular disease incidence.

Biometry↗

PubMed1995

Comparison of models of odor interaction.

Subjects rated the overall perceived intensity of concentrations of the odorants cineole, geraniol, hexyl salicylate, and linalyl acetate smelled alone and in binary mixtures. The subjects also rated intensity of specified constituents (e.g. amount of cineole in cineole, and in mixtures of cineole and linalyl acetate). The intensity of the stronger component alone offered a close description of perceived intensity. In addition to the Stronger Component model, two other psychological models (Vector and U model) and two psychophysical models (UPL2 and Equiratio Mixture model) offered descriptions ranging from fair to very good. Psychological models gave better fits, but lack explanatory power. Some results indicated that weaker odors add more potently than stronger odors, an outcome incompatible with these models. The psychophysical models, based on the additivity of single components, generally overestimated perceived intensity. Judgments of individual qualities gave only slight encouragement to any expectation of differences in masking or maskability among odorants. The results highlight the need to test particular critical hypotheses regarding how people perceive mixtures.

Acyclic Monoterpenes↗

PubMed2005

Applications of support vector machines to cancer classification with microarray data.

Microarray gene expression data usually have a large number of dimensions, e.g., over ten thousand genes, and a small number of samples, e.g., a few tens of patients. In this paper, we use the support vector machine (SVM) for cancer classification with microarray data. Dimensionality reduction methods, such as principal components analysis (PCA), class-separability measure, Fisher ratio, and t-test, are used for gene selection. A voting scheme is then employed to do multi-group classification by k(k - 1) binary SVMs. We are able to obtain the same classification accuracy but with much fewer features compared to other published results.

Algorithms↗

PubMedDate not supplied

[The susceptibility of mosquitoes for Plasmodium gallinaceum in the joint use of biologically active substances].

Making use of a model pair Aedes aegypti--Plasmodium gallinaceum, the authors assess the susceptibility of mosquito female survivors to malaria agent after treatment of larvae with various bioactive substances. Eight binary combinations of 6 preparations have been tried: dimilin and uvemon, insect development regulators; fundosol and copper sulfate, fungicides; phytobacteriomicin (PBM), a larvicidal antibiotic; bactoculicide, a bacterial agent. Combinations of PBM with compounds differing by their mechanisms of action were found to inhibit the specific effect of PBM on the vector, PBM specific effect consisting in depression of mosquito susceptibility to P. gallinaceum. PBM combinations with some agents may alter other parameters of the vector potential: combinations of copper sulfate or uvemon with low concentrations of PBM potentiated the larvicidal effect, and PBM mixtures with fungicides reduces the activity of female attacks.

Aedes↗

PubMed2004

Classification of brain tumours using short echo time 1H MR spectra.

The purpose was to objectively compare the application of several techniques and the use of several input features for brain tumour classification using Magnetic Resonance Spectroscopy (MRS). Short echo time 1H MRS signals from patients with glioblastomas (n = 87), meningiomas (n = 57), metastases (n = 39), and astrocytomas grade II (n = 22) were provided by six centres in the European Union funded INTERPRET project. Linear discriminant analysis, least squares support vector machines (LS-SVM) with a linear kernel and LS-SVM with radial basis function kernel were applied and evaluated over 100 stratified random splittings of the dataset into training and test sets. The area under the receiver operating characteristic curve (AUC) was used to measure the performance of binary classifiers, while the percentage of correct classifications was used to evaluate the multiclass classifiers. The influence of several factors on the classification performance has been tested: L2- vs. water normalization, magnitude vs. real spectra and baseline correction. The effect of input feature reduction was also investigated by using only the selected frequency regions containing the most discriminatory information, and peak integrated values. Using L2-normalized complete spectra the automated binary classifiers reached a mean test AUC of more than 0.95, except for glioblastomas vs. metastases. Similar results were obtained for all classification techniques and input features except for water normalized spectra, where classification performance was lower. This indicates that data acquisition and processing can be simplified for classification purposes, excluding the need for separate water signal acquisition, baseline correction or phasing.

Brain Chemistry↗

PubMedDate not supplied

Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance.

A molecular similarity searching technique based on atom environments, information-gain-based feature selection, and the naive Bayesian classifier has been applied to a series of diverse datasets and its performance compared to those of alternative searching methods. Atom environments are count vectors of heavy atoms present at a topological distance from each heavy atom of a molecular structure. In this application, using a recently published dataset of more than 100000 molecules from the MDL Drug Data Report database, the atom environment approach appears to outperform fusion of ranking scores as well as binary kernel discrimination, which are both used in combination with Unity fingerprints. Overall retrieval rates among the top 5% of the sorted library are nearly 10% better (more than 14% better in relative numbers) than those of the second best method, Unity fingerprints and binary kernel discrimination. In 10 out of 11 sets of active compounds the combination of atom environments and the naive Bayesian classifier appears to be the superior method, while in the remaining dataset, data fusion and binary kernel discrimination in combination with Unity fingerprints is the method of choice. Binary kernel discrimination in combination with Unity fingerprints generally comes second in performance overall. The difference in performance can largely be attributed to the different molecular descriptors used. Atom environments outperform Unity fingerprints by a large margin if the combination of these descriptors with the Tanimoto coefficient is compared. The naive Bayesian classifier in combination with information-gain-based feature selection and selection of a sensible number of features performs about as well as binary kernel discrimination in experiments where these classification methods are compared. When used on a monoaminooxidase dataset, atom environments and the naive Bayesian classifier perform as well as binary kernel discrimination in the case of a 50/50 split of training and test compounds. In the case of sparse training data, binary kernel discrimination is found to be superior on this particular dataset. On a third dataset, the atom environment descriptor shows higher retrieval rates than other 2D fingerprints tested here when used in combination with the Tanimoto similarity coefficient. Feature selection is shown to be a crucial step in determining the performance of the algorithm. The representation of molecules by atom environments is found to be more effective than Unity fingerprints for the type of biological receptor similarity calculations examined here. Combining information prior to scoring and including information about inactive compounds, as in the Bayesian classifier and binary kernel discrimination, is found to be superior to posterior data fusion (in the datasets tested here).

Journal Article↗

PubMed2002

Feature selection for structure-activity correlation using binary particle swarms.

We present a new feature selection algorithm for structure-activity and structure-property correlation based on particle swarms. Particle swarms explore the search space through a population of individuals that adapt by returning stochastically toward previously successful regions, influenced by the success of their neighbors. This method, which was originally intended for searching multidimensional continuous spaces, is adapted to the problem of feature selection by viewing the location vectors of the particles as probabilities and employing roulette wheel selection to construct candidate subsets. The algorithm is applied in the construction of parsimonious quantitative structure-activity relationship (QSAR) models based on feed-forward neural networks and is tested on three classical data sets from the QSAR literature. It is shown that the method compares favorably with simulated annealing and is able to identify a better and more diverse set of solutions given the same amount of simulation time.

Algorithms↗

PubMed1999

Evolution of speckle during spinodal decomposition.

Time-dependent properties of the speckled intensity patterns created by scattering coherent radiation from materials undergoing spinodal decomposition are investigated by numerical integration of the Cahn-Hilliard-Cook equation. For binary systems which obey a local conservation law, the characteristic domain size is known to grow in time tau as R=[Btau](n) with n=1/3, where B is a constant. The intensities of individual speckles are found to be nonstationary, persistent time series. The two-time intensity covariance at wave vector k can be collapsed onto a scaling function Cov(deltat,t), where deltat=k(1/n)B(tau(2)-tau(1)) and t=k(1/n)B(tau(1)+tau(2))/2. Both analytically and numerically, the covariance is found to depend on deltat only through deltat/t in the small-t limit and deltat/t (1-n) in the large-t limit, consistent with a simple theory of moving interfaces that applies to any universality class described by a scalar order parameter. The speckle-intensity covariance is numerically demonstrated to be equal to the square of the two-time structure factor of the scattering material, for which an analytic scaling function is obtained for large t. In addition, the two-time, two-point order-parameter correlation function is found to scale as C(r/(B(n)sqaureroot[tau1(2n)+tau2(2n)]),tau1/tau2), even for quite large distances r. The asymptotic power-law exponent for the autocorrelation function is found to be lambda approximately 4.47, violating an upper bound conjectured by Fisher and Huse.

Journal Article↗

PubMed1999

Interaction between the F plasmid TraA (F-pilin) and TraQ proteins.

Elaboration of conjugative (F) pili by F+ strains of Escherichia coli requires the activities of over a dozen F-encoded DNA transfer (Tra) proteins. The organization and functions of these proteins are largely unknown. Using the yeast two-hybrid assay, we have begun to analyse binary interactions among the Tra proteins required for F-pilus formation. We focus here on interactions involving F-pilin, the only known F-pilus subunit. Using a library of F tra DNA fragments that contained all the F genes required for F pilus formation in a yeast GAL4 activation domain vector (pACTII), we transformed yeast containing a plasmid (pAS1CYH2traA) encoding a GAL4 DNA-binding domain-F-pilin fusion. Doubly transformed cells were screened for GAL4-dependent gene expression. This screen repeatedly identified only a single Tra protein, TraQ, previously identified as a likely F-pilin chaperone. The F-pilin-TraQ interaction appeared to be specific, as no transcriptional activation was detected in yeast transformants containing pACTIItraQ plasmids and the Salmonella typhi pED208 traA gene cloned in pAS1CYH2. Two traQ segments isolated in the screen against F-pilin were tested for complementation of a traQ null allele in E. coli. One, lacking the first 11 (of 94) TraQ amino acids, restored DNA donor activity, donor-specific bacteriophage sensitivity and membrane F-pilin accumulation to wild-type levels. The second, lacking the first 21 amino acids, was much less effective in these assays. Both TraQ polypeptides accumulated in E. coli as transmembrane proteins. The longer, biologically active segment was fused to the GAL4 DNA-binding domain gene of pAS1CYH2 and used to screen the tra fragment library. The only positives from this screen identified traA segments. The fusion sites between the traA and GAL4 segments identified the hydrophobic, C-terminal domain IV of F-pilin as sufficient for the interaction. As TraQ is the only Tra protein required for the accumulation of inner membrane F-pilin, the interaction probably reflects a specific, chaperone-like function for TraQ in E. coli. Attempts to isolate an F-pilin-TraQ complex from E. coli were unsuccessful, suggesting that the interaction between the two is normally transient, as expected from previous studies of the kinetics of TraA membrane insertion and processing to F-pilin.

Amino Acid Sequence↗

PubMed2003

Classification of multiple cancer types by multicategory support vector machines using gene expression data.

MOTIVATION: High-density DNA microarray measures the activities of several thousand genes simultaneously and the gene expression profiles have been used for the cancer classification recently. This new approach promises to give better therapeutic measurements to cancer patients by diagnosing cancer types with improved accuracy. The Support Vector Machine (SVM) is one of the classification methods successfully applied to the cancer diagnosis problems. However, its optimal extension to more than two classes was not obvious, which might impose limitations in its application to multiple tumor types. We briefly introduce the Multicategory SVM, which is a recently proposed extension of the binary SVM, and apply it to multiclass cancer diagnosis problems. RESULTS: Its applicability is demonstrated on the leukemia data (Golub et al., 1999) and the small round blue cell tumors of childhood data (Khan et al., 2001). Comparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods. SUPPLEMENTARY INFORMATION: http://www.stat.ohio-state.edu/~yklee/msvm.htm

Algorithms↗

PubMed1997

Cloning and expression of the Bacillus sphaericus 2362 mosquitocidal genes in a non-toxic unicellular cyanobacterium, Synechococcus PCC6301.

Genes encoding the mosquitocidal binary toxin of Bacillus sphaericus 2362 were introduced into Synechococcus PCC6301, a cyanobacterium that can tolerate a number of potential variations in the mosquito breeding environment, and can serve as a food source for mosquito larvae. The toxin genes, preceded by a Synechococcus rbcL promoter, were located on a mobilizable Escherichia coli Synechococcus shuttle vector, which was introduced into Synechococcus PCC6301 at frequencies of 10(-5)-10(-7) exconjugants/recipient, depending on the selective conditions used. Recombinant Synechococcus exhibited significant toxicity against 2-day-old and 6-day-old Culex quinquefasciatus larvae, the concentration required to kill 50% of larvae (LC50) being 2.1 x 10(5) and 1.3 x 10(5) cells/ml respectively. Mosquitocidal activity decreased tenfold after 20 generations of non-selective growth.

Animals↗

PubMedDate not supplied

Virtual screening using binary kernel discrimination: analysis of pesticide data.

This paper discusses the use of binary kernel discrimination (BKD) for identifying potential active compounds in lead-discovery programs. BKD was compared with established virtual screening methods in a series of experiments using pesticide data from the Syngenta corporate database. It was found to be superior to methods based on similarity searching and substructural analysis but inferior to a support vector machine. Similar conclusions resulted from application of the methods to a pesticide data set for which categorical activity data were available.

Algorithms↗

PubMedDate not supplied

Six high-priority organochlorine pesticides, either singly or in combination, are nonestrogenic in transfected HeLa cells.

There have been increasing concerns that environmental chemicals may adversely affect the health of humans and wildlife by acting as endocrine modulators. These concerns have been augmented by the realization that human exposure occurs not just to single chemical agents, but typically to mixtures of chemicals that could exhibit estrogenic activity qualitatively and/or quantitatively different from that of individual components. To address these concerns, we have evaluated the ability of six organochlorine pesticides (4, 4'-DDT, 4,4'-DDD, 4,4'-DDE, aldrin, dieldrin, or endrin, all classified high priority by ATSDR) to modulate transcriptional activation of an estrogen-responsive reporter gene in transfected HeLa cells. In these assays, HeLa cells cotransfected with an expression vector encoding estrogen receptor and an estrogen-responsive chloramphenicol acetyltransferase (CAT) reporter plasmid were exposed to these pesticides individually and in defined combinations. While estradiol consistently elicited 10- to 23-fold dose-dependent inductions in these assays, the six organochlorine pesticides showed no detectable dose-related response when tested individually. When tested in binary combinations, the pesticide mixtures showed no additional estrogenicity. Thus, the pesticides tested, singly or as mixtures, showed virtually no evidence of estrogenicity.

Aldrin↗

PubMed1986

Polyamine depletion following exposure to DL-alpha-difluoromethylornithine both in vivo and in vitro initiates morphological alterations and mitochondrial activation in a monomorphic strain of Trypanosoma brucei brucei.

DL-alpha-difluoromethylornithine (DFMO), a specific irreversible inhibitor of ornithine decarboxylase (ODC), rapidly depletes cells of intracellular putrescine. When administered to animals and humans, DFMO cures acute infections of trypanosomiasis. In order to determine if the mechanism of drug action is related to initiation of transformation and biochemical alterations subsequent to polyamine depletion, trypanosome morphology and mitochondrial activation were studied in a monomorphic strain of Trypanosoma brucei brucei. Exposure of trypanosomes to DFMO in vivo in infected rodents or in vitro in culture resulted in a depletion of intracellular putrescine and a cessation of cell division without specific cytotoxicity. These events were followed by a transformation of the long slender bloodstream form to a short stumpy form via an intermediate morphology. Putrescine, the product of the ODC reaction, abrogates this effect. When introduced into SDM-79 medium, the intermediate form is capable of further transformation to an "insect" procyclic trypomastigote whereas the long slender form and short stumpy form are not. Short stumpy forms are incapable of binary fission and have lost their infectivity for the vertebrate host. In addition, the mitochondrial marker enzyme, NAD diaphorase, was found only in the short stumpy and intermediate forms. We hypothesize that the short stumpy phenotype may not be a viable stage in the natural transformation of the trypanosome from its mammalian host to the insect vector.

Animals↗

PubMed2004

Dynamic proximity of spatio-temporal sequences.

Recurrent networks can generate spatio-temporal neural sequences of very large cycles, having an apparent random behavior. Nonetheless a proximity measure between these sequences may be defined through comparison of the synaptic weight matrices that generate them. Following the dynamic neural filter (DNF) formalism we demonstrate this concept by comparing teacher and student recurrent networks of binary neurons. We show that large sequences, providing a training set well exceeding the Cover limit, allow for good determination of the synaptic matrices. Alternatively, assuming the matrices to be known, very fast determination of the biases can be achieved. Thus, a spatio-temporal sequence may be regarded as spatio-temporal encoding of the bias vector. We introduce a linear support vector machine (SVM) variant of the DNF in order to specify an optimal weight matrix. This approach allows us to deal with noise. Spatio-temporal sequences generated by different DNFs with the same number of neurons may be compared by calculating correlations of the synaptic matrices of the reconstructed DNFs. Other types of spatio-temporal sequences need the introduction of hidden neurons, and/or the use of a kernel variant of the SVM approach. The latter is being defined as a recurrent support vector network (RSVN).

Action Potentials↗

PubMed1999

Ternary complex factors Elk-1 and Sap-1a mediate growth hormone-induced transcription of egr-1 (early growth response factor-1) in 3T3-F442A preadipocytes.

In our search for transcription factors induced by GH, we have analyzed immediate early gene activation in a model of GH-dependent differentiation. Here we describe the activation of early growth response factor-1 (egr-1) in GH-stimulated 3T3-F442A preadipocytes and the transcription factors responsible for its transactivation. Binding activity of egr-1 in electrophoretic mobility shift assay (EMSA) increased transiently 1 h after GH stimulation, accompanied by a concomitant increase in egr-1 mRNA. egr-1 induction appeared not to be related to proliferation since it was amplified in quiescent preadipocytes at a time when cells were refractive to GH-stimulated DNA synthesis. Truncations of the proximal 1 kb of the egr-1 promoter revealed that a 374-bp region (-624 to -250) contributes about 80% of GH inducibility in 3T3-F442A cells and approximately 90% inducibility in CHO-K1 cells. This region contains three juxtaposed SRE (serum response element)/Ets site pairs known to be important for egr-1 activity in response to exogenous stimuli. Site-specific mutations of individual SRE and Ets sites within this region each reduced GH inducibility of the promoter. Use of these site-specific mutations in EMSA showed that disruption of either Ets or SRE sites abrogated ternary complex formation at the composite sites. DNA binding of ternary complexes, but not binary complexes, in EMSA was rapidly and transiently increased by GH. EMSA supershifts indicated these ternary complexes contained serum response factor (SRF) and the Ets factors Elk-1 and Sap-1a. Coexpression of Sap-1a and Elk-1 resulted in a marked increase in GH induction of egr-1 promoter activity, although transfection with expression vectors for either Ets factor alone did not significantly enhance the GH response. We conclude that GH stimulates transcription of egr-1 primarily through activation of these Ets factors at multiple sites on the promoter and that stabilization of ternary complexes with SRF at these sites maximizes this response.

Adipocytes↗

PubMed1998

The introduction into bacillus sphaericus of the Bacillus thuringiensis subsp. medellin Cyt1Ab1 gene results in higher susceptibility of resistant mosquito larva populations to B. sphaericus.

The fragment containing the gene encoding the cytolytic Cyt1Ab1 protein from Bacillus thuringiensis subsp. medellin and its flanking sequences (I. Thiery, A. Delécluse, M. C. Tamayo, and S. Orduz, Appl. Environ. Microbiol. 63:468-473, 1997) was introduced into Bacillus sphaericus toxic strains 2362, 2297, and Iab872 by electroporation with the shuttle vector pMK3. Only small amounts of the protein were produced in recombinant strains 2362 and Iab872. The protein was detected in these strains only by Western blotting and immunodetection with antibody raised against Cyt1Ab1 protein. Large amounts of Cyt1Ab1 protein were produced in B. sphaericus recombinant strain 2297, and there was an additional crystal, other than that of the binary toxin, within the exosporium. The production of the Cyt1Ab1 protein in addition to the binary toxin did not increase the larvicidal activity of the B. sphaericus recombinant strain against susceptible mosquito populations of Culex pipiens or Aedes aegypti. However, it partially restored (10 to 20 times) susceptibility of the resistant mosquito populations of C. pipiens (SPHAE) and Culex quinquefasciatus (GeoR) to the binary toxin. The Cyt1Ab1 protein produced in recombinant B. thuringiensis SPL407(pcyt1Ab1) was synthesized in two types of crystal-one round and with various dense areas, surrounded by an envelope, and the other a regular cuboid crystal, very similar to that found in the B. sphaericus recombinant strain.

Aedes↗