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Results for “binary vectorization”

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PubMed2001

Adenovirus-mediated Bak gene transfer induces apoptosis in mesothelioma cell lines.

OBJECTIVE: Conventional treatment for mesothelioma is largely ineffective. We therefore evaluated the novel approach of adenoviral gene transfer of the proapoptotic Bcl-2 family member Bak in mesothelioma cancer cell lines, which are sensitive and resistant to adenoviral p53. METHODS: Binary adenoviral Bak (Ad/GT-Bak and Ad/GV16) and LacZ (Ad/GT-LacZ and Ad/GV16) vectors were used for transduction of the mesothelioma cell lines I-45 (p53 resistant) and REN (p53 sensitive). Protein levels were determined by Western blotting. Apoptosis was assessed by morphologic changes, caspase-3 cleavage, and fluorescence-activated cell sorter analysis of subdiploid populations. Cell viability was determined with the XTT assay. Statistical analysis was performed with analysis of variance and the Student t test. RESULTS: High levels of Bak gene transfer were seen after coadministration of Ad/GT-Bak and Ad/GV16 in both mesothelioma cell lines. Apoptosis was induced 24 hours after Bak but not LacZ gene transfer ([Bak: I-45, 36%; REN, 25%] vs [LacZ: I-45, 1%; REN, 3%], P <.05]) in p53-sensitive (REN) and p53-resistant (I-45) cell lines. Cellular viability was significantly decreased 48 to 72 hours after Bak gene transfer compared with control vector in both cell lines (72 hours: Bak I-45, 1.4% +/- 1.0%, and Bak REN, 4.7% +/- 1%, vs Lac-Z I-45, 83% +/- 3%, and Lac-Z REN, 100% +/- 1%; P <.05). CONCLUSIONS: Adenovirus-mediated overexpression of the Bak gene induces apoptosis and decreased cellular viability in p53-sensitive and p53-resistant mesothelioma cells. These data suggest that the gene transfer of proapoptotic Bcl-2 family members may represent a novel gene therapy strategy to treat mesothelioma.

Adenoviridae↗

PubMed2001

An automatic sequential recognition method for cortical auditory evoked potentials.

The detection of cortical auditory evoked potentials (CAEP), which are part of the electroencephalogram (EEG) in reaction to acoustic stimuli, has important applications such as determining objective audiograms. The detection is usually performed by a human operator, with support from often basic signal processing methods. This paper presents a novel mechanism for the detection of CAEPs, which is fully automatic and stops the measurement when a given confidence is reached. This proposed detector comprises of three stages. First, a feature extraction by a wavelet transform parameterizes the time domain EEG signal by only few transform coefficients. This feature vector is then classified by a neural network which yields a binary vote on every EEG segment. Finally, a sequential statistical test is performed on successive classifications; this stops the measurement if a specified decision confidence has been reached. The adjustment of the detector according to a clinical database is discussed. Thus adjusted, the proposed CAEP detection scheme is applied to a study, and compared with a human operator. The results demonstrate that this method can attain similar results, but outperforms the human expert for stimulation levels close to the hearing threshold.

Adult↗

PubMed2006

Multivariate extensions of McNemar's test.

This article considers global tests of differences between paired vectors of binomial probabilities, based on data from two dependent multivariate binary samples. Difference is defined as either an inhomogeneity in the marginal distributions or asymmetry in the joint distribution. For detecting the first type of difference, we propose a multivariate extension of McNemar's test and show that it is a generalized score test under a generalized estimating equations (GEE) approach. Univariate features such as the relationship between the Wald and score tests and the dropout of pairs with the same response carry over to the multivariate case and the test does not depend on the working correlation assumption among the components of the multivariate response. For sparse or imbalanced data, such as occurs when the number of variables is large or the proportions are close to zero, the test is best implemented using a bootstrap, and if this is computationally too complex, a permutation distribution. We apply the test to safety data for a drug, in which two doses are evaluated by comparing multiple responses by the same subjects to each one of them.

Biometry↗

PubMed2005

Comparison of antireflection surfaces based on two-dimensional binary gratings and thin-film coatings.

A comparison of antireflection surfaces based on the two-dimensional binary gratings and thin-film coatings is presented. First, a two-dimensional hybrid binary grating is proposed and analyzed by use of a vector-based implementation of the rigorous coupled-wave analysis method. The optimum parameters of the structure are determined and the effects that changing them have on spectral characteristics of the structure are studied. Then this structure is compared with multilayer thin-film antireflection filters. These filters are designed by genetic algorithm and needle methods, which are powerful methods for multilayer filter design. The comparison results show that the sensitivity of the grating to changes in the incident wavelength is high. However, a reflectance of the order of 10(-3)% at the design wavelength can be achieved. The sensitivity of designed antireflection thin-film filters to wavelength changes is lower, however, and the minimum achievable reflectance is higher.

Journal Article↗

PubMedDate not supplied

A pH-sensitive polymer that enhances cationic lipid-mediated gene transfer.

The efficient release of nonviral gene carriers from endosomes is an important step for the successful delivery of DNA into the cell nucleus. A synthetic pH-sensitive anionic polymer, poly(propylacrylic acid) (PPAA), was designed to aid in endosomal escape of nonviral vectors and improve the transfection efficiencies with these vectors. Transfection of NIH3T3 fibroblasts with ternary physical mixtures of the cationic lipid DOTAP, pCMVbeta plasmid DNA, and PPAA showed marked enhancement of both gene expression levels and fraction of cells transfected compared to binary control mixtures of DOTAP and DNA. PPAA also significantly improved the serum-stability of DOTAP/DNA vectors. The DOTAP/DNA/PPAA vectors maintained high levels of transfection in media containing up to 50% serum. The striking enhancement of transfection efficiency with cationic lipid/DNA/PPAA mixtures, along with the enhanced serum-stability, suggests that PPAA may provide significant improvements for the in vivo intracellular delivery of drugs such as DNA, oligonucleotides, proteins, and peptides.

3T3 Cells↗

PubMed2006

A second independent resistance mechanism to Bacillus sphaericus binary toxin targets its alpha-glucosidase receptor in Culex quinquefasciatus.

The entomopathogen Bacillus sphaericus is an important tool for the vector control of Culex sp., and its effectiveness has been validated in field trials. The appearance of resistance to this bacterium, however, remains a threat to its use, and attempts have been made to understand the resistance mechanisms. Previous work showed that the resistance to B. sphaericus in a Culex quinquefasciatus colony is associated with the absence of the approximately 60-kDa binary toxin receptor in larvae midgut microvilli. Here, the gene encoding the C. quinquefasciatus toxin receptor, Cqm1, was cloned and sequenced from a susceptible colony. The deduced amino-acid sequence confirmed its identity as an alpha-glucosidase, and analysis of the corresponding gene sequence from resistant larvae implicated a 19-nucleotide deletion as the basis for resistance. This deletion changes the ORF and originates a premature stop codon, which prevents the synthesis of the full-length Cqm1. Expression of the truncated protein, however, was not detected when whole larvae extracts were probed with antibodies raised against an N-terminal 45-kDa recombinant fragment of Cqm1. It seems that the premature stop codon directs the mutated cqm1 to the nonsense-mediated decay pathway of mRNA degradation. In-gel assays confirmed that a single alpha-glucosidase protein is missing from the resistant colony. Further in vitro affinity assays showed that the recombinant fragment binds to the toxin, and mapped the binding site to the N-terminus of the receptor.

Amino Acid Sequence↗

PubMed2006

Quantum solvation dynamics of HCN in a helium-4 droplet.

Ultracold nanodroplets of helium-4, containing several thousands of He atoms, offer considerable promise as microscopic cryogenic chambers. Potential applications include the creation of tailor-made chemical or biomolecular complexes and studies of superfluidity in nanoscale systems. Recent experiments have succeeded in interrogating droplets of quantum solvent which consist of as few as 1-20 helium-4 atoms and which contain a single solute molecule. This allows the transition from a floppy, but essentially molecular, complex to a dissolved molecule to be followed and, surprisingly, the transition is found to occur quite rapidly, in some cases for as few as N = 7-20 solvent atoms. For example, in experiments on helium-4 droplets seeded with CO molecules [Tang and McKellar, J. Chem. Phys. 119, 754 (2003)], two series of transitions are observed which correlate with the a-type (Delta K = 0) and b-type (Delta K = +/-1) lines of the binary complex, CO-He (K is the quantum number associated with the projection of the total angular momentum onto the vector connecting the atom and the molecular center of mass). The a-type series, which evolves from the end-over-end rotational motion of the CO-He binary complex, saturates to the nanodroplet limit for as few as 10-15 helium-4 atoms, i.e., the effective moment of inertia of the molecule converges to its asymptotic (solvated) value quite rapidly. In contrast, the b-type series, which evolves from the free-molecule rotational mode, disappears altogether for N approximately 7 atoms. Similar behavior is observed in recent computational studies of HCN(4He)N droplets [Paolini et al., J. Chem. Phys. 123, 114306 (2005)]. In this article the quantum solvation of HCN in small helium-4 droplets is studied using a new fixed-node diffusion Monte Carlo (DMC) procedure. In this approach a Born-Oppenheimer-type separation of radial and angular motions is introduced as a means of computing nodal surfaces of the many-body wave functions which are required in the fixed-node DMC method. Excited rotational energies are calculated for HCN(4He)N droplets with N = 1-20: the adiabatic node approach also allows concrete physical mechanisms to be proposed for the predicted disappearance of the b-type series as well as the rapid convergence of the a-type series to the nanodroplet limit with increasing N. The behavior of the a-type series is traced directly to the mechanics of angular momentum coupling-and decoupling-between identical bosons and the molecular rotor. For very small values of N there exists significant angular momentum coupling between the molecule and the helium atoms: at N approximately 10 solvation appears to be complete as evidenced by significant decoupling of the molecule and solvent angular momenta. The vanishing of the b-type series is predicted to be a result of increasing He-He repulsion as the number of solvent atoms increases.

Journal Article↗

PubMed2005

Construction of linkage maps in full-sib families of diploid outbreeding species by minimizing the number of recombinations in hidden inheritance vectors.

This article investigates the construction of linkage maps by means of the reconstruction of hidden inheritance vectors. An inheritance vector provides a description of the origin of marker alleles in an individual in terms of a binary code indicating the grandparental origin of the alleles. The practical application that is considered is the full-sib family of a diploid outbreeding species. Essentially, map construction is considered as an optimization problem in which marker data are used as restrictions on hidden inheritance vectors. Simulated annealing, a form of combinatorial optimization, is used to minimize the number of recombinations between adjacent markers. The new algorithm is applied to simulated data as well as to practical data obtained from a cross between two apple cultivars. For the practical data, a detailed procedure for examining the reliability of individual markers and their positions on the map is presented. Extensions of the method for more complicated population structures are discussed.

Algorithms↗

PubMed2003

Regulating gene expression using self-inactivating lentiviral vectors containing the mifepristone-inducible system.

Methods to regulate gene expression in vitro and in vivo are currently areas of intense research. The present study, therefore, was designed to determine the efficacy of transgene expression using the GeneSwitch mifepristone-regulatable system within the context of an integrating HIV-1 vector. Lentiviral transfer plasmids expressing the red (DsRed2) and green fluorescent protein (EGFP) markers were constructed for in vitro assessment on the basal and mifepristone-induced cell activation levels by FACS analyses. In our design, efficient cell activation and transgene expression were found using a binary lentivector system i.e., the trans-activator, Switch, and the inducible promoter-transgene expression cassette were cloned into separate vectors. Note that the Switch trans-activator performed optimally when cloned into the reverse-orientation, but the inducible promoter containing lentivector did not appear to be dependent upon the orientation within the lentivector backbone. This binary lentivector system resulted in tightly regulated transgene expression, with low basal cell activation in the absence of mifepristone (MFP). Upon induction, a 41- to 275-fold increase in the number of DsRed2- and EGFP-positive cells were detected (n=3). To determine the inducing ability of the GeneSwitch, we cloned the human alpha(1)-antitrypsin cDNA into the optimal lentiviral vector and transduced HeLa and Huh7 cells at increasing lentivector doses as determined by p24 Gag ELISA. We found that MFP could induce the expression of hAAT protein in HeLa cells from 310 to 15,000 ng hAAT/10(6) cells/24 h, which was a 48-fold induction. Similar results were observed in huH7 cells. In all, this study demonstrates that the GeneSwitch system can be designed within the context of a lentiviral vector for in vitro gene transfer, and this may also provide a viable method for temporally regulating gene expression for therapeutic applications in vivo or ex vivo.

Cell Line↗

PubMed2006

Robust and accurate vectorization of line drawings.

This paper presents a method for vectorizing the graphical parts of paper-based line drawings. The method consists of separating the input binary image into layers of homogeneous thickness, skeletonizing each layer, segmenting the skeleton by a method based on random sampling, and simplifying the result. The segmentation method is robust with a best bound of 50 percent noise reached for indefinitely long primitives. Accurate estimation of the recognized vector's parameters is enabled by explicitly computing their feasibility domains. Theoretical performance analysis and expression of the complexity of the segmentation method are derived. Experimental results and comparisons with other vectorization systems are also provided.

Algorithms↗

PubMed1999

Crystallization and preliminary X-ray diffraction studies of the 51 kDa protein of the mosquito-larvicidal binary toxin from Bacillus sphaericus.

Certain strains of Bacillus sphaericus produce a highly toxic mosquito-larvicidal protein during sporulation which is active against vectors of dengue, encephalitis and malaria. This toxin is initially expressed as 51 and 42 kDa proteins and is converted to 43 and 39 kDa proteins, respectively, which form the active heterodimer complex. For a better understanding of the toxicity mechanism at the molecular level, the 51 kDa protein of the binary toxin of B. sphaericus strain 2297 was expressed as a glutathione-S-transferase fusion protein and purified by affinity chromatography. Protein crystals were grown from an amorphous precipitate in five months using the hanging-drop vapor-diffusion method. The protein crystals were dissolved and were found to be composed of a proteolytically modified 45.2 kDa derivative similar to the active form of this protein. The crystals form in space group P43212 (or P41212) and diffract to 2.6 A, with unit-cell dimensions a = b = 133.48, c = 69. 76 A.

Animals↗

PubMed2005

Analysis of alcoholism data using support vector machines.

A supervised learning method, support vector machine, was used to analyze the microsatellite marker dataset of the Collaborative Study on the Genetics of Alcoholism Problem 1 for the Genetic Analysis Workshop 14. Twelve binary-valued phenotype variables were chosen for analyses using the markers from all autosomal chromosomes. Using various polynomial kernel functions of the support vector machine and randomly divided genome regions, we were able to observe the association of some marker sets with the chosen phenotypes and thus reduce the size of the dataset. The successful classifications established with the chosen support vector machine kernel function had high levels of correctness for each prediction, e.g., 96% in the fourfold cross-validations. However, owing to the limited sample data, we were not able to test the predictions of the classifiers in the new sample data.

Alcoholism↗

PubMed2005

Diagrammatic formulation of the kinetic theory of fluctuations in equilibrium classical fluids. V. The short time approximation for the memory function.

The correlation function for density fluctuations in a monatomic fluid obeys a formally exact kinetic equation containing a memory function. A previously derived short time approximation (STA) for this memory function is tested by comparing its predictions with the results of molecular dynamic simulations of a dense Lennard-Jones fluid at a variety of temperatures. This approximation takes into account the contribution to the correlation function of uncorrelated repulsive binary collisions. The qualitative changes of predicted correlation functions with temperature and wave vector are generally correct. The major exception to this is the transverse current correlation function for small wave vector. The quantitative accuracy is better at short times than long times and better at high temperatures than low temperatures. The major failing of the STA is its underestimation of the amplitudes of the negative dips in the current autocorrelation functions and of the temperature dependence of the amplitudes of the dips. Despite its deficiencies in predicting the time dependence of current correlation functions, the STA gives accurate results for the self-diffusion coefficient and the shear viscosity coefficient at the highest temperatures studied.

Journal Article↗

PubMed2002

Identifying spots in microarray images.

Microarray technology has provided a way to quantitate the simultaneous expression of a large number of genes. This approach is dependent on reproducible, accurate identification and quantitation of spot intensities. In this paper, clustering-based image segmentation is described to extract the target intensity of the microarray spots. While the technique is generic, its effectiveness on extracting spot intensities on arrays obtained from a two-color (Cy3/Cy5) experiment is discussed. The approximate boundaries of the spots are determined initially by manual alignment of rectangular grids. The pixel intensities of the image (I) inside a grid, is mapped onto a one-dimensional vector (v). The k-means clustering technique is applied to generate a binary partition of v. The median value of the pixel intensities inside each of the clusters for a given spot determines its foreground and the local background intensity. The difference in the median value of the foreground and the background intensity is the desired target intensity of the spot. The results are compared against those obtained using a region growing approach.

Algorithms↗

PubMed2004

Accurate classification of protein structural families using coherent subgraph analysis.

Protein structural annotation and classification is an important problem in bioinformatics. We report on the development of an efficient subgraph mining technique and its application to finding characteristic substructural patterns within protein structural families. In our method, protein structures are represented by graphs where the nodes are residues and the edges connect residues found within certain distance from each other. Application of subgraph mining to proteins is challenging for a number reasons: (1) protein graphs are large and complex, (2) current protein databases are large and continue to grow rapidly, and (3) only a small fraction of the frequent subgraphs among the huge pool of all possible subgraphs could be significant in the context of protein classification. To address these challenges, we have developed an information theoretic model called coherent subgraph mining. From information theory, the entropy of a random variable X measures the information content carried by X and the Mutual Information (MI) between two random variables X and Y measures the correlation between X and Y. We define a subgraph X as coherent if it is strongly correlated with every sufficiently large sub-subgraph Y embedded in it. Based on the MI metric, we have designed a search scheme that only reports coherent subgraphs. To determine the significance of coherent protein subgraphs, we have conducted an experimental study in which all coherent subgraphs were identified in several protein structural families annotated in the SCOP database (Murzin et al, 1995). The Support Vector Machine algorithm was used to classify proteins from different families under the binary classification scheme. We find that this approach identifies spatial motifs unique to individual SCOP families and affords excellent discrimination between families.

Algorithms↗

PubMed2004

Two-promoter vector is highly efficient for overproduction of protein complexes.

The use of bicistronic vectors, which contain two target genes under one promoter, has been the most common practice for the heterologous production of binary protein complexes. The major problem of this method is the much lower expression of the second gene compared with that of the first gene next to the promoter. We tested a simple idea of whether inclusion of an additional promoter in front of the second gene may remove the problem. Compared with bicistronic vectors, corresponding two-promoter vectors yielded four to nine times larger amounts of the complexes between BCL-2 family proteins, BCL-X(L):BAD, BCL-X(L):BIM-S, and CED-9:EGL-1 in bacterial cells as a result of significantly increased expression of the second genes in a manner independent of the order of the target genes. With the two-promoter system, we produced two other complexes in large quantity suitable for extensive crystallization trial. The method does not accompany any technical disadvantages, and represents a significant improvement from the conventional method, which should enjoy wide application for the coexpression of binary or higher order protein complexes by extension.

Circular Dichroism↗

PubMed2002

Prediction trees with soft nodes for binary outcomes.

Consider the problem of predicting the occurrence of an event, the onset of diabetes mellitus, say, from a vector of continuous and discrete predictors. We propose a new algorithm for the construction of a tree-structured predictor for the event of interest, which uses a new approach for dealing with continuous predictors. The novelty is that the tree uses splits for continuous variables. This means that at each node an individual goes to the right branch with a certain probability, function of a predictor. The predictor as well as the particular shape of the function is chosen from the data by the proposed algorithm. We evaluate its performance on several real data sets, in particular comparing it with a standard tree-growing algorithm. We also present an analysis of a well-known data set, the Pima Indian diabetes data set, to illustrate the application of the method in biostatistics.

Aged↗

PubMed1995

Bayesian sequential monitoring designs for single-arm clinical trials with multiple outcomes.

We present a Bayesian approach for monitoring multiple outcomes in single-arm clinical trials. Each patient's response may include both adverse events and efficacy outcomes, possibly occurring at different study times. We use a Dirichlet-multinomial model to accommodate general discrete multivariate responses. We present Bayesian decision criteria and monitoring boundaries for early termination of studies with unacceptably high rates of adverse outcomes or with low rates of desirable outcomes. Each stopping rule is constructed either to maintain equivalence or to achieve a specified level of improvement of a particular event rate for the experimental treatment, compared with that of standard therapy. We avoid explicit specification of costs and a loss function. We evaluate the joint behaviour of the multiple decision rules using frequentist criteria. One chooses a design by considering several parameterizations under relevant fixed values of the multiple outcome probability vector. Applications include trials where response is the cross-product of multiple simultaneous binary outcomes, and hierarchical structures that reflect successive stages of treatment response, disease progression and survival. We illustrate the approach with a variety of single-arm cancer trials, including bio-chemotherapy acute leukaemia trials, bone marrow transplantation trials, and an anti-infection trial. The number of elementary patient outcomes in each of these trials varies from three to seven, with as many as four monitoring boundaries running simultaneously. We provide general guidelines for eliciting and parameterizing Dirichlet priors and for specifying design parameters.

Bayes Theorem↗