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PubMed2005

A new fractional wavelet approach for the simultaneous determination of ampicillin sodium and sulbactam sodium in a binary mixture.

A new application of the fractional wavelet transform (FWT) was proposed for the simultaneous determination of ampicillin (AP) and sulbactam (SB) in a pharmaceutical combination for injection. FWT approach is a new powerful tool for removing noise and irrelevant information from the absorption spectra. Cardinal information having higher peak amplitude, eliminated noise, sharp peaks with shrinking width of spectral range was obtained by the application of FWT procedure to the original absorption spectra. In this paper, FWT approach was subjected to the data vector of the UV-signals obtained from AP and SB in the wavelength range of 211.5-313.8 nm. Derivative transform was applied to the original absorption signal together with its FWT generalization. The calibration graphs for AP and SB were obtained by measuring the FWT and usual derivative amplitudes at zero-crossing points. The method validation was carried out by using the synthetic mixture analysis. Our proposed FWT approach was compared with the usual derivative spectrophotometry and chemometric methods (CLS, PCR and PLS) and a good agreement was reported.

Absorption↗

PubMed1990

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. II. Relationships between chemical model and partition function algorithm.

The relationships between the chemical properties of a system and the partition function algorithm as applied to the description of multiple equilibria in solution are explained. The partition functions ZM, ZA, and ZH are obtained from powers of the binary generating functions Jj = (1 + kappa j gamma j,i[Y])i tau j, where i tau j = p tau j, q tau j, or r tau j represent the maximum number of sites in sites in class j, for Y = M, A, or H, respectively. Each term of the generating function can be considered an element (ij) of a vector Jj and each power of the cooperativity factor gamma ij,i can be considered an element of a diagonal cooperativity matrix gamma j. The vectors Jj are combined in tensor product matrices L tau = (J1) [J2]...[Jj]..., thus representing different receptor-ligand combinations. The partition functions are obtained by summing elements of the tensor matrices. The relationship of the partition functions with the total chemical amounts TM, TA, and TH has been found. The aim is to describe the total chemical amounts TM, TA, and TH as functions of the site affinity constants kappa j and cooperativity coefficients bj. The total amounts are calculated from the sum of elements of tensor matrices Ll. Each set of indices (pj..., qj..., rj...) represents one element of a tensor matrix L tau and defines each term of the summation. Each term corresponds to the concentration of a chemical microspecies. The distinction between microspecies MpjAqjHrj with ligands bound on specific sites and macrospecies MpAqHR corresponding to a chemical stoichiometric composition is shown. The translation of the properties of chemical model schemes into the algorithms for the generation of partition functions is illustrated with reference to a series of examples of gradually increasing complexity. The equilibria examined concern: (1) a unique class of sites; (2) the protonation of a base with two classes of sites; (3) the simultaneous binding of ligand A and proton H to a macromolecule or receptor M with four classes of sites; and (4) the binding to a macromolecule M of ligand A which is in turn a receptor for proton H. With reference to a specific example, it is shown how a computer program for least-squares refinement of variables kappa j and bj can be organized. The chemical model from the free components M, A, and H to the saturated macrospecies MpAQHR, with possible complex macrospecies MpAq and AHR, is defined first.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed2002

Tumor-specific transcriptional targeting of suicide gene therapy.

Transcriptional targeting of gene expression has been plagued by the weakness of tissue-specific promoters. Thus, to increase promoter strength while maintaining tissue specificity, we constructed a recombinant adenovirus containing a binary promoter system with a tumor-specific promoter (CEA; carcinoembryonic antigen) driving a transcription transactivator, which then activates a minimal promoter to express a suicide gene (HSV-tk; herpes simplex virus thymidine kinase). This ADV/binary-tk induced equal or greater cell killing in a CEA-specific manner in vitro compared with the CEA-independent killing of a vector with a constitutive viral promoter driving HSV-tk (ADV/RSV-tk). To monitor adenovirus-mediated HSV-tk gene expression in vivo, we employed noninvasive nuclear imaging using a radioiodinated nucleoside analog ([((1)31)I]-FIAU) serving as a substrate for HSV-tk. [((1)31)I]-FIAU-derived radioactivity accumulated after intratumoral injection of ADV/binary-tk only in the area of CEA-positive tumors with significantly less spread to the adjacent liver tissue than after administration of the universally expressed ADV/RSV-tk. Both viruses exhibited similar antitumor efficacy upon injection of liver metastases. Importantly, in vivo dose escalation studies demonstrated significantly reduced toxicity after intravenous administration of ADV/binary-tk versus ADV/RSV-tk. In summary, the increased therapeutic index of this novel, amplified CEA-driven suicide gene therapy vector is a proof of principle for the powerful enhancement of a weak tissue-specific promoter for effective tumor restricted gene expression.

Adenoviridae↗

PubMed2006

Partial clustering in binary two-dimensional colloidal suspensions.

Strongly interacting binary mixtures of superparamagnetic colloidal particles confined to a two-dimensional water-air interface are examined by theory, computer simulation, and experiment. The mixture exhibits a partial clustering in equilibrium: in the voids of the matrix of unclustered big particles, the small particles form subclusters with a spongelike topology which is accompanied by a characteristic small-wave vector peak in the small-small structure factor. This partial clustering is a general phenomenon occurring for strongly coupled negatively nonadditive mixtures.

Colloids↗

PubMed2005

Comparative application of wavelet approaches to absorption and ratio spectra for the simultaneous determination of diminazene aceturate and phenazone in veterinary granules for injection.

A comparison of two wavelet approaches, Daubechies and reverse Biorthogonal, is described for the quantitative resolution of a binary mixture of diminazene aceturate (DIMA) and phenazone (PHE) in veterinary granules for injection without any chemical separation. These two approaches were specified as db4 (a = 180) and rbior3.7 (a = 125) respectively, after testing the signal analysis parameters for the overlapping absorption spectra and ratio spectra. In the first step db4 (a = 180) was applied to the original absorbance data vector of DIMA and PHE. In the second step rbio3.7 (a = 125) was applied to the ratio spectra data vectors of DIMA using the divisor PHE. The same approach was also subjected to the ratio spectra of PHE using the divisor DIMA. The db4 (a = 180) and rbior3.7 (a = 125) calibration graphs were constructed using the transformation values obtained in the wavelet domain. In the method validation, the wavelet calibration functions were tested using synthetic mixtures and the standard addition technique. The simultaneous quantitative analysis of DIMA and PHE in the commercial veterinary preparation was achieved by the elaborated methods. The assay results were compared with each other and good agreement was observed.

Algorithms↗

PubMed2005

Prospective recruitment of patients with congestive heart failure using an ad-hoc binary classifier.

This paper addresses a very specific problem of identifying patients diagnosed with a specific condition for potential recruitment in a clinical trial or an epidemiological study. We present a simple machine learning method for identifying patients diagnosed with congestive heart failure and other related conditions by automatically classifying clinical notes dictated at Mayo Clinic. This method relies on an automatic classifier trained on comparable amounts of positive and negative samples of clinical notes previously categorized by human experts. The documents are represented as feature vectors, where features are a mix of demographic information as well as single words and concept mappings to MeSH and HICDA classification systems. We compare two simple and efficient classification algorithms (Naïve Bayes and Perceptron) and a baseline term spotting method with respect to their accuracy and recall on positive samples. Depending on the test set, we find that Naïve Bayes yields better recall on positive samples (95 vs. 86%) but worse accuracy than Perceptron (57 vs. 65%). Both algorithms perform better than the baseline with recall on positive samples of 71% and accuracy of 54%.

Artificial Intelligence↗

PubMed2002

A statistical procedure for the analysis of microbial communities based on phenotypic properties of isolates.

A novel statistical procedure for the analysis of microbial communities based on phenotypic properties of randomly collected isolates is presented and discussed. The procedure allows the representation of the microbial communities as a set of ellipses in a bidimensional graph. This representation is obtained by the following steps: (a) measurement of a set of binary phenotypic properties for n isolates belonging to k samples, each representing a different community; (b) repeated sampling by bootstrapping of the m samples, thus obtaining, for each community, i subsamples of j isolates; (c) calculation of the frequency of positive results for each test for each subsample; (d) calculation of the matrix of Euclidean distances between the k x i frequency vectors; (e) use of multidimensional scaling (MDS) to obtain a representation in two dimensions of the distance relationships between the frequency vectors; (f) plotting of the 95% confidence ellipses for the i frequency vectors of each of the k communities. By using both simple, synthetic microbial communities, and samples of lactic acid bacteria isolated from natural microbial communities (sourdoughs, compressed yeast, fermented sausages), it was demonstrated that the position and shape of the ellipses are clearly related to the composition of the community, while the relationship between the size of the ellipses and the phenotypical diversity of the community is less straightforward: while communities with very different diversity (measured with the Functional Evenness index and the mean taxonomic distance) had ellipses that were very different in size, there was no strict proportionality between the size of the ellipse and the diversity of the community. Nevertheless, the representation of microbial communities obtained by bootstrapping and multidimensional scaling appears to be superior to the more usual representation based on tabulation of the frequencies of isolates belonging to different clusters.

Animals↗

PubMed2006

Scattering for mixtures of hard spheres: comparison of total scattering intensities with model.

The angular dependence of the intensity of x-rays scattered from binary and ternary hard sphere mixtures is investigated and compared to the predictions of two scattering models. Mixture ratio and total volume fraction dependent effects are investigated for size ratios equal to 0.51 and 0.22. Comparisons of model predictions with experimental results indicate the significant impact of the role of particle size distributions in interpreting the angular dependence of the scattering at wave vectors probing density fluctuations intermediate between the sizes of the particles in the mixture.

Journal Article↗

PubMed2002

Gene induction studies and toxicity of chemical mixtures.

As part of its mixtures program, the Agency for Toxic Substances and Disease Registry (ATSDR) supports in vitro and limited in vivo toxicity testing to further our understanding of the toxicity and health effects of chemical mixtures. There are increasing concerns that environmental chemicals adversely affect the health of humans and wildlife. These concerns have been augmented by the realization that exposure to chemicals often occurs to mixtures of these chemicals that may exhibit complex synergistic or antagonistic interactions. To address such concerns, we have conducted two studies with techniques that are being used increasingly in experimental toxicology. In the first study, six organochlorine pesticides (4,4 -DDT, 4,4 -DDD, 4,4 -DDE, aldrin, dieldrin, or endrin) were selected from the ATSDR Comprehensive Environmental Response, Compensation and Liability Act of 1980 (or Superfund) priority list and tested for their ability 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 dosed with and without selected environmental chemicals either individually or in defined combinations. Estradiol consistently elicited 10- to 23-fold dose-dependent inductions in this assay. By contrast, all six of the organochlorine pesticides showed no detectable dose-related response when tested either individually or in binary combinations. Thus, these chemicals as binary mixtures do not exhibit any additional estrogenicity at the levels tested in these assays. In the second study, arsenic [As(V)], cadmium [Cd(II)], chromium [Cr(III, VI)], and lead [Pb(II)] were tested in a commercially developed assay system, CAT-Tox (L), to identify metal-responsive promoters and to determine whether the pattern of gene expression changed with a mixture of these metals. This assay employs a battery of recombinant HepG2 cell lines to test the transcriptional activation capacity of xenobiotics in any of 13 different signal-transduction pathways. Singly, As(V), Cd(II), Cr(III, VI), and Pb(II) produced complex induction profiles in these assays. However, no evidence of synergistic activity was detected with a mixture of Cd(II), Cr(III), and Pb(II). These results have shown metal activation of gene expression through several previously unreported signal-transduction pathways and thus suggest new directions for future studies into their biochemical mechanisms of toxicity. In conclusion, the (italic)in vitro(/italic) methods used in these studies provide insights into complex interactions that occur in cellular systems and could be used to identify biomarkers of exposure to other environmental chemical mixtures.

Biomarkers↗

PubMed1985

Differentiation in Trypanosoma brucei: host-parasite cell junctions and their persistence during acquisition of the variable antigen coat.

Acquisition of the variable antigen-containing surface coat of Trypanosoma brucei occurs at the metacyclic stage in the salivary glands of the tsetse fly vector. The differentiation of the metacyclic trypanosome in the gland has been studied by scanning electron microscopy and by transmission electron microscopy of thin sections and freeze-fracture replicas. The uncoated epimastigote trypanosomes (with a prenuclear kinetoplast) divide while attached to the salivary gland epithelium brush border by elaborate branched flagellar outgrowths, which ramify between the host cell microvilli and form punctate hemidesmosome-like attachment plaques where they are indented by the microvilli. These outgrowths become reduced as the epimastigotes transform to uncoated trypomastigotes (with postnuclear kinetoplast), which remain attached and capable of binary fission. The flagellar outgrowths disappear but the attachment plaques persist as the uncoated trypomastigotes (premetacyclics) stop dividing and acquire the surface coat to become 'nascent metacyclics'. Coat acquisition therefore occurs in the attached trypanosome and not, as previously believed, after detachment. Coating is accompanied by morphological changes in the glycosomes and mitochondrion of the parasite. Freeze-fracture replicas of the host-parasite junctional complexes show membrane particle aggregates on the host membrane but not on the parasite membrane. It is suggested that disruption of the complex occurs when maximum packing of the glycoprotein molecules has been achieved in the trypanosome surface coat, releasing the metacyclic trypanosome into the lumen of the gland.

Animals↗

PubMed2001

Molecular dynamics study of the longitudinal modes in disparate-mass binary liquid mixtures.

A series of molecular dynamics simulations of simple liquid binary mixtures of soft spheres with disparate-mass particles were carried out to investigate the origin of the marked differences between the dynamic structure factors of some liquid binary mixtures such as the Li0.7Mg0.3 and Li0.8Pb0.2 alloys. It is shown that the facility for observing peaks associated with fast-propagating modes in the partial Li-Li dynamic structure factor of Li0.8Pb0.2 should be mainly attributed to the structure of this alloy, which is characterized by an incipient ABAB ordering as found in molten salts. The longitudinal dispersion relations at intermediate wave vectors obtained from the longitudinal current spectra are very similar for the two alloys and reflect the existence of both fast-and slow-propagating modes of kinetic character associated with light and heavy particles, respectively. The influence of the hardness of the repulsive potential cores as well as the composition of the mixture on the longitudinal collective modes is also discussed.

Journal Article↗

PubMed2000

Gaussian processes for classification: mean-field algorithms.

We derive a mean-field algorithm for binary classification with gaussian processes that is based on the TAP approach originally proposed in statistical physics of disordered systems. The theory also yields an approximate leave-one-out estimator for the generalization error, which is computed with no extra computational cost. We show that from the TAP approach, it is possible to derive both a simpler "naive" mean-field theory and support vector machines (SVMs) as limiting cases. For both mean-field algorithms and support vector machines, simulation results for three small benchmark data sets are presented. They show that one may get state-of-the-art performance by using the leave-one-out estimator for model selection and the built-in leave-one-out estimators are extremely precise when compared to the exact leave-one-out estimate. The second result is taken as strong support for the internal consistency of the mean-field approach.

Algorithms↗

PubMed2004

Secure holographic memory by double-random polarization encryption.

A novel optical encryption based on polarization is proposed and applied to a holographic memory system. Original binary data are described as two orthogonal linear polarization states. These input polarization states can be modulated by use of two polarization-modulation masks located at the input and the Fourier planes. Each modulation mask can convert an input polarization state into a random polarization state. Once encrypted, the polarization state is recorded as a hologram. For the decryption, the hologram can generate a vector phase-conjugate beam. When the same polarization-modulation masks are used, the vector phase-conjugate readout can cancel the polarization modulation at each mask, and the original polarization state can be recovered. The encryption of the proposed method is evaluated numerically. We also present experimental results by demonstrating holographic recording in a bacteriorhodopsin film.

Journal Article↗

PubMed2006

Laboratory evaluation of pyriproxyfen and spinosad, alone and in combination, against Aedes aegypti larvae.

In this study, the efficacy of pyriproxyfen and spinosad, alone and in combination, was evaluated against the dengue vector Aedes aegypti (L.). Larval bioassays were carried out on susceptible mosquito larvae to determine the concentration-mortality responses of mosquitoes exposed to each insecticide alone and in mixture. Synergism between pyriproxyfen and spinosad was determined by the calculation of a combination index (CI) by using the isobologram method. For pyriproxyfen, LC50 and LC95 were 1.1 x 10(-4) (1.0 x 10(-4)-1.1 x 10(-4)) and 3.2 x 10(-4) (2.9 x 10(-4)-3.6 x 10(-4)) mg/liter, respectively. Pyriproxyfen acted at very low concentrations by inhibiting the adult emergence of Ae. aegypti (97% inhibition rates at 3.3 x 10(-4) mg/liter). Spinosad activity was -500 times lower than that of pyriproxyfen against the Bora strain, with LC50 and LC95 values estimated at 0.055 (0.047-0.064) and 0.20 (0.15-0.27) mg/liter, respectively. A binary mixture of pyriproxyfen and spinosad was realized at the ratio 1:500 by considering the values of the LC50 obtained for each product. The LC50 and LC95 of the mixture were 0.019 (0.016 - 0.022) and 0.050 (0.040 - 0.065) mg/liter, respectively. The mixture combined both the larvicidal activity of spinosad and the juvenoid action of pyriproxyfen. From the LC70 to LC99 a significant synergism effect was observed between the two insecticides (CI ranged from 0.74 to 0.31). This strong synergism observed at high concentrations allows a reduction by five and nine-fold of pyriproxyfen and spinosad amounts to kill almost 100% mosquitoes. Combination of pyriproxyfen and spinosad may then represent a promising strategy to improve mosquito control in situations with insecticide-resistant Aedes dengue vectors.

Aedes↗

PubMed2006

Insecticidal toxins from Photorhabdus bacteria and their potential use in agriculture.

Most of the insecticidal toxins used in agriculture come from a single bacterium Bacillus thuringiensis or 'Bt'. Here we review our work on the array of toxins produced by Photorhabdus and Xenorhabdus bacteria that are symbiotic with entomopathogenic nematodes, and discuss their potential for use in agriculture as alternatives to Bt. Despite the fact that both Photorhabdus and Xenorhabdus are introduced directly into the insect blood stream by their nematode vectors, they produce a range of toxins with both oral and injectable insecticidal activity. The toxin complexes (Tc's) are large orally active toxins that are displayed on the outer surface of the bacterium. They require three components (A-C) for full toxicity and one 'A' component has been successfully expressed in transgenic Arabidopsis to confer insect resistance. One such group of Tc's, the PirAB binary toxins, have oral activity against mosquitoes and some caterpillar pests. Their mode of action is not known but they show significant sequence similarity to a recently described neurotoxin beta-leptinotarsin-h isolated from the blood of the Colorado potato beetle. Other toxins such as 'makes caterpillars floppy' (Mcf) and proteins encoded by the 'Photorhabdus virulence cassettes' (PVCs) only show injectable activity. Mcf1 promotes apoptosis in a wide range of cells and appears to mimic mammalian BH3 domain-only proteins in the mitochondrion whereas the mode of action of the PVCs remains undetermined. The likely biological reasons for the massive functional redundancy in Photorhabdus insecticidal toxins are discussed.

Agriculture↗

PubMed2001

Spinodal decomposition in a binary polymer mixture: dynamic self-consistent-field theory and Monte Carlo simulations.

We investigate how the dynamics of a single chain influences the kinetics of early stage phase separation in a symmetric binary polymer mixture. We consider quenches from the disordered phase into the region of spinodal instability. On a mean field level we approach this problem with two methods: a dynamical extension of the self-consistent-field theory for Gaussian chains, with the density variables evolving in time, and the method of the external potential dynamics where the effective external fields are propagated in time. Different wave vector dependencies of the kinetic coefficient are taken into account. These early stages of spinodal decomposition are also studied through Monte Carlo simulations employing the bond fluctuation model that maps the chains-in our case with 64 effective segments-on a coarse grained lattice. The results obtained through self-consistent-field calculations and Monte Carlo simulations can be compared because the time, length, and temperature scales are mapped onto each other through the diffusion constant, the chain extension, and the energy of mixing. The quantitative comparison of the relaxation rate of the global structure factor shows that a kinetic coefficient according to the Rouse model gives a much better agreement than a local, i.e., wave vector independent, kinetic factor. Including fluctuations in the self-consistent-field calculations leads to a shorter time span of spinodal behavior and a reduction of the relaxation rate for smaller wave vectors and prevents the relaxation rate from becoming negative for larger values of the wave vector. This is also in agreement with the simulation results.

Journal Article↗

PubMed2006

Cytolytic toxin Cyt1Aa of Bacillus thuringiensis synergizes the mosquitocidal toxin Mtx1 of Bacillus sphaericus.

Using the shuttle vector pBU4, the mosquitocidal toxin gene mtx1 from Bacillus sphaericus strain SSII-1 was introduced into an acrystalliferous strain of B. thuringiensis both individually and in combination with the accessory protein gene p20 and the cytolytic protein gene cyt1Aa from B. thuringiensis subsp. israelensis. Bioassay results indicated that the recombinants B-pMT4(Mtx1) and B-pMT9(Mtx1), both individually containing mtx1, had moderate toxicities to binary toxin susceptible and binary toxin resistant Culex quinquefasciatus larvae during the vegetative growth stage, but that their toxicities declined rapidly during the sporulation phase. The LC50 values were 2.5 and 4.8 mg/ml respectively, against 3-4 instar susceptible and resistant larvae for the final sporulated cultures of recombinants B-pMT9(Mtx1), and little toxicity was detected for B-pMT4(Mtx1). Meanwhile, the recombinant B-pMPX2(Mtx1+Cyt1Aa) expressing Mtx1, P20 alone, and Cyt1Aa in combination had stable toxicities during both the vegetative phase and the sporulation phase, with a LC50 ranging from 0.45-0.58 mg/ml. Furthermore, expression of Cyt1Aa appeared to enhance the activity of Mtx1 to target mosquito larvae, suggesting a synergism between Cyt1Aa and Mtx1 toxins.

Animals↗

PubMed1987

Cloning of the genes involved in synthesis of coenzyme pyrrolo-quinoline-quinone from Acinetobacter calcoaceticus.

Mutants of Acinetobacter calcoaceticus LMD79.41 were isolated that are defective in the synthesis of the coenzyme pyrrolo-quinoline-quinone (PQQ). A gene bank of the wild-type. A. calcoaceticus genome was constructed with the binary plasmid system pLV21-RP4 delta Km. The DNA of A. calcoaceticus LMD79.41 was partially digested with Sau3A, and fragments of about 15 kilobases were inserted into the BamHI site of pLV21. The hybrid plasmids maintained in Escherichia coli were transferred by conjugation to the PQQ- mutants of A. calcoaceticus. One hybrid plasmid was isolated that complements all isolated PQQ- mutants. Subcloning of this plasmid in the vector pRK290 resulted in an insert of 5 kilobases on which at least four different genes involved in PQQ synthesis could be indicated. With Tn5 insertions the four PQQ genes were mapped, and it was shown that these genes are most probably located in three operons.

Acinetobacter↗