Mobile Technology Affinity in Renal Transplant Recipients.

Science.gov (United States)

Reber, S; Scheel, J; Stoessel, L; Schieber, K; Jank, S; Lüker, C; Vitinius, F; Grundmann, F; Eckardt, K-U; Prokosch, H-U; Erim, Y

Medication nonadherence is a common problem in renal transplant recipients (RTRs). Mobile health approaches to improve medication adherence are a current trend, and several medication adherence apps are available. However, it is unknown whether RTRs use these technologies and to what extent. In the present study, the mobile technology affinity of RTRs was analyzed. We hypothesized significant age differences in mobile technology affinity and that mobile technology affinity is associated with better cognitive functioning as well as higher educational level. A total of 109 RTRs (63% male) participated in the cross-sectional study, with an overall mean age of 51.8 ± 14.2 years. The study included the Technology Experience Questionnaire (TEQ) for the assessment of mobile technology affinity, a cognitive test battery, and sociodemographic data. Overall, 57.4% of the patients used a smartphone or tablet and almost 45% used apps. The TEQ sum score was 20.9 in a possible range from 6 (no affinity to technology) to 30 (very high affinity). Younger patients had significantly higher scores in mobile technology affinity. The only significant gender difference was found in having fun with using electronic devices: Men enjoyed technology more than women did. Mobile technology affinity was positively associated with cognitive functioning and educational level. Young adult patients might profit most from mobile health approaches. Furthermore, high educational level and normal cognitive functioning promote mobile technology affinity. This should be kept in mind when designing mobile technology health (mHealth) interventions for RTRs. For beneficial mHealth interventions, further research on potential barriers and desired technologic features is necessary to adapt apps to patients' needs. Copyright © 2017 Elsevier Inc. All rights reserved.

Affine and quasi-affine frames for rational dilations

DEFF Research Database (Denmark)

Bownik, Marcin; Lemvig, Jakob

2011-01-01

In this paper we extend the investigation of quasi-affine systems, which were originally introduced by Ron and Shen [J. Funct. Anal. 148 (1997), 408-447] for integer, expansive dilations, to the class of rational, expansive dilations. We show that an affine system is a frame if, and only if......, the corresponding family of quasi-affine systems are frames with uniform frame bounds. We also prove a similar equivalence result between pairs of dual affine frames and dual quasi-affine frames. Finally, we uncover some fundamental differences between the integer and rational settings by exhibiting an example...

High-affinity receptors for bombesin-like peptides in normal guinea pig lung membranes

International Nuclear Information System (INIS)

Lach, E.; Trifilieff, A.; Landry, Y.; Gies, J.P.

1991-01-01

The binding of the radiolabeled bombesin analogue [ 125 I-Tyr 4 ]bombesin to guinea-pig lung membranes was investigated. Binding of [ 125 I-Tyr 4 ]bombesin was specific, saturable, reversible and linearly related to the protein concentration. Scatchard analysis of equilibrium binding data at 25C indicated the presence of a single class of non-interacting binding sites for bombesin (B max = 7.7 fmol/mg protein). The value of the equilibrium dissociation constant (K D = 90 pM) agrees with a high-affinity binding site. Bombesin and structurally related peptides such as [ 125 I-Tyr 4 ]bombesin, neuromedin B and neuromedin C inhibited the binding of [ 125 I-Tyr 4 ]bombesin in an order of potencies as follows: [ 125 I-Tyr 4 ]bombesin > bombesin ≥ neuromedin C much-gt neuromedin B. These results indicate that guinea-pig lung membranes possess a single class of bombesin receptors with a high affinity for bombesin and a lower one for neuromedin B

Microfluidics in the selection of affinity reagents for the detection of cancer: paving a way towards future diagnostics.

Science.gov (United States)

Hung, Lien-Yu; Wang, Chih-Hung; Fu, Chien-Yu; Gopinathan, Priya; Lee, Gwo-Bin

2016-08-07

Microfluidic technologies have miniaturized a variety of biomedical applications, and these chip-based systems have several significant advantages over their large-scale counterparts. Recently, this technology has been used for automating labor-intensive and time-consuming screening processes, whereby affinity reagents, including aptamers, peptides, antibodies, polysaccharides, glycoproteins, and a variety of small molecules, are used to probe for molecular biomarkers. When compared to conventional methods, the microfluidic approaches are faster, more compact, require considerably smaller quantities of samples and reagents, and can be automated. Furthermore, they allow for more precise control of reaction conditions (e.g., pH, temperature, and shearing forces) such that more efficient screening can be performed. A variety of affinity reagents for targeting cancer cells or cancer biomarkers are now available and will likely replace conventional antibodies. In this review article, the selection of affinity reagents for cancer cells or cancer biomarkers on microfluidic platforms is reviewed with the aim of highlighting the utility of such approaches in cancer diagnostics.

Comparative characterization of molecular varieties of thyroxine-binding human globulin

International Nuclear Information System (INIS)

Ermolenko, M.N.; Sviridov, O.V.; Strel'chenok, O.A.

1986-01-01

Two molecular varieties of thyroxine-binding globulin (TBG) of human retroplacental blood, obtained as a result of fractionation of pure TBG on concanavalin A-Sepharose, were studied. It was shown that these varieties (TBG-1 and TBG-2) are immunologically identical; they have the same molecular weight and amino acid composition, exhibit the same affinity for thyroid hormones, and are indistinguishable in spectral characteristics. And yet, TBG-1 and TBG-2 have differences in charge, detectable in isoelectrofocusing, and a different monosaccharide composition. The existence of molecular varieties of TBG during pregnancy is apparently due to the peculiarities of the glycosylation of the polypeptide chain during TBG biosynthesis

Class of the affine line is a zero divisor in the Grothendieck ring

OpenAIRE

Borisov, Lev

2014-01-01

We show that the class of the affine line is a zero divisor in the Grothendieck ring of algebraic varieties over complex numbers. The argument is based on the Pfaffian-Grassmannian double mirror correspondence.

Molecular electron affinities

International Nuclear Information System (INIS)

Fukuda, E.K.

1983-01-01

Molecular electron affinities have historically been difficult quantities to measure accurately. These difficulties arise from differences in structure between the ion and neutral as well as the existence of excited negative ion states. To circumvent these problems, relative electron affinities were determined in this dissertation by studying equilibrium electron transfer reactions using a pulsed ion cyclotron resonance (ICR) spectrometer. Direct measurement of ion and neutral concentrations for reactions of the general type, A - + B = B - + A, allow calculation of the equilibrium constant and, therefore, the free energy change. The free energy difference is related to the difference in electron affinities between A and B. A relative electron affinity scale covering a range of about 45 kcal/mol was constructed with various substituted p-benzoquinones, nitrobenzenes, anhydrides, and benzophenones. To assign absolute electron affinities, various species with accurately known electron affinities are tied to the scale via ion-cyclotron double resonance bracketing techniques. After the relative scale is anchored to these species with well-known electron affinities, the scale is then used as a check on other electron affinity values as well as generating new electron affinity values. Many discrepancies were found between the electron affinities measured using the ICR technique and previous literature determinations

Affinity purification using recombinant PXR as a tool to characterize environmental ligands.

Science.gov (United States)

Dagnino, Sonia; Bellet, Virginie; Grimaldi, Marina; Riu, Anne; Aït-Aïssa, Sélim; Cavaillès, Vincent; Fenet, Hélène; Balaguer, Patrick

2014-02-01

Many environmental endocrine disrupting compounds act as ligands for nuclear receptors. The human pregnane X receptor (hPXR), for instance, is activated by a variety of environmental ligands such as steroids, pharmaceutical drugs, pesticides, alkylphenols, polychlorinated biphenyls and polybromo diethylethers. Some of us have previously reported the occurrence of hPXR ligands in environmental samples but failed to identify them. The aim of this study was to test whether a PXR-affinity column, in which recombinant hPXR was immobilized on solid support, could help the purification of these chemicals. Using PXR ligands of different affinity (10 nM < EC50 < 10 μM), we demonstrated that the PXR-affinity preferentially column captured ligands with medium to high affinities (EC50 < 1 μM). Furthermore, by using the PXR-affinity column to analyze an environmental sample containing ERα, AhR, AR, and PXR activities, we show that (i) half of the PXR activity of the sample was due to compounds with medium to high affinity for PXR and (ii) PXR shared ligands with ERα, AR, and AhR. These findings demonstrate that the newly developed PXR-affinity column coupled to reporter cell lines represents a valuable tool for the characterization of the nature of PXR active compounds and should therefore guide and facilitate their further analysis. Copyright © 2012 Wiley Periodicals, Inc., a Wiley company.

The choroid plexus in normal full-term neonate : a study of morphological variety on sonography

International Nuclear Information System (INIS)

Lee, Young Seok; Kim, Ji Hye

1999-01-01

differences with regard to gender and side. We have observed the morphological variety of the choroid plexus in normal full-term neonates on ultrasonograms and believe that a knowledge of the various sonographic patterns involved can help differentiating normal choroid plexus from intraventricular hemorrhage or choroidal abnormality

The choroid plexus in normal full-term neonate : a study of morphological variety on sonography

Energy Technology Data Exchange (ETDEWEB)

Lee, Young Seok [Dankook Univ. Hospital, Seoul (Korea, Republic of); Kim, Ji Hye [Chunganggil Hospital, Seoul (Korea, Republic of)

1999-04-01

statistical differences with regard to gender and side. We have observed the morphological variety of the choroid plexus in normal full-term neonates on ultrasonograms and believe that a knowledge of the various sonographic patterns involved can help differentiating normal choroid plexus from intraventricular hemorrhage or choroidal abnormality.

Report: Affinity Chromatography.

Science.gov (United States)

Walters, Rodney R.

1985-01-01

Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

Evaluation of selected nursery traits in combination rootstocks and variety for Asian pear trees

Directory of Open Access Journals (Sweden)

Tomáš Nečas

2012-01-01

Full Text Available Evaluation of the nursery traits of rootstocks and varieties is an important tool for optimisation of the fruit orchard plants final growing. The present experiment evaluated the standard and progressive rootstocks for the pear trees in combination with the Asian varieties of P. pyrifolia Nakai. a P. ussuriensis Maxim. in comparison with the control variety ‘Conference’ P. communis L. The evaluation was focused on such properties as affinity, growth of the tree propagated by budding, thickness of the root crown at the rootstock and the root suckering. Their interactions were tested statistically. The highest values of affinity within the nursery were achieved with the following rootstocks: ‘BET’ (96.6%, ‘FOX 11’ (95.5 %, and ‘MA’ (94.4 %. ‘Hosui’ was identified as the variety with the greatest growing capacity, with an average gain of 1238.2 mm. The most supported variety growth was exhibited by the ‘FOX 11’ rootstock, with an average gain of the trees propagated by budding of 1388.8 mm. The growth intensity itself was demonstrated most in the thickness of the root crown of the ‘BET’ (P. betulifolia rootstock, namely 15.8 mm. The rootstock that exhibited the strongest root suckering was also ‘BET’ with 6.2 suckers per rootstock. The identified differences between the varieties and rootstocks were confirmed as statistically significant or even highly statistically significant.

Simulated electron affinity tuning in metal-insulator-metal (MIM) diodes

Science.gov (United States)

Mistry, Kissan; Yavuz, Mustafa; Musselman, Kevin P.

2017-05-01

Metal-insulator-metal diodes for rectification applications must exhibit high asymmetry, nonlinearity, and responsivity. Traditional methods of improving these figures of merit have consisted of increasing insulator thickness, adding multiple insulator layers, and utilizing a variety of metal contact combinations. However, these methods have come with the price of increasing the diode resistance and ultimately limiting the operating frequency to well below the terahertz regime. In this work, an Airy Function Transfer Matrix simulation method was used to observe the effect of tuning the electron affinity of the insulator as a technique to decrease the diode resistance. It was shown that a small increase in electron affinity can result in a resistance decrease in upwards of five orders of magnitude, corresponding to an increase in operating frequency on the same order. Electron affinity tuning has a minimal effect on the diode figures of merit, where asymmetry improves or remains unaffected and slight decreases in nonlinearity and responsivity are likely to be greatly outweighed by the improved operating frequency of the diode.

Robotic high-throughput purification of affinity-tagged recombinant proteins.

Science.gov (United States)

Wiesler, Simone C; Weinzierl, Robert O J

2015-01-01

Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories.

Hirota's solitons in the affine and the conformal affine Toda models

International Nuclear Information System (INIS)

Aratyn, H.; Constantinidis, C.P.; Ferreira, L.A.; Gomes, J.F.; Zimerman, A.H.

1993-01-01

We use Hirota's method formulated as a recursive scheme to construct a complete set of soliton solutions for the affine Toda field theory based on an arbitrary Lie algebra. Our solutions include a new class of solitons connected with two different types of degeneracies encountered in Hirota's perturbation approach. We also derive an universal mass formula for all Hirota's solutions to the affine Toda model valid for all underlying Lie groups. Embedding of the affine Toda model in the conformal affine Toda model plays a crucial role in this analysis. (orig.)

Using color histogram normalization for recovering chromatic illumination-changed images.

Science.gov (United States)

Pei, S C; Tseng, C L; Wu, C C

2001-11-01

We propose a novel image-recovery method using the covariance matrix of the red-green-blue (R-G-B) color histogram and tensor theories. The image-recovery method is called the color histogram normalization algorithm. It is known that the color histograms of an image taken under varied illuminations are related by a general affine transformation of the R-G-B coordinates when the illumination is changed. We propose a simplified affine model for application with illumination variation. This simplified affine model considers the effects of only three basic forms of distortion: translation, scaling, and rotation. According to this principle, we can estimate the affine transformation matrix necessary to recover images whose color distributions are varied as a result of illumination changes. We compare the normalized color histogram of the standard image with that of the tested image. By performing some operations of simple linear algebra, we can estimate the matrix of the affine transformation between two images under different illuminations. To demonstrate the performance of the proposed algorithm, we divide the experiments into two parts: computer-simulated images and real images corresponding to illumination changes. Simulation results show that the proposed algorithm is effective for both types of images. We also explain the noise-sensitive skew-rotation estimation that exists in the general affine model and demonstrate that the proposed simplified affine model without the use of skew rotation is better than the general affine model for such applications.

Color-weak compensation using local affine isometry based on discrimination threshold matching

OpenAIRE

Mochizuki, Rika; Kojima, Takanori; Lenz, Reiner; Chao, Jinhui

2015-01-01

We develop algorithms for color-weak compensation and color-weak simulation based on Riemannian geometry models of color spaces. The objective function introduced measures the match of color discrimination thresholds of average normal observers and a color-weak observer. The developed matching process makes use of local affine maps between color spaces of color-normal and color-weak observers. The method can be used to generate displays of images that provide color-normal and color-weak obser...

The solutions of affine and conformal affine Toda field theory

International Nuclear Information System (INIS)

Papadopoulos, G.; Spence, B.

1994-02-01

We give new formulations of the solutions of the field equations of the affine Toda and conformal affine Toda theories on a cylinder and two-dimensional Minkowski space-time. These solutions are parameterised in terms of initial data and the resulting covariant phase spaces are diffeomorphic to the Hamiltonian ones. We derive the fundamental Poisson brackets of the parameters of the solutions and give the general static solutions for the affine theory. (authors). 10 refs

Selective high-affinity polydentate ligands and methods of making such

Energy Technology Data Exchange (ETDEWEB)

Denardo, Sally J.; Denardo, Gerald L.; Balhorn, Rodney L.

2018-02-06

This invention provides novel polydentate selective high affinity ligands (SHALs) that can be used in a variety of applications in a manner analogous to the use of antibodies. SHALs typically comprise a multiplicity of ligands that each bind different region son the target molecule. The ligands are joined directly or through a linker thereby forming a polydentate moiety that typically binds the target molecule with high selectivity and avidity.

hPEPT1 Affinity and Translocation of Selected Gln-Sar and Glu-Sar Dipeptide Derivatives

DEFF Research Database (Denmark)

Eriksson, A. H.; Elm, Peter L.; Begtrup, Mikael

2005-01-01

using 14C-labeled Gly-Sar. Translocation was measured as fluorescence ratios induced by the substrates using the fluorescent probe BCECF and an epifluorescence microscope setup. All compounds showed high affinity to hPEPT1, but only the amides l-Gln(N,N-dimethyl)-Sar and l-Gln(N-piperidinyl)-Sar were...... been suggested. However, these are not necessarily predictive of compounds that are actually translocated by hPEPT1. More information on affinity to and translocation via hPEPT1 of side-chain-modified dipeptides may be gained by conducting a study of selected dipeptide derivatives with variety in size...... translocated by hPEPT1. hPEPT1 is very susceptible to modifications of the N-terminal amino acid side chain of dipeptidomimetic substrates, in terms of achieving compounds with high affinity for the transporter. However, as affinity is not predictive of translocation, derivatization in this position must...

Lectin affinity electrophoresis.

Science.gov (United States)

Kobayashi, Yuka

2014-01-01

An interaction or a binding event typically changes the electrophoretic properties of a molecule. Affinity electrophoresis methods detect changes in the electrophoretic pattern of molecules (mainly macromolecules) that occur as a result of biospecific interactions or complex formation. Lectin affinity electrophoresis is a very effective method for the detection and analysis of trace amounts of glycobiological substances. It is particularly useful for isolating and separating the glycoisomers of target molecules. Here, we describe a sensitive technique for the detection of glycoproteins separated by agarose gel-lectin affinity electrophoresis that uses antibody-affinity blotting. The technique is tested using α-fetoprotein with lectin (Lens culinaris agglutinin and Phaseolus vulgaris agglutinin)-agarose gels.

Lp-dual affine surface area

Science.gov (United States)

Wei, Wang; Binwu, He

2008-12-01

According to the notion of Lp-affine surface area by Lutwak, in this paper, we introduce the concept of Lp-dual affine surface area. Further, we establish the affine isoperimetric inequality and the Blaschke-Santaló inequality for Lp-dual affine surface area. Besides, the dual Brunn-Minkowski inequality for Lp-dual affine surface area is presented.

Guanine nucleotide regulation of dopamine receptor agonist affinity states in rat estradiol-induced pituitary tumors

International Nuclear Information System (INIS)

Di Paolo, T.; Falardeau, P.

1987-01-01

The authors have investigated dopamine (DA) receptor agonist high- and low-affinity states in female rate estradiol-induced prolactin (PRL)-secreting pituitary tumors and intact pituitary tissue. Estradiol treatment increased the anterior pituitary weight 9-fold and plasma prolactin levels 74-fold and these measures are correlated (R = 0.745, n = 73, p 3 H]-spiperone binding to the DA receptor by apomorphine was compared in normal and adenomatous pituitary tissue. The inhibition constants (Ki) and the proportions of the two apomorphine sites are unchanged in tumors compared to intact pituitary tissue. Guanosine 5'-[β-γ-imino]triphosphate (Gpp(NH)p) causes complete conversion of the high into low affinity dopaminergic agonist site in normal pituitary and in tumors. These results suggest that rats with primary estradiol-induced pituitary tumors have normal and functional DA receptors. 9 references, 2 tables

Electrochemical affinity biosensors for detection of mycotoxins: A review.

Science.gov (United States)

Vidal, Juan C; Bonel, Laura; Ezquerra, Alba; Hernández, Susana; Bertolín, Juan R; Cubel, Carlota; Castillo, Juan R

2013-11-15

This review discusses the current state of electrochemical biosensors in the determination of mycotoxins in foods. Mycotoxins are highly toxic secondary metabolites produced by molds. The acute toxicity of these results in serious human and animal health problems, although it has been only since early 1960s when the first studied aflatoxins were found to be carcinogenic. Mycotoxins affect a broad range of agricultural products, most important cereals and cereal-based foods. A majority of countries, mentioning especially the European Union, have established preventive programs to control contamination and strict laws of the permitted levels in foods. Official methods of analysis of mycotoxins normally requires sophisticated instrumentation, e.g. liquid chromatography with fluorescence or mass detectors, combined with extraction procedures for sample preparation. For about sixteen years, the use of simpler and faster analytical procedures based on affinity biosensors has emerged in scientific literature as a very promising alternative, particularly electrochemical (i.e., amperometric, impedance, potentiometric or conductimetric) affinity biosensors due to their simplicity and sensitivity. Typically, electrochemical biosensors for mycotoxins use specific antibodies or aptamers as affinity ligands, although recombinant antibodies, artificial receptors and molecular imprinted polymers show potential utility. This article deals with recent advances in electrochemical affinity biosensors for mycotoxins and covers complete literature from the first reports about sixteen years ago. Copyright © 2013 Elsevier B.V. All rights reserved.

NK1 receptor fused to beta-arrestin displays a single-component, high-affinity molecular phenotype.

Science.gov (United States)

Martini, Lene; Hastrup, Hanne; Holst, Birgitte; Fraile-Ramos, Alberto; Marsh, Mark; Schwartz, Thue W

2002-07-01

Arrestins are cytosolic proteins that, upon stimulation of seven transmembrane (7TM) receptors, terminate signaling by binding to the receptor, displacing the G protein and targeting the receptor to clathrin-coated pits. Fusion of beta-arrestin1 to the C-terminal end of the neurokinin NK1 receptor resulted in a chimeric protein that was expressed to some extent on the cell surface but also accumulated in transferrin-labeled recycling endosomes independently of agonist stimulation. As expected, the fusion protein was almost totally silenced with respect to agonist-induced signaling through the normal Gq/G11 and Gs pathways. The NK1-beta-arrestin1 fusion construct bound nonpeptide antagonists with increased affinity but surprisingly also bound two types of agonists, substance P and neurokinin A, with high, normal affinity. In the wild-type NK1 receptor, neurokinin A (NKA) competes for binding against substance P and especially against antagonists with up to 1000-fold lower apparent affinity than determined in functional assays and in homologous binding assays. When the NK1 receptor was closely fused to G proteins, this phenomenon was eliminated among agonists, but the agonists still competed with low affinity against antagonists. In contrast, in the NK1-beta-arrestin1 fusion protein, all ligands bound with similar affinity independent of the choice of radioligand and with Hill coefficients near unity. We conclude that the NK1 receptor in complex with arrestin is in a high-affinity, stable, agonist-binding form probably best suited to structural analysis and that the receptor can display binding properties that are nearly theoretically ideal when it is forced to complex with only a single intracellular protein partner.

An Affine Invariant Bivariate Version of the Sign Test.

Science.gov (United States)

1987-06-01

words: affine invariance, bivariate quantile, bivariate symmetry, model,. generalized median, influence function , permutation test, normal efficiency...calculate a bivariate version of the influence function , and the resulting form is bounded, as is the case for the univartate sign test, and shows the...terms of a blvariate analogue of IHmpel’s (1974) influence function . The latter, though usually defined as a von-Mises derivative of certain

Guanine nucleotide regulation of dopamine receptor agonist affinity states in rat estradiol-induced pituitary tumors

Energy Technology Data Exchange (ETDEWEB)

Di Paolo, T.; Falardeau, P.

1987-08-31

The authors have investigated dopamine (DA) receptor agonist high- and low-affinity states in female rate estradiol-induced prolactin (PRL)-secreting pituitary tumors and intact pituitary tissue. Estradiol treatment increased the anterior pituitary weight 9-fold and plasma prolactin levels 74-fold and these measures are correlated (R = 0.745, n = 73, p < 0.001). Competition for (/sup 3/H)-spiperone binding to the DA receptor by apomorphine was compared in normal and adenomatous pituitary tissue. The inhibition constants (Ki) and the proportions of the two apomorphine sites are unchanged in tumors compared to intact pituitary tissue. Guanosine 5'-(..beta..-..gamma..-imino)triphosphate (Gpp(NH)p) causes complete conversion of the high into low affinity dopaminergic agonist site in normal pituitary and in tumors. These results suggest that rats with primary estradiol-induced pituitary tumors have normal and functional DA receptors. 9 references, 2 tables.

Continuous affine processes

DEFF Research Database (Denmark)

Buchardt, Kristian

2016-01-01

Affine processes possess the property that expectations of exponential affine transformations are given by a set of Riccati differential equations, which is the main feature of this popular class of processes. In this paper we generalise these results for expectations of more general transformati...

Affinity in electrophoresis.

Science.gov (United States)

Heegaard, Niels H H

2009-06-01

The journal Electrophoresis has greatly influenced my approaches to biomolecular affinity studies. The methods that I have chosen as my main tools to study interacting biomolecules--native gel and later capillary zone electrophoresis--have been the topic of numerous articles in Electrophoresis. Below, the role of the journal in the development and dissemination of these techniques and applications reviewed. Many exhaustive reviews on affinity electrophoresis and affinity CE have been published in the last few years and are not in any way replaced by the present deliberations that are focused on papers published by the journal.

The metric-affine gravitational theory as the gauge theory of the affine group

International Nuclear Information System (INIS)

Lord, E.A.

1978-01-01

The metric-affine gravitational theory is shown to be the gauge theory of the affine group, or equivalently, the gauge theory of the group GL(4,R) of tetrad deformations in a space-time with a locally Minkowskian metric. The identities of the metric-affine theory, and the relationship between them and those of general relativity and Sciama-Kibble theory, are derived. (Auth.)

Engineering an antibody with picomolar affinity to DOTA chelates of multiple radionuclides for pretargeted radioimmunotherapy and imaging

Energy Technology Data Exchange (ETDEWEB)

Orcutt, Kelly Davis; Slusarczyk, Adrian L. [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Cieslewicz, Maryelise [Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Ruiz-Yi, Benjamin [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Bhushan, Kumar R. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Frangioni, John V. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Wittrup, K. Dane, E-mail: wittrup@mit.ed [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

2011-02-15

Introduction: In pretargeted radioimmunotherapy (PRIT), a bifunctional antibody is administered and allowed to pre-localize to tumor cells. Subsequently, a chelated radionuclide is administered and captured by cell-bound antibody while unbound hapten clears rapidly from the body. We aim to engineer high-affinity binders to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelates for use in PRIT applications. Methods: We mathematically modeled antibody and hapten pharmacokinetics to analyze hapten tumor retention as a function of hapten binding affinity. Motivated by model predictions, we used directed evolution and yeast surface display to affinity mature the 2D12.5 antibody to DOTA, reformatted as a single chain variable fragment (scFv). Results: Modeling predicts that for high antigen density and saturating bsAb dose, a hapten-binding affinity of 100 pM is needed for near-maximal hapten retention. We affinity matured 2D12.5 with an initial binding constant of about 10 nM to DOTA-yttrium chelates. Affinity maturation resulted in a 1000-fold affinity improvement to biotinylated DOTA-yttrium, yielding an 8.2{+-}1.9 picomolar binder. The high-affinity scFv binds DOTA complexes of lutetium and gadolinium with similar picomolar affinity and indium chelates with low nanomolar affinity. When engineered into a bispecific antibody construct targeting carcinoembryonic antigen, pretargeted high-affinity scFv results in significantly higher tumor retention of a {sup 111}In-DOTA hapten compared to pretargeted wild-type scFv in a xenograft mouse model. Conclusions: We have engineered a versatile, high-affinity, DOTA-chelate-binding scFv. We anticipate it will prove useful in developing pretargeted imaging and therapy protocols to exploit the potential of a variety of radiometals.

Theory of affine projection algorithms for adaptive filtering

CERN Document Server

Ozeki, Kazuhiko

2016-01-01

This book focuses on theoretical aspects of the affine projection algorithm (APA) for adaptive filtering. The APA is a natural generalization of the classical, normalized least-mean-squares (NLMS) algorithm. The book first explains how the APA evolved from the NLMS algorithm, where an affine projection view is emphasized. By looking at those adaptation algorithms from such a geometrical point of view, we can find many of the important properties of the APA, e.g., the improvement of the convergence rate over the NLMS algorithm especially for correlated input signals. After the birth of the APA in the mid-1980s, similar algorithms were put forward by other researchers independently from different perspectives. This book shows that they are variants of the APA, forming a family of APAs. Then it surveys research on the convergence behavior of the APA, where statistical analyses play important roles. It also reviews developments of techniques to reduce the computational complexity of the APA, which are important f...

A Generalized Affine Isoperimetric Inequality

OpenAIRE

Chen, Wenxiong; Howard, Ralph; Lutwak, Erwin; Yang, Deane; Zhang, Gaoyong

2004-01-01

A purely analytic proof is given for an inequality that has as a direct consequence the two most important affine isoperimetric inequalities of plane convex geometry: The Blaschke-Santalo inequality and the affine isoperimetric inequality of affine differential geometry.

Fatty acid and drug binding to a low-affinity component of human serum albumin, purified by affinity chromatography

DEFF Research Database (Denmark)

Vorum, H; Pedersen, A O; Honoré, B

1992-01-01

Binding equilibria for decanoate to a defatted, commercially available human serum albumin preparation were investigated by dialysis exchange rate determinations. The binding isotherm could not be fitted by the general binding equation. It was necessary to assume that the preparation was a mixture...... of two albumin components about 40% of the albumin having high affinity and about 60% having low affinity. By affinity chromatography we succeeded in purifying the low-affinity component from the mixture. The high-affinity component, however, could not be isolated. We further analyzed the fatty acid...... and drug binding abilities of the low-affinity component. The fatty acids decanoate, laurate, myristate and palmitate were bound with higher affinity to the mixture than to the low-affinity component. Diazepam was bound with nearly the same affinity to the low-affinity component as to the albumin mixture...

Lp-mixed affine surface area

Science.gov (United States)

Wang, Weidong; Leng, Gangsong

2007-11-01

According to the three notions of mixed affine surface area, Lp-affine surface area and Lp-mixed affine surface area proposed by Lutwak, in this article, we give the concept of ith Lp-mixed affine surface area such that the first and second notions of Lutwak are its special cases. Further, some Lutwak's results are extended associated with this concept. Besides, applying this concept, we establish an inequality for the volumes and dual quermassintegrals of a class of star bodies.

Identification of high-affinity anti-IL-1 α autoantibodies in normal human serum as an interfering substance in a sensitive enzyme-linked immunosorbent assay for IL-1 α

International Nuclear Information System (INIS)

Mae, N.; Liberato, D.J.; Chizzonite, R.; Satoh, H.

1991-01-01

A highly reproducible, sensitive, and specific sandwich enzyme-linked immunosorbent assay (ELISA) for recombinant human IL-1 α (rhIL-1 alpha) has been developed. Results from this ELISA have demonstrated that the concentration of rhIL-1 α added to normal human serum (NHS) decreased by 16.3% after 3 h and 24.9% after 6 h at room temperature. Molecular exclusion column chromatography with Sephacryl S-300 HR revealed that 125I-labeled IL-1 α added to normal human serum rapidly formed higher molecular weight complexes without indication of proteolytic degradation. The observed reduction in immunoreactivity was correlated with this protein complex formation and accounted for the apparent instability of rhIL-1 α in NHS. Immunoblot analysis indicated that the molecular weight of the binding protein was 150-160K, and the IL-1 α binding activity was removed and recovered from NHS by Protein-G affinity chromatography; indicating that the binding protein was IL-1 α-specific IgG. The binding of 125I-labeled IL-1 α to the serum binding proteins could be inhibited by unlabeled IL-1 alpha (IC50 = 7.4 x 10(-11) M) but not by unlabeled IL-1 β. Kinetic analysis with 125I-labeled IL-1 alpha revealed that the average binding affinity of these IL-1 α-specific IgGs was 4.7 x 10(10) M-1. These results suggest that these autoantibodies may interfere with the detection of IL-1 α in human serum by various assay systems and also could be a regulator of circulating IL-1 α

Mapping Affinities in Academic Organizations

Directory of Open Access Journals (Sweden)

Dario Rodighiero

2018-02-01

Full Text Available Scholarly affinities are one of the most fundamental hidden dynamics that drive scientific development. Some affinities are actual, and consequently can be measured through classical academic metrics such as co-authoring. Other affinities are potential, and therefore do not leave visible traces in information systems; for instance, some peers may share interests without actually knowing it. This article illustrates the development of a map of affinities for academic collectives, designed to be relevant to three audiences: the management, the scholars themselves, and the external public. Our case study involves the School of Architecture, Civil and Environmental Engineering of EPFL, hereinafter ENAC. The school consists of around 1,000 scholars, 70 laboratories, and 3 institutes. The actual affinities are modeled using the data available from the information systems reporting publications, teaching, and advising scholars, whereas the potential affinities are addressed through text mining of the publications. The major challenge for designing such a map is to represent the multi-dimensionality and multi-scale nature of the information. The affinities are not limited to the computation of heterogeneous sources of information; they also apply at different scales. The map, thus, shows local affinities inside a given laboratory, as well as global affinities among laboratories. This article presents a graphical grammar to represent affinities. Its effectiveness is illustrated by two actualizations of the design proposal: an interactive online system in which the map can be parameterized, and a large-scale carpet of 250 square meters. In both cases, we discuss how the materiality influences the representation of data, in particular the way key questions could be appropriately addressed considering the three target audiences: the insights gained by the management and their consequences in terms of governance, the understanding of the scholars’ own

Affine field theories

International Nuclear Information System (INIS)

Cadavid, A.C.

1989-01-01

The author constructs a non-Abelian field theory by gauging a Kac-Moody algebra, obtaining an infinite tower of interacting vector fields and associated ghosts, that obey slightly modified Feynman rules. She discusses the spontaneous symmetry breaking of such theory via the Higgs mechanism. If the Higgs particle lies in the Cartan subalgebra of the Kac-Moody algebra, the previously massless vectors acquire a mass spectrum that is linear in the Kac-Moody index and has additional fine structure depending on the associated Lie algebra. She proceeds to show that there is no obstacle in implementing the affine extension of supersymmetric Yang-Mills theories. The result is valid in four, six and ten space-time dimensions. Then the affine extension of supergravity is investigated. She discusses only the loop algebra since the affine extension of the super-Poincare algebra appears inconsistent. The construction of the affine supergravity theory is carried out by the group manifold method and leads to an action describing infinite towers of spin 2 and spin 3/2 fields that interact subject to the symmetries of the loop algebra. The equations of motion satisfy the usual consistency check. Finally, she postulates a theory in which both the vector and scalar fields lie in the loop algebra of SO(3). This theory has an expanded soliton sector, and corresponding to the original 't Hooft-Polyakov solitonic solutions she now finds an infinite family of exact, special solutions of the new equations. She also proposes a perturbation method for obtaining an arbitrary solution of those equations for each level of the affine index

Electron affinities: theoretical

International Nuclear Information System (INIS)

Kaufman, J.J.

1976-01-01

A brief description is given of the conceptual background and formalism of the various ab-initio and semi-ab-initio quantum computational techniques for calculating atomic and molecular electron affinities: Hartree--Fock--Roothaan SCF, configuration interaction (CI), multiconfiguration SCF (MC-SCF), Bethe--Goldstone, superposition of configurations (SOC), ab-initio effective core model potentials, Xα-MS, plus other less common methods. Illustrative and comparative examples of electron affinities calculated by these various methods are presented

Hemoglobin affinity in Andean rodents

Directory of Open Access Journals (Sweden)

HRVOJ OSTOJIC

2002-01-01

Full Text Available Blood hemoglobin oxygen affinity (P50 was measured in three Andean species and in the laboratory rat (control, all raised near sea level. Chinchilla lanigera (Molina, 1792 has an altitudinal habitat range from low Andean slopes up to 3000 m., while Chinchilla brevicaudata (Waterhouse, 1848 has an altitudinal range from 3000 to 5000 m. The laboratory type guinea pig, wild type guinea pig (Cavia porcellus, (Waterhouse, 1748, and laboratory rat (Rattus norvegicus were also raised at sea level. The Andean species had high hemoglobin oxygen affinities (low P50 compared with the rat. Chinchilla brevicaudata had a higher affinity than Chinchilla lanigera. The wild type guinea pig had a higher affinity than the laboratory type. As has been shown in other species, this is another example of an inverse correlation between the altitude level and the P50 values. This is the first hemoglobin oxygen affinity study in Chinchilla brevicaudata.

A Quick and Affine Invariance Matching Method for Oblique Images

Directory of Open Access Journals (Sweden)

XIAO Xiongwu

2015-04-01

Full Text Available This paper proposed a quick, affine invariance matching method for oblique images. It calculated the initial affine matrix by making full use of the two estimated camera axis orientation parameters of an oblique image, then recovered the oblique image to a rectified image by doing the inverse affine transform, and left over by the SIFT method. We used the nearest neighbor distance ratio(NNDR, normalized cross correlation(NCC measure constraints and consistency check to get the coarse matches, then used RANSAC method to calculate the fundamental matrix and the homography matrix. And we got the matches that they were interior points when calculating the homography matrix, then calculated the average value of the matches' principal direction differences. During the matching process, we got the initial matching features by the nearest neighbor(NN matching strategy, then used the epipolar constrains, homography constrains, NCC measure constrains and consistency check of the initial matches' principal direction differences with the calculated average value of the interior matches' principal direction differences to eliminate false matches. Experiments conducted on three pairs of typical oblique images demonstrate that our method takes about the same time as SIFT to match a pair of oblique images with a plenty of corresponding points distributed evenly and an extremely low mismatching rate.

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

Directory of Open Access Journals (Sweden)

C. Ruben Vosmeer

2014-01-01

Full Text Available Binding affinity prediction of potential drugs to target and off-target proteins is an essential asset in drug development. These predictions require the calculation of binding free energies. In such calculations, it is a major challenge to properly account for both the dynamic nature of the protein and the possible variety of ligand-binding orientations, while keeping computational costs tractable. Recently, an iterative Linear Interaction Energy (LIE approach was introduced, in which results from multiple simulations of a protein-ligand complex are combined into a single binding free energy using a Boltzmann weighting-based scheme. This method was shown to reach experimental accuracy for flexible proteins while retaining the computational efficiency of the general LIE approach. Here, we show that the iterative LIE approach can be used to predict binding affinities in an automated way. A workflow was designed using preselected protein conformations, automated ligand docking and clustering, and a (semi-automated molecular dynamics simulation setup. We show that using this workflow, binding affinities of aryloxypropanolamines to the malleable Cytochrome P450 2D6 enzyme can be predicted without a priori knowledge of dominant protein-ligand conformations. In addition, we provide an outlook for an approach to assess the quality of the LIE predictions, based on simulation outcomes only.

Accurate determination of the oxidative phosphorylation affinity for ADP in isolated mitochondria.

Directory of Open Access Journals (Sweden)

Gilles Gouspillou

Full Text Available BACKGROUND: Mitochondrial dysfunctions appear strongly implicated in a wide range of pathologies. Therefore, there is a growing need in the determination of the normal and pathological integrated response of oxidative phosphorylation to cellular ATP demand. The present study intends to address this issue by providing a method to investigate mitochondrial oxidative phosphorylation affinity for ADP in isolated mitochondria. METHODOLOGY/PRINCIPAL FINDINGS: The proposed method is based on the simultaneous monitoring of substrate oxidation (determined polarographically and phosphorylation (determined using the glucose-hexokinase glucose-6-phosphate dehydrogenase-NADP(+ enzymatic system rates, coupled to the determination of actual ADP and ATP concentrations by bioluminescent assay. This enzymatic system allows the study of oxidative phosphorylation during true steady states in a wide range of ADP concentrations. We demonstrate how the application of this method allows an accurate determination of mitochondrial affinity for ADP from both oxidation (K(mVox and phosphorylation (K(mVp rates. We also demonstrate that determination of K(mVox leads to an important overestimation of the mitochondrial affinity for ADP, indicating that mitochondrial affinity for ADP should be determined using phosphorylation rate. Finally, we show how this method allows the direct and precise determination of the mitochondrial coupling efficiency. Data obtained from rat skeletal muscle and liver mitochondria illustrate the discriminating capabilities of this method. CONCLUSIONS/SIGNIFICANCE: Because the proposed method allows the accurate determination of mitochondrial oxidative phosphorylation affinity for ADP in isolated mitochondria, it also opens the route to a better understanding of functional consequences of mitochondrial adaptations/dysfunctions arising in various physiological/pathophysiological conditions.

Selective induction of high-ouabain-affinity isoform of Na+-K+-ATPase by thyroid hormone

International Nuclear Information System (INIS)

Haber, R.S.; Loeb, J.N.

1988-01-01

The administration of thyroid hormone is known to result in an induction of the Na + -K + -adenosinetriphosphatase (Na + -K + -ATPase) in rat skeletal muscle and other thyroid hormone-responsive tissues. Since the Na + -K + -ATPase in a variety of mammalian tissues has recently been reported to exist in at least two forms distinguishable by differing affinities for the inhibitory cardiac glycoside ouabain. The authors have studied the effects of 3,3',5-triiodo-L-thyronine (T 3 ) treatment on these two forms of the enzyme in rat diaphragm. The inhibition of Na + -K + -ATPase activity in a crude membrane fraction by varying concentrations of ouabain conformed to a biphasic pattern consistent with the presence of two distinct isoforms with inhibition constants (K I s) for ouabain of ∼10 -7 and 10 -4 M, respectively. Measurement of the specific binding of [ 3 H]ouabain to these membranes confirmed the presence of a class of high-affinity ouabain binding sites with a dissociation constant (K d ) of slightly less than 10 -7 M, whose maximal binding capacity was increased by T 3 treatment by 185%. Binding studies in unfractionated homogenates of diaphragm similarly demonstrated the presence of high-affinity sites whose maximal binding capacity was increased by T 3 treatment. Quantitation of both the high- and low-ouabain-affinity forms of the Na + -K + -ATPase by ouabain-dependent phosphorylation from [ 32 P]orthophosphate confirmed that T 3 treatment markedly increased the number of high-affinity sites while having little effect on the number of low-affinity sites. These observations provide, to our knowledge, the first demonstration that these two forms of the Na + -K + -ATPase are subject to selective hormonal induction

2017 Guralp Affinity Digitizer Evaluation.

Energy Technology Data Exchange (ETDEWEB)

Merchant, Bion J.

2018-03-01

Sandia National Laboratories has tested and evaluated two Guralp Affinity digitizers. The Affinity digitizers are intended to record sensor output for seismic and infrasound monitoring applications. The purpose of this digitizer evaluation is to measure the performance characteristics in such areas as power consumption, input impedance, sensitivity, full scale, self- noise, dynamic range, system noise, response, passband, and timing. The Affinity digitizers are being evaluated for potential use in the International Monitoring System (IMS) of the Comprehensive Nuclear Test-Ban-Treaty Organization (CTBTO).

Two-parameter quantum affine algebra Ur,s(sln-circumflex), Drinfeld realization and quantum affine Lyndon basis

International Nuclear Information System (INIS)

Hu Naihong; Rosso, M.; Zhang Honglian

2006-12-01

We further find the defining structure of a two-parameter quantum affine algebra U r,s (sl n -circumflex) (n > 2) in the sense of Benkart-Witherspoon [BW1] after the work of [BGH1], [HS] and [BH], which turns out to be a Drinfeld double. Of more importance for the 'affine' cases is that we work out the compatible two-parameter version of the Drinfeld realization as a quantum affinization of U r,s (sl n ) and establish the Drinfeld isomorphism Theorem in the two-parameter setting via developing a new remarkable combinatorial approach - quantum 'affine' Lyndon basis with an explicit valid algorithm, based on the Drinfeld realization. (author)

Study of nuclear proteins in normal and xeroderma pigmentosum lymphoblastoid cells

International Nuclear Information System (INIS)

Amari, N.M.B.

1985-01-01

Nuclear histone and nonhistone (NHP) proteins from normal human and xeroderma pigmentosum, complementation group A (XP-A) lymphoblastoid cells were compared both qualitatively, quantitatively and for binding affinity for DNA. Histones and four NHP fractions (NHP/sub 1-4/) were isolated from purified cell nuclei. Binding affinity to [ 3 H] melanoma DNA of histones and each NHP fraction was then determined using gradient dialysis followed by a filter assay. Histones and each NHP fraction were then sub-fractionated by polyacrylamide gel electrophoresis. Densitometric scans of the separation of these proteins on the gels were qualitatively, and quantitatively analyzed and compared between the two cell lines. No qualitative or quantitative differences were observed between histones from XP-A or normal cells

Representations of affine Hecke algebras

CERN Document Server

Xi, Nanhua

1994-01-01

Kazhdan and Lusztig classified the simple modules of an affine Hecke algebra Hq (q E C*) provided that q is not a root of 1 (Invent. Math. 1987). Ginzburg had some very interesting work on affine Hecke algebras. Combining these results simple Hq-modules can be classified provided that the order of q is not too small. These Lecture Notes of N. Xi show that the classification of simple Hq-modules is essentially different from general cases when q is a root of 1 of certain orders. In addition the based rings of affine Weyl groups are shown to be of interest in understanding irreducible representations of affine Hecke algebras. Basic knowledge of abstract algebra is enough to read one third of the book. Some knowledge of K-theory, algebraic group, and Kazhdan-Lusztig cell of Cexeter group is useful for the rest

Action of carbon monoxide on the affinity of hemoglobin for oxygen

Energy Technology Data Exchange (ETDEWEB)

Vanuxem, D.; Weiller, P.J.; Guillot, C.; Grimaud, C.

1982-01-01

The authors have studied the action of carbon monoxide on the affinity of hemoglobin for oxygen by measuring P50 in whole blood and in stripped hemoglobin before and after exposition of blood samples from heavy smokers and polycythemic patients with high levels of HbCO to hyperbaric oxygen (2.2 ata). The concentration of 2,3-diphosphoglycerate was normal although P50 was significantly lowered, not only in whole blood but also in stripped hemoglobin. Hyperbaric oxygen normalized P50 by removing CO radicals from stripped hemoglobin. This may indicate that CO radicals exert a direct action on the hemoglobin molecule, at least at the HbCO levels studied in this work.

Antisymmetric tensor generalizations of affine vector fields.

Science.gov (United States)

Houri, Tsuyoshi; Morisawa, Yoshiyuki; Tomoda, Kentaro

2016-02-01

Tensor generalizations of affine vector fields called symmetric and antisymmetric affine tensor fields are discussed as symmetry of spacetimes. We review the properties of the symmetric ones, which have been studied in earlier works, and investigate the properties of the antisymmetric ones, which are the main theme in this paper. It is shown that antisymmetric affine tensor fields are closely related to one-lower-rank antisymmetric tensor fields which are parallelly transported along geodesics. It is also shown that the number of linear independent rank- p antisymmetric affine tensor fields in n -dimensions is bounded by ( n + 1)!/ p !( n - p )!. We also derive the integrability conditions for antisymmetric affine tensor fields. Using the integrability conditions, we discuss the existence of antisymmetric affine tensor fields on various spacetimes.

Braided affine geometry and q-analogs of wave operators

International Nuclear Information System (INIS)

Gurevich, Dimitri; Saponov, Pavel

2009-01-01

The main goal of this review is to compare different approaches to constructing the geometry associated with a Hecke type braiding (in particular, with that related to the quantum group U q (sl(n))). We place emphasis on the affine braided geometry related to the so-called reflection equation algebra (REA). All objects of such a type of geometry are defined in the spirit of affine algebraic geometry via polynomial relations on generators. We begin by comparing the Poisson counterparts of 'quantum varieties' and describe different approaches to their quantization. Also, we exhibit two approaches to introducing q-analogs of vector bundles and defining the Chern-Connes index for them on quantum spheres. In accordance with the Serre-Swan approach, the q-vector bundles are treated as finitely generated projective modules over the corresponding quantum algebras. Besides, we describe the basic properties of the REA used in this construction and compare different ways of defining q-analogs of partial derivatives and differentials on the REA and algebras close to them. In particular, we present a way of introducing a q-differential calculus via Koszul type complexes. The elements of the q-calculus are applied to defining q-analogs of some relativistic wave operators. (topical review)

Enhancement of the cytotoxicity of radiosensitizers by modest hyperthermia: the electron-affinity relationship

Energy Technology Data Exchange (ETDEWEB)

Rajaratnam, S.; Adams, G.E.; Stratford, I.J.; Clarke, C.

1982-01-01

The cytotoxicity of 3 electron-affinic radiosensitizers has been studied in Chinese hamster V-79 cells as a function of pH and modest hyperthermia. When equitoxic concentrations were used and temperature was increased from 34 to 41/sup 0/C metronidazole, the compound with the lowest electron affinity showed the greatest enhancement of hypoxic-cell toxicity, and nitrofurantoin, the compound with the highest electron affinity, the least. The results can be explained if the mechanisms of toxicity involves a redox reaction, since it would be expected that the least toxic compound (lowest electron affinity) would have the largest activation energy and hence the greatest temperature effect. This appears to hold for these 3 compounds. Experiments also showed that nitrofurantoin which exhibits no increase in toxicity when the temperature was increased from 37 to 41/sup 0/C at pH 7.4, showed an increase in toxicity for the same temperature change at the pH of 7.0 and 6.6. Under aerobic conditions only metronidazole showed significant toxicity at 41/sup 0/C, where the differential between aerobic and hypoxic cell toxicity was minimal, both at pH 7.4, and at the low pH values of 7.0 and 6.6. In the clinical setting there is evidence that tumor cells are at a lower pH than their surrounding normal tissues. Hypoxic-cell cytotoxicity is enhanced at low pH, and even further enhanced at low pH in combination with a temperature of 41/sup 0/C. However, this finding correlates conversely with electron affinity.

Affine LIBOR Models with Multiple Curves

DEFF Research Database (Denmark)

Grbac, Zorana; Papapantoleon, Antonis; Schoenmakers, John

2015-01-01

are specified following the methodology of the affine LIBOR models and are driven by the wide and flexible class of affine processes. The affine property is preserved under forward measures, which allows us to derive Fourier pricing formulas for caps, swaptions, and basis swaptions. A model specification...... with dependent LIBOR rates is developed that allows for an efficient and accurate calibration to a system of caplet prices....

MR guided spatial normalization of SPECT scans

International Nuclear Information System (INIS)

Crouch, B.; Barnden, L.R.; Kwiatek, R.

2010-01-01

Full text: In SPECT population studies where magnetic resonance (MR) scans are also available, the higher resolution of the MR scans allows for an improved spatial normalization of the SPECT scans. In this approach, the SPECT images are first coregistered to their corresponding MR images by a linear (affine) transformation which is calculated using SPM's mutual information maximization algorithm. Non-linear spatial normalization maps are then computed either directly from the MR scans using SPM's built in spatial normalization algorithm, or, from segmented TI MR images using DARTEL, an advanced diffeomorphism based spatial normalization algorithm. We compare these MR based methods to standard SPECT based spatial normalization for a population of 27 fibromyalgia patients and 25 healthy controls with spin echo T 1 scans. We identify significant perfusion deficits in prefrontal white matter in FM patients, with the DARTEL based spatial normalization procedure yielding stronger statistics than the standard SPECT based spatial normalization. (author)

Affinity Programs and the Real Estate Brokerage Industry

OpenAIRE

G Stacy Sirmans; David A. Macpherson

2001-01-01

This study surveys active real estate brokers obtaining information on involvement in affinity programs and referral/relocation networks. Some results regarding affinity involvement are: (a) 13% of respondents reported affinity affilliations, 75% reported no affiliations, and 12% indicated plans to become involved within the next year; (b) about half having affinity affiliations were involved with 2-4 groups; (c) affinity relationships were most often with membership organizations, corporatio...

Frobenius splitting and geometry of G-Schubert varieties

DEFF Research Database (Denmark)

He, Xuhua; Thomsen, Jesper Funch

Let be an equivariant embedding of a connected reductive group over an algebraically closed field of positive characteristic. Let denote a Borel subgroup of . A -Schubert variety in is a subvariety of the form , where is a -orbit closure in . In the case where is the wonderful compactification of....... Although this indicates that -Schubert varieties have nice singularities we give an example, in the wonderful compactification of a group of adjoint type, which is not normal. Finally we also extend the Frobenius splitting results to the more general class of -Schubert varieties....

Engineering of bispecific affinity proteins with high affinity for ERBB2 and adaptable binding to albumin.

Directory of Open Access Journals (Sweden)

Johan Nilvebrant

Full Text Available The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein.

Using Affinity Diagrams to Evaluate Interactive Prototypes

DEFF Research Database (Denmark)

Lucero, Andrés

2015-01-01

our particular use of affinity diagramming in prototype evaluations. We reflect on a decade’s experience using affinity diagramming across a number of projects, both in industry and academia. Our affinity diagramming process in interaction design has been tailored and consists of four stages: creating...

The construction of normal expectations

DEFF Research Database (Denmark)

Quitzau, Maj-Britt; Røpke, Inge

2008-01-01

The gradual upward changes of standards in normal everyday life have significant environmental implications, and it is therefore important to study how these changes come about. The intention of the article is to analyze the social construction of normal expectations through a case study. The case...... concerns the present boom in bathroom renovations in Denmark, which offers an excellent opportunity to study the interplay between a wide variety of consumption drivers and social changes pointing toward long-term changes of normal expectations regarding bathroom standards. The study is problemoriented...... and transdisciplinary and draws on a wide range of sociological, anthropological, and economic theories. The empirical basis comprises a combination of statistics, a review of magazine and media coverage, visits to exhibitions, and qualitative interviews. A variety of consumption drivers are identified. Among...

Single-step affinity purification for fungal proteomics.

Science.gov (United States)

Liu, Hui-Lin; Osmani, Aysha H; Ukil, Leena; Son, Sunghun; Markossian, Sarine; Shen, Kuo-Fang; Govindaraghavan, Meera; Varadaraj, Archana; Hashmi, Shahr B; De Souza, Colin P; Osmani, Stephen A

2010-05-01

A single-step protein affinity purification protocol using Aspergillus nidulans is described. Detailed protocols for cell breakage, affinity purification, and depending on the application, methods for protein release from affinity beads are provided. Examples defining the utility of the approaches, which should be widely applicable, are included.

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells

Directory of Open Access Journals (Sweden)

Wei Shi

2014-12-01

Full Text Available Clonal population expansion of T cells during an immune response is dependent on the affinity of the T cell receptor (TCR for its antigen [1]. However, there is little understanding of how this process is controlled transcriptionally. We found that the transcription factor IRF4 was induced in a manner dependent on TCR-affinity and was critical for the clonal expansion and maintenance of effector function of antigen-specific CD8+ T cells. We performed a genome-wide expression profiling experiment using RNA sequencing technology (RNA-seq to interrogate global expression changes when IRF4 was deleted in CD8+ T cells activated with either a low or high affinity peptide ligand. This allowed us not only to determine IRF4-dependent transcriptional changes but also to identify transcripts dependent on TCR-affinity [2]. Here we describe in detail the analyses of the RNA-seq data, including quality control, read mapping, quantification, normalization and assessment of differential gene expression. The RNA-seq data can be accessed from Gene Expression Omnibus database (accession number GSE49929.

Connections between quantized affine algebras and superalgebras

International Nuclear Information System (INIS)

Zhang, R.B.

1992-08-01

Every affine superalgebra with a symmetrizable Cartan matrix is closely related to an ordinary affine algebra with the same Cartan matrix. It is shown that the quantum supergroup associated with the former is essentially isomorphic to the quantum group associated with the latter in an appropriate class of representations. At the classical level, each integrable irreducible highest weight representation of the affine superalgebra has a corresponding irreducible representation of the affine algebra, which has the same weight space decomposition. (author). 5 refs, 3 tabs

Electrochemical Affinity Biosensors Based on Disposable Screen-Printed Electrodes for Detection of Food Allergens

Science.gov (United States)

Vasilescu, Alina; Nunes, Gilvanda; Hayat, Akhtar; Latif, Usman; Marty, Jean-Louis

2016-01-01

Food allergens are proteins from nuts and tree nuts, fish, shellfish, wheat, soy, eggs or milk which trigger severe adverse reactions in the human body, involving IgE-type antibodies. Sensitive detection of allergens in a large variety of food matrices has become increasingly important considering the emergence of functional foods and new food manufacturing technologies. For example, proteins such as casein from milk or lysozyme and ovalbumin from eggs are sometimes used as fining agents in the wine industry. Nonetheless, allergen detection in processed foods is a challenging endeavor, as allergen proteins are degraded during food processing steps involving heating or fermentation. Detection of food allergens was primarily achieved via Enzyme-Linked Immuno Assay (ELISA) or by chromatographic methods. With the advent of biosensors, electrochemical affinity-based biosensors such as those incorporating antibodies and aptamers as biorecognition elements were also reported in the literature. In this review paper, we highlight the success achieved in the design of electrochemical affinity biosensors based on disposable screen-printed electrodes towards detection of protein allergens. We will discuss the analytical figures of merit for various disposable screen-printed affinity sensors in relation to methodologies employed for immobilization of bioreceptors on transducer surface. PMID:27827963

Selective induction of high-ouabain-affinity isoform of Na sup + -K sup + -ATPase by thyroid hormone

Energy Technology Data Exchange (ETDEWEB)

Haber, R.S.; Loeb, J.N. (Columbia Univ., New York, NY (USA))

1988-12-01

The administration of thyroid hormone is known to result in an induction of the Na{sup +}-K{sup +}-adenosinetriphosphatase (Na{sup +}-K{sup +}-ATPase) in rat skeletal muscle and other thyroid hormone-responsive tissues. Since the Na{sup +}-K{sup +}-ATPase in a variety of mammalian tissues has recently been reported to exist in at least two forms distinguishable by differing affinities for the inhibitory cardiac glycoside ouabain. The authors have studied the effects of 3,3{prime},5-triiodo-L-thyronine (T{sub 3}) treatment on these two forms of the enzyme in rat diaphragm. The inhibition of Na{sup +}-K{sup +}-ATPase activity in a crude membrane fraction by varying concentrations of ouabain conformed to a biphasic pattern consistent with the presence of two distinct isoforms with inhibition constants (K{sub I}s) for ouabain of {approximately}10{sup {minus}7} and 10{sup {minus}4} M, respectively. Measurement of the specific binding of ({sup 3}H)ouabain to these membranes confirmed the presence of a class of high-affinity ouabain binding sites with a dissociation constant (K{sub d}) of slightly less than 10{sup {minus}7}M, whose maximal binding capacity was increased by T{sub 3} treatment by 185%. Binding studies in unfractionated homogenates of diaphragm similarly demonstrated the presence of high-affinity sites whose maximal binding capacity was increased by T{sub 3} treatment. Quantitation of both the high- and low-ouabain-affinity forms of the Na{sup +}-K{sup +}-ATPase by ouabain-dependent phosphorylation from ({sup 32}P)orthophosphate confirmed that T{sub 3} treatment markedly increased the number of high-affinity sites while having little effect on the number of low-affinity sites. These observations provide, to our knowledge, the first demonstration that these two forms of the Na{sup +}-K{sup +}-ATPase are subject to selective hormonal induction.

Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

Science.gov (United States)

Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

2016-08-26

Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

Affine Fullerene C60 in a GS-Quasigroup

Directory of Open Access Journals (Sweden)

Vladimir Volenec

2014-01-01

Full Text Available It will be shown that the affine fullerene C60, which is defined as an affine image of buckminsterfullerene C60, can be obtained only by means of the golden section. The concept of the affine fullerene C60 will be constructed in a general GS-quasigroup using the statements about the relationships between affine regular pentagons and affine regular hexagons. The geometrical interpretation of all discovered relations in a general GS-quasigroup will be given in the GS-quasigroup C(1/2(1+5.

Affinity Spaces and 21st Century Learning

Science.gov (United States)

Gee, James Paul

2017-01-01

This article discusses video games as "attractors" to "affinity spaces." It argues that affinity spaces are key sites today where people teach and learn 21st Century skills. While affinity spaces are proliferating on the Internet as interest-and-passion-driven sites devoted to a common set of endeavors, they are not new, just…

Identification of high-affinity calmodulin-binding proteins in rat liver

International Nuclear Information System (INIS)

Hanley, R.M.; Dedman, J.R.; Shenolikar, S.

1987-01-01

The Ca 2+ -dependent binding of [ 125 I] calmodulin (CaM) to hepatic proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was utilized to identify CaM binding or acceptor proteins or CAPs. Two proteins of apparent molecular weight of 60,000 (CAP-60) and 45,000 (CAP-45) comprised > 80% of the Ca 2+ -dependent CaM binding in rat liver cytosol. CAP-60 and CAP-45 were partially purified by a variety of chromatographic steps, including affinity chromatography on CaM Sepharose. CAP-60 possessed a native molecular size of 400,000, indicating it to be the CaM-binding subunit of a larger oligomeric complex. In contrast, CAP-45 was monomeric as judged by gel filtration. Neither CAP-60 nor CAP-45 possessed chromatographic properties consistent with known CaM-dependent enzymes reported in the literature. Two-dimensional peptide mapping provided convincing evidence that CAP-60 and CAP-45 were unrelated to other well-characterized CAPs, namely Ca 2+ (CaM)-dependent protein kinase II, calcineurin, or the CaM-dependent cyclic nucleotide phosphodiesterase. The relative abundance and high affinity for CaM could suggest that these novel target proteins, CAP-60 and CAP-45, represent a dominant pathway for CaM action in the mammalian liver

Fanconi anemia complementation group A (FANCA) protein has intrinsic affinity for nucleic acids with preference for single-stranded forms.

Science.gov (United States)

Yuan, Fenghua; Qian, Liangyue; Zhao, Xinliang; Liu, Jesse Y; Song, Limin; D'Urso, Gennaro; Jain, Chaitanya; Zhang, Yanbin

2012-02-10

The Fanconi anemia complementation group A (FANCA) gene is one of 15 disease-causing genes and has been found to be mutated in ∼60% of Fanconi anemia patients. Using purified protein, we report that human FANCA has intrinsic affinity for nucleic acids. FANCA binds to both single-stranded (ssDNA) and double-stranded (dsDNA) DNAs; however, its affinity for ssDNA is significantly higher than for dsDNA in an electrophoretic mobility shift assay. FANCA also binds to RNA with an intriguingly higher affinity than its DNA counterpart. FANCA requires a certain length of nucleic acids for optimal binding. Using DNA and RNA ladders, we determined that the minimum number of nucleotides required for FANCA recognition is ∼30 for both DNA and RNA. By testing the affinity between FANCA and a variety of DNA structures, we found that a 5'-flap or 5'-tail on DNA facilitates its interaction with FANCA. A patient-derived FANCA truncation mutant (Q772X) has diminished affinity for both DNA and RNA. In contrast, the complementing C-terminal fragment of Q772X, C772-1455, retains the differentiated nucleic acid-binding activity (RNA > ssDNA > dsDNA), indicating that the nucleic acid-binding domain of FANCA is located primarily at its C terminus, where most disease-causing mutations are found.

Fanconi Anemia Complementation Group A (FANCA) Protein Has Intrinsic Affinity for Nucleic Acids with Preference for Single-stranded Forms*

Science.gov (United States)

Yuan, Fenghua; Qian, Liangyue; Zhao, Xinliang; Liu, Jesse Y.; Song, Limin; D'Urso, Gennaro; Jain, Chaitanya; Zhang, Yanbin

2012-01-01

The Fanconi anemia complementation group A (FANCA) gene is one of 15 disease-causing genes and has been found to be mutated in ∼60% of Fanconi anemia patients. Using purified protein, we report that human FANCA has intrinsic affinity for nucleic acids. FANCA binds to both single-stranded (ssDNA) and double-stranded (dsDNA) DNAs; however, its affinity for ssDNA is significantly higher than for dsDNA in an electrophoretic mobility shift assay. FANCA also binds to RNA with an intriguingly higher affinity than its DNA counterpart. FANCA requires a certain length of nucleic acids for optimal binding. Using DNA and RNA ladders, we determined that the minimum number of nucleotides required for FANCA recognition is ∼30 for both DNA and RNA. By testing the affinity between FANCA and a variety of DNA structures, we found that a 5′-flap or 5′-tail on DNA facilitates its interaction with FANCA. A patient-derived FANCA truncation mutant (Q772X) has diminished affinity for both DNA and RNA. In contrast, the complementing C-terminal fragment of Q772X, C772–1455, retains the differentiated nucleic acid-binding activity (RNA > ssDNA > dsDNA), indicating that the nucleic acid-binding domain of FANCA is located primarily at its C terminus, where most disease-causing mutations are found. PMID:22194614

On the structure of self-affine convex bodies

Energy Technology Data Exchange (ETDEWEB)

Voynov, A S [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

2013-08-31

We study the structure of convex bodies in R{sup d} that can be represented as a union of their affine images with no common interior points. Such bodies are called self-affine. Vallet's conjecture on the structure of self-affine bodies was proved for d = 2 by Richter in 2011. In the present paper we disprove the conjecture for all d≥3 and derive a detailed description of self-affine bodies in R{sup 3}. Also we consider the relation between properties of self-affine bodies and functional equations with a contraction of an argument. Bibliography: 10 titles.

Traceless affinity labeling of endogenous proteins for functional analysis in living cells.

Science.gov (United States)

Hayashi, Takahiro; Hamachi, Itaru

2012-09-18

affinity labeling method and allows for real-time monitoring of protein activity. With the high target specificity and biocompatibility of this technique, we have achieved individual labeling and imaging of endogenously expressed proteins in samples of high biological complexity. We also highlight applications in which our current approach enabled the monitoring of important biological events, such as ligand binding, in living cells. These novel chemical labeling techniques are expected to provide a molecular toolbox for studying a wide variety of proteins and beyond in living cells.

Polynomials associated with equilibria of affine Toda-Sutherland systems

International Nuclear Information System (INIS)

Odake, S; Sasaki, R

2004-01-01

An affine Toda-Sutherland system is a quasi-exactly solvable multi-particle dynamics based on an affine simple root system. It is a 'cross' between two well-known integrable multi-particle dynamics, an affine Toda molecule (exponential potential, periodic nearest-neighbour interaction) and a Sutherland system (inverse sine-square interaction). Polynomials describing the equilibrium positions of affine Toda-Sutherland systems are determined for all affine simple root systems

Different endothelin receptor affinities in dog tissues

International Nuclear Information System (INIS)

Loeffler, B.M.L.; Loehrer, W.

1991-01-01

Endothelin (ET) is a long-lasting potent vasoconstrictor-peptide. Here the authors report different binding affinities of endothelin-1 (ET-1) to ET-receptors of various dog tissues. Crude microsomal fractions were prepared after homogenisation of dog tissues in 50 mM Tris/HCl, 20 mM MnCl2, 1 mM EDTA, pH 7.4 by differential centrifugation. Aliquots of microsomal fractions (70 micrograms of protein) were incubated at 25 degrees C for 180 min in the presence of 20 pM 125I-ET-1 and various concentrations of cold ET-1. Four different ET-1 receptor binding affinities were found: adrenals, cerebrum, liver, heart, skeletal muscle and stomach microsomal membranes contained high affinity binding sites (Kd 50 - 80 pM, Bmax 60 - 250 fmol/mg). In cerebellum and spleen medium affinity ET-1 receptors (Kd 350 pM, Bmax 880 and 1200 fmol/mg respectively) were present. In comparison lung and kidney microsomes contained a low affinity ET-1 receptor (Kd 800 and 880 pM, Bmax 1600 and 350 fmol/mg). Receptors of even lower affinity were present in heart, intestine and liver microsomes with Kd values of 3 - 6 nM

Duals of Affine Grassmann Codes and Their Relatives

DEFF Research Database (Denmark)

Beelen, P.; Ghorpade, S. R.; Hoholdt, T.

2012-01-01

Affine Grassmann codes are a variant of generalized Reed-Muller codes and are closely related to Grassmann codes. These codes were introduced in a recent work by Beelen Here, we consider, more generally, affine Grassmann codes of a given level. We explicitly determine the dual of an affine...... Grassmann code of any level and compute its minimum distance. Further, we ameliorate the results by Beelen concerning the automorphism group of affine Grassmann codes. Finally, we prove that affine Grassmann codes and their duals have the property that they are linear codes generated by their minimum......-weight codewords. This provides a clean analogue of a corresponding result for generalized Reed-Muller codes....

A Novel Vertex Affinity for Community Detection

Energy Technology Data Exchange (ETDEWEB)

Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-10-05

We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

On affine non-negative matrix factorization

DEFF Research Database (Denmark)

Laurberg, Hans; Hansen, Lars Kai

2007-01-01

We generalize the non-negative matrix factorization (NMF) generative model to incorporate an explicit offset. Multiplicative estimation algorithms are provided for the resulting sparse affine NMF model. We show that the affine model has improved uniqueness properties and leads to more accurate id...

Affinity-based biosensors as promising tools for gene doping detection.

Science.gov (United States)

Minunni, Maria; Scarano, Simona; Mascini, Marco

2008-05-01

Innovative bioanalytical approaches can be foreseen as interesting means for solving relevant emerging problems in anti-doping control. Sport authorities fear that the newer form of doping, so-called gene doping, based on a misuse of gene therapy, will be undetectable and thus much less preventable. The World Anti-Doping Agency has already asked scientists to assist in finding ways to prevent and detect this newest kind of doping. In this Opinion article we discuss the main aspects of gene doping, from the putative target analytes to suitable sampling strategies. Moreover, we discuss the potential application of affinity sensing in this field, which so far has been successfully applied to a variety of analytical problems, from clinical diagnostics to food and environmental analysis.

Improving image segmentation by learning region affinities

Energy Technology Data Exchange (ETDEWEB)

Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.

2010-11-03

We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

Selection of imprinted nanoparticles by affinity chromatography.

Science.gov (United States)

Guerreiro, António R; Chianella, Iva; Piletska, Elena; Whitcombe, Michael J; Piletsky, Sergey A

2009-04-15

Soluble molecularly imprinted nanoparticles were synthesised via iniferter initiated polymerisation and separated by size via gel permeation chromatography. Subsequent fractionation of these particles by affinity chromatography allowed the separation of high affinity fractions from the mixture of nanoparticles. Fractions selected this way possess affinity similar to that of natural antibodies (K(d) 6.6x10(-8)) M and were also able to discriminate between related functional analogues of the template.

Immunostimulatory CpG-oligonucleotides induce functional high affinity IL-2 receptors on B-CLL cells: costimulation with IL-2 results in a highly immunogenic phenotype.

Science.gov (United States)

Decker, T; Schneller, F; Kronschnabl, M; Dechow, T; Lipford, G B; Wagner, H; Peschel, C

2000-05-01

CpG-oligodeoxynucleotides (CpG-ODN) have been shown to induce proliferation, cytokine production, and surface molecule regulation in normal and malignant human B cells. In the present study, we investigated the potential of CpG-ODN to induce functional high-affinity receptors in leukemic and normal B cells and the effects of costimulation with IL-2 on proliferation, cytokine secretion, and surface molecule regulation. Highly purified B cells from B-CLL patients and normal controls were stimulated with CpG-ODN with or without IL-2. Expression of CD25 was determined using FACS, and the presence of high-affinity IL-2 receptors was determined by scatchard analysis. Costimulatory effects of IL-2 and CpG-ODN were investigated using proliferation assays, ELISA (IL-6, TNF-alpha), and FACS analysis (CD80, CD86 expression). Reactivity of autologous and allogeneic T cells toward activated B-CLL cells was determined in mixed lymphocyte reactions and Interferon-gamma Elispot assays. The CpG-ODN DSP30 caused a significantly stronger induction of the IL-2 receptor alpha chain in malignant as compared with normal B cells (p = 0.03). This resulted in the expression of functional high-affinity IL-2 receptors in B-CLL cells, but fewer numbers of receptors with less affinity were expressed in normal B cells. Although addition of IL-2 to CpG-ODN-stimulated cells augmented proliferation in both normal B cells and B-CLL cells, no costimulatory effect on cytokine production or surface molecule expression could be observed in normal B cells. In contrast, TNF-alpha and IL-6 production was increased in B-CLL cells, and the expression of CD80 and CD86 was further enhanced when IL-2 was used as a costimulus. Autologous and allogeneic immune recognition of B-CLL cells stimulated with CpG-ODN and IL-2 was increased compared with B-CLL cells stimulated with CpG-ODN alone. Stimulation of B-CLL cells with CpG-ODN and IL-2 might be an attractive strategy for potential immunotherapies for B

Synthesis of site-heterologous haptens for high-affinity anti-pyraclostrobin antibody generation.

Science.gov (United States)

Mercader, Josep V; Agulló, Consuelo; Abad-Somovilla, Antonio; Abad-Fuentes, Antonio

2011-03-07

The design and synthesis of functional chemical derivatives of small organic molecules is usually a key step for the intricate production of a variety of bioconjugates. In this respect, the derivatization site at which the spacer arm is introduced in immunizing conjugates constitutes a highly critical parameter for the generation of high-affinity and selective antibodies. However, due to the usual complexity of the required synthetic procedures, the appropriate comparison of alternative tethering positions has often been neglected. In the present study, meticulous strategies were followed to prepare synthetic derivatives of pyraclostrobin with the same linkers located at diverse rationally-chosen sites. Activity appraisal of antibodies and bioconjugates was carried out by bidimensional competitive direct and indirect immunoassays, and a superior performance of two of the three synthesized haptens was found. Finally, a detailed analysis of the conformations of the target molecule and the synthesized haptens in aqueous solution was done using computer assisted molecular modeling techniques. This study suggested that the lower titers and affinities of one set of antibodies are most probably due to conformational effects of the spacer arm in the immunizing bioconjugate.

Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives

Science.gov (United States)

Lettieri, R.; D'Abramo, M.; Stella, L.; La Bella, A.; Leonelli, F.; Giansanti, L.; Venanzi, M.; Gatto, E.

2018-04-01

Thymidine phosphorylase (TP) is an enzyme that is up-regulated in a wide variety of solid tumors, including breast and colorectal cancers. It is involved in tumor growth and metastasis, for this reason it is one of the key enzyme to be inhibited, in an attempt to prevent tumor proliferation. However, it also plays an active role in cancer treatment, through its contribution in the conversion of the anti-cancer drug 5-fluorouracil (5-FU) to an irreversible inhibitor of thymidylate synthase (TS), responsible of the inhibition of the DNA synthesis. In this work, the intrinsic TP fluorescence has been investigated for the first time and exploited to study TP binding affinity for the unsubstituted 5-FU and for two 5-FU derivatives, designed to expose this molecule on liposomal membranes. These molecules were obtained by functionalizing the nitrogen atom with a chain consisting of six (1) or seven (2) units of glycol, linked to an alkyl moiety of 12 carbon atoms. Derivatives (1) and (2) exhibited an affinity for TP in the micromolar range, 10 times higher than the parent compound, irrespective of the length of the polyoxyethylenic spacer. This high affinity was maintained also when the compounds were anchored in liposomal membranes. Experimental results were supported by molecular dynamics simulations and docking calculations, supporting a feasible application of the designed supramolecular lipid structure in selective targeting of TP, to be potentially used as a drug delivery system or sensor device.

Global affine differential geometry of hypersurfaces

CERN Document Server

Li, An-Min; Zhao, Guosong; Hu, Zejun

2015-01-01

This book draws a colorful and widespread picture of global affine hypersurface theory up to the most recent state. Moreover, the recent development revealed that affine differential geometry- as differential geometry in general- has an exciting intersection area with other fields of interest, like partial differential equations, global analysis, convex geometry and Riemann surfaces.

Fatty acid uptake in normal human myocardium

International Nuclear Information System (INIS)

Vyska, K.; Meyer, W.; Stremmel, W.; Notohamiprodjo, G.; Minami, K.; Machulla, H.J.; Gleichmann, U.; Meyer, H.; Koerfer, R.

1991-01-01

Fatty acid binding protein has been found in rat aortic endothelial cell membrane. It has been identified to be a 40-kDa protein that corresponds to a 40-kDa fatty acid binding protein with high affinity for a variety of long chain fatty acids isolated from rat heart myocytes. It is proposed that this endothelial membrane fatty acid binding protein might mediate the myocardial uptake of fatty acids. For evaluation of this hypothesis in vivo, influx kinetics of tracer-labeled fatty acids was examined in 15 normal subjects by scintigraphic techniques. Variation of the plasma fatty acid concentration and plasma perfusion rate has been achieved by modulation of nutrition state and exercise conditions. The clinical results suggest that the myocardial fatty acid influx rate is saturable by increasing fatty acid plasma concentration as well as by increasing plasma flow. For analysis of these data, functional relations describing fatty acid transport from plasma into myocardial tissue in the presence and absence of an unstirred layer were developed. The fitting of these relations to experimental data indicate that the free fatty acid influx into myocardial tissue reveals the criteria of a reaction on a capillary surface in the vicinity of flowing plasma but not of a reaction in extravascular space or in an unstirred layer and that the fatty acid influx into normal myocardium is a saturable process that is characterized by the quantity corresponding to the Michaelis-Menten constant, Km, and the maximal velocity, Vmax, 0.24 ± 0.024 mumol/g and 0.37 ± 0.013 mumol/g(g.min), respectively. These data are compatible with a nondiffusional uptake process mediated by the initial interaction of fatty acids with the 40-kDa membrane fatty acid binding protein of cardiac endothelial cells

Birationally rigid varieties. I. Fano varieties

International Nuclear Information System (INIS)

Pukhlikov, A V

2007-01-01

The theory of birational rigidity of rationally connected varieties generalises the classical rationality problem. This paper gives a survey of the current state of this theory and traces its history from Noether's theorem and the Lueroth problem to the latest results on the birational superrigidity of higher-dimensional Fano varieties. The main components of the method of maximal singularities are considered.

Skeletal affinity of Tc(V)-DMS is bone cell mediated and pH dependent.

Science.gov (United States)

Horiuchi-Suzuki, Kazuko; Konno, Aya; Ueda, Mayumi; Fukuda, Yoko; Nishio, Saori; Hashimoto, Kazuyuki; Saji, Hideo

2004-03-01

In spite of recent advances in bone cellular and molecular biology, there is still a poor correlation between these parameters and data obtained from bone scintigraphy. Diphosphonate derivatives radiolabelled with technetium-99m (Tc-BPs) have long been recognised as bone-seeking agents with an affinity for areas of active mineralisation. However, during clinical trials with a pH-sensitive tumour agent, the pentavalent technetium complex of dimercaptosuccinic acid [Tc(V)-DMS] showed a noticeable osteotropic character only in bone pathologies (bone metastases, Paget's diseases) and lacked accumulation in normal mature bone. To decipher the osteotropic character of Tc(V)-DMS, a study at the cellular level was considered necessary. Moreover, to learn more about the role of Tc bone agents, acid-base regulation by bone tissue or cells was studied. First, biological parameters in body fluid were measured under systemic acidosis, induced by glucose administration, in normal and Ehrlich ascites tumour (EAT)-bearing mice. Then, in vivo biodistribution studies using Tc(V)-DMS or a conventional Tc-BP agent were carried out. The effect of glucose-mediated acidification on the skeletal distribution of the Tc agents in the mice provided valuable hints regarding the differential mediation of bone cells in skeletal tissue affinity for the agents. Thereafter, in vitro studies on osteoblast and osteoclast cells were performed and the comparative affinity of Tc(V)-DMS and Tc-BP was screened under diverse acidification conditions. Moreover, studies were also carried out on acid-base parameters related to the cellular uptake mechanism. Very specific pH-sensitive Tc(V)-DMS accumulation only in the osteoclastic system was detected, and use of Tc(V)-DMS in the differential detection of osteoblastic and osteoclastic metastases is discussed.

New unitary affine-Virasoro constructions

International Nuclear Information System (INIS)

Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M.; Yamron, J.P.

1990-01-01

This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g

PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

Science.gov (United States)

Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei

2012-01-01

Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

Haemoglobin Rahere (beta Lys-Thr): A new high affinity haemoglobin associated with decreased 2, 3-diphosphoglycerate binding and relative polycythaemia.

Science.gov (United States)

Lorkin, P A; Stephens, A D; Beard, M E; Wrigley, P F; Adams, L; Lehmann, H

1975-01-01

A new haemoglobin with increased oxygen affinity, beta82 (EF6) lysine leads to threonine (Hb Rahere), was found during the investigation of a patient who was found to have a raised haemoglobin concentration after a routine blood count. The substitution affects one of the 2, 3-diphosphoglycerate binding sites, resulting in an increased affinity for oxygen, but both the haem-haem interaction and the alkaline Bohr effect are normal in the haemolysate. This variant had the same mobility as haemoglobin A on electrophoresis at alkaline pH but was detected by measuring the whole blood oxygen affinity; it could be separated from haemoglobin A, however, by electrophoresis in agar at acid pH. The raised haemoglobin concentration was mainly due to a reduction in plasma volume (a relative polycythaemia) and was associated with a persistently raised white blood count. This case emphasises the need to measure the oxygen affinity of haemoglobin in all patients with absolute or relative polycythaemia when some obvious cause is not evident. PMID:124

Alternative affinity tools: more attractive than antibodies?

NARCIS (Netherlands)

Ruigrok, V.J.B.; Levisson, M.; Eppink, M.H.M.; Smidt, H.; Oost, van der J.

2011-01-01

Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids

Affine stochastic mortality

NARCIS (Netherlands)

Schrager, D.F.

2006-01-01

We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

Energy Technology Data Exchange (ETDEWEB)

Wang, Deng-Liang [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Yang, Hai-Tao; Wang, Jiang-Jie [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yao, Pei-Sen [Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Pan, Ru-Jun [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yang, Chaoyong James, E-mail: cyyang@xmu.edu.cn [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Kang, De-Zhi, E-mail: kdzy99988@163.com [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China)

2014-10-31

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K{sub d} 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K{sub d} 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

International Nuclear Information System (INIS)

Wang, Deng-Liang; Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan; Yang, Hai-Tao; Wang, Jiang-Jie; Yao, Pei-Sen; Pan, Ru-Jun; Yang, Chaoyong James; Kang, De-Zhi

2014-01-01

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K d 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K d 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy

Electron affinities, molecular structures, and thermochemistry of the fluorine, chlorine and bromine substituted methyl radicals

Science.gov (United States)

Li, Qian-Shu; Zhao, Jun-Fang; Xie, Yaoming; Schaefer, Henry F., III

Four independent density functional theory (DFT) methods have been employed to study the structures and electron affinities of the methyl and F-, Cl- and Br-substituted methyl radicals and their anions. The methods used have been carefully calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews, 2002, 102, 231). The first dissociation energies together with the vibrational frequencies of these species are also reported. The basis sets used in this work are of double- ζ plus polarization quality with additional s- and p-type diffuse functions, labelled as DZP++. Previously observed trends in the prediction of bond lengths by the DFT methods are also demonstrated for the F-, Cl- and Br-substituted methyl radicals and their anions. Generally, the Hartree-Fock/DFT hybrid methods predict shorter and more reliable bond lengths than the pure DFT methods. Neutral-anion energy differences reported in this work are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Compared with the available experimental electron affinities, the BHLYP method predicts much lower values, while the other methods predict values (EAad, EAvert, VDE) close to each other and almost within the experimental range. For those systems without reliable experimental measurements, our best adiabatic EAs predicted by BLYP are 0.78 (CHF2), 1.23 (CHFCl), 1.44 (CHFBr), 1.61 (CHClBr), 2.24 (CF2Cl), 2.42 (CF2Br), 2.56 (CFBr2), 2.36 (CCl2Br), 2.46 (CClBr2), and 2.44 eV (CFClBr). The most striking feature of these predictions is that they display an inverse relationship between halogen electronegativity and EA. The DZP++ B3LYP method determines the vibrational frequencies in best agreement with available experimental results for this series, with an average relative error of ~2%. The value of using a variety of DFT methods is observed in that BHLYP does best for geometries, BLYP for electron

Cadmium uptake and speciation changes in the rhizosphere of cadmium accumulator and non-accumulator oilseed rape varieties

Institute of Scientific and Technical Information of China (English)

SU Dechun; XING Jianping; JIAO Weiping; WONG Woonchung

2009-01-01

Characteristics of cadmium (Cd) uptake kinetics and distribution of Cd speciation in the rhizosphere for Cd accumulator and non-accumulator oilseed rape varieties were investigated under nutrient solution and rhizobox soil culture conditions.The results showed that the maximal influx (Vmax) for Cd2+ and Km were significantly different for the two oilseed rape varieties.The value of Vmax for Cd accumulator oilseed rape Zhucang Huazi was two-fold greater than that for oilseed rape Chuangyou II-93.The exchangeable Cd concentration in the rhizosphere was significantly lower than in non-rhizospheric soils supplemented with Cd as CdSO4 for both the varieties.Carbonate-bound Cd in the rhizosphere of Cd accumulator oilseed rape was significantly higher than that in the rhizosphere of non-accumulator oilseed rape and non-rhizospheric soil.Cd accumulator oilseed rape had a higher Cd2+ affinity and more ability to uptake insoluble Cd in the soil than the non-accumulator oilseed rape.

Rank Two Affine Manifolds in Genus 3

OpenAIRE

Aulicino, David; Nguyen, Duc-Manh

2016-01-01

We complete the classification of rank two affine manifolds in the moduli space of translation surfaces in genus three. Combined with a recent result of Mirzakhani and Wright, this completes the classification of higher rank affine manifolds in genus three.

[Affinity of the elements in group VI of the periodic table to tumors and organs].

Science.gov (United States)

Ando, A; Hisada, K; Ando, I

1976-10-01

In order to investigate the tumor affinity radioisotopes, chromium (51Cr), molybdenum (99Mo), tungsten (181W), selenium (75Se) and tellurium (127mTe)--the elements of group VI in the periodic table--were examined, using the rats which were subcutaneously transplanted with Yoshida sarcoma. Seven preprarations, sodium chromate (Na251CrO4), chromium chloride (51CrCl3), normal ammonium molybdate ((NH4)299MoO7), sodium tungstate (Na2181WO4), sodium selenate (Na275SeO4), sodium selenite (Na275SeO3) and tellurous acid (H2127mTeO3) were injected intravenously to each group of tumor bearing rats. These rats were sacrificed at various periods after injection of each preparation: 3 hours, 24 hours and 48 hours in all preparations. The radioactivities of the tumor, blood, muscle, liver, kidney and spleen were measured by a well-type scintillation counter, and retention values (in every tissue including the tumor) were calculated in percent of administered dose per g-tissue weight. All of seven preparations did not have any affinity for malignant tumor. Na251CrO4 and H2127mTeO3 had some affinity for the kidneys, and Na275SeO3 had some affinity for the liver. Na2181WO4 and (NH4)299MoO4 disappeared very rapidly from the blood and soft tissue, and about seventy-five percent of radioactivity was excreted in urine within first 3 hours.

Dynamics of Open Systems with Affine Maps

International Nuclear Information System (INIS)

Zhang Da-Jian; Liu Chong-Long; Tong Dian-Min

2015-01-01

Many quantum systems of interest are initially correlated with their environments and the reduced dynamics of open systems are an interesting while challenging topic. Affine maps, as an extension of completely positive maps, are a useful tool to describe the reduced dynamics of open systems with initial correlations. However, it is unclear what kind of initial state shares an affine map. In this study, we give a sufficient condition of initial states, in which the reduced dynamics can always be described by an affine map. Our result shows that if the initial states of the combined system constitute a convex set, and if the correspondence between the initial states of the open system and those of the combined system, defined by taking the partial trace, is a bijection, then the reduced dynamics of the open system can be described by an affine map. (paper)

USING MICROSCALE THERMOPHORESIS TO EASILY MEASURE BINDING AFFINITY

Directory of Open Access Journals (Sweden)

Dennis Breitsprecher*

2018-03-01

Full Text Available While it’s very common for biologists and chemists to test whether or not two molecules interact with each other, it’s much more useful to gather information on the nature of that interaction. How strong is it? How long will it last? What does that mean for its biological function? One way to answer these questions is to study affinity. Binding affinity is defined as the strength of the binding interaction between a single biomolecule to its binding partner, or ligand, and it can be quantifiably measured, providing information on whether or not molecules are interacting, as well as assigning a value to the affinity. When measuring binding affinity, there are several parameters to look at, but the dissociation constant (Kd, which defines the likelihood that an interaction between two molecules will break, is a very common measurement. The smaller the dissociation constant, the more tightly bound the ligand is, and the higher the affinity is between the two molecules.

Single-Step Affinity Purification for Fungal Proteomics ▿ †

OpenAIRE

Liu, Hui-Lin; Osmani, Aysha H.; Ukil, Leena; Son, Sunghun; Markossian, Sarine; Shen, Kuo-Fang; Govindaraghavan, Meera; Varadaraj, Archana; Hashmi, Shahr B.; De Souza, Colin P.; Osmani, Stephen A.

2010-01-01

A single-step protein affinity purification protocol using Aspergillus nidulans is described. Detailed protocols for cell breakage, affinity purification, and depending on the application, methods for protein release from affinity beads are provided. Examples defining the utility of the approaches, which should be widely applicable, are included.

The Structure of Affine Buildings

CERN Document Server

Weiss, Richard M

2009-01-01

In The Structure of Affine Buildings, Richard Weiss gives a detailed presentation of the complete proof of the classification of Bruhat-Tits buildings first completed by Jacques Tits in 1986. The book includes numerous results about automorphisms, completions, and residues of these buildings. It also includes tables correlating the results in the locally finite case with the results of Tits's classification of absolutely simple algebraic groups defined over a local field. A companion to Weiss's The Structure of Spherical Buildings, The Structure of Affine Buildings is organized around the clas

The dynamics of metric-affine gravity

International Nuclear Information System (INIS)

Vitagliano, Vincenzo; Sotiriou, Thomas P.; Liberati, Stefano

2011-01-01

Highlights: → The role and the dynamics of the connection in metric-affine theories is explored. → The most general second order action does not lead to a dynamical connection. → Including higher order invariants excites new degrees of freedom in the connection. → f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy

Spectral affinity in protein networks.

Science.gov (United States)

Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu

2009-11-29

Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to quickly find nodes closest to a queried vertex in any protein

Multiprocessor Real-Time Scheduling with Hierarchical Processor Affinities

OpenAIRE

Bonifaci , Vincenzo; Brandenburg , Björn; D'Angelo , Gianlorenzo; Marchetti-Spaccamela , Alberto

2016-01-01

International audience; Many multiprocessor real-time operating systems offer the possibility to restrict the migrations of any task to a specified subset of processors by setting affinity masks. A notion of " strong arbitrary processor affinity scheduling " (strong APA scheduling) has been proposed; this notion avoids schedulability losses due to overly simple implementations of processor affinities. Due to potential overheads, strong APA has not been implemented so far in a real-time operat...

nth roots with Hilbert-Schmidt defect operator of normal contractions

International Nuclear Information System (INIS)

Duggal, B.P.

1992-08-01

Let T be a normal contraction (on a complex separable Hilbert space H into itself) with an nth root A such that the defect operator D A =(1-A*A) 1/2 is of the Hilbert-Schmidt class C 2 . Then either A is normal or A is similar to a normal contraction. In the case in which T is hyponormal, A n =T and D A is an element of C 2 , A is a ''coupling'' of a contraction similar to a normal contraction and a contraction which is the quasi-affine transform of a unilateral shift. These results are applied to prove a (Putnam-Fuglede type) commutatively theorem for operator valued roots of commutative analytic functions and hyponormal contractions T which have an nth root with Hilbert-Schmidt defect operator. 23 refs

Affine fractal functions as bases of continuous funtions | Navascues ...

African Journals Online (AJOL)

The objective of the present paper is the study of affine transformations of the plane, which provide self-affine curves as attractors. The properties of these curves depend decisively of the coefficients of the system of affinities involved. The corresponding functions are continuous on a compact interval. If the scale factors are ...

Antibody Affinity Maturation in Fishes—Our Current Understanding

Directory of Open Access Journals (Sweden)

Brad G. Magor

2015-07-01

Full Text Available It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig mutator enzyme activation-induced cytidine deaminase (AID. We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes.

Thermokinetic model of borosilicate glass dissolution: contextual affinity

International Nuclear Information System (INIS)

Advocat, T.; Vernaz, E.; Crovisier, J.L.; Fritz, B.

1989-01-01

Short and long-term geochemical interactions of R7T7 nuclear glass with water at 100 0 C were simulated with the DISSOL thermokinetic computer code. Both the dissolved glass quantity and the resulting water composition, saturation states and mineral quantities produced were calculated as a function of time. The rate equation used in the simulation was first proposed by Aagaard and Helgeson. It simulates a gradually diminishing dissolution rate as the reaction affinity diminishes. The best agreement with 1-year experimental data was obtained with a reaction affinity calculated from silica activity (Grambow's hypothesis) rather than taking into account the activity of all the glass components as proposed by Jantzen and Plodinec. The concept of residual affinity was introduced by Grambow to express the fact that the glass dissolution rate does not cease. We prefer to replace the term residual affinity by contextual affinity, which expresses the influence on the dissolution rate of three factors: the solution chemistry, the metastability of SiO 2 (m), and the possible precipitation of certain aluminosilicates such as zeolites. 19 refs

Affinity Strings: Enterprise Data for Resource Recommendations

Directory of Open Access Journals (Sweden)

Shane Nackerud

2008-12-01

Full Text Available The University of Minnesota Libraries have created a MyLibrary portal, with databases and e-journals targeted to users, based on their affiliations. The University's enterprise authentication system provides an "affinity string", now used to personalize the MyLibrary portal. This affinity string automates discovery of a user's relationship to the University--describing a user's academic department and degree program or position at the University. Affinity strings also provide the Libraries with an anonymized view of resource usage, allowing data collection that respects users' privacy and lays the groundwork for automated recommendation of relevant resources based on the practices and habits of their peers.

Detecting anomalies in crowded scenes via locality-constrained affine subspace coding

Science.gov (United States)

Fan, Yaxiang; Wen, Gongjian; Qiu, Shaohua; Li, Deren

2017-07-01

Video anomaly event detection is the process of finding an abnormal event deviation compared with the majority of normal or usual events. The main challenges are the high structure redundancy and the dynamic changes in the scenes that are in surveillance videos. To address these problems, we present a framework for anomaly detection and localization in videos that is based on locality-constrained affine subspace coding (LASC) and a model updating procedure. In our algorithm, LASC attempts to reconstruct the test sample by its top-k nearest subspaces, which are obtained by segmenting the normal samples space using a clustering method. A sample with a large reconstruction cost is detected as abnormal by setting a threshold. To adapt to the scene changes over time, a model updating strategy is proposed. We experiment on two public datasets: the UCSD dataset and the Avenue dataset. The results demonstrate that our method achieves competitive performance at a 700 fps on a single desktop PC.

Compound immobilization and drug-affinity chromatography.

Science.gov (United States)

Rix, Uwe; Gridling, Manuela; Superti-Furga, Giulio

2012-01-01

Bioactive small molecules act through modulating a yet unpredictable number of targets. It is therefore of critical importance to define the cellular target proteins of a compound as an entry point to understanding its mechanism of action. Often, this can be achieved in a direct fashion by chemical proteomics. As with any affinity chromatography, immobilization of the bait to a solid support is one of the earliest and most crucial steps in the process. Interfering with structural features that are important for identification of a target protein will be detrimental to binding affinity. Also, many molecules are sensitive to heat or to certain chemicals, such as acid or base, and might be destroyed during the process of immobilization, which therefore needs to be not only efficient, but also mild. The subsequent affinity chromatography step needs to preserve molecular and conformational integrity of both bait compound and proteins in order to result in the desired specific enrichment while ensuring a high level of compatibility with downstream analysis by mass spectrometry. Thus, the right choice of detergent, buffer, and protease inhibitors is also essential. This chapter describes a widely applicable procedure for the immobilization of small molecule drugs and for drug-affinity chromatography with subsequent protein identification by mass spectrometry.

Affine coherent states and Toeplitz operators

Science.gov (United States)

Hutníková, Mária; Hutník, Ondrej

2012-06-01

We study a parameterized family of Toeplitz operators in the context of affine coherent states based on the Calderón reproducing formula (= resolution of unity on L_2( {R})) and the specific admissible wavelets (= affine coherent states in L_2( {R})) related to Laguerre functions. Symbols of such Calderón-Toeplitz operators as individual coordinates of the affine group (= upper half-plane with the hyperbolic geometry) are considered. In this case, a certain class of pseudo-differential operators, their properties and their operator algebras are investigated. As a result of this study, the Fredholm symbol algebras of the Calderón-Toeplitz operator algebras for these particular cases of symbols are described. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’.

Removal of an endogenous antigen from an antibody to increase its effective affinity constant, as illustrated by Triiodothyronine assay

International Nuclear Information System (INIS)

Oliver, L.K.; Cano, C.

1977-01-01

Antisera to triiodothyronine were shown to contain large quantities of the hormone, well in excess of normal circulating concentrations. Extracting the triiodothyronine from the antiserum with alkaline ethanol yielded an antibody of increased affinity. Use of this antibody in a radioimmunoassay resulted in a fourfold increase in sensitivity as compared with the unextracted material

Affinity between information retrieval system and search topic

International Nuclear Information System (INIS)

Ebinuma, Yukio

1979-01-01

Ten search profiles are tested on the INIS system at the Japan Atomic Energy Research Institute. The results are plotted on recall-precision chart ranging from 100% recall to 100% precision. The curves are not purely systems-dependent nor search-dependent, and are determined substantially by the ''affinity'' between the system and the search topic. The curves are named ''Affinity curves of search topics with information retrieval systems'', and hence retrieval affinity factors are derived. They are obtained not only for individual search topics but also for averages in the system. By such a quantitative examination, the difference of affinity among search topics in a given system, that of the same search topic among various systems, and that of systems to the same group of search topics can be compared reasonably. (author)

Affine group formulation of the Standard Model coupled to gravity

Energy Technology Data Exchange (ETDEWEB)

Chou, Ching-Yi, E-mail: l2897107@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China); Ita, Eyo, E-mail: ita@usna.edu [Department of Physics, US Naval Academy, Annapolis, MD (United States); Soo, Chopin, E-mail: cpsoo@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China)

2014-04-15

In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

Affine.m—Mathematica package for computations in representation theory of finite-dimensional and affine Lie algebras

Science.gov (United States)

Nazarov, Anton

2012-11-01

In this paper we present Affine.m-a program for computations in representation theory of finite-dimensional and affine Lie algebras and describe implemented algorithms. The algorithms are based on the properties of weights and Weyl symmetry. Computation of weight multiplicities in irreducible and Verma modules, branching of representations and tensor product decomposition are the most important problems for us. These problems have numerous applications in physics and we provide some examples of these applications. The program is implemented in the popular computer algebra system Mathematica and works with finite-dimensional and affine Lie algebras. Catalogue identifier: AENA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENB_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 24 844 No. of bytes in distributed program, including test data, etc.: 1 045 908 Distribution format: tar.gz Programming language: Mathematica. Computer: i386-i686, x86_64. Operating system: Linux, Windows, Mac OS, Solaris. RAM: 5-500 Mb Classification: 4.2, 5. Nature of problem: Representation theory of finite-dimensional Lie algebras has many applications in different branches of physics, including elementary particle physics, molecular physics, nuclear physics. Representations of affine Lie algebras appear in string theories and two-dimensional conformal field theory used for the description of critical phenomena in two-dimensional systems. Also Lie symmetries play a major role in a study of quantum integrable systems. Solution method: We work with weights and roots of finite-dimensional and affine Lie algebras and use Weyl symmetry extensively. Central problems which are the computations of weight multiplicities, branching and fusion coefficients are solved using one general recurrent

Spectral affinity in protein networks

Directory of Open Access Journals (Sweden)

Teng Shang-Hua

2009-11-01

Full Text Available Abstract Background Protein-protein interaction (PPI networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. Results We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. Conclusion We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to

Quantitative relationship between antibody affinity and antibody avidity

International Nuclear Information System (INIS)

Griswold, W.R.

1987-01-01

The relationship between antibody avidity, measured by the dissociation of the antigen-antibody bond in antigen excess, and antibody affinity was studied. Complexes of radiolabelled antigen and antibody of known affinity were prepared in vitro and allowed to stand for seven days to reach equilibrium. Then nonlabelled antigen in one hundred fold excess was added to dissociate the complexes. After an appropriate incubation the fraction of antigen bound to antibody was measured by the ammonium sulfate precipitation method. The dissociation index was the fraction bound in the experimental sample divided by the fraction bound in the control. The correlation coefficient between the dissociation index and the antibody binding constant was 0.92 for early dissociation and 0.98 for late dissociation. The regression equation relating the binding constant to the dissociation index was K = 6.4(DI) + 6.25, where DI is the late dissociation index and K is the logarithm to the base 10 of the binding constant. There is a high correlation between avidity and affinity of antibody. Antibody affinity can be estimated from avidity data. The stability of antigen-antibody complexes can be predicted from antibody affinity

Thermokinetic model of borosilicate glass dissolution: Contextual affinity

International Nuclear Information System (INIS)

Advocat, T.; Vernaz, E.; Crovisier, J.L.; Fritz, B.

1990-01-01

Short and long-term geochemical interactions of R7T7 nuclear glass with water at 100C were simulated with the DISSOL thermokinetic computer code. Both the dissolved glass quantity and the resulting water composition, saturation states and mineral quantities produced were calculated as a function of time. The rate equation used in the simulation was first proposed by Aagaard and Hegelson: v = k + · S · a( H + ) -n · (1 - e -(A/RT) ). It simulates a gradually diminishing dissolution rate as the reaction affinity diminishes. The best agreement with 1-year experimental data was obtained with a reaction affinity calculated from silica activity (Grambow's hypothesis) rather than taking into account the activity of all the glass components as proposed by Jantzen and Plodinec. The concept of residual affinity was introduced by Grambow to express the fact that the glass dissolution rate does not cease. The authors prefer to replace the term residual affinity by contextual affinity, which expresses the influence on the dissolution rate of three factors: the solution chemistry, the metastability of SiO 2 (m), and the possible precipitation of certain aluminosilicates such as zeolites

Breeding for Quality Protein Maize (QPM Varieties: A Review

Directory of Open Access Journals (Sweden)

Liliane N. Tandzi

2017-11-01

Full Text Available The nutritional evaluation of quality protein maize (QPM in feeding trials has proved its nutritional superiority over non-QPM varieties for human and livestock consumption. The present paper reviews some of the most recent achievements in development of QPM varieties using both conventional and molecular breeding under stressed and non-stressed environments. It is evident that numerous QPM varieties have been developed and released around the world over the past few decades. While the review points out some gaps in information or research efforts, challenges associated with adoption QPM varieties are highlighted and suggestions to overcome them are presented. The adoption of released varieties and challenges facing QPM production at the farmer level are also mentioned. Several breeding methods have been conventionally used to develop QPM varieties in stressed (drought, low soil nitrogen, resistance to grey leaf spot, Turcicum leaf blight, ear rot, and Striga and non-stressed environments. At least three genetic loci have been found to be implicated in controlling the levels of a protein synthesis factor correlated with lysine. They have been mapped on chromosomes 2, 4, and 7. While the use of molecular approaches will improve the efficiency and speed of variety development, the cost implications might limit the use of these technologies in the developing world. More emphasis should be given to breeding QPM for tolerance to environmental stresses, such as low soil pH, heat, and combined heat and drought stress. The post-harvest attack of QPM grains should also be considered. The adoption of QPM genotypes by farmers has been found to be limited mainly due to the minimal collaboration between maize breeders, farmers, agricultural extension workers, and other relevant stakeholders, as well as the need for isolating QPM varieties from normal maize. Therefore, there is need to use participatory plant breeding (PPB and/or participatory variety

Calculation of protein-ligand binding affinities.

Science.gov (United States)

Gilson, Michael K; Zhou, Huan-Xiang

2007-01-01

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.

Soybean varieties discrimination using non-imaging hyperspectral sensor

Science.gov (United States)

da Silva Junior, Carlos Antonio; Nanni, Marcos Rafael; Shakir, Muhammad; Teodoro, Paulo Eduardo; de Oliveira-Júnior, José Francisco; Cezar, Everson; de Gois, Givanildo; Lima, Mendelson; Wojciechowski, Julio Cesar; Shiratsuchi, Luciano Shozo

2018-03-01

Infrared region of electromagnetic spectrum has remarkable applications in crop studies. Infrared along with Red band has been used to develop certain vegetation indices. These indices like NDVI, EVI provide important information on any crop physiological stages. The main objective of this research was to discriminate 4 different soybean varieties (BMX Potência, NA5909, FT Campo Mourão and Don Mario) using non-imaging hyperspectral sensor. The study was conducted in four agricultural areas in the municipality of Deodápolis (MS), Brazil. For spectral analysis, 2400 field samples were taken from soybean leaves by means of FieldSpec 3 JR spectroradiometer in the range from 350 to 2500 nm. The data were evaluated through multivariate analysis with the whole set of spectral curves isolated by blue, green, red and near infrared wavelengths along with the addition of vegetation indices like (Enhanced Vegetation Index - EVI, Normalized Difference Vegetation Index - NDVI, Green Normalized Difference Vegetation Index - GNDVI, Soil-adjusted Vegetation Index - SAVI, Transformed Vegetation Index - TVI and Optimized Soil-Adjusted Vegetation Index - OSAVI). A number of the analysis performed where, discriminant (60 and 80% of the data), simulated discriminant (40 and 20% of data), principal component (PC) and cluster analysis (CA). Discriminant and simulated discriminant analyze presented satisfactory results, with average global hit rates of 99.28 and 98.77%, respectively. The results obtained by PC and CA revealed considerable associations between the evaluated variables and the varieties, which indicated that each variety has a variable that discriminates it more effectively in relation to the others. There was great variation in the sample size (number of leaves) for estimating the mean of variables. However, it was possible to observe that 200 leaves allow to obtain a maximum error of 2% in relation to the mean.

ASIFT: An Algorithm for Fully Affine Invariant Comparison

Directory of Open Access Journals (Sweden)

Guoshen Yu

2011-02-01

Full Text Available If a physical object has a smooth or piecewise smooth boundary, its images obtained by cameras in varying positions undergo smooth apparent deformations. These deformations are locally well approximated by affine transforms of the image plane. In consequence the solid object recognition problem has often been led back to the computation of affine invariant image local features. The similarity invariance (invariance to translation, rotation, and zoom is dealt with rigorously by the SIFT method The method illustrated and demonstrated in this work, Affine-SIFT (ASIFT, simulates a set of sample views of the initial images, obtainable by varying the two camera axis orientation parameters, namely the latitude and the longitude angles, which are not treated by the SIFT method. Then it applies the SIFT method itself to all images thus generated. Thus, ASIFT covers effectively all six parameters of the affine transform.

Applications of Affine and Weyl geometry

CERN Document Server

García-Río, Eduardo; Nikcevic, Stana

2013-01-01

Pseudo-Riemannian geometry is, to a large extent, the study of the Levi-Civita connection, which is the unique torsion-free connection compatible with the metric structure. There are, however, other affine connections which arise in different contexts, such as conformal geometry, contact structures, Weyl structures, and almost Hermitian geometry. In this book, we reverse this point of view and instead associate an auxiliary pseudo-Riemannian structure of neutral signature to certain affine connections and use this correspondence to study both geometries. We examine Walker structures, Riemannia

Theoretical determination of proton affinity differences in zeolites

NARCIS (Netherlands)

Kramer, G.J.; Santen, van R.A.

1993-01-01

An important factor in zeolite catalysis is the proton affinity, i.e., the energy required to remove a proton from the zeolite lattice. Differences in proton affinity are expected to influence the catalytic activity of acid sites, making the catalytically active sites inhomogeneous (within one

Pseudo-affinity chromatography of rumen microbial cellulase on ...

African Journals Online (AJOL)

Pseudo-affinity chromatography of rumen microbial cellulase on Sepharose- Cibacron Blue F3GA. ... African Journal of Biotechnology ... Pseudo affinity adsorption of bioproducts on Sepharose-cibacron blue F3-GA was subjected to rumen microbial enzyme evaluation through batch binding and column chromatography of ...

Realization of Robertson-Walker spacetimes as affine hypersurfaces

International Nuclear Information System (INIS)

Chen Bangyen

2007-01-01

Due to the growing interest in embeddings of spacetimes in higher dimensional spaces, we consider a special type of embedding. We prove that Robertson-Walker spacetimes can be embedded as centroaffine hypersurfaces and graph hypersurfaces in some affine spaces in such a way that the induced relative metrics are exactly the Lorentzian metrics on the Robertson-Walker spacetimes. Such realizations allow us to view Robertson-Walker spacetimes and their submanifolds as affine submanifolds in a natural way. Consequently, our realizations make it possible to apply the tools of affine differential geometry to study Robertson-Walker spacetimes and their submanifolds

On affine variety codes from the Klein quartic

DEFF Research Database (Denmark)

Geil, Hans Olav; Ozbudak, Ferruh

2018-01-01

as the best known codes according to Grassl (2007) and in the remaining few cases the parameters are almost as good. To establish the code parameters we apply the footprint bound (Geil and Høholdt, IEEE Trans. Inform. Theory 46(2), 635–641, 2000 and Høholdt 1998) from Gröbner basis theory and for this purpose...

Methyl Cation Affinities of Neutral and Anionic Maingroup-Element Hydrides: Trends Across the Periodic Table and Correlation with Proton Affinities

NARCIS (Netherlands)

Mulder, R. Joshua; Guerra, Celia Fonseca; Bickelhaupt, F. Matthias

2010-01-01

We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and

Mathematical analysis of frontal affinity chromatography in particle and membrane configurations.

Science.gov (United States)

Tejeda-Mansir, A; Montesinos, R M; Guzmán, R

2001-10-30

The scaleup and optimization of large-scale affinity-chromatographic operations in the recovery, separation and purification of biochemical components is of major industrial importance. The development of mathematical models to describe affinity-chromatographic processes, and the use of these models in computer programs to predict column performance is an engineering approach that can help to attain these bioprocess engineering tasks successfully. Most affinity-chromatographic separations are operated in the frontal mode, using fixed-bed columns. Purely diffusive and perfusion particles and membrane-based affinity chromatography are among the main commercially available technologies for these separations. For a particular application, a basic understanding of the main similarities and differences between particle and membrane frontal affinity chromatography and how these characteristics are reflected in the transport models is of fundamental relevance. This review presents the basic theoretical considerations used in the development of particle and membrane affinity chromatography models that can be applied in the design and operation of large-scale affinity separations in fixed-bed columns. A transport model for column affinity chromatography that considers column dispersion, particle internal convection, external film resistance, finite kinetic rate, plus macropore and micropore resistances is analyzed as a framework for exploring further the mathematical analysis. Such models provide a general realistic description of almost all practical systems. Specific mathematical models that take into account geometric considerations and transport effects have been developed for both particle and membrane affinity chromatography systems. Some of the most common simplified models, based on linear driving-force (LDF) and equilibrium assumptions, are emphasized. Analytical solutions of the corresponding simplified dimensionless affinity models are presented. Particular

Generalized Warburg impedance on realistic self-affine fractals ...

Indian Academy of Sciences (India)

2016-08-26

Aug 26, 2016 ... We analyse the problem of impedance for a diffusion controlled charge transfer process across an irregular interface. These interfacial irregularities are characterized as two class of random fractals: (i) a statistically isotropic self-affine fractals and (ii) a statistically corrugated self-affine fractals.

Weak affinity chromatography for evaluation of stereoisomers in early drug discovery.

Science.gov (United States)

Duong-Thi, Minh-Dao; Bergström, Maria; Fex, Tomas; Svensson, Susanne; Ohlson, Sten; Isaksson, Roland

2013-07-01

In early drug discovery (e.g., in fragment screening), recognition of stereoisomeric structures is valuable and guides medicinal chemists to focus only on useful configurations. In this work, we concurrently screened mixtures of stereoisomers and estimated their affinities to a protein target (thrombin) using weak affinity chromatography-mass spectrometry (WAC-MS). Affinity determinations by WAC showed that minor changes in stereoisomeric configuration could have a major impact on affinity. The ability of WAC-MS to provide instant information about stereoselectivity and binding affinities directly from analyte mixtures is a great advantage in fragment library screening and drug lead development.

Generalized Warburg impedance on realistic self-affine fractals

Indian Academy of Sciences (India)

We analyse the problem of impedance for a diffusion controlled charge transfer process across an irregular interface. These interfacial irregularities are characterized as two class of random fractals: (i) a statistically isotropic self-affine fractals and (ii) a statistically corrugated self-affine fractals. The information about the ...

Proteolysis inside the membrane is a rate-governed reaction not driven by substrate affinity.

Science.gov (United States)

Dickey, Seth W; Baker, Rosanna P; Cho, Sangwoo; Urban, Siniša

2013-12-05

Enzymatic cleavage of transmembrane anchors to release proteins from the membrane controls diverse signaling pathways and is implicated in more than a dozen diseases. How catalysis works within the viscous, water-excluding, two-dimensional membrane is unknown. We developed an inducible reconstitution system to interrogate rhomboid proteolysis quantitatively within the membrane in real time. Remarkably, rhomboid proteases displayed no physiological affinity for substrates (K(d) ~190 μM/0.1 mol%). Instead, ~10,000-fold differences in proteolytic efficiency with substrate mutants and diverse rhomboid proteases were reflected in k(cat) values alone. Analysis of gate-open mutant and solvent isotope effects revealed that substrate gating, not hydrolysis, is rate limiting. Ultimately, a single proteolytic event within the membrane normally takes minutes. Rhomboid intramembrane proteolysis is thus a slow, kinetically controlled reaction not driven by transmembrane protein-protein affinity. These properties are unlike those of other studied proteases or membrane proteins but are strikingly reminiscent of one subset of DNA-repair enzymes, raising important mechanistic and drug-design implications. Copyright © 2013 Elsevier Inc. All rights reserved.

Affine pairings on ARM

NARCIS (Netherlands)

Acar, T.; Lauter, K.; Naehrig, M.; Shumow, D.

2011-01-01

Pairings on elliptic curves are being used in an increasing number of cryptographic applications on many different devices and platforms, but few performance numbers for cryptographic pairings have been reported on embedded and mobile devices. In this paper we give performance numbers for affine and

High blood oxygen affinity in the air-breathing swamp eel Monopterus albus.

Science.gov (United States)

Damsgaard, Christian; Findorf, Inge; Helbo, Signe; Kocagoz, Yigit; Buchanan, Rasmus; Huong, Do Thi Thanh; Weber, Roy E; Fago, Angela; Bayley, Mark; Wang, Tobias

2014-12-01

The Asian swamp eel (Monopterus albus, Zuiew 1793) is a facultative air-breathing fish with reduced gills. Previous studies have shown that gas exchange seems to occur across the epithelium of the buccopharyngeal cavity, the esophagus and the integument, resulting in substantial diffusion limitations that must be compensated by adaptations in others steps of the O₂ transport system to secure adequate O₂ delivery to the respiring tissues. We therefore investigated O₂ binding properties of whole blood, stripped hemoglobin (Hb), two major isoHb components and the myoglobin (Mb) from M. albus. Whole blood was sampled using indwelling catheters for blood gas analysis and determination of O₂ equilibrium curves. Hb was purified to assess the effects of endogenous allosteric effectors, and Mb was isolated from heart and skeletal muscle to determine its O₂ binding properties. The blood of M. albus has a high O₂ carrying capacity [hematocrit (Hct) of 42.4±4.5%] and binds O₂ with an unusually high affinity (P₅₀=2.8±0.4mmHg at 27°C and pH7.7), correlating with insensitivity of the Hb to the anionic allosteric effectors that normally decrease Hb-O₂ affinity. In addition, Mb is present at high concentrations in both heart and muscle (5.16±0.99 and 1.08±0.19mg ∙ g wet tissue⁻¹, respectively). We suggest that the high Hct and high blood O₂ affinity serve to overcome the low diffusion capacity in the relatively inefficient respiratory surfaces, while high Hct and Mb concentration aid in increasing the O₂ flux from the blood to the muscles. Copyright © 2014 Elsevier Inc. All rights reserved.

ODE/IM correspondence and modified affine Toda field equations

Energy Technology Data Exchange (ETDEWEB)

Ito, Katsushi; Locke, Christopher

2014-08-15

We study the two-dimensional affine Toda field equations for affine Lie algebra g{sup ^} modified by a conformal transformation and the associated linear equations. In the conformal limit, the associated linear problem reduces to a (pseudo-)differential equation. For classical affine Lie algebra g{sup ^}, we obtain a (pseudo-)differential equation corresponding to the Bethe equations for the Langlands dual of the Lie algebra g, which were found by Dorey et al. in study of the ODE/IM correspondence.

Evaluation of nitrogen sources (15 N) on three wheat varieties in an andisol and an ultisol in the IX Region. II: Isotopic parameters and fertilizer use efficiency

International Nuclear Information System (INIS)

Pino N, Ines; Buneder B, Mirta; Peyrelongue C, Amelia

1996-01-01

A field study was carried out in order to evaluate different N fertilizers sources in three wheat varieties considering an Andisol and an Ultisol soils, in the IX Region of the country. The dilution isotopic techniques was used, with AS, 10% at rates of 20 kg ha -1 of N. The isotopic parameters such as N in the plant derived from the nitrogen sources, the N in the plant derived from the soil, the fertilizer use efficiencies and the agronomic evaluation between them were determined. The Nddfu (%) was associated to the varieties and to the soils. In the Ultisol, Dalcahue variety had a better behaviour with SS and, in the Andisol, Laurel variety showed an special affinity with U. In three varieties, the higher % of N derived from the sources it was in the grain, showing Dalcahue variety a better translocation.The fertilizer use efficiency (FUE) and the physiological efficiency, determined according the isotopic parameters, were higher than the values determined according the conventional methodology. (author)

Evaluation of nitrogen sources (15 N) on three wheat varieties in an andisol and an ultisol, in the IX region. 2. Isotopic parameters and fertilizer use efficiency

International Nuclear Information System (INIS)

Pino N, Ines; Peyrelongue C, A.; Buneder B, Mirta

1997-01-01

Full text: A field study was carried out in order to evaluate different N fertilizers sources un three wheat varieties, considering an Andisol and Ultisol soils, in the IX Region of the country. The dilution isotopic techniques was used, with As, 10% at rates of 20 kg ha -1 of N. The isotopic parameters such as N in the plant derived from the nitrogen sources, the N in the plant derived from the soil, the fertilizer use efficiencies and the agronomic evaluation between them were determined. The Nddfu (%) was associated to the varieties and to the soils. In the Ultisol, Dalcahue variety had a better behaviour with SS and, in the Andisol, Laurel variety showed an special affinity with U. In the three varieties, the higher % of N derived from the sources it was in the grain, showing Dalcahue variety a better translocation. The fertilizer use efficiency (FUE) and the physiological efficiency, determined according the isotopic parameters, were higher than the values determined according the conventional methodology

RMT Assessments of the Market Latent Information Embedded in the Stocks' Raw, Normalized, and Partial Correlations

Directory of Open Access Journals (Sweden)

Dror Y. Kenett

2009-01-01

Full Text Available We present here assessment of the latent market information embedded in the raw, affinity (normalized, and partial correlations. We compared the Zipf plot, spectrum, and distribution of the eigenvalues for each matrix with the results of the corresponding random matrix. The analysis was performed on stocks belonging to the New York and Tel Aviv Stock Exchange, for the time period of January 2000 to March 2009. Our results show that in comparison to the raw correlations, the affinity matrices highlight the dominant factors of the system, and the partial correlation matrices contain more information. We propose that significant stock market information, which cannot be captured by the raw correlations, is embedded in the affinity and partial correlations. Our results further demonstrate the differences between NY and TA markets.

Characterization of self-affinity in the global regime

Science.gov (United States)

Neimark, Alexander V.

1994-11-01

Methods for characterization of self-affine surfaces and measurements of their roughness exponents H are developed. It is shown that for smoothed surfaces, which underwent particular coarse graining or averaging of the small-scale fluctuations, the excess surface area Sex and the mean square root radius of curvature ac are related by two distinct asymptotic power laws if ac is well below or well above a certain crossover scale acr. In the local regime of self-affinity, when acSex~(ac/acr)-(1-H). In the global regime of self-affinity, when ac>>acr, Sex~(ac/acr)-2(1-H)/(2-H). The former scaling relationship is consistent with the well known definition of local fractal dimensions dloc=dtop+1-H. The latter scaling relationship offers alternatives for characterization of self-affinity over large scales by means of excess dimensions defined as dex=dtop+2(1-H)/(2-H) and can be used for determination of roughness exponents from the measurements provided in the global regime. The thermodynamic method of fractal analysis, proposed earlier for self-similar surfaces (A.V. Neimark, Pis'ma Zh. Eksp. Teor. Fiz. 51, 535 (1990) [JETP Lett. 51, 607 (1990)]; Physica A 191, 258 (1992)), is extended for self-affine surfaces for determination of fractal dimensions and roughness exponents from adsorption and capillary experimental data.

Agrochemicals and genetic aging of crop varieties (Juxtaposition)

International Nuclear Information System (INIS)

Mirza, M.Y.; Ali, N.; Khan, A.R.; Qayyum, A.; Manzoor, W.

2002-01-01

Agrochemicals are indispensable in agriculture, but their frequent and indiscriminate use incurs caryological irregularities and mutagenic effects on cell-cytongenetic apparatus. These kinds of abnormalities at chromosome level disturb the normal process of their packaging and distribution at the time of cell-division, create phenotypic alterations in the plant and inflict genetic aging upon the crop-varieties. Thus, laboratory-testing of the agrochemicals for their cytotoxicity must be a regular feature in the country and the least cytotoxic formulation should only be recommended for commercial use. (author)

In vitro evaluation of different varieties of maize fodder for their methane generation potential and digestibility with goat rumen liquor.

Science.gov (United States)

Vaswani, Shalini; Kumar, Ravindra; Kumar, Vinod; Roy, Debashis; Kumar, Muneendra

2016-11-01

To evaluate the methane generation potential and digestibility of different (normal and three high-quality protein maize [HQPM]) varieties of maize fodder with goat rumen liquor in vitro . Methane production potential and digestibility of different varieties of maize fodder were tested in in vitro gas production test. Seven varieties of maize, four normal (HTHM 5101, DHM 117, HM 5, and Shaktiman/900 M Gold), and three high-quality protein (HQPM 5, HQPM 7, and HQPM 9/Vivek) were grown in different plots under the same environmental and agro-climatic conditions. Fodders were harvested at 45-50 days of sowing, and the representative samples of fodder from different varieties of maize were collected for analysis. Dried and grinded form of these maize fodder varieties was tested for gas, methane, and digestibility using goat rumen microflora in in vitro gas syringes. Gas production (ml/g dry matter [DM]) was highest for HM5 variety (97.66, whereas lowest for HQPM 9 variety (64.22). Gas production (ml/g degraded DM [DDM]) and methane (%) were statistically similar in different varieties of maize fodder. The methane production expressed as ml/g DM and ml/g DDM was significantly (pproduction.

Methyl cation affinities of neutral and anionic maingroup-element hydrides: trends across the periodic table and correlation with proton affinities.

Science.gov (United States)

Mulder, R Joshua; Guerra, Célia Fonseca; Bickelhaupt, F Matthias

2010-07-22

We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and corresponding entropies) at 298 K of all anionic (XH(n-1)(-)) and neutral bases (XH(n)) constituted by maingroup-element hydrides of groups 14-17 and the noble gases (i.e., group 18) along the periods 2-6. The cation affinity of the bases decreases from H(+) to CH(3)(+). To understand this trend, we have carried out quantitative bond energy decomposition analyses (EDA). Quantitative correlations are established between the MCA and PA values.

DAYA ANTIBAKTERI EKSTRAK ETANOL DAUN SENGGANI (Melastoma affine D. Don

Directory of Open Access Journals (Sweden)

Ika Trisharyanti Dian Kusumowati

2014-08-01

Full Text Available Melastoma affine D. Don had some activities such as anthelmintic, antibacteria, antiinfiammation, antifungal, and antitumor. The aims of this research was determine antibacteria activity of ethanolic extract of Melastoma affine D. Don. The antimicrobial activity was tested by solid dilution method to get Minimum Inhibition Concentration (MIC. The compounds in Melastoma affine D. Don was analyzed by tube test method and Thin Layer Chromatography (TLC with chloroform : methanol : formic acid (8,5:1,5:0,5 as mobile phase and silica gel GF254 as stationary phase. The result showed ethanolic extract of Melastoma affine D. Don contains alkaloid, polyphenol, fiavonoid, saponin, and essential oil. The MIC of Senggani against Staphylococcus aureus was 2% and 3% against Escherichia coli and the extract could not inhibit Staphylococcus aureus and Escherichia coli multiresistant until concentration 7% extract ethanol. Keywords: Melastoma affine D. Don, Staphylococcus aureus, Escherichia coli

Monitoring the normal body

DEFF Research Database (Denmark)

Nissen, Nina Konstantin; Holm, Lotte; Baarts, Charlotte

2015-01-01

of practices for monitoring their bodies based on different kinds of calculations of weight and body size, observations of body shape, and measurements of bodily firmness. Biometric measurements are familiar to them as are health authorities' recommendations. Despite not belonging to an extreme BMI category...... provides us with knowledge about how to prevent future overweight or obesity. This paper investigates body size ideals and monitoring practices among normal-weight and moderately overweight people. Methods : The study is based on in-depth interviews combined with observations. 24 participants were...... recruited by strategic sampling based on self-reported BMI 18.5-29.9 kg/m2 and socio-demographic factors. Inductive analysis was conducted. Results : Normal-weight and moderately overweight people have clear ideals for their body size. Despite being normal weight or close to this, they construct a variety...

Computation of piecewise affine terminal cost functions for model predictive control

NARCIS (Netherlands)

Brunner, F.D.; Lazar, M.; Allgöwer, F.; Fränzle, Martin; Lygeros, John

2014-01-01

This paper proposes a method for the construction of piecewise affine terminal cost functions for model predictive control (MPC). The terminal cost function is constructed on a predefined partition by solving a linear program for a given piecewise affine system, a stabilizing piecewise affine

Cambrian trilobites with Siberian affinities, southwestern Alaska

Energy Technology Data Exchange (ETDEWEB)

Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

1985-02-01

Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

On Affine Fusion and the Phase Model

Directory of Open Access Journals (Sweden)

Mark A. Walton

2012-11-01

Full Text Available A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the su(n Wess-Zumino-Novikov-Witten (WZNW conformal field theories appears in a simple integrable system known as the phase model. The Yang-Baxter equation leads to the construction of commuting operators as Schur polynomials, with noncommuting hopping operators as arguments. The algebraic Bethe ansatz diagonalizes them, revealing a connection to the modular S matrix and fusion of the su(n WZNW model. The noncommutative Schur polynomials play roles similar to those of the primary field operators in the corresponding WZNW model. In particular, their 3-point functions are the su(n fusion multiplicities. We show here how the new phase model realization of affine fusion makes obvious the existence of threshold levels, and how it accommodates higher-genus fusion.

Evaluation of primary and secondary metabolites in selected varieties of potatoes.

Directory of Open Access Journals (Sweden)

Ján Mareček

2016-01-01

Full Text Available The aim of study was to determine primary and secondary metabolites in selected varieties of potatoes. Potatoes (Solanum tuberosum L. are good source of bioactive compounds, mainly phenols as one of the most important components. The chemical composition with reducing sugar, starch, ascorbic acid, total polyphenol and flavonoid content were analyzed in five potato varieties (Agria, Marabel, Red Anna, Picasso, Princess. Values of dry matter content ranged from 20.34 to 23.64%. In terms of tubers storage, its content above 20% is required. The highest level of starch was detected in variety Princess (16.82%. The lowest reducing sugar content was recorded by variety Marabel (0.08%. Similarly, low values reached varieties Princess (0.12%, Agria (0.14 and Red Anna (0.16%. These would be appropriate to use for food processing and for production of fried potato chips or fries. Variety Red Anna reached the highest amount of vitamin C (73.72 mg.kg-1. The lower levels of this vitamin showed tubers of varieties Picasso (35.02 mg.kg-1 and Princess (36.89 mg.kg-1. The antioxidant activity was measured with radical scavenging assays using 1,1-diphenyl-2-picrylhydrazyl (DPPH radical as well as phosphomolybdenic assay. Potato varieties contained high levels of total polyphenols (0.474 – 1.550 mg GAE per dry weight and flavonoids (1.407 – 15.933 μg QE per dry weight. The consumption of potatoes can provide nutritional value along with antioxidant potential that can be helpful for proper functioning of the body physiological systems. Statistical evaluation by the single factor analysis of variance detected high significant impact of variety on the content of all the analytical parameters in evaluated varieties of potato tubers. Normal 0 21 false false false SK X-NONE X-NONE

Capillary electrophoresis-based assessment of nanobody affinity and purity

NARCIS (Netherlands)

Haselberg, Rob; Oliveira, Sabrina; van der Meel, Roy; Somsen, Govert W; de Jong, Gerhardus J

2014-01-01

Drug purity and affinity are essential attributes during development and production of therapeutic proteins. In this work, capillary electrophoresis (CE) was used to determine both the affinity and composition of the biotechnologically produced "nanobody" EGa1, the binding fragment of a

Specificity and affinity quantification of protein-protein interactions.

Science.gov (United States)

Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

2013-05-01

Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

Exploring Girls' Science Affinities Through an Informal Science Education Program

Science.gov (United States)

Todd, Brandy; Zvoch, Keith

2017-10-01

This study examines science interests, efficacy, attitudes, and identity—referred to as affinities, in the context of an informal science outreach program for girls. A mixed methods design was used to explore girls' science affinities before, during, and after participation in a cohort-based summer science camp. Multivariate analysis of survey data revealed that girls' science affinities varied as a function of the joint relationship between family background and number of years in the program, with girls from more affluent families predicted to increase affinities over time and girls from lower income families to experience initial gains in affinities that diminish over time. Qualitative examination of girls' perspectives on gender and science efficacy, attitudes toward science, and elements of science identities revealed a complex interplay of gendered stereotypes of science and girls' personal desires to prove themselves knowledgeable and competent scientists. Implications for the best practice in fostering science engagement and identities in middle school-aged girls are discussed.

Neutron RBE for normal tissues

International Nuclear Information System (INIS)

Field, S.B.; Hornsey, S.

1979-01-01

RBE for various normal tissues is considered as a function of neutron dose per fraction. Results from a variety of centres are reviewed. It is shown that RBE is dependent on neutron energy and is tissue dependent, but is not specially high for the more critical tissues or for damage occurring late after irradiation. (author)

For deliberative disagreement: Its venues, varieties and values

DEFF Research Database (Denmark)

Kock, Christian Erik J

2017-01-01

this follows several characteristics, primarily that there will normally be good reasons on both sides of an issue. I criticize prevalent conceptions of argumentation and outline an alternative, discussing contexts and varieties of deliberation and proposing normative criteria based on a citizen-centered view......I outline a theory of deliberative debate, its distinctive features and the kind of normative criteria that may be posited for it in light of its distinctive features. Deliberative debate is a type of practical reasoning: ultimately it is not about what is true, but about what to do. From...

Affine pairings on ARM

NARCIS (Netherlands)

Acar, T.; Lauter, K.; Naehrig, M.; Shumow, D.; Abdalla, M.; Lange, T.

2013-01-01

We report on relative performance numbers for affine and projective pairings on a dual-core Cortex A9 ARM processor. Using a fast inversion in the base field and doing inversion in extension fields by using the norm map to reduce to inversions in smaller fields, we find a very low ratio of

Selection of appropriate template for spatial normalization of brain images: tensor based morphometry

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong; Chung, June Key; Lee, Myung Chul [College of Medicine, Seoul National University, Seoul (Korea, Republic of)

2004-07-01

Although there have been remarkable advances in spatial normalization techniques, the differences in the shape of the hemispheres and the sulcal pattern of brains relative to age, gender, races, and diseases cannot be fully overcome by the nonlinear spatial normalization techniques. T1 SPGR MR images in 16 elderly male normal volunteers (>55 y. mean age: = 61.8 {+-} 3.5 y) were spatially normalized onto the age/gender specific Korean templates, and the Caucasian MNI template and the extent of the deformations were compared. These particular subjects were never included in the development of the templates. First , the images were matched into the templates using an affine transformation to eliminate the global difference between the templates and source images. Second the affine registration was followed by an estimation of nonlinear deformation. Determinants of the Jacobian matrices of the nonlinear deformation were then calculated for every voxel to estimate the regional volume change during the nonlinear transformation Jacobian determinant images highlighted the great magnitude of the relative local volume changes obtained when the elderly brains were spatially normalized onto the young/midlife male or female templates. They reflect the enlargement of CSF space in the lateral ventricles, sylvian fissures and cisterna magna, and the shrinkage of the cortex noted mainly in frontal, insular and lateral temporal cortexes, and the cerebellums in the aged brains. In the Jacobian determinant images, a regional shrinkage of the brain in the left middle prefrontal cortex was observed in addition to the regional expansion in the ventricles and sylvian fissures, which may be due to the age differences between the template and source images. The regional anatomical difference between template and source images could impose an extreme deformation of the source images during the spatial normalization and therefore. Individual brains should be placed into the appropriate

Selection of appropriate template for spatial normalization of brain images: tensor based morphometry

International Nuclear Information System (INIS)

Lee, Jae Sung; Lee, Dong Soo; Kim, Yu Kyeong; Chung, June Key; Lee, Myung Chul

2004-01-01

Although there have been remarkable advances in spatial normalization techniques, the differences in the shape of the hemispheres and the sulcal pattern of brains relative to age, gender, races, and diseases cannot be fully overcome by the nonlinear spatial normalization techniques. T1 SPGR MR images in 16 elderly male normal volunteers (>55 y. mean age: = 61.8 ± 3.5 y) were spatially normalized onto the age/gender specific Korean templates, and the Caucasian MNI template and the extent of the deformations were compared. These particular subjects were never included in the development of the templates. First , the images were matched into the templates using an affine transformation to eliminate the global difference between the templates and source images. Second the affine registration was followed by an estimation of nonlinear deformation. Determinants of the Jacobian matrices of the nonlinear deformation were then calculated for every voxel to estimate the regional volume change during the nonlinear transformation Jacobian determinant images highlighted the great magnitude of the relative local volume changes obtained when the elderly brains were spatially normalized onto the young/midlife male or female templates. They reflect the enlargement of CSF space in the lateral ventricles, sylvian fissures and cisterna magna, and the shrinkage of the cortex noted mainly in frontal, insular and lateral temporal cortexes, and the cerebellums in the aged brains. In the Jacobian determinant images, a regional shrinkage of the brain in the left middle prefrontal cortex was observed in addition to the regional expansion in the ventricles and sylvian fissures, which may be due to the age differences between the template and source images. The regional anatomical difference between template and source images could impose an extreme deformation of the source images during the spatial normalization and therefore. Individual brains should be placed into the appropriate template

Affine planes, ternary rings, and examples of non-Desarguesian planes

OpenAIRE

Ivanov, Nikolai V.

2016-01-01

The paper is devoted to a detailed self-contained exposition of a part of the theory of affine planes leading to a construction of affine (or, equivalently, projective) planes not satisfying the Desarques axiom. It is intended to complement the introductory expositions of the theory of affine and projective planes. A novelty of our exposition is a new notation for the ternary operation in a ternary ring, much more suggestive than the standard one.

Insulin binding properties of normal and transformed human epidermal cultured keratinocytes

International Nuclear Information System (INIS)

Verrando, P.; Ortonne, J.P.

1985-01-01

Insulin binding to its receptors was studied in cultured normal and transformed (A431 line) human epidermal keratinocytes. The specific binding was a temperature-dependent, saturable process. Normal keratinocytes possess a mean value of about 80,000 receptors per cell. Fifteen hours exposure of the cells to insulin lowered their receptor number (about 65% loss in available sites); these reappeared when the hormone was removed from the culture medium. In the A431 epidermoid carcinoma cell line, there is a net decrease in insulin binding (84% of the initial bound/free hormone ratio in comparison with normal cells) essentially related to a loss in receptor affinity for insulin. Thus, cultured human keratinocytes which express insulin receptors may be a useful tool in understanding skin pathology related to insulin disorders

Fermionic construction of vertex operators for twisted affine algebras

International Nuclear Information System (INIS)

Frappat, L.; Sorba, P.; Sciarrino, A.

1988-03-01

We construct vertex operator representations of the twisted affine algebras in terms of fermionic (or parafermionic in some cases) elementary fields. The folding method applied to the extended Dynkin diagrams of the affine algebras allows us to determine explicitly these fermionic fields as vertex operators

Excited state electron affinity calculations for aluminum

Science.gov (United States)

Hussein, Adnan Yousif

2017-08-01

Excited states of negative aluminum ion are reviewed, and calculations of electron affinities of the states (3s^23p^2)^1D and (3s3p^3){^5}{S}° relative to the (3s^23p)^2P° and (3s3p^2)^4P respectively of the neutral aluminum atom are reported in the framework of nonrelativistic configuration interaction (CI) method. A priori selected CI (SCI) with truncation energy error (Bunge in J Chem Phys 125:014107, 2006) and CI by parts (Bunge and Carbó-Dorca in J Chem Phys 125:014108, 2006) are used to approximate the valence nonrelativistic energy. Systematic studies of convergence of electron affinity with respect to the CI excitation level are reported. The calculated value of the electron affinity for ^1D state is 78.675(3) meV. Detailed Calculations on the ^5S°c state reveals that is 1216.8166(3) meV below the ^4P state.

k-Schur functions and affine Schubert calculus

CERN Document Server

Lam, Thomas; Morse, Jennifer; Schilling, Anne; Shimozono, Mark; Zabrocki, Mike

2014-01-01

This book gives an introduction to the very active field of combinatorics of affine Schubert calculus, explains the current state of the art, and states the current open problems. Affine Schubert calculus lies at the crossroads of combinatorics, geometry, and representation theory. Its modern development is motivated by two seemingly unrelated directions. One is the introduction of k-Schur functions in the study of Macdonald polynomial positivity, a mostly combinatorial branch of symmetric function theory. The other direction is the study of the Schubert bases of the (co)homology of the affine Grassmannian, an algebro-topological formulation of a problem in enumerative geometry. This is the first introductory text on this subject. It contains many examples in Sage, a free open source general purpose mathematical software system, to entice the reader to investigate the open problems. This book is written for advanced undergraduate and graduate students, as well as researchers, who want to become familiar with ...

Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics.

Science.gov (United States)

Garnett, Graham A E; Starke, Melissa J; Shaurya, Alok; Li, Janessa; Hof, Fraser

2016-04-05

Proteome-wide studies of post-translationally methylated species using mass spectrometry are complicated by high sample diversity, competition for ionization among peptides, and mass redundancies. Antibody-based enrichment has powered methylation proteomics until now, but the reliability, pan-specificity, polyclonal nature, and stability of the available pan-specific antibodies are problematic and do not provide a standard, reliable platform for investigators. We have invented an anionic supramolecular host that can form host-guest complexes selectively with methyllysine-containing peptides and used it to create a methylysine-affinity column. The column resolves peptides on the basis of methylation-a feat impossible with a comparable commercial cation-exchange column. A proteolyzed nuclear extract was separated on the methyl-affinity column prior to standard proteomics analysis. This experiment demonstrates that such chemical methyl-affinity columns are capable of enriching and improving the analysis of methyllysine residues from complex protein mixtures. We discuss the importance of this advance in the context of biomolecule-driven enrichment methods.

Affine-projective field laws

International Nuclear Information System (INIS)

Murphy, G.L.

1975-01-01

The general topic of geometric unified field theories is discussed in the first section. Some reasons are given for pursuing such theories, and some criticisms are considered. The second section develops the fundamental equations of a purely affine theory which is invariant under projective transformations of the affine connection. This theory is a generalization of that of Schrodinger. Possible identifications for the space-time metric are considered in Sec. III. Sections IV and V deal with the limits of pure gravitation and electrodynamics. In the symmetric limit, Einstein's vacuum equations with cosmological term are recovered. The theory also contains a generalized electrodynamic set of equations which is very similar to the Born-Infeld set. In the weak-field approximation, a finite mass must be attributed to the photon. The problem of motion for charges is discussed here, and it is argued that criticisms of unified field theories because of a supposed inability to produce the Lorentz force law are probably not justified. Three more speculative sections deal with possible explanations of nuclear forces, the spin-torsion relation, and particle structure

PRINCIPLES OF AFFINITY-BASED BIOSENSORS

Science.gov (United States)

Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...

Polynomial Primal-Dual Cone Affine Scaling for Semidefinite Programming

NARCIS (Netherlands)

A.B. Berkelaar (Arjan); J.F. Sturm; S. Zhang (Shuzhong)

1996-01-01

textabstractIn this paper we generalize the primal--dual cone affine scaling algorithm of Sturm and Zhang to semidefinite programming. We show in this paper that the underlying ideas of the cone affine scaling algorithm can be naturely applied to semidefinite programming, resulting in a new

Control and estimation of piecewise affine systems

CERN Document Server

Xu, Jun

2014-01-01

As a powerful tool to study nonlinear systems and hybrid systems, piecewise affine (PWA) systems have been widely applied to mechanical systems. Control and Estimation of Piecewise Affine Systems presents several research findings relating to the control and estimation of PWA systems in one unified view. Chapters in this title discuss stability results of PWA systems, using piecewise quadratic Lyapunov functions and piecewise homogeneous polynomial Lyapunov functions. Explicit necessary and sufficient conditions for the controllability and reachability of a class of PWA systems are

Non-contact adhesion to self-affine surfaces: A theoretical model

Energy Technology Data Exchange (ETDEWEB)

Makeev, Maxim A., E-mail: makeev@umich.edu

2013-11-22

Strength of adhesion between materials is known to be strongly influenced by interface irregularities. In this work, I devise a perturbative approach to describe the effect of self-affine roughness on non-contact adhesive interactions. The hierarchy of the obtained analytical solutions is the following. First, analytical formulae are deduced to describe roughness corrections to the van der Waals interaction energies between a hemi-space adherend, bounded by a self-affine surface, and a point-like adherent. Second, the problem of two hemi-spaces, one of which has a planar surface, and the other is bounded by a self-affine surface, is solved analytically. In the latter case, a numerical analysis is performed to delineate the behavior of the roughness corrections as a function of the parameters, characterizing self-affine fractal surface roughness. The problem of two hemi-spaces, both bounded by self-affine fractal surfaces, is also addressed in this work. The model's predictions are compared with previously reported theoretical results and available experimental data.

Detection-Guided Fast Affine Projection Channel Estimator for Speech Applications

Directory of Open Access Journals (Sweden)

Yan Wu Jennifer

2007-04-01

Full Text Available In various adaptive estimation applications, such as acoustic echo cancellation within teleconferencing systems, the input signal is a highly correlated speech. This, in general, leads to extremely slow convergence of the NLMS adaptive FIR estimator. As a result, for such applications, the affine projection algorithm (APA or the low-complexity version, the fast affine projection (FAP algorithm, is commonly employed instead of the NLMS algorithm. In such applications, the signal propagation channel may have a relatively low-dimensional impulse response structure, that is, the number m of active or significant taps within the (discrete-time modelled channel impulse response is much less than the overall tap length n of the channel impulse response. For such cases, we investigate the inclusion of an active-parameter detection-guided concept within the fast affine projection FIR channel estimator. Simulation results indicate that the proposed detection-guided fast affine projection channel estimator has improved convergence speed and has lead to better steady-state performance than the standard fast affine projection channel estimator, especially in the important case of highly correlated speech input signals.

Self-affine roughness influence on redox reaction charge admittance

NARCIS (Netherlands)

Palasantzas, G

2005-01-01

In this work we investigate the influence of self-affine electrode roughness on the admittance of redox reactions during facile charge transfer kinetics. The self-affine roughness is characterized by the rms roughness amplitude w, the correlation length xi and the roughness exponent H (0

Affine Toda equations and solutions in the homogeneous grading

Czech Academy of Sciences Publication Activity Database

Zuevsky, Alexander

2018-01-01

Roč. 542, April 1 (2018), s. 149-161 ISSN 0024-3795 Institutional support: RVO:67985840 Keywords : affine Lie gebras * affine Toda modes * solitons Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.973, year: 2016 https://www.sciencedirect.com/science/article/pii/S0024379517302100

Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis

Energy Technology Data Exchange (ETDEWEB)

Bray, J.J.; Drachman, D.B.

1982-01-01

Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the range of 10/sup 10/ M/sup -1/, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r/sup 2/>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG.

An Affinity Propagation Clustering Algorithm for Mixed Numeric and Categorical Datasets

Directory of Open Access Journals (Sweden)

Kang Zhang

2014-01-01

Full Text Available Clustering has been widely used in different fields of science, technology, social science, and so forth. In real world, numeric as well as categorical features are usually used to describe the data objects. Accordingly, many clustering methods can process datasets that are either numeric or categorical. Recently, algorithms that can handle the mixed data clustering problems have been developed. Affinity propagation (AP algorithm is an exemplar-based clustering method which has demonstrated good performance on a wide variety of datasets. However, it has limitations on processing mixed datasets. In this paper, we propose a novel similarity measure for mixed type datasets and an adaptive AP clustering algorithm is proposed to cluster the mixed datasets. Several real world datasets are studied to evaluate the performance of the proposed algorithm. Comparisons with other clustering algorithms demonstrate that the proposed method works well not only on mixed datasets but also on pure numeric and categorical datasets.

An improved affine projection algorithm for active noise cancellation

Science.gov (United States)

Zhang, Congyan; Wang, Mingjiang; Han, Yufei; Sun, Yunzhuo

2017-08-01

Affine projection algorithm is a signal reuse algorithm, and it has a good convergence rate compared to other traditional adaptive filtering algorithm. There are two factors that affect the performance of the algorithm, which are step factor and the projection length. In the paper, we propose a new variable step size affine projection algorithm (VSS-APA). It dynamically changes the step size according to certain rules, so that it can get smaller steady-state error and faster convergence speed. Simulation results can prove that its performance is superior to the traditional affine projection algorithm and in the active noise control (ANC) applications, the new algorithm can get very good results.

Phosphopeptide enrichment by immobilized metal affinity chromatography

DEFF Research Database (Denmark)

Thingholm, Tine E.; Larsen, Martin R.

2016-01-01

Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively...... charged metal ions such as Fe3+, Ga3+, Al3+, Zr4+, and Ti4+ has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from...

Satake diagrams of affine Kac-Moody algebras

Energy Technology Data Exchange (ETDEWEB)

Tripathy, L K [S B R Government Womens' College, Berhampur, Orissa 760 001 (India); Pati, K C [Department of Physics, Khallikote College, Berhampur, Orissa 760 001 (India)

2006-02-10

Satake diagrams of affine Kac-Moody algebras (untwisted and twisted) are obtained from their Dynkin diagrams. These diagrams give a classification of restricted root systems associated with these algebras. In the case of simple Lie algebras, these root systems and Satake diagrams correspond to symmetric spaces which have recently found many physical applications in quantum integrable systems, quantum transport problems, random matrix theories etc. We hope these types of root systems may have similar applications in theoretical physics in future and may correspond to symmetric spaces analogue of affine Kac-Moody algebras if they exist.

CT findings of normal pancreatic tail: variety of morphology and location

Energy Technology Data Exchange (ETDEWEB)

Han, Hye Seung; Son, San Hoo; Moon, Gae Hyuk; Kim, Hu Ho; Gong Jae Chul; Yang Jae Boum [Inchon Christian Hospital, Inchon (Korea, Republic of); Park, Mee Sook [Jaesung Hospital. (Korea, Republic of)

1998-02-01

To determine the morphology and location of normal pancreatic tail, as seen on abdominal CT. A hundred and one patients without pancreatic disease underwent CT scanning. We then determined how to relate the location of the pancreatic tail with the splenic hilum, left kidney, and pancreatic body. We compared the thickness of the tail with that of the body and analysed of the morphology of the tail. Seventy-seven percent of all pancreatic tails were located below the splenic hilum, with 59% of this proportion located 1 to 2 cm below. Fifty percent of tails were located at the level of the uppermost quarter of the left kidney, and a further 27% at the level of the second quarter; 75 % were located in the ventrolateral portion of this kidney and 23% in the ventral portion. In 48% of patients, the pancreatic tail and body were the same thickness, and in a further 48 %, the tail was thicker than the body. In 34% of patients, the tail showed focal bulging, and in another 32%, it tapered smoothly. Forty seven percent of tails were located below the pancreatic body and a further 37% were found at the same level as the body. Abdominal CT scans showed differing morphology and location of the pancreatic tail. The recognition of these variations will diminish speculation as to their true nature. (author). 12 refs., 4 figs.

The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

Directory of Open Access Journals (Sweden)

Xiliang Zheng

2015-04-01

Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity.

Science.gov (United States)

Wang, Deng-Liang; Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan; Yang, Hai-Tao; Wang, Jiang-Jie; Yao, Pei-Sen; Pan, Ru-Jun; Yang, Chaoyong James; Kang, De-Zhi

2014-10-31

Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher's attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with Kd 56±7.3nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy. Copyright © 2014 Elsevier Inc. All rights reserved.

ODE/IM correspondence and Bethe ansatz for affine Toda field equations

Directory of Open Access Journals (Sweden)

Katsushi Ito

2015-07-01

Full Text Available We study the linear problem associated with modified affine Toda field equation for the Langlands dual gˆ∨, where gˆ is an untwisted affine Lie algebra. The connection coefficients for the asymptotic solutions of the linear problem are found to correspond to the Q-functions for g-type quantum integrable models. The ψ-system for the solutions associated with the fundamental representations of g leads to Bethe ansatz equations associated with the affine Lie algebra gˆ. We also study the A2r(2 affine Toda field equation in massless limit in detail and find its Bethe ansatz equations as well as T–Q relations.

Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold

DEFF Research Database (Denmark)

Graversen, Jonas Heilskov; Jacobsen, C; Sigurskjold, B W

2000-01-01

-type lectin-like domain of tetranectin, involving Lys-148, Glu-150, and Asp-165, which mediates calcium-sensitive binding to plasminogen kringle 4. Here, we investigate the effect of conservative substitutions of these and a neighboring amino acid residue. Substitution of Thr-149 in tetranectin...... with a tyrosine residue considerably increases the affinity for plasminogen kringle 4, and, in addition, confers affinity for plasminogen kringle 2. As shown by isothermal titration calorimetry analysis, this new interaction is stronger than the binding of wild-type tetranectin to plasminogen kringle 4...

Integrable deformations of affine Toda theories and duality

International Nuclear Information System (INIS)

Fateev, V.A.

1996-01-01

We introduce and study five series of one-parameter families of two-dimensional integrable quantum field theories. These theories have a Lagrangian description in terms of the massive Thirring model coupled with non-simply laced affine Toda theories. Perturbative calculations, analysis of the factorized scattering theory and the Bethe ansatz technique are used to show that these field theories possess the dual representation available for the perturbative analysis in the strong coupling limit. The dual theory can be formulated as the non-linear sigma model with Witten's Euclidean black hole metric (complex sinh-Gordon theory) coupled with non-simply laced affine Toda theories. Lie algebras associated with these ''dual'' Toda theories belong to the dual series of affine algebras but have a smaller rank. The exact relation between coupling constants in the dual theories is conjectured. (orig.)

2D Affine and Projective Shape Analysis.

Science.gov (United States)

Bryner, Darshan; Klassen, Eric; Huiling Le; Srivastava, Anuj

2014-05-01

Current techniques for shape analysis tend to seek invariance to similarity transformations (rotation, translation, and scale), but certain imaging situations require invariance to larger groups, such as affine or projective groups. Here we present a general Riemannian framework for shape analysis of planar objects where metrics and related quantities are invariant to affine and projective groups. Highlighting two possibilities for representing object boundaries-ordered points (or landmarks) and parameterized curves-we study different combinations of these representations (points and curves) and transformations (affine and projective). Specifically, we provide solutions to three out of four situations and develop algorithms for computing geodesics and intrinsic sample statistics, leading up to Gaussian-type statistical models, and classifying test shapes using such models learned from training data. In the case of parameterized curves, we also achieve the desired goal of invariance to re-parameterizations. The geodesics are constructed by particularizing the path-straightening algorithm to geometries of current manifolds and are used, in turn, to compute shape statistics and Gaussian-type shape models. We demonstrate these ideas using a number of examples from shape and activity recognition.

Local uncontrollability for affine control systems with jumps

Science.gov (United States)

Treanţă, Savin

2017-09-01

This paper investigates affine control systems with jumps for which the ideal If(g1, …, gm) generated by the drift vector field f in the Lie algebra L(f, g1, …, gm) can be imbedded as a kernel of a linear first-order partial differential equation. It will lead us to uncontrollable affine control systems with jumps for which the corresponding reachable sets are included in explicitly described differentiable manifolds.

An {Mathematical expression} iteration bound primal-dual cone affine scaling algorithm for linear programmingiteration bound primal-dual cone affine scaling algorithm for linear programming

NARCIS (Netherlands)

J.F. Sturm; J. Zhang (Shuzhong)

1996-01-01

textabstractIn this paper we introduce a primal-dual affine scaling method. The method uses a search-direction obtained by minimizing the duality gap over a linearly transformed conic section. This direction neither coincides with known primal-dual affine scaling directions (Jansen et al., 1993;

The topological entropy of iterated piecewise affine maps is uncomputable

Directory of Open Access Journals (Sweden)

Pascal Koiran

2001-12-01

Full Text Available We show that it is impossible to compute (or even to approximate the topological entropy of a continuous piecewise affine function in dimension four. The same result holds for saturated linear functions in unbounded dimension. We ask whether the topological entropy of a piecewise affine function is always a computable real number, and conversely whether every non-negative computable real number can be obtained as the topological entropy of a piecewise affine function. It seems that these two questions are also open for cellular automata.

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

NARCIS (Netherlands)

Bosdriesz, Evert; Wortel, Meike T.; Haanstra, Jurgen R.; Wagner, Marijke J.; De La Torre Cortés, Pilar; Teusink, Bas

2018-01-01

Many organisms have several similar transporters with different affinities for the same substrate. Typically, high-affinity transporters are expressed when substrate is scarce and low-affinity ones when it is abundant. The benefit of using low instead of high-affinity transporters remains unclear,

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

NARCIS (Netherlands)

Bosdriesz, Evert; Wortel, M.T.; Haanstra, Jurgen R.; Wagner, Marijke J.; De La Torre, P.; Teusink, Bas

2018-01-01

Many organisms have several similar transporters with different affinities for the same substrate. Typically, high-affinity transporters are expressed when substrate is scarce and low-affinity ones when it is abundant. The benefit of using low instead of high-affinity transporters remains

Antibody affinity maturation

DEFF Research Database (Denmark)

Skjødt, Mette Louise

Yeast surface display is an effective tool for antibody affinity maturation because yeast can be used as an all-in-one workhorse to assemble, display and screen diversified antibody libraries. By employing the natural ability of yeast Saccharomyces cerevisiae to efficiently recombine multiple DNA...... laboratory conditions. A particular emphasis was put on using molecular techniques in conjunction with microenvironmental measurements (O2, pH, irradiance), a combination that is rarely found but provides a much more detailed understanding of “cause and effect” in complex natural systems...

RMT Assessments of the Market Latent Information Embedded in the Stocks' Raw, Normalized, and Partial Correlations

OpenAIRE

Kenett, Dror Y.; Shapira, Yoash; Ben-Jacob, Eshel

2009-01-01

We present here assessment of the latent market information embedded in the raw, affinity (normalized), and partial correlations. We compared the Zipf plot, spectrum, and distribution of the eigenvalues for each matrix with the results of the corresponding random matrix. The analysis was performed on stocks belonging to the New York ...

The affine quantum gravity programme

CERN Document Server

Klauder, J R

2002-01-01

The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix left brace g-hat sub a sub b (x)right brace composed of the spatial components of the local metric operator. On spectral grounds, canonical commutation relations are incompatible with this principle, and they must be replaced by noncanonical, affine commutation relations. Due to the partial second-class nature of the quantum gravitational constraints, it is advantageous to use the recently developed projection operator method, which treats all quantum constraints on an equal footing. Using this method, enforcement of regularized versions of the gravitational operator constraints is formulated quite naturally by means of a novel and relatively well-defined functional integral involving only the same set of variables that appears in the usual classical formulation. It is anticipated that skills and insight to study this formulation can be developed by studying special, reduced-variable models that sti...

Affinity resins as new tools for identifying target proteins of ascorbic acid.

Science.gov (United States)

Iwaoka, Yuji; Nishino, Kohei; Ishikawa, Takahiro; Ito, Hideyuki; Sawa, Yoshihiro; Tai, Akihiro

2018-02-12

l-Ascorbic acid (AA) has diverse physiological functions, but little is known about the functional mechanisms of AA. In this study, we synthesized two types of affinity resin on which AA is immobilized in a stable form to identify new AA-targeted proteins, which can provide important clues for elucidating unknown functional mechanisms of AA. To our knowledge, an affinity resin on which AA as a ligand is immobilized has not been prepared, because AA is very unstable and rapidly degraded in an aqueous solution. By using the affinity resins, cytochrome c (cyt c) was identified as an AA-targeted protein, and we showed that oxidized cyt c exhibits specific affinity for AA. These results suggest that two kinds of AA-affinity resin can be powerful tools to identify new target proteins of AA.

Hereditary stomatocytosis: association of low 2,3-diphosphoglycerate with increased cation pumping by the red cell.

Science.gov (United States)

Wiley, J S; Cooper, R A; Adachi, K; Asakura, T

1979-01-01

The levels of glycolytic intermediates have been measured in red cells from patients with both overhydrated and dehydrated varieties of the hereditary stomatocytosis syndrome. Red cell 2,3-diphosphoglycerate was reduced by 33% below normal in all patients with either stomatocyte or target cell morphologies (i.e. over or under hydrated varieties respectively). The relative decrement in 2,3-diphosphoglycerate was even greater when abnormal cells were compared with control cells with similar reticulocytosis. Red cell ADP concentrations in stomatocytosis were significantly increased above normal but ATP concentrations were not significantly changed. Whole blood oxygen affinity in stomatocytosis was increased in proportion to the lowered content of diphosphoglycerate. Some new parameters of membrane transport in hereditary stomatocytosis have been measured. Platelet K+ and Na+ concentrations and platelet K+ permeability were normal in stomatocytosis. The number of 3H-uridine transport sites in stomatocytes were increased by 9-39% above normal and this increment was the same as the increment in red cell lipids (0-38%). Hereditary stomatocytes contain 2-10-fold more cation pumps than normal and the increased active cation pumping may explain the high ADP, the low 2,3-diphosphoglycerate concentration and the increased oxygen affinity in this syndrome.

Molecular analysis of quality protein (QPM) and normal maize ...

African Journals Online (AJOL)

Jane

2011-10-24

Oct 24, 2011 ... genetic variation among QPM and normal maize varieties is important for an efficient selection and .... olymerase chain reaction (PCR) amplifications of RAPD and ISSR ..... Genetic characterization of Malawian cowpea.

Computing Tropical Varieties

DEFF Research Database (Denmark)

Speyer, D.; Jensen, Anders Nedergaard; Bogart, T.

2005-01-01

The tropical variety of a d-dimensional prime ideal in a polynomial ring with complex coefficients is a pure d-dimensional polyhedral fan. This fan is shown to be connected in codimension one. We present algorithmic tools for computing the tropical variety, and we discuss our implementation...

Online identification of continuous bimodal and trimodal piecewise affine systems

NARCIS (Netherlands)

Le, Q.T.; van den Boom, A.J.J.; Baldi, S.; Rantzer, Anders; Bagterp Jørgensen, John; Stoustrup, Jakob

2016-01-01

This paper investigates the identification of continuous piecewise affine systems in state space form with jointly unknown partition and subsystem matrices. The partition of the system is generated by the so-called centers. By representing continuous piecewise affine systems in the max-form and

A Novel Affinity Tag, ABTAG, and Its Application to the Affinity Screening of Single-Domain Antibodies Selected by Phage Display

Directory of Open Access Journals (Sweden)

Greg Hussack

2017-10-01

Full Text Available ABTAG is a camelid single-domain antibody (sdAb that binds to bovine serum albumin (BSA with low picomolar affinity. In surface plasmon resonance (SPR analyses using BSA surfaces, bound ABTAG can be completely dissociated from the BSA surfaces at low pH, over multiple cycles, without any reduction in the capacity of the BSA surfaces to bind ABTAG. A moderate throughput, SPR-based, antibody screening assay exploiting the unique features of ABTAG is described. Anti-carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6 sdAbs were isolated from a phage-displayed sdAb library derived from the heavy chain antibody repertoire of a llama immunized with CEACAM6. Following one or two rounds of panning, enriched clones were expressed as ABTAG fusions in microtiter plate cultures. The sdAb-ABTAG fusions from culture supernatants were captured on BSA surfaces and CEACAM6 antigen was then bound to the captured molecules. The SPR screening method gives a read-out of relative expression levels of the fusion proteins and kinetic and affinity constants for CEACAM6 binding by the captured molecules. The library was also panned and screened by conventional methods and positive clones were subcloned and expressed for SPR analysis. Compared to conventional panning and screening, the SPR-based ABTAG method yielded a considerably higher diversity of binders, some with affinities that were three orders of magnitude higher affinity than those identified by conventional panning.

Succinate production positively correlates with the affinity of the global transcription factor Cra for its effector FBP in Escherichia coli.

Science.gov (United States)

Wei, Li-Na; Zhu, Li-Wen; Tang, Ya-Jie

2016-01-01

Effector binding is important for transcription factors, affecting both the pattern and function of transcriptional regulation to alter cell phenotype. Our previous work suggested that the affinity of the global transcription factor catabolite repressor/activator (Cra) for its effector fructose-1,6-bisphosphate (FBP) may contribute to succinate biosynthesis. To support this hypothesis, single-point and three-point mutations were proposed through the semi-rational design of Cra to improve its affinity for FBP. For the first time, a positive correlation between succinate production and the affinity of Cra for FBP was revealed in Escherichia coli . Using the best-fit regression function, a cubic equation was used to examine and describe the relationship between succinate production and the affinity of Cra for FBP, demonstrating a significant positive correlation between the two factors (coefficient of determination R 2  = 0.894, P  = 0.000 Cra and DNA showed that Cra bound to the promoter regions of pck and aceB to activate the corresponding genes. Normally, Cra-regulated operons under positive control are deactivated in the presence of FBP. Therefore, theoretically, the enhanced affinity of Cra for FBP will inhibit the activation of pck and aceB . However, the activation of genes involved in CO 2 fixation and the glyoxylate pathway was further improved by the Cra mutant, ultimately contributing to succinate biosynthesis. Enhanced binding of Cra to FBP or active site mutations may eliminate the repressive effect caused by FBP, thus leading to increased activation of genes associated with succinate biosynthesis in the Cra mutant. This work demonstrates an important transcriptional regulation strategy in the metabolic engineering of succinate production and provides useful information for better understanding of the regulatory mechanisms of transcription factors.

Affinity of Iresine herbstii and Brugmansia arborea extracts on different cerebral receptors.

Science.gov (United States)

Nencini, Cristina; Cavallo, Federica; Bruni, Giancarlo; Capasso, Anna; De Feo, Vincenzo; De Martino, Laura; Giorgi, Giorgio; Micheli, Lucia

2006-05-24

Iresine herbstii Hook. (Amaranthaceae) and Brugmansia arborea (L.) Lagerheim (Solanaceae) are used in the northern Peruvian Andes for magic-therapeutical purposes. The traditional healers use Iresine herbstii with the ritual aim to expel bad spirits from the body. Furthermore, Iresine herbstii was used in association with other plants, such as Trichocereus pachanoi Britt. et Rose, for divination, to diagnose diseases, and to take possession of another identity. Also, species of Brugmansia have been reported to be used during ritual practices for magical and curative purposes. Given the above evidence, the aim of the present study is to evaluate if the central effects of Iresine herbstii and Brugmansia arborea could be associated with interaction with SNC receptors. Two Iresine herbstii extracts (methanolic and aqueous) and one Brugmansia arborea aqueous extract were tested for in vitro affinity on 5-HT(1A), 5-HT(2A), 5-HT(2C), D1, D2, alpha(1), and alpha(2) receptors by radioligand binding assays. The biological materials for binding assay (cerebral cortex) were taken from male Sprague-Dawley rats. The extracts affinity for receptors is definite as inhibition percentage of radioligand/receptor binding and measured as the radioactivity of remaining complex radioligand/receptor. The data obtained for Iresine extracts have shown a low affinity for the 5-HT(1A) receptor and no affinity for 5-HT(2A) receptor. Otherwise the methanolic extract showed affinity for 5-HT(2C) receptor (IC(50): 34.78 microg/ml) and for D1 receptor (IC(50): 19.63 microg/ml), instead the Iresine aqueous extract displayed a lower affinity for D1 (48.3% at the maximum concentration tested) and a higher value of affinity for D2 receptors (IC(50): 32.08 microg/ml). The Brugmansia aqueous extract displayed affinity for D1 receptors (IC(50): 17.68 microg/ml), D2 receptors (IC(50): 15.95 microg/ml) and weak affinity for the serotoninergic receptors. None of the three extracts showed relevant affinity

Biochemical method for fast affinity diagnosis in grape-vine transplantation

International Nuclear Information System (INIS)

Lilov, D.

1977-01-01

Long term experiments have proved the affinity of cv. Mavroud in transplantations on various root stocks. Best affinity was observed in the combination cv. Mavroud X Riparia tomanteau, followed, in a descending order, by the combinations Mavroud X Mavroud (autotransplantation), Mavroud X Berlandieri X Riparia Kobber SBB and Mavroud X Riparia 33 EM. In view to establish indices for predicting the transplantation affinity a great number of physiological-biochemical and morphological-anatomical studies were carried out. The results obtained showed that a most clearly expressed positive, statistically significant correlation exists between the amount of 15 N transported from the root stock to the scions, shoots and leaves. As a result, a biochemical method for fast affinity diagnosis in grape-vine transplantation has been developed. The reliability of the method has been checked up also with other cultivars. Up to the present no such method was known in grape-vine science and practice. (author)

Methods for quantifying T cell receptor binding affinities and thermodynamics

Science.gov (United States)

Piepenbrink, Kurt H.; Gloor, Brian E.; Armstrong, Kathryn M.; Baker, Brian M.

2013-01-01

αβ T cell receptors (TCRs) recognize peptide antigens bound and presented by class I or class II major histocompatibility complex (MHC) proteins. Recognition of a peptide/MHC complex is required for initiation and propagation of a cellular immune response, as well as the development and maintenance of the T cell repertoire. Here we discuss methods to quantify the affinities and thermodynamics of interactions between soluble ectodomains of TCRs and their peptide/MHC ligands, focusing on titration calorimetry, surface plasmon resonance, and fluorescence anisotropy. As TCRs typically bind ligand with weak-to-moderate affinities, we focus the discussion on means to enhance the accuracy and precision of low affinity measurements. In addition to further elucidating the biology of the T cell mediated immune response, more reliable low affinity measurements will aid with more probing studies with mutants or altered peptides that can help illuminate the physical underpinnings of how TCRs achieve their remarkable recognition properties. PMID:21609868

Novel trends in affinity biosensors: current challenges and perspectives

International Nuclear Information System (INIS)

Arugula, Mary A; Simonian, Aleksandr

2014-01-01

Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ‘aptamers’ and ‘phages’ which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives. (topical review)

Targeting Anti-Cancer Active Compounds: Affinity-Based Chromatographic Assays

OpenAIRE

de Moraes, Marcela Cristina; Cardoso, Carmen Lucia; Seidl, Claudia; Moaddel, Ruin; Cass, Quezia Bezerra

2016-01-01

Affinity-based chromatography assays encompass the use of solid supports containing immobilized biological targets to monitor binding events in the isolation , identification and/or characterization of bioactive compounds. This powerful bioanalytical technique allows the screening of potential binders through fast analyses that can be directly performed using isolated substances or complex matrices. An overview of the recent researches in frontal and zonal affinity-based chromatography screen...

A theoretical model for the effects of reduced hemoglobin-oxygen affinity on tumor oxygenation

International Nuclear Information System (INIS)

Kavanagh, Brian D.; Secomb, Timothy W.; Hsu, Richard; Lin, P.-S.; Venitz, Jurgen; Dewhirst, Mark W.

2002-01-01

Purpose: To develop a theoretical model for oxygen delivery to tumors, and to use the model to simulate the effects of changing the affinity of hemoglobin for oxygen on tumor oxygenation. Methods and Materials: Hemoglobin affinity is expressed in terms of P 50 , the partial pressure of oxygen (Po 2 ) at half saturation. Effects of changing P 50 on arterial Po 2 are predicted using an effective vessel approach to describe diffusive oxygen transport in the lungs, assuming fixed systemic oxygen demand and fixed blood flow rate. The decline in oxygen content of blood as it flows through normal tissue before entering the tumor region is assumed fixed. The hypoxic fraction of the tumor region is predicted using a three-dimensional simulation of diffusion from a network of vessels whose geometry is derived from observations of tumor microvasculature in the rat. Results: In air-breathing rats, predicted hypoxic fraction decreases with moderate increases in P 50 , but increases with further increases of P 50 , in agreement with previous experimental results. In rats breathing hyperoxic gases, and in humans breathing either normoxic or hyperoxic gases, increased P 50 is predicted to improve tumor oxygenation. Conclusions: The results support the administration of synthetic agents to increase P 50 during radiation treatment of tumors

Varieties of English.

Science.gov (United States)

Brook, G. L.

The English language is not a monolithic entity but an amalgam of many different varieties that can be associated respectively with groups of speakers, with individuals, and with the occasion. Among such varieties are slang, regional and class dialects, the language of children, and the language used by public speakers, journalists, lawyers,…

Quantum image encryption based on generalized affine transform and logistic map

Science.gov (United States)

Liang, Hao-Ran; Tao, Xiang-Yang; Zhou, Nan-Run

2016-07-01

Quantum circuits of the generalized affine transform are devised based on the novel enhanced quantum representation of digital images. A novel quantum image encryption algorithm combining the generalized affine transform with logistic map is suggested. The gray-level information of the quantum image is encrypted by the XOR operation with a key generator controlled by the logistic map, while the position information of the quantum image is encoded by the generalized affine transform. The encryption keys include the independent control parameters used in the generalized affine transform and the logistic map. Thus, the key space is large enough to frustrate the possible brute-force attack. Numerical simulations and analyses indicate that the proposed algorithm is realizable, robust and has a better performance than its classical counterpart in terms of computational complexity.

Ecoinformatics Can Infer Causal Effects of Crop Variety on Insect Attack by Capitalizing on 'Pseudoexperiments' Created When Different Crop Varieties Are Interspersed: A Case Study in Almonds.

Science.gov (United States)

Rosenheim, Jay A; Higbee, Bradley S; Ackerman, Jonathan D; Meisner, Matthew H

2017-12-05

Capturing the complementary strengths of observational and experimental research methods usually requires the researcher to gather separate experimental and observational data sets. In some cases, however, commercial agricultural practices produce the spatial and temporal mixing of 'treatments' independently of other possibly covarying factors that is normally achieved only with formal experimentation. The resulting 'pseudoexperiments' can provide strong evidence for causal relationships. Here, we analyze a large observational data set that creates a series of such pseudoexperiments to assess the effect of different commercial varieties of almond, Prunus dulcis (Mill.) on the impact of two key lepidopteran pests, the navel orangeworm Amyelois transitella (Walker) (Lepidoptera: Pyralidae), and the peach twig borer Anarsia lineatella Zeller (Lepidoptera: Gelechiidae). Almonds are universally planted as polycultures of different varieties to obtain efficient cross-pollination. We find substantial differences across almond varieties in the rates of infestation of almond hulls and nutmeats by the two pests. We find no support for the hypothesis that earlier-maturing varieties sustain higher attack; for A. transitella, later-maturing varieties instead had more frequent infestation. On many almond varieties, A. lineatella reaches high infestation levels by feeding almost exclusively on the hulls, rather than nutmeats. Given the importance of these pests in directly destroying almond nuts and in promoting aflatoxin-producing Aspergillus sp. fungal infections of almonds, further work exploring the impact of these pests is warranted. Because many crops requiring cross-pollination are planted as mixtures of different varieties, commercial agricultural production data hold great potential for studying within-crop variation in susceptibility to insect attack. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights

Enhancing Community Detection By Affinity-based Edge Weighting Scheme

Energy Technology Data Exchange (ETDEWEB)

Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-10-05

Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.

APPLICATION OF IMMUNOGLOBULIN-BINDING PROTEINS A, G, L IN THE AFFINITY CHROMATOGRAPHY

Directory of Open Access Journals (Sweden)

О. V. Sviatenko

2014-04-01

Full Text Available Proteins A, G and L are native or recombinant proteins of microbial origin that bind to mammalian immunoglobulins. Preferably recombinant variants of proteins A, G, L are used in biotechnology for affinity sorbents production. Сomparative characteristics of proteins A, G, L and affinity sorbents on the basis of them, advantages and disadvantages of these proteins application as ligands in the affinity chromatography are done. Analysis of proteins A, G, L properties is presented. Binding specificities and affinities of these proteins differ between species and antibody subclass. Protein А has high affinity to human IgG1, IgG2, IgG4, mouse IgG2a, IgG2b, IgG3, goat and sheep IgG2, dog, cat, guinea pig, rabbit IgG. Protein G binds strongly to human, mouse, cow, goat, sheep and rabbit IgG. Protein L has ability of strong binding to immunoglobulin kappa-chains of human, mouse, rat and pig. Expediency of application of affinity chromatography with usage of sorbents on the basis of immobilized proteins A, G, L are shown for isolation and purification of antibodies different classes. Previously mentioned method is used as an alternative to conventional methods of protein purification, such as ion-exchange, hydrophobic interactions, metal affinity chromatography, ethanol precipitation due to simplicity in usage, possibility of one-step purification process, obtaining of proteins high level purity, multiuse at maintenance of proper storage and usage conditions. Affinity sorbents on the basis of immobilized proteins A, G, L are used not only for antibodies purification, but also for extraction of different antibodies fractions from blood serum.

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers.

Science.gov (United States)

Holstein, Carly A; Chevalier, Aaron; Bennett, Steven; Anderson, Caitlin E; Keniston, Karen; Olsen, Cathryn; Li, Bing; Bales, Brian; Moore, David R; Fu, Elain; Baker, David; Yager, Paul

2016-02-01

To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.

ANALYSIS OF DRUG-PROTEIN BINDING BY ULTRAFAST AFFINITY CHROMATOGRAPHY USING IMMOBILIZED HUMAN SERUM ALBUMIN

Science.gov (United States)

Mallik, Rangan; Yoo, Michelle J.; Briscoe, Chad J.; Hage, David S.

2010-01-01

Human serum albumin (HSA) was explored for use as a stationary phase and ligand in affinity microcolumns for the ultrafast extraction of free drug fractions and the use of this information for the analysis of drug-protein binding. Warfarin, imipramine, and ibuprofen were used as model analytes in this study. It was found that greater than 95% extraction of all these drugs could be achieved in as little as 250 ms on HSA microcolumns. The retained drug fraction was then eluted from the same column under isocratic conditions, giving elution in less than 40 s when working at 4.5 mL/min. The chromatographic behavior of this system gave a good fit with that predicted by computer simulations based on a reversible, saturable model for the binding of an injected drug with immobilized HSA. The free fractions measured by this method were found to be comparable to those determined by ultrafiltration, and equilibrium constants estimated by this approach gave good agreement with literature values. Advantages of this method include its speed and the relatively low cost of microcolumns that contain HSA. The ability of HSA to bind many types of drugs also creates the possibility of using the same affinity microcolumn to study and measure the free fractions for a variety of pharmaceutical agents. These properties make this technique appealing for use in drug binding studies and in the high-throughput screening of new drug candidates. PMID:20227701

Affinity of antibody secreted by a single cell

International Nuclear Information System (INIS)

Doran, D.M.

1978-01-01

It was the intention of this research to measure the affinity of antibody secreted by a single cell, and to describe the spectrum of affinities displayed in response to antigenic stimulation. The single cell secreting specific antibody was isolated by means of the hemolytic plaque assay. The amount of antibody secreted by the cell was to be measured through the use of a solid phase radioimmunoassay. The affinity of the antibody would be estimated by comparing the diameter of the plaque, and the amount of antibody secreted, with a mathematical theory of the formation of a plaque in agar. As a test system, a solid phase radioimmunoassay was developed for human serum albumin using antibody coupled to Sephadex. A sensitivity of 1 nanogram was attained with this assay. A solid phase radioimmunoassay for mouse immunoglobulin M was developed, using antibody coupled to Sepharose. The sensitivity attained with this assay was only on the order of 10 micrograms. The mouse immunoglobulin M radioimmunoassay was not sensitive enough to measure the amount of antibody secreted by a single cell. From a theoretical equation, the relationship between antibody affinity, plaque diameter and antibody secretion rate was calculated for the experimental conditions used in this research. By assuming a constant antibody secretion rate, an effective binding constant for the antibody was estimated from the average plaque diameters. This effective binding constant was observed to increase during the immune response

Experimental and theoretical binding affinity between polyvinylpolypyrrolidone and selected phenolic compounds from food matrices.

Science.gov (United States)

Durán-Lara, Esteban F; López-Cortés, Xaviera A; Castro, Ricardo I; Avila-Salas, Fabián; González-Nilo, Fernando D; Laurie, V Felipe; Santos, Leonardo S

2015-02-01

Polyvinylpolypyrrolidone (PVPP) is a fining agent, widely used in winemaking and brewing, whose mode of action in removing phenolic compounds has not been fully characterised. The aim of this study was to evaluate the experimental and theoretical binding affinity of PVPP towards six phenolic compounds representing different types of phenolic species. The interaction between PVPP and phenolics was evaluated in model solutions, where hydroxyl groups, hydrophobic bonding and steric hindrance were characterised. The results of the study indicated that PVPP exhibits high affinity for quercetin and catechin, moderate affinity for epicatechin, gallic acid and lower affinity for 4-methylcatechol and caffeic acid. The affinity has a direct correlation with the hydroxylation degree of each compound. The results show that the affinity of PVPP towards phenols is related with frontier orbitals. This work demonstrates a direct correlation between the experimental affinity and the interaction energy calculations obtained through computational chemistry methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the Lp affine isoperimetric inequalities

Indian Academy of Sciences (India)

surface area measure on convex bodies. We also establish the reverse version of -Petty projection inequality and an affine isoperimetric inequality of − p K . Author Affiliations. Wuyang Yu1 Gangsong Leng2. Institute of Management Decision ...

Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

Directory of Open Access Journals (Sweden)

Xiakun Chu

2014-08-01

Full Text Available Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less flexibility leads to weaker (stronger coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.

Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin

Directory of Open Access Journals (Sweden)

Mora Xavier

2007-05-01

Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for

Quantifying high-affinity binding of hydrophobic ligands by isothermal titration calorimetry.

Science.gov (United States)

Krainer, Georg; Broecker, Jana; Vargas, Carolyn; Fanghänel, Jörg; Keller, Sandro

2012-12-18

A fast and reliable quantification of the binding thermodynamics of hydrophobic high-affinity ligands employing a new calorimetric competition experiment is described. Although isothermal titration calorimetry is the method of choice for a quantitative characterization of intermolecular interactions in solution, a reliable determination of a dissociation constant (K(D)) is typically limited to the range 100 μM > K(D) > 1 nM. Interactions displaying higher or lower K(D) values can be assessed indirectly, provided that a suitable competing ligand is available whose K(D) falls within the directly accessible affinity window. This established displacement assay, however, requires the high-affinity ligand to be soluble at high concentrations in aqueous buffer and, consequently, poses serious problems in the study of protein binding involving small-molecule ligands dissolved in organic solvents--a familiar case in many drug-discovery projects relying on compound libraries. The calorimetric competition assay introduced here overcomes this limitation, thus allowing for a detailed thermodynamic description of high-affinity receptor-ligand interactions involving poorly water-soluble compounds. Based on a single titration of receptor into a dilute mixture of the two competing ligands, this competition assay provides accurate and precise values for the dissociation constants and binding enthalpies of both high- and moderate-affinity ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation and high-affinity protein-inhibitor interactions, and explore its potential and limitations with the aid of simulations and statistical analyses.

Normal variants and artifacts in bone scan: potential for errors in interpretation

International Nuclear Information System (INIS)

Sohn, Myung Hee

2004-01-01

Bone scan is one of the most frequently performed studies in nuclear medicine. In bone scan, the amount of radioisotope taken up by lesion depends primarily on the local rate of bone turnover rather than on the bone mass. Bone scan is extremely sensitive for detecting bony abnormalities. However, abnormalities that appear on bone scan may not always represent disease. The normal scan appearances may be affected not only by skeletal physiology and anatomy but also by a variety of technical factors which can influence image quality. Many normal variants and artifacts may appear on bone scan. They could simulate a pathologic process and could mislead into the wrong diagnostic interpretation. Therefore, their recognition is necessary to avoid misdiagnosis. A nuclear medicine physician should be aware of variable appearance of the normal variants and artifacts on bone scan. In this article, a variety of normal variants and artifacts mimicking real pathologic lesion in bone scan interpretation are discussed and illustrated

Affinity functions for modeling glass dissolution rates

Energy Technology Data Exchange (ETDEWEB)

Bourcier, W.L. [Lawrence Livermore National Lab., CA (United States)

1997-07-01

Glass dissolution rates decrease dramatically as glass approach ''saturation'' with respect to the leachate solution. Most repository sites are chosen where water fluxes are minimal, and therefore the waste glass is most likely to dissolve under conditions close to ''saturation''. The key term in the rate expression used to predict glass dissolution rates close to ''saturation'' is the affinity term, which accounts for saturation effects on dissolution rates. Interpretations of recent experimental data on the dissolution behaviour of silicate glasses and silicate minerals indicate the following: 1) simple affinity control does not explain the observed dissolution rate for silicate minerals or glasses; 2) dissolution rates can be significantly modified by dissolved cations even under conditions far from saturation where the affinity term is near unity; 3) the effects of dissolved species such as Al and Si on the dissolution rate vary with pH, temperature, and saturation state; and 4) as temperature is increased, the effect of both pH and temperature on glass and mineral dissolution rates decrease, which strongly suggests a switch in rate control from surface reaction-based to diffusion control. Borosilicate glass dissolution models need to be upgraded to account for these recent experimental observations. (A.C.)

On $L_p$ Affine Surface Area and Curvature Measures

OpenAIRE

Zhao, Yiming

2015-01-01

The relationship between $L_p$ affine surface area and curvature measures is investigated. As a result, a new representation of the existing notion of $L_p$ affine surface area depending only on curvature measures is derived. Direct proofs of the equivalence between this new representation and those previously known are provided. The proofs show that the new representation is, in a sense, "polar" to that of Lutwak's and "dual" to that of Sch\\"utt & Werner's.

Role of the multichain IL-2 receptor complex in the control of normal and malignant T-cell proliferation

International Nuclear Information System (INIS)

Waldmann, T.A.

1987-01-01

Antigen-induced activation of resting T-cells induces the synthesis of interleukin-2 (IL-2), as well as the expression of specific cell surface receptors for this lymphokine. There are at least two forms of the cellular receptors for IL-2, one with a very high affinity and the other with a lower affinity. The authors have identified two IL-2 binding peptides, a 55-kd peptide reactive with the anti-Tac monoclonal antibody, and a novel 75-kd non-Tac IL-2 binding peptide. Cell lines bearing either the p55, Tac, or the p75 peptide along manifested low-affinity IL-2 binding, whereas cell lines bearing both peptides manifested both high- and low-affinity receptors. Fusion of cell membranes from low-affinity IL-2 binding cells bearing the Tac peptide alone with membranes from a cell line bearing the p75 peptide alone generates hybrid membranes bearing high-affinity receptors. They propose a multichain model for the high-affinity IL-2 receptor in which both the Tac and the p75 IL-2 binding peptides are associated in a receptor complex. In contrast to resting T-cells, human T-cell lymphotropic virus I-associated adult T-cell leukemia cells constitutively express large numbers of IL-2 receptors. Because IL-2 receptors are present on the malignant T-cells but not on normal resting cells, clinical trials have been initiated in which patients with adult T-cell leukemia are being treated with either unmodified or toxin-conjugated forms of anti-Tac monoclonal antibody directed toward this growth factor receptor. Cross-linking studies were done using [ 125 I] IL-2

[An examination of the determinants of social withdrawal and affinity for social withdrawal].

Science.gov (United States)

Watanabe, Asami; Matsui, Yutaka; Takatsuka, Yusuke

2010-12-01

This study examined the determinants of social withdrawal using data from a survey by the Tokyo Metropolitan Government Office for Youth Affairs and Public Safety (2008). In addition, this study identified young people who showed an affinity for social withdrawal although they were not in a state of withdrawal, and examined the determinants of an affinity for social withdrawal. The results of stepwise discriminant analysis showed that factors such as social phobia, depression, violence, and emotional bonds with family differentiated between the general youth group and the social withdrawal group and the "affinity group". Social phobia, violence, and refusal to be interfered in self-decision making differentiated between the social withdrawal group and the "affinity group". This study shows that an "affinity group" should be cared as well as an actual withdrawal group.

Affinity chromatography: A versatile technique for antibody purification.

Science.gov (United States)

Arora, Sushrut; Saxena, Vikas; Ayyar, B Vijayalakshmi

2017-03-01

Antibodies continue to be extremely utilized entities in myriad applications including basic research, imaging, targeted delivery, chromatography, diagnostics, and therapeutics. At production stage, antibodies are generally present in complex matrices and most of their intended applications necessitate purification. Antibody purification has always been a major bottleneck in downstream processing of antibodies, due to the need of high quality products and associated high costs. Over the years, extensive research has focused on finding better purification methodologies to overcome this holdup. Among a plethora of different techniques, affinity chromatography is one of the most selective, rapid and easy method for antibody purification. This review aims to provide a detailed overview on affinity chromatography and the components involved in purification. An array of support matrices along with various classes of affinity ligands detailing their underlying working principles, together with the advantages and limitations of each system in purifying different types of antibodies, accompanying recent developments and important practical methodological considerations to optimize purification procedure are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Pepper seed variety identification based on visible/near-infrared spectral technology

Science.gov (United States)

Li, Cuiling; Wang, Xiu; Meng, Zhijun; Fan, Pengfei; Cai, Jichen

2016-11-01

Pepper is a kind of important fruit vegetable, with the expansion of pepper hybrid planting area, detection of pepper seed purity is especially important. This research used visible/near infrared (VIS/NIR) spectral technology to detect the variety of single pepper seed, and chose hybrid pepper seeds "Zhuo Jiao NO.3", "Zhuo Jiao NO.4" and "Zhuo Jiao NO.5" as research sample. VIS/NIR spectral data of 80 "Zhuo Jiao NO.3", 80 "Zhuo Jiao NO.4" and 80 "Zhuo Jiao NO.5" pepper seeds were collected, and the original spectral data was pretreated with standard normal variable (SNV) transform, first derivative (FD), and Savitzky-Golay (SG) convolution smoothing methods. Principal component analysis (PCA) method was adopted to reduce the dimension of the spectral data and extract principal components, according to the distribution of the first principal component (PC1) along with the second principal component(PC2) in the twodimensional plane, similarly, the distribution of PC1 coupled with the third principal component(PC3), and the distribution of PC2 combined with PC3, distribution areas of three varieties of pepper seeds were divided in each twodimensional plane, and the discriminant accuracy of PCA was tested through observing the distribution area of samples' principal components in validation set. This study combined PCA and linear discriminant analysis (LDA) to identify single pepper seed varieties, results showed that with the FD preprocessing method, the discriminant accuracy of pepper seed varieties was 98% for validation set, it concludes that using VIS/NIR spectral technology is feasible for identification of single pepper seed varieties.

In vitro evaluation of different varieties of maize fodder for their methane generation potential and digestibility with goat rumen liquor

Directory of Open Access Journals (Sweden)

Shalini Vaswani

2016-11-01

Full Text Available Aim: To evaluate the methane generation potential and digestibility of different (normal and three high-quality protein maize [HQPM] varieties of maize fodder with goat rumen liquor in vitro. Materials and Methods: Methane production potential and digestibility of different varieties of maize fodder were tested in in vitro gas production test. Seven varieties of maize, four normal (HTHM 5101, DHM 117, HM 5, and Shaktiman/900 M Gold, and three high-quality protein (HQPM 5, HQPM 7, and HQPM 9/Vivek were grown in different plots under the same environmental and agro-climatic conditions. Fodders were harvested at 45-50 days of sowing, and the representative samples of fodder from different varieties of maize were collected for analysis. Dried and grinded form of these maize fodder varieties was tested for gas, methane, and digestibility using goat rumen microflora in in vitro gas syringes. Results: Gas production (ml/g dry matter [DM] was highest for HM5 variety (97.66, whereas lowest for HQPM 9 variety (64.22. Gas production (ml/g degraded DM [DDM] and methane (% were statistically similar in different varieties of maize fodder. The methane production expressed as ml/g DM and ml/g DDM was significantly (p<0.05 highest for HM 5 (14.22 and 26.62 and lowest for DHM 117 variety (7.47 and 14.13. The in vitro DM digestibility (% and in vitro organic matter digestibility (% varied from 47.48 (HQPM 5 to 52.05 (HQPM 9 and 50.03 (HQPM 7 to 54.22 (HM 5, respectively. Conclusion: The present study concluded that DHM 117 maize variety fodder has lowest methane generation potential and incorporating it in the dietary regime of ruminants may contribute to lower methane production.

DFT study on the effect of exocyclic substituents on the proton affinity of 1-methylimidazole

International Nuclear Information System (INIS)

Liu, Haining; Bara, Jason E.; Turner, C. Heath

2013-01-01

Highlights: • DFT calculations are used to predict the proton affinity of 1-methylimidazoles. • The electron-withdrawing groups dominate the predicted proton affinity. • The effects of multiple substituents on the proton affinity can be accurately predicted. • Large compound libraries can be screened for imidazoles with tailored reactivity. - Abstract: A deeper understanding of the acid/base properties of imidazole derivatives will aid the development of solvents, polymer membranes and other materials that can be used for CO 2 capture and acid gas removal. In this study, we employ density functional theory calculations to investigate the effect of various electron-donating and electron-withdrawing groups on the proton affinity of 1-methylimidazole. We find that electron-donating groups are able to increase the proton affinity relative to 1-methylimidazole, i.e., making the molecule more basic. In contrast, electron-withdrawing groups cause a decrease of the proton affinity. When multiple substituents are present, their effects on the proton affinity were found to be additive. This finding offers a quick approach for predicting and targeting the proton affinities of this series of molecules, and we show the strong correlation between the calculated proton affinities and experimental pK a values

Density-conserving affine continuous cellular automata solving the relaxed density classification problem

International Nuclear Information System (INIS)

Wolnik, Barbara; Dembowski, Marcin; Bołt, Witold; Baetens, Jan M; De Baets, Bernard

2017-01-01

The focus of this paper is on the density classification problem in the context of affine continuous cellular automata. Although such cellular automata cannot solve this problem in the classical sense, most density-conserving affine continuous cellular automata with a unit neighborhood radius are valid solutions of a slightly relaxed version of this problem. This result follows from a detailed study of the dynamics of the density-conserving affine continuous cellular automata that we introduce. (paper)

High affinity binding of [3H]cocaine to rat liver microsomes

International Nuclear Information System (INIS)

El-Maghrabi, E.A.; Calligaro, D.O.; Eldefrawi, M.E.

1988-01-01

] 3 H]cocaine bound reversible, with high affinity and stereospecificity to rat liver microsomes. Little binding was detected in the lysosomal, mitochondrial and nuclear fractions. The binding kinetics were slow and the kinetically calculated K/sub D/ was 2 nM. Induction of mixed function oxidases by phenobarbital did not produce significant change in [ 3 H]cocaine binding. On the other hand, chronic administration of cocaine reduced [ 3 H]cocaine binding drastically. Neither treatment affected the affinity of the liver binding protein for cocaine. Microsomes from mouse and human livers had less cocaine-binding protein and lower affinity for cocaine than those from rat liver. Binding of [ 3 H]cocaine to rat liver microsomes was insensitive to monovalent cations and > 10 fold less sensitive to biogenic amines than the cocaine receptor in rat striatum. However, the liver protein had higher affinity for cocaine and metabolites except for norcocaine. Amine uptake inhibitors displaced [ 3 H]cocaine binding to liver with a different rank order of potency than their displacement of [ 3 H]cocaine binding to striatum. This high affinity [ 3 H]cocaine binding protein in liver is not likely to be monooxygenase, but may have a role in cocaine-induced hepatotoxicity

Evaluation of SDS depletion using an affinity spin column and IMS-MS detection

Energy Technology Data Exchange (ETDEWEB)

Hengel, Shawna M.; Floyd, Erica A.; Baker, Erin Shammel; Zhao, Rui; Wu, Si; Pasa-Tolic, Ljiljana

2012-11-01

While the use of detergents is necessary for a variety of protein isolation preparation protocols, often prior to mass spectral (MS) analysis, they are not compatible with MS analysis due to ion suppression and adduct formation. This manuscript describes optimization of detergent removal, using commercially available SDS depletion spin columns containing an affinity resin, providing for both increased protein recovery and thorough SDS removal. Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) allowed for a concurrent analysis of both analyte and detergent. In the case of both proteins and peptides, higher detergent concentrations than previously reported provided an increase of sample recovery; however there was a limit as SDS was detected by IMS-MS at higher levels of SDS indicating incomplete detergent depletion. The results also suggest optimal conditions for SDS removal are dependent on the sample concentration. Overall, this study provides a useful guide for proteomic studies where SDS is required for efficient sample preparation.

Changes in erythrocyte insulin receptors in normal dogs and keeshond dogs with inheritable, early onset, insulin dependent diabetes mellitus

International Nuclear Information System (INIS)

Klaassen, J.K.

1986-01-01

Validation of a procedure to evaluate insulin receptors on erythrocytes (RBC-IR) in dogs is described. The specific binding of ( 125 I)iodoinsulin to RBC-IR of normal dogs is significantly greater than binding in keeshonds with an inheritable form of early onset diabetes mellitus. This decreased binding was due to a significant decrease in RBC-IR affinity in the diabetic keeshonds. To determine the effect on RBC-IR, normal dogs were treated with either dexamethasone (0.1 mg/kg) or prednisone (0.3 mg/kg) for 10 days: concentrations of plasma cortisol, glucose, and insulin, plus binding characteristics of RBC-IR were determined. In the dexamethasone treated group, plasma glucose concentrations were elevated significantly by day 6 and continued through day 10. Insulin concentrations were elevated significantly by day 3 and remained elevated through day 10. In the prednisone treated group, glucose concentrations were elevated significantly by day 3, while insulin concentrations were elevated significantly by day 8. Maximum binding of RBC-IR was unaffected by prednisone and neither affinities nor receptor numbers were significantly different from day 1. No changes in plasma cortisol concentration were seen. Diabetic keeshonds on daily insulin treatment were removed from exogenous insulin therapy for 48 hours. Significant increases in glucose concentrations were observed, but no significant changes in cortisol, insulin, average receptor binding affinity, or RBC-IR number per cell occurred

Na+,K+-ATPase Na+ affinity in rat skeletal muscle fiber types

DEFF Research Database (Denmark)

Kristensen, Michael; Juel, Carsten

2010-01-01

Previous studies in expression systems have found different ion activation of the Na(+)/K(+)-ATPase isozymes, which suggest that different muscles have different ion affinities. The rate of ATP hydrolysis was used to quantify Na(+),K(+)-ATPase activity, and the Na(+) affinity of Na(+),K(+)-ATPase...

Paper-based immune-affinity arrays for detection of multiple mycotoxins in cereals.

Science.gov (United States)

Li, Li; Chen, Hongpu; Lv, Xiaolan; Wang, Min; Jiang, Xizhi; Jiang, Yifei; Wang, Heye; Zhao, Yongfu; Xia, Liru

2018-03-01

Mycotoxins produced by different species of fungi may coexist in cereals and feedstuffs, and could be highly toxic for humans and animals. For quantification of multiple mycotoxins in cereals, we developed a paper-based mycotoxin immune-affinity array. First, paper-based microzone arrays were fabricated by photolithography. Then, monoclonal mycotoxin antibodies were added in a copolymerization reaction with a cross-linker to form an immune-affinity monolith on the paper-based microzone array. With use of a competitive immune-response format, paper-based mycotoxin immune-affinity arrays were successfully applied to detect mycotoxins in samples. The detection limits for deoxynivalenol, zearalenone, T-2 toxin, and HT-2 toxin were 62.7, 10.8, 0.36, and 0.23 μg·kg -1 , respectively, which meet relevant requirements for these compounds in food. The recovery rates were 81-86% for deoxynivalenol, 89-117% for zearalenone, 79-86% for T-2 toxin, and 78-83% for HT-2 toxin, and showed the paper-based immune-affinity arrays had good reproducibility. In summary, the paper-based mycotoxin immune-affinity array provides a sensitive, rapid, accurate, stable, and convenient platform for detection of multiple mycotoxins in agro-foods. Graphical abstract Paper-based immune-affinity monolithic array. DON deoxynivalenol, HT-2 HT-2 toxin, T-2 T-2 toxin, PEGDA polyethylene glycol diacrylate, ZEN zearalenone.

Kennicutt-Schmidt Relation Variety and Star-forming Cloud Fraction

Energy Technology Data Exchange (ETDEWEB)

Morokuma-Matsui, Kana [Chile Observatory, National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka-shi, Tokyo 181-8588 (Japan); Muraoka, Kazuyuki, E-mail: kana.matsui@nao.ac.jp [Department of Physical Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan)

2017-03-10

The observationally derived Kennicutt-Schmidt (KS) relation slopes differ from study to study, ranging from sublinear to superlinear. We investigate the KS-relation variety (slope and normalization) as a function of integrated intensity ratio, R {sub 31} = CO( J = 3–2)/CO( J = 1–0) using spatially resolved CO( J = 1–0), CO( J = 3–2), H i, H α, and 24 μ m data of three nearby spiral galaxies (NGC 3627, NGC 5055, and M83). We find that (1) the slopes for each subsample with a fixed R {sub 31} are shallower, but the slope for all data sets combined becomes steeper, (2) normalizations for high R {sub 31} subsamples tend to be high, (3) R {sub 31} correlates with star formation efficiency, therefore the KS relation depends on the distribution in R {sub 31}–Σ{sub gas} space of the samples: no Σ{sub gas} dependence of R {sub 31} results in a linear slope of the KS relation, whereas a positive correlation between Σ{sub gas} and R {sub 31} results in a superlinear slope of the KS relation, and (4) R {sub 31}–Σ{sub gas} distributions are different from galaxy to galaxy and within a galaxy: galaxies with prominent galactic structure tend to have large R {sub 31} and Σ{sub gas}. Our results suggest that the formation efficiency of a star-forming cloud from molecular gas is different among galaxies as well as within a galaxy, and it is one of the key factors inducing the variety in galactic KS relation.

Fragment-based quantum mechanical calculation of protein-protein binding affinities.

Science.gov (United States)

Wang, Yaqian; Liu, Jinfeng; Li, Jinjin; He, Xiao

2018-04-29

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Two distinct affinity binding sites for IL-1 on human cell lines

International Nuclear Information System (INIS)

Bensimon, C.; Wakasugi, N.; Tagaya, Y.; Takakura, K.; Yodoi, J.; Tursz, T.; Wakasugi, H.

1989-01-01

We used two human cell lines, NK-like YT-C3 and an EBV-containing B cell line, 3B6, as models to study the receptor(s) for IL-1. Two distinct types of saturable binding sites were found on both cell lines at 37 degrees C. Between 1 pM and 100 pM of 125I-IL-1-alpha concentration, saturable binding sites were detected on the YT-C3 cells with a K of 4 x 10(-11) M. The K found for the IL-1-alpha binding sites on 3B6 cells was 7.5 x 10(-11) M. An additional binding curve was detected above 100 pM on YT-C3 cells with a K of 7 x 10(-9) M and on 3B6 cells with a K of 5 x 10(-9) M. Scatchard plot analysis revealed 600 sites/cell with high affinity binding and 7000 sites/cell with low affinity for YT-C3 cells and 300 sites/cell with high affinity binding and 6000 sites/cell with low affinity for 3B6 cells. At 37 degrees C, the internalization of 125I-labeled IL-1 occurred via both high and low affinity IL-1R on both YT-C3 and 3B6 cells, whereas the rates of internalization for high affinity binding sites on YT-C3 cells were predominant in comparison to that of low affinity binding sites. In chemical cross-linking studies of 125 I-IL-1-alpha to 3B6 and YT-C3 cells, two protein bands were immunoprecipitated with Mr around 85 to 90 kDa leading to an estimation of the Mr of the IL-1R around 68 to 72 kDa. In similar experiments, the Mr found for the IL-1R expressed on the murine T cell line EL4 was slightly higher (around 80 kDa). Whether these distinct affinity binding sites are shared by a single molecule or by various chains remains to be elucidated

[The content of phenolic acids in the edible parts of selected varieties of apples].

Science.gov (United States)

Malik, Agnieszka; Kiczorowska, Bozena; Zdyb, Justyna

2009-01-01

Fruits and vegetables are essential sources of many nutritive substances which are necessary for normal function of the organism. One of the mostly consumed fruits in many European countries, including Poland is apples. The prohealthy properties of apples are associated with the contents of polyphenolic compounds, thus including in parts phenolic acids which have antioxidant properties. The concentration of these compounds depends on many factors such as variety climate and soil conditions, maturity as well as agro technical operations. The aim of this investigation was to compare the concentrations of phenolic acids and epicatechin in the varieties of apple Champion and Jonica, which were collected from different orchards around Lublin. The phenolic compounds were assayed using a Symmetry column carrier RP-C18 (Waters) integrated with a high pressure liquid chromatography apparatus. The dominant phenolic acids found in the Champion variety was chlorogenic acid, whereas in the Jonica variety, chlorogenic and homovanilic acids were the dominate once. The highest concentrations of chlorogenic acid was detected in the pulp of an apple (Jonica variety) collected from the orchards around the cities of Puławy and Lublin, whereas homovanilic acid was the highest in the other samples collected from the orchards in the vicinity of Stryjno and Góry Markuszowskie. Among the Jonica and Champion varieties of apples collected from various orchards in the vicinity of Lublin, the highest content of epicatechin (13,12 mg/kg) was found in the pulps of Champions variety collected in Puławy. In general, the Champion variety was the best source of phenolic acids and epicatechin compared to the Jonica variety independent of the harvest zone.

Channel normalization technique for speech recognition in mismatched conditions

CSIR Research Space (South Africa)

Kleynhans, N

2008-11-01

Full Text Available , where one wishes to use any available training data for a variety of purposes. Research into a new channel normalization (CN) technique for channel mismatched speech recognition is presented. A process of inverse linear filtering is used in order...

Accurate and sensitive quantification of protein-DNA binding affinity.

Science.gov (United States)

Rastogi, Chaitanya; Rube, H Tomas; Kribelbauer, Judith F; Crocker, Justin; Loker, Ryan E; Martini, Gabriella D; Laptenko, Oleg; Freed-Pastor, William A; Prives, Carol; Stern, David L; Mann, Richard S; Bussemaker, Harmen J

2018-04-17

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes. Copyright © 2018 the Author(s). Published by PNAS.

On singularities of lattice varieties

OpenAIRE

Mukherjee, Himadri

2013-01-01

Toric varieties associated with distributive lattices arise as a fibre of a flat degeneration of a Schubert variety in a minuscule. The singular locus of these varieties has been studied by various authors. In this article we prove that the number of diamonds incident on a lattice point $\\a$ in a product of chain lattices is more than or equal to the codimension of the lattice. Using this we also show that the lattice varieties associated with product of chain lattices is smooth.

[Study on discrimination of varieties of fire resistive coating for steel structure based on near-infrared spectroscopy].

Science.gov (United States)

Xue, Gang; Song, Wen-qi; Li, Shu-chao

2015-01-01

In order to achieve the rapid identification of fire resistive coating for steel structure of different brands in circulating, a new method for the fast discrimination of varieties of fire resistive coating for steel structure by means of near infrared spectroscopy was proposed. The raster scanning near infrared spectroscopy instrument and near infrared diffuse reflectance spectroscopy were applied to collect the spectral curve of different brands of fire resistive coating for steel structure and the spectral data were preprocessed with standard normal variate transformation(standard normal variate transformation, SNV) and Norris second derivative. The principal component analysis (principal component analysis, PCA)was used to near infrared spectra for cluster analysis. The analysis results showed that the cumulate reliabilities of PC1 to PC5 were 99. 791%. The 3-dimentional plot was drawn with the scores of PC1, PC2 and PC3 X 10, which appeared to provide the best clustering of the varieties of fire resistive coating for steel structure. A total of 150 fire resistive coating samples were divided into calibration set and validation set randomly, the calibration set had 125 samples with 25 samples of each variety, and the validation set had 25 samples with 5 samples of each variety. According to the principal component scores of unknown samples, Mahalanobis distance values between each variety and unknown samples were calculated to realize the discrimination of different varieties. The qualitative analysis model for external verification of unknown samples is a 10% recognition ration. The results demonstrated that this identification method can be used as a rapid, accurate method to identify the classification of fire resistive coating for steel structure and provide technical reference for market regulation.

Constraints on the affinity term for modeling long-term glass dissolution rates

International Nuclear Information System (INIS)

Bourcier, W.L.; Carroll, S.A.; Phillips, B.L.

1993-11-01

Predictions of long-term glass dissolution rates are highly dependent on the form of the affinity term in the rate expression. Analysis of the quantitative effect of saturation state on glass dissolution rate for CSG glass (a simple analog of SRL-165 glass), shows that a simple (1-Q/K) affinity term does not match experimental results. Our data at 100 degree C show that the data is better fit by an affinity term having the form (1 - (Q/K) 1 /σ) where σ = 10

Identification of an adeno-associated virus binding epitope for AVB sepharose affinity resin

Directory of Open Access Journals (Sweden)

Qiang Wang

Full Text Available Recent successes of adeno-associated virus (AAV–based gene therapy have created a demand for large-scale AAV vector manufacturing and purification techniques for use in clinical trials and beyond. During the development of purification protocols for rh.10, hu.37, AAV8, rh.64R1, AAV3B, and AAV9 vectors, based on a widely used affinity resin, AVB sepharose (GE, we found that, under the same conditions, different serotypes have different affinities to the resin, with AAV3B binding the best and AAV9 the poorest. Further analysis revealed a surface-exposed residue (amino acid number 665 in AAV8 VP1 numbering differs between the high-affinity AAV serotypes (serine in AAV3B, rh.10, and hu.37 and the low-affinity ones (asparagine in AAV8, rh.64R1, and AAV9. The residue locates within a surface-exposed, variable epitope flanked by highly conserved residues. The substitution of the epitope in AAV8, rh.64R1, and AAV9 with the corresponding epitope of AAV3B (SPAKFA resulted in greatly increased affinity to AVB sepharose with no reduction in the vectors’ in vitro potency. The presence of the newly identified AVB-binding epitope will be useful for affinity resin selection for the purification of novel AAV serotypes. It also suggests the possibility of vector engineering to yield a universal affinity chromatography purification method for multiple AAV serotypes.

Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags

DEFF Research Database (Denmark)

Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji

2014-01-01

Thioredoxins (Trx) are small redox proteins that reduce disulfide bonds in various target proteins and maintain cellular thiol redox control. Here, a thiol-specific labeling and affinity enrichment approach for identification and relative quantification of Trx target disulfides in complex protein...... reduction is determined by LC-MS/MS-based quantification of tryptic peptides labeled with "light" (12C) and "heavy" (13C) ICAT reagents. The methodology can be adapted to monitor the effect of different reductants or oxidants on the redox status of thiol/disulfide proteomes in biological systems....... extracts is described. The procedure utilizes the isotope-coded affinity tag (ICAT) reagents containing a thiol reactive iodoacetamide group and a biotin affinity tag to target peptides containing reduced cysteine residues. The identification of substrates for Trx and the extent of target disulfide...

Affinity purification of recombinant human plasminogen activator ...

African Journals Online (AJOL)

Affinity purification of recombinant human plasminogen activator from ... Screening antibody was performed using rhPA milk in an ELISA-elution assay. ... useful for purifying other tPA mutants or other novel recombinant milkderived proteins.

The Purification of a Blood Group A Glycoprotein: An Affinity Chromatography Experiment.

Science.gov (United States)

Estelrich, J.; Pouplana, R.

1988-01-01

Describes a purification process through affinity chromatography necessary to obtain specific blood group glycoproteins from erythrocytic membranes. Discusses the preparation of erythrocytic membranes, extraction of glycoprotein from membranes, affinity chromatography purification, determination of glycoproteins, and results. (CW)

The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair.

Science.gov (United States)

Breslin, Claire; Mani, Rajam S; Fanta, Mesfin; Hoch, Nicolas; Weinfeld, Michael; Caldecott, Keith W

2017-09-29

The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism.

Science.gov (United States)

Boughlala, Zakaria; Fonseca Guerra, Célia; Bickelhaupt, F Matthias

2016-06-01

We have analyzed the structure and bonding of gas-phase Cl-X and [HCl-X](+) complexes for X(+)= H(+), CH3 (+), Li(+), and Na(+), using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl(-) and HCl for the various cations. The Cl-X bond becomes longer and weaker along X(+) = H(+), CH3 (+), Li(+), and Na(+). Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn-Sham molecular orbital (KS-MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities.

Quantum deformation of the affine transformation algebra

International Nuclear Information System (INIS)

Aizawa, N.; Sato, Haru-Tada

1994-01-01

We discuss a quantum deformation of the affine transformation algebra in one-dimensional space. It is shown that the quantum algebra has a non-cocommutative Hopf algebra structure, simple realizations and quantum tensor operators. (orig.)

Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

International Nuclear Information System (INIS)

Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.; Horne, David A.; Williams, John C.

2016-01-01

An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex

Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

Energy Technology Data Exchange (ETDEWEB)

Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.; Horne, David A.; Williams, John C., E-mail: jcwilliams@coh.org [Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010 (United States)

2016-05-23

An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.

Spinal cord normalization in multiple sclerosis.

Science.gov (United States)

Oh, Jiwon; Seigo, Michaela; Saidha, Shiv; Sotirchos, Elias; Zackowski, Kathy; Chen, Min; Prince, Jerry; Diener-West, Marie; Calabresi, Peter A; Reich, Daniel S

2014-01-01

Spinal cord (SC) pathology is common in multiple sclerosis (MS), and measures of SC-atrophy are increasingly utilized. Normalization reduces biological variation of structural measurements unrelated to disease, but optimal parameters for SC volume (SCV)-normalization remain unclear. Using a variety of normalization factors and clinical measures, we assessed the effect of SCV normalization on detecting group differences and clarifying clinical-radiological correlations in MS. 3T cervical SC-MRI was performed in 133 MS cases and 11 healthy controls (HC). Clinical assessment included expanded disability status scale (EDSS), MS functional composite (MSFC), quantitative hip-flexion strength ("strength"), and vibration sensation threshold ("vibration"). SCV between C3 and C4 was measured and normalized individually by subject height, SC-length, and intracranial volume (ICV). There were group differences in raw-SCV and after normalization by height and length (MS vs. HC; progressive vs. relapsing MS-subtypes, P normalization by length (EDSS:r = -.43; MSFC:r = .33; strength:r = .38; vibration:r = -.40), and height (EDSS:r = -.26; MSFC:r = .28; strength:r = .22; vibration:r = -.29), but diminished with normalization by ICV (EDSS:r = -.23; MSFC:r = -.10; strength:r = .23; vibration:r = -.35). In relapsing MS, normalization by length allowed statistical detection of correlations that were not apparent with raw-SCV. SCV-normalization by length improves the ability to detect group differences, strengthens clinical-radiological correlations, and is particularly relevant in settings of subtle disease-related SC-atrophy in MS. SCV-normalization by length may enhance the clinical utility of measures of SC-atrophy. Copyright © 2014 by the American Society of Neuroimaging.

IA-2 autoantibody affinity in children at risk for type 1 diabetes.

Science.gov (United States)

Krause, Stephanie; Chmiel, Ruth; Bonifacio, Ezio; Scholz, Marlon; Powell, Michael; Furmaniak, Jadwiga; Rees Smith, Bernard; Ziegler, Anette-G; Achenbach, Peter

2012-12-01

Autoantibodies to insulinoma-associated protein 2 (IA-2A) are associated with increased risk for type 1 diabetes. Here we examined IA-2A affinity and epitope specificity to assess heterogeneity in response intensity in relation to pathogenesis and diabetes risk in 50 children who were prospectively followed from birth. At first IA-2A appearance, affinity ranged from 10(7) to 10(11)L/mol and was high (>1.0×10(9)L/mol) in 41 (82%) children. IA-2A affinity was not associated with epitope specificity or HLA class II haplotype. On follow-up, affinity increased or remained high, and IA-2A were commonly against epitopes within the protein tyrosine phosphatase-like IA-2 domain and the homologue protein IA-2β. IA-2A were preceded or accompanied by other islet autoantibodies in 49 (98%) children, of which 34 progressed to diabetes. IA-2A affinity did not stratify diabetes risk. In conclusion, the IA-2A response in children is intense with rapid maturation against immunogenic epitopes and a strong association with diabetes development. Copyright © 2012 Elsevier Inc. All rights reserved.

Lucerne varieties for continuous grazing

DEFF Research Database (Denmark)

Søegaard, Karen

2012-01-01

severe grazing with heifers in two cutting/grazing managements. Two new varieties, Verbena and Camporegio, and an older variety Luzelle were established in 2009 in pure stands and in two different mixtures with perennial ryegrass (Lolium perenne). Camporegio had the lowest yield, the lowest competitive...... strength, the lowest plant density in spring, and the density was most reduced during grazing. The results could not confirm significant differences between the new and the older varieties. The results for Luzelle were generally between Verbena and Camporegio. The varieties did not differ in herbage...

Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada.

Science.gov (United States)

Jeffery, Nicholas W; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J

2011-01-01

The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.

Complex Algebraic Varieties

CERN Document Server

Peternell, Thomas; Schneider, Michael; Schreyer, Frank-Olaf

1992-01-01

The Bayreuth meeting on "Complex Algebraic Varieties" focussed on the classification of algebraic varieties and topics such as vector bundles, Hodge theory and hermitian differential geometry. Most of the articles in this volume are closely related to talks given at the conference: all are original, fully refereed research articles. CONTENTS: A. Beauville: Annulation du H(1) pour les fibres en droites plats.- M. Beltrametti, A.J. Sommese, J.A. Wisniewski: Results on varieties with many lines and their applications to adjunction theory.- G. Bohnhorst, H. Spindler: The stability of certain vector bundles on P(n) .- F. Catanese, F. Tovena: Vector bundles, linear systems and extensions of (1).- O. Debarre: Vers uns stratification de l'espace des modules des varietes abeliennes principalement polarisees.- J.P. Demailly: Singular hermitian metrics on positive line bundles.- T. Fujita: On adjoint bundles of ample vector bundles.- Y. Kawamata: Moderate degenerations of algebraic surfaces.- U. Persson: Genus two fibra...

Influence of bone affinity on the skeletal distribution of fluorescently labeled bisphosphonates in vivo.

Science.gov (United States)

Roelofs, Anke J; Stewart, Charlotte A; Sun, Shuting; Błażewska, Katarzyna M; Kashemirov, Boris A; McKenna, Charles E; Russell, R Graham G; Rogers, Michael J; Lundy, Mark W; Ebetino, Frank H; Coxon, Fraser P

2012-04-01

Bisphosphonates are widely used antiresorptive drugs that bind to calcium. It has become evident that these drugs have differing affinities for bone mineral; however, it is unclear whether such differences affect their distribution on mineral surfaces. In this study, fluorescent conjugates of risedronate, and its lower-affinity analogues deoxy-risedronate and 3-PEHPC, were used to compare the localization of compounds with differing mineral affinities in vivo. Binding to dentine in vitro confirmed differences in mineral binding between compounds, which was influenced predominantly by the characteristics of the parent compound but also by the choice of fluorescent tag. In growing rats, all compounds preferentially bound to forming endocortical as opposed to resorbing periosteal surfaces in cortical bone, 1 day after administration. At resorbing surfaces, lower-affinity compounds showed preferential binding to resorption lacunae, whereas the highest-affinity compound showed more uniform labeling. At forming surfaces, penetration into the mineralizing osteoid was found to inversely correlate with mineral affinity. These differences in distribution at resorbing and forming surfaces were not observed at quiescent surfaces. Lower-affinity compounds also showed a relatively higher degree of labeling of osteocyte lacunar walls and labeled lacunae deeper within cortical bone, indicating increased penetration of the osteocyte canalicular network. Similar differences in mineralizing surface and osteocyte network penetration between high- and low-affinity compounds were evident 7 days after administration, with fluorescent conjugates at forming surfaces buried under a new layer of bone. Fluorescent compounds were incorporated into these areas of newly formed bone, indicating that "recycling" had occurred, albeit at very low levels. Taken together, these findings indicate that the bone mineral affinity of bisphosphonates is likely to influence their distribution within the

On dynamic equations for interaction of the affinor field with affine connection

International Nuclear Information System (INIS)

Pestov, A.B.

1987-01-01

The Lagrangian of interaction of an affinor field with an affine connection is constructed and the equations of motion and conservation laws are derived. It is shown that there exists a symmetric conserved tensor of the affine-connection energy-momentum

Affinity for Quantitative Tools: Undergraduate Marketing Students Moving beyond Quantitative Anxiety

Science.gov (United States)

Tarasi, Crina O.; Wilson, J. Holton; Puri, Cheenu; Divine, Richard L.

2013-01-01

Marketing students are known as less likely to have an affinity for the quantitative aspects of the marketing discipline. In this article, we study the reasons why this might be true and develop a parsimonious 20-item scale for measuring quantitative affinity in undergraduate marketing students. The scale was administered to a sample of business…

Modifiers of hemoglobin/oxygen affinity as sensitizers of tumors to radiation

International Nuclear Information System (INIS)

Hirst, D.G.; Wood, P.J.

1987-01-01

A powerful mechanism in the control of oxygen delivery to tissues is the allosteric modification of hemoglobin. Increased or decreased release of oxygen can be achieved by altering the affinity of hemoglobin for oxygen. Several studies have shown that tumor radiosensitivity is dependent on this relationship. The authors studied affinity changes produced in two distinctly different ways. Tumor bearing mice were given isovolemic exchange blood transfusions with the blood from donor mice which had been exposed to abnormal oxygen tensions, leading to increased or slightly decreased levels of 2,3-diphosphoglycerate (2,3 DPG) in their blood. When the recipient mice were irradiated, those receiving the blood with higher 2,3 DPG levels showed greater tumor sensitivity to radiation. An alternative strategy is the use of drugs which directly alter hemoglobin/oxygen affinity. The authors studied three antihyperlipoproteinemia drugs, all of which have produced markedly reduced affinities in vivo. Preliminary data indicate that the radiosensitization produced by at least one of these compounds is less than would have been expected from the 2,3 DPG experiments

Solitons and the energy-momentum tensor for affine Toda theory

Science.gov (United States)

Olive, D. I.; Turok, N.; Underwood, J. W. R.

1993-07-01

Following Leznov and Saveliev, we present the general solution to Toda field theories of conformal, affine or conformal affine type, associated with a simple Lie algebra g. These depend on a free massless field and on a group element. By putting the former to zero, soliton solutions to the affine Toda theories with imaginary coupling constant result with the soliton data encoded in the group element. As this requires a reformulation of the affine Kac-Moody algebra closely related to that already used to formulate the physical properties of the particle excitations, including their scattering matrices, a unified treatment of particles and solitons emerges. The physical energy—momentum tensor for a general solution is broken into a total derivative plus a part dependent only on the derivatives of the free field. Despite the non-linearity of the field equations and their complex nature the energy and momentum of the N-soliton solution is shown to be real, equalling the sum of contributions from the individual solitons. There are rank-g species of soliton, with masses given by a generalisation of a formula due to Hollowood, being proportional to the components of the left Perron-Frobenius eigenvector of the Cartan matrix of g.

Solitons and the energy-momentum tensor for affine Toda theory

International Nuclear Information System (INIS)

Olive, D.I.; Turok, N.; Underwood, J.W.R.

1993-01-01

Following Leznov and Saveliev, we present the general solution to Toda field theories of conformal, affine or conformal affine type, associated with a simple Lie algebra g. These depend on a free massless field and on a group element. By putting the former to zero, soliton solutions to the affine Toda theories with imaginary coupling constant result with the soliton data encoded in the group element. As this requires a reformulation of the affine Kac-Moodyy algebra closely related to that already used to formulate the physical properties of the particle excitations, including their scattering matrices, a unified treatment of particles and solitons emerges. The physical energy-momentum tensor for a general solution is broken into a total derivative plus a part dependent only on the derivatives of the free field. Despite the non-linearity of the field equations and their complex nature the energy and momentum of the N-soliton solution is shown to be real, equalling the sum of contributions from the individual solitons. There are rank-g species of soliton, with masses given by a generalisation of a formula due to Hollowood, being proportional to the components of the left Perron-Frobenius eigenvector of the Cartan matrix of g. (orig.)

Affine invariants of convex polygons.

Science.gov (United States)

Flusser, Jan

2002-01-01

In this correspondence, we prove that the affine invariants, for image registration and object recognition, proposed recently by Yang and Cohen (see ibid., vol.8, no.7, p.934-46, July 1999) are algebraically dependent. We show how to select an independent and complete set of the invariants. The use of this new set leads to a significant reduction of the computing complexity without decreasing the discrimination power.

Specific capture of uranyl protein targets by metal affinity chromatography

International Nuclear Information System (INIS)

Basset, C.; Dedieu, A.; Guerin, P.; Quemeneur, E.; Meyer, D.; Vidaud, C.

2008-01-01

To improve general understanding of biochemical mechanisms in the field of uranium toxicology, the identification of protein targets needs to be intensified. Immobilized metal affinity chromatography (IMAC) has been widely developed as a powerful tool for capturing metal binding proteins from biological extracts. However uranyl cations (UO 2 2+ ) have particular physico-chemical characteristics which prevent them from being immobilized on classical metal chelating supports. We report here on the first development of an immobilized uranyl affinity chromatography method, based on the cation-exchange properties of amino-phosphonate groups for uranyl binding. The cation distribution coefficient and loading capacity on the support were determined. Then the stability of the uranyl-bonded phase under our chromatographic conditions was optimized to promote affinity mechanisms. The successful enrichment of uranyl binding proteins from human serum was then proven using proteomic and mass spectral analysis. (authors)

DNA-repair, cell killing and normal tissue damage

International Nuclear Information System (INIS)

Dahm-Daphi, J.; Dikomey, E.; Brammer, I.

1998-01-01

Background: Side effects of radiotherapy in normal tissue is determined by a variety of factors of which cellular and genetic contributions are described here. Material and methods: Review. Results: Normal tissue damage after irradiation is largely due to loss of cellular proliferative capacity. This can be due to mitotic cell death, apoptosis, or terminal differentiation. Dead or differentiated cells release cytokines which additionally modulate the tissue response. DNA damage, in particular non-reparable or misrepaired double-strand breaks are considered the basic lesion leading to G1-arrest and ultimately to cell inactivation. Conclusion: Evidence for genetic bases of normal tissue response, cell killing and DNA-repair capacity is presented. However, a direct link of all 3 endpoints has not yet been proved directly. (orig.) [de

Use of Intrinsic Viscosity for evaluation of polymer-solvent affinity

DEFF Research Database (Denmark)

Marani, Debora; Hjelm, Johan; Wandel, Marie

2013-01-01

The objective of the current paper was to define a rheological method for the study of the solvent/binder affinity. The adopted strategy involves the study of the intrinsic viscosity [η] of polymer solutions. [η] was estimated via an extrapolation procedure using the Huggins and Kramer equations....... The intrinsic viscosity and the Mark-Houwink shape parameter were estimated for the three polymers and used as criteria for estimating the polymer/solvent affinity....

Normal postperative computed tomography findings after avariety of pancreatic surgeries

Energy Technology Data Exchange (ETDEWEB)

Seo, Ji Won; Hwang, Ho Kyoung; Lee, Min Wook; Kim, Ki Whang; Kang, Chang Moo; Kim, Myeong Jin; Chung, Yong Eun [Yonsei University College of Medicine, Seoul (Korea, Republic of)

2017-04-15

Pancreatic surgery remains the only curative treatment for pancreatic neoplasms, and plays an important role in the management of medically intractable diseases. Since the original Whipple operation in the 20th century, surgical techniques have advanced, resulting in decreased postoperative complications and better clinical outcomes. Normal postoperative imaging findings vary greatly depending on the surgical technique used. Radiologists are required to be familiar with the normal postoperative imaging findings, in order to distinguish from postoperative complications or tumor recurrence. In this study, we briefly review a variety of surgical techniques for the pancreas, and present the normal postoperative computed tomography findings.

AHP 44: THE VITALITY OF KHAMS TIBETAN VARIETIES IN WEIXI COUNTY

Directory of Open Access Journals (Sweden)

Hiroyuki Suzuki

2017-02-01

Full Text Available This article presents an overview of the multilingual situation of Weixi County, Yunnan Province, in the southeastern Tibetosphere, and discusses the vitality of several Tibetan varieties currently used by Tibetans in Weixi who live alongside Naxi, Lisu, Bai, Yi, and Pumi people. In this borderland area, most Tibetans are multilingual, speaking Lisu and/or Naxi in addition to Yunnanese, a dialect of Mandarin. I focus on two local Tibetan varieties: Gagatang and Tacheng. The former has become endangered, while many speakers still use the latter. Intergenerational transmission of Gagatang appears to be declining, and community attitudes towards the language are increasingly negative, whereas Tacheng Tibetan appears relatively vital, speakers of this variety have strong positive attitudes towards their mother tongue, and generally consider multilingualism to be normal. I identify two factors that contribute to Gagatang's endangerment. First is the local demographic context, where none of the minority languages are supported by the majority of villagers. A second factor is the lack of strong identities attached to local languages. This research suggests that minority languages are more valued in communities that also value ethnic diversity, thus suggesting that a key to maintaining linguistic diversity in the Tibetosphere is the retention of diverse identities.

Preparation of Affinity Column Based on Zr4+ Ion for Phosphoproteins Isolation

International Nuclear Information System (INIS)

Lee, Seon Mi; Bae, In Ae; Park, Jung Hyen; Kim, Tae Dong; Choi, Seong Ho

2009-01-01

This paper has described about preparation of Zr 4+ affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr 4+ ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr 4+ -immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr 4+ affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr 4+ affinity polymeric microsphere by liquid chromatography. This Zr 4+ affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography

Complex multi-projective variety and entanglement

International Nuclear Information System (INIS)

Heydari, Hoshang; Bjoerk, Gunnar

2005-01-01

In this paper, we will show that a vanishing generalized concurrence of a separable state can be seen as an algebraic variety called the Segre variety. This variety defines a quadric space which gives a geometric picture of separable states. For pure, bi- and three-partite states the variety equals the generalized concurrence. Moreover, we generalize the Segre variety to a general multipartite state by relating to a quadric space defined by two-by-two subdeterminants

The geometric and arithmetic volume of Shimura varieties of orthogonal type

CERN Document Server

Hörmann, Fritz

2015-01-01

This book outlines a functorial theory of integral models of (mixed) Shimura varieties and of their toroidal compactifications, for odd primes of good reduction. This is the integral version, developed in the author's thesis, of the theory invented by Deligne and Pink in the rational case. In addition, the author develops a theory of arithmetic Chern classes of integral automorphic vector bundles with singular metrics using the work of Burgos, Kramer and Kühn. The main application is calculating arithmetic volumes or "heights" of Shimura varieties of orthogonal type using Borcherds' famous modular forms with their striking product formula-an idea due to Bruinier-Burgos-Kühn and Kudla. This should be seen as an Arakelov analogue of the classical calculation of volumes of orthogonal locally symmetric spaces by Siegel and Weil. In the latter theory, the volumes are related to special values of (normalized) Siegel Eisenstein series. In this book, it is proved that the Arakelov analogues are related to special d...

Einstein’s gravity from a polynomial affine model

Science.gov (United States)

Castillo-Felisola, Oscar; Skirzewski, Aureliano

2018-03-01

We show that the effective field equations for a recently formulated polynomial affine model of gravity, in the sector of a torsion-free connection, accept general Einstein manifolds—with or without cosmological constant—as solutions. Moreover, the effective field equations are partially those obtained from a gravitational Yang–Mills theory known as Stephenson–Kilmister–Yang theory. Additionally, we find a generalization of a minimally coupled massless scalar field in General Relativity within a ‘minimally’ coupled scalar field in this affine model. Finally, we present a brief (perturbative) analysis of the propagators of the gravitational theory, and count the degrees of freedom. For completeness, we prove that a Birkhoff-like theorem is valid for the analyzed sector.

Establishing the proteome of normal human cerebrospinal fluid.

Directory of Open Access Journals (Sweden)

Steven E Schutzer

2010-06-01

Full Text Available Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal.We applied immunoaffinity separation and high sensitivity and resolution liquid chromatography-mass spectrometry to examine CSF from healthy normal individuals. 2630 proteins in CSF from normal subjects were identified, of which 56% were CSF-specific, not found in the much larger set of 3654 proteins we have identified in plasma. We also examined CSF from groups of subjects previously examined by others as surrogates for normals where neurologic symptoms warranted a lumbar puncture but where clinical laboratory were reported as normal. We found statistically significant differences between their CSF proteins and our non-neurological normals. We also examined CSF from 10 volunteer subjects who had lumbar punctures at least 4 weeks apart and found that there was little variability in CSF proteins in an individual as compared to subject to subject.Our results represent the most comprehensive characterization of true normal CSF to date. This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features.

Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications.

Science.gov (United States)

Hage, David S

2017-06-01

The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. © 2016 American Association for Clinical Chemistry.

Masturbation, sexuality, and adaptation: normalization in adolescence.

Science.gov (United States)

Shapiro, Theodore

2008-03-01

During adolescence the central masturbation fantasy that is formulated during childhood takes its final form and paradoxically must now be directed outward for appropriate object finding and pair matching in the service of procreative aims. This is a step in adaptation that requires a further developmental landmark that I have called normalization. The path toward airing these private fantasies is facilitated by chumship relationships as a step toward further exposure to the social surround. Hartmann's structuring application of adaptation within psychoanalysis is used as a framework for understanding the process that simultaneously serves intrapsychic and social demands and permits goals that follow evolutionary principles. Variations in the normalization process from masturbatory isolation to a variety of forms of sexual socialization are examined in sociological data concerning current adolescent sexual behavior and in case examples that indicate some routes to normalized experience and practice.

The affine quantum gravity programme

International Nuclear Information System (INIS)

Klauder, John R

2002-01-01

The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix { g-hat ab (x)} composed of the spatial components of the local metric operator. On spectral grounds, canonical commutation relations are incompatible with this principle, and they must be replaced by noncanonical, affine commutation relations. Due to the partial second-class nature of the quantum gravitational constraints, it is advantageous to use the recently developed projection operator method, which treats all quantum constraints on an equal footing. Using this method, enforcement of regularized versions of the gravitational operator constraints is formulated quite naturally by means of a novel and relatively well-defined functional integral involving only the same set of variables that appears in the usual classical formulation. It is anticipated that skills and insight to study this formulation can be developed by studying special, reduced-variable models that still retain some basic characteristics of gravity, specifically a partial second-class constraint operator structure. Although perturbatively nonrenormalizable, gravity may possibly be understood nonperturbatively from a hard-core perspective that has proved valuable for specialized models. Finally, developing a procedure to pass to the genuine physical Hilbert space involves several interconnected steps that require careful coordination

Sugawara construction for affine SL(N,1)

International Nuclear Information System (INIS)

Henningson, M.

1990-01-01

We investigate the sl(N,1) superalgebras, their affine extensions and their representations. This is used to perform a Sugawara construction of the Virasoro algebra. The allowed values of the conformal anomaly and the conformal dimension are computed. (orig.)

Normal modes and continuous spectra

International Nuclear Information System (INIS)

Balmforth, N.J.; Morrison, P.J.

1994-12-01

The authors consider stability problems arising in fluids, plasmas and stellar systems that contain singularities resulting from wave-mean flow or wave-particle resonances. Such resonances lead to singularities in the differential equations determining the normal modes at the so-called critical points or layers. The locations of the singularities are determined by the eigenvalue of the problem, and as a result, the spectrum of eigenvalues forms a continuum. They outline a method to construct the singular eigenfunctions comprising the continuum for a variety of problems

High Affinity, Developability and Functional Size: The Holy Grail of Combinatorial Antibody Library Generation

Directory of Open Access Journals (Sweden)

Kathrin Tissot

2011-05-01

Full Text Available Since the initial description of phage display technology for the generation of human antibodies, a variety of selection methods has been developed. The most critical parameter for all in vitro-based approaches is the quality of the antibody library. Concurrent evolution of the libraries has allowed display and selection technologies to reveal their full potential. They come in different flavors, from naïve to fully synthetic and differ in terms of size, quality, method of preparation, framework and CDR composition. Early on, the focus has mainly been on affinities and thus on library size and diversity. Subsequently, the increased awareness of developability and cost of goods as important success factors has spurred efforts to generate libraries with improved biophysical properties and favorable production characteristics. More recently a major focus on reduction of unwanted side effects through reduced immunogenicity and improved overall biophysical behavior has led to a re-evaluation of library design.

High-throughput fragment screening by affinity LC-MS.

Science.gov (United States)

Duong-Thi, Minh-Dao; Bergström, Maria; Fex, Tomas; Isaksson, Roland; Ohlson, Sten

2013-02-01

Fragment screening, an emerging approach for hit finding in drug discovery, has recently been proven effective by its first approved drug, vemurafenib, for cancer treatment. Techniques such as nuclear magnetic resonance, surface plasmon resonance, and isothemal titration calorimetry, with their own pros and cons, have been employed for screening fragment libraries. As an alternative approach, screening based on high-performance liquid chromatography separation has been developed. In this work, we present weak affinity LC/MS as a method to screen fragments under high-throughput conditions. Affinity-based capillary columns with immobilized thrombin were used to screen a collection of 590 compounds from a fragment library. The collection was divided into 11 mixtures (each containing 35 to 65 fragments) and screened by MS detection. The primary screening was performed in 3500 fragments per day). Thirty hits were defined, which subsequently entered a secondary screening using an active site-blocked thrombin column for confirmation of specificity. One hit showed selective binding to thrombin with an estimated dissociation constant (K (D)) in the 0.1 mM range. This study shows that affinity LC/MS is characterized by high throughput, ease of operation, and low consumption of target and fragments, and therefore it promises to be a valuable method for fragment screening.

Gaussian and Affine Approximation of Stochastic Diffusion Models for Interest and Mortality Rates

Directory of Open Access Journals (Sweden)

Marcus C. Christiansen

2013-10-01

Full Text Available In the actuarial literature, it has become common practice to model future capital returns and mortality rates stochastically in order to capture market risk and forecasting risk. Although interest rates often should and mortality rates always have to be non-negative, many authors use stochastic diffusion models with an affine drift term and additive noise. As a result, the diffusion process is Gaussian and, thus, analytically tractable, but negative values occur with positive probability. The argument is that the class of Gaussian diffusions would be a good approximation of the real future development. We challenge that reasoning and study the asymptotics of diffusion processes with affine drift and a general noise term with corresponding diffusion processes with an affine drift term and an affine noise term or additive noise. Our study helps to quantify the error that is made by approximating diffusive interest and mortality rate models with Gaussian diffusions and affine diffusions. In particular, we discuss forward interest and forward mortality rates and the error that approximations cause on the valuation of life insurance claims.

High affinity hemoglobin and Parkinson's disease.

Science.gov (United States)

Graham, Jeffrey; Hobson, Douglas; Ponnampalam, Arjuna

2014-12-01

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra (SN) region of the midbrain. Oxidative damage in this region has been shown to play an important role in the pathogenesis of this disease. Human neurons have been discovered to contain hemoglobin, with an increased concentration seen in the neurons of the SN. High affinity hemoglobin is a clinical entity resulting from mutations that create a functional increase in the binding of hemoglobin to oxygen and an inability to efficiently unload it to tissues. This can result in a number of metabolic compensatory changes, including an elevation in circulating hemoglobin and an increase in the molecule 2,3-diphosphoglycerate (2,3-DPG). Population based studies have revealed that patients with PD have elevated hemoglobin as well as 2,3-DPG levels. Based on these observations, we hypothesize that the oxidative damage seen in PD is related to an underlying high affinity hemoglobin subtype. Copyright © 2014 Elsevier Ltd. All rights reserved.

Online Normalization Algorithm for Engine Turbofan Monitoring

Science.gov (United States)

2014-10-02

Online Normalization Algorithm for Engine Turbofan Monitoring Jérôme Lacaille 1 , Anastasios Bellas 2 1 Snecma, 77550 Moissy-Cramayel, France...understand the behavior of a turbofan engine, one first needs to deal with the variety of data acquisition contexts. Each time a set of measurements is...it auto-adapts itself with piecewise linear models. 1. INTRODUCTION Turbofan engine abnormality diagnosis uses three steps: reduction of

Food and value motivation: Linking consumer affinities to different types of food products.

Science.gov (United States)

de Boer, Joop; Schösler, Hanna

2016-08-01

This study uses the consumer affinity concept to examine the multiple motives that may shape consumers' relationships with food. The concept was applied in a study on four broad product types in the Netherlands, which cover a wide range of the market and may each appeal to consumers with different affinities towards foods. These product types may be denoted as 'conventional', 'efficient', 'gourmet' and 'pure'. A comparative analysis, based on Higgins' Regulatory Focus Theory, was performed to examine whether food-related value motivations could explain different consumer affinities for these product types. The affinities of consumers were measured by means of a non-verbal, visual presentation of four samples of food products in a nationwide survey (n = 742) among consumers who were all involved in food purchasing and/or cooking. The affinities found could be predicted fairly well from a number of self-descriptions relating to food and eating, which expressed different combinations of type of value motivation and involvement with food. The analysis demonstrated the contrasting role of high and low involvement as well as the potential complementarity of promotion- and prevention-focused value motivation. It is suggested that knowledge of the relationships between product types, consumer affinities and value motivation can help improve the effectiveness of interventions that seek to promote healthy and sustainable diets in developed countries. Copyright © 2016 Elsevier Ltd. All rights reserved.

Providing affinity

DEFF Research Database (Denmark)

Guglielmi, Michel; Johannesen, Hl

2004-01-01

, Essex, Hertfordshire, Norfolk and Suffolk. Research found that there was a lack of identity or sense of belonging and nothing anchoring people to the region as a whole. Common affinity is somehow forced to the people of East England and thereby we came to the conclusion that a single landmark...... and potential situations but also virtual events that calls for an undeterminated process of resolution. This process is activated by the user who co-produces the actualisation as an answer to a virtual reality that we defined at the first place. The potential situations or the possible it is a fantomatic real....... The possible is like the real. It is determinated and it only lakes existence. While the possible is already made, the virtual is like a problematic which needs to be resolved and actualized. Our installations are based on high tech interactivity where we use sensors and remote communication to offer a sense...

Haemoglobin Pierre-Benite--a high affinity variant associated with relative polycythaemia.

Science.gov (United States)

Beard, M E; Potter, H C; Spearing, R L; Brennan, S O

2001-12-01

This is the second reported example of Hb Pierre--Benite (beta90 Glu-->Asp). This mutation is associated with increased oxygen affinity and polycythaemia. No instability was found and there was no charge shift detected by cellulose acetate electrophoresis at pH 8.3. The mutation was however, clearly indicated by electrospray ionization mass spectrometry (ESI MS), which showed an abnormal beta chain with a 14 Da decrease in mass. Blood volume studies documented a relative rather than a true polycythaemia and this finding has been reported in at least two other high affinity haemoglobin variants--Hb Heathrow and Hb Rahere. This finding led to delay in diagnosis because high oxygen affinity variants are conventionally considered to cause a true polycythaemia.

Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals.

Science.gov (United States)

Wright, Traver J; Davis, Randall W

2015-07-01

Myoglobin (Mb) is an oxygen binding protein found in vertebrate skeletal muscle, where it facilitates intracellular transport and storage of oxygen. This protein has evolved to suit unique physiological needs in the muscle of diving vertebrates that express Mb at much greater concentrations than their terrestrial counterparts. In this study, we characterized Mb oxygen affinity (P50) from 25 species of aquatic and terrestrial birds and mammals. Among diving species, we tested for correlations between Mb P50 and routine dive duration. Across all species examined, Mb P50 ranged from 2.40 to 4.85 mmHg. The mean P50 of Mb from terrestrial ungulates was 3.72±0.15 mmHg (range 3.70-3.74 mmHg). The P50 of cetaceans was similar to terrestrial ungulates ranging from 3.54 to 3.82 mmHg, with the exception of the melon-headed whale, which had a significantly higher P50 of 4.85 mmHg. Among pinnipeds, the P50 ranged from 3.23 to 3.81 mmHg and showed a trend for higher oxygen affinity in species with longer dive durations. Among diving birds, the P50 ranged from 2.40 to 3.36 mmHg and also showed a trend of higher affinities in species with longer dive durations. In pinnipeds and birds, low Mb P50 was associated with species whose muscles are metabolically active under hypoxic conditions associated with aerobic dives. Given the broad range of potential globin oxygen affinities, Mb P50 from diverse vertebrate species appears constrained within a relatively narrow range. High Mb oxygen affinity within this range may be adaptive for some vertebrates that make prolonged dives. © 2015. Published by The Company of Biologists Ltd.

Proadifen-sensitive high affinity binding of 3H-alaproclate to liver membranes

International Nuclear Information System (INIS)

Ross, S.B.

1987-01-01

3 H-alaproclate, a selective 5 h ydroxytryptamine uptake inhibitor, was found to bind to microsomal membranes from the rat liver with high affinity (K D -=3 nM) and large capacity (B max about 2 nmol/g liver). This binding was stereoselective since S-( - )-alaproclate was 30 times more potent than the R-( + )-enantiomer to displace the 3 H-labelled racemate. Proadifen (SKF 525A), an inhibitor of cytochrome P-450, displaced the 3 H-alaproclate binding with the same, high affinity (K i =3 nM) as alaproclate itself. Repeated treatment with phenobarbital sodium (5x75 mg/kg intraperitoneally) increased the number of alaproclate binding sites 7-8 times without changing the affinity. However, most of the phenobarbital induced 3 H-alaproclate binding was not displaceable by proadifen, showing the presence of at least two different high affinity binding sites. The possible involvement of cytochrome P-450 in the alaproclate binding is discussed. (author)

Novosadski golozrni, a spring oat variety

Directory of Open Access Journals (Sweden)

Pržulj Novo

2001-01-01

Full Text Available The naked oat variety Novosadski golozrni was developed from a cross between the variety Adam and a spring-type naked oat line from Canada. The variety is early, medium tall, with excellent resistance to lodging. The yield of Novosadski golozrni is 30-40% lower than that of the hulled standard and it is to the largest measure dependent on the interaction variety x year x location. The variety has high contents of proteins and fats (19.2% DM and 6.2% DM, respectively and a low cellulose content (2.8% DM. .

Ferromagnetic Levan Composite: An Affinity Matrix to Purify Lectin

Directory of Open Access Journals (Sweden)

Renata Angeli

2009-01-01

Full Text Available A simple and inexpensive procedure used magnetite and levan to synthesize a composite recovered by a magnetic field. Lectins from Canavalia ensiformis (Con A and Cratylia mollis (Cramoll 1 and Cramoll 1,4 did bind specifically to composite. The magnetic property of derivative favored washing out contaminating proteins and recovery of pure lectins with glucose elution. Cramoll 1 was purified by this affinity binding procedure in two steps instead of a previous three-step protocol with ammonium sulfate fractionation, affinity chromatography on Sephadex G-75, and ion exchange chromatography through a CM-cellulose column.

It's the peptide-MHC affinity, stupid.

Science.gov (United States)

Kammertoens, Thomas; Blankenstein, Thomas

2013-04-15

Adoptively transferred T cells can reject large established tumors, but recurrence due to escape variants frequently occurs. In this issue of Cancer Cell, Engels et al. demonstrate that the affinity of the target peptide to the MHC molecule determines whether large tumors will relapse following adoptive T cell therapy. Copyright © 2013 Elsevier Inc. All rights reserved.

Engineering a novel multifunctional green fluorescent protein tag for a wide variety of protein research.

Directory of Open Access Journals (Sweden)

Takuya Kobayashi

Full Text Available BACKGROUND: Genetically encoded tag is a powerful tool for protein research. Various kinds of tags have been developed: fluorescent proteins for live-cell imaging, affinity tags for protein isolation, and epitope tags for immunological detections. One of the major problems concerning the protein tagging is that many constructs with different tags have to be made for different applications, which is time- and resource-consuming. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a novel multifunctional green fluorescent protein (mfGFP tag which was engineered by inserting multiple peptide tags, i.e., octa-histidine (8xHis, streptavidin-binding peptide (SBP, and c-Myc tag, in tandem into a loop of GFP. When fused to various proteins, mfGFP monitored their localization in living cells. Streptavidin agarose column chromatography with the SBP tag successfully isolated the protein complexes in a native form with a high purity. Tandem affinity purification (TAP with 8xHis and SBP tags in mfGFP further purified the protein complexes. mfGFP was clearly detected by c-Myc-specific antibody both in immunofluorescence and immuno-electron microscopy (EM. These findings indicate that mfGFP works well as a multifunctional tag in mammalian cells. The tag insertion was also successful in other fluorescent protein, mCherry. CONCLUSIONS AND SIGNIFICANCE: The multifunctional fluorescent protein tag is a useful tool for a wide variety of protein research, and may have the advantage over other multiple tag systems in its higher expandability and compatibility with existing and future tag technologies.

Bowman Capsule Volume and Related Factors in Adults With Normal Renal Function

Directory of Open Access Journals (Sweden)

Takaya Sasaki

2018-03-01

Conclusion: In the normal adult kidney, there may be an optimal BV to GV ratio for maintaining effective filtration in a variety of clinical situations, including advanced age, obesity, and hypertension.

Color and Contrast Enhancement by Controlled Piecewise Affine Histogram Equalization

Directory of Open Access Journals (Sweden)

Jose-Luis Lisani

2012-10-01

Full Text Available This paper presents a simple contrast enhancement algorithm based on histogram equalization (HE. The proposed algorithm performs a piecewise affine transform of the intensity levels of a digital image such that the new cumulative distribution function will be approximately uniform (as with HE, but where the stretching of the range is locally controlled to avoid brutal noise enhancement. We call this algorithm Piecewise Affine Equalization (PAE. Several experiments show that, in general, the new algorithm improves HE results.

Salt modulates the stability and lipid binding affinity of the adipocyte lipid-binding proteins

Science.gov (United States)

Schoeffler, Allyn J.; Ruiz, Carmen R.; Joubert, Allison M.; Yang, Xuemei; LiCata, Vince J.

2003-01-01

Adipocyte lipid-binding protein (ALBP or aP2) is an intracellular fatty acid-binding protein that is found in adipocytes and macrophages and binds a large variety of intracellular lipids with high affinity. Although intracellular lipids are frequently charged, biochemical studies of lipid-binding proteins and their interactions often focus most heavily on the hydrophobic aspects of these proteins and their interactions. In this study, we have characterized the effects of KCl on the stability and lipid binding properties of ALBP. We find that added salt dramatically stabilizes ALBP, increasing its Delta G of unfolding by 3-5 kcal/mol. At 37 degrees C salt can more than double the stability of the protein. At the same time, salt inhibits the binding of the fluorescent lipid 1-anilinonaphthalene-8-sulfonate (ANS) to the protein and induces direct displacement of the lipid from the protein. Thermodynamic linkage analysis of the salt inhibition of ANS binding shows a nearly 1:1 reciprocal linkage: i.e. one ion is released from ALBP when ANS binds, and vice versa. Kinetic experiments show that salt reduces the rate of association between ANS and ALBP while simultaneously increasing the dissociation rate of ANS from the protein. We depict and discuss the thermodynamic linkages among stability, lipid binding, and salt effects for ALBP, including the use of these linkages to calculate the affinity of ANS for the denatured state of ALBP and its dependence on salt concentration. We also discuss the potential molecular origins and potential intracellular consequences of the demonstrated salt linkages to stability and lipid binding in ALBP.

Development of a nonlinear model for the prediction of response times of glucose affinity sensors using concanavalin A and dextran and the development of a differential osmotic glucose affinity sensor

Science.gov (United States)

Reis, Louis G.

With the increasing prevalence of diabetes in the United States and worldwide, blood glucose monitoring must be accurate and reliable. Current enzymatic sensors have numerous disadvantages that make them unreliable and unfavorable among patients. Recent research in glucose affinity sensors correct some of the problems that enzymatic sensors experience. Dextran and concanavalin A are two of the more common components used in glucose affinity sensors. When these sensors were first explored, a model was derived to predict the response time of a glucose affinity sensor using concanavalin A and dextran. However, the model assumed the system was linear and fell short of calculating times representative of the response times determined through experimental tests with the sensors. In this work, a new model that uses the Stokes-Einstein Equation to demonstrate the nonlinear behavior of the glucose affinity assay was developed to predict the response times of similar glucose affinity sensors. In addition to the device tested by the original linear model, additional devices were identified and tested with the proposed model. The nonlinear model was designed to accommodate the many different variations between systems. The proposed model was able to accurately calculate response times for sensors using the concanavalin A-dextran affinity assay with respect to the experimentally reported times by the independent research groups. Parameter studies using the nonlinear model were able to identify possible setbacks that could compromise the response of thesystem. Specifically, the model showed that the improper use of asymmetrical membranes could increase the response time by as little as 20% or more as the device is miniaturized. The model also demonstrated that systems using the concanavalin Adextran assay would experience higher response times in the hypoglycemic range. This work attempted to replicate and improve an osmotic glucose affinity sensor. The system was designed to

The elution of certain protein affinity tags with millimolar concentrations of diclofenac.

Science.gov (United States)

Baliova, Martina; Juhasova, Anna; Jursky, Frantisek

2015-12-01

Diclofenac (2-[(2, 6-dichlorophenyl)amino] benzeneacetic acid) is a sparingly soluble, nonsteroidal anti-inflammatory drug therapeutically acting at low micromolar concentrations. In pH range from 8 to 11, its aqueous solubility can be increased up to 200 times by the presence of counter ions such as sodium. Our protein interaction studies revealed that a millimolar concentration of sodium diclofenac is able to elute glutathione S-transferase (GST), cellulose binding protein (CBD), and maltose binding protein (MBP) but not histidine-tagged or PDZ-tagged proteins from their affinity resins. The elution efficiency of diclofenac is comparable with the eluting agents normally used at similar concentrations. Native gel electrophoresis of sodium diclofenac-treated proteins showed that the interaction is non-covalent and non-denaturing. These results suggest that sodium diclofenac, in addition to its pharmaceutical applications, can also be exploited as a lead for the development of new proteomics reagents. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of Sowing Date and Limited Irrigation on Yield and Yield Components of Five Rainfed Wheat Varieties in Maragheh Region

Directory of Open Access Journals (Sweden)

A. R. Tavakkoli

2013-03-01

Full Text Available In order to investigate the effects of sowing date (SD and single irrigation (SI amounts on yield and yield components of rainfed wheat varieties, a field experiment was conducted as split-split plots arranged in a randomized complete blocks design with three replications during 2002-2004 at main station of Dryland Agricultural Research Institute in Maragheh, Iran. Treatments included three sowing dates (early, normal and late, three levels of single irrigation (rainfed, 50 mm and 100 mm only at planting time and five wheat varieties (three numbered lines, Azar2 and double-cross Shahi. Results revealed that interactions of SD, SI and wheat varieties were significant for grain yield, number of kernels per spike and water productivity (P≤0.01. Single irrigation at normal planting time increased grain yield, straw, biomass, harvest index, and water productivity. Grain yield and water productivity were increased by 131% and 84.8%, respectively. Single irrigation at late planting time was not significant on agronomic traits and produced low water productivity. Regarding the reaction of wheat to planting date and single irrigation, results showed that normal single irrigation can improve yield, yield components and water productivity index. The effectiveness of single irrigation under dryland conditions can be observed in all wheat cultivars. Although this effectiveness on yield and yield components is observable, but it is necessary to select the time of irrigation properly.

Affine Kac-Moody algebras and their representations

International Nuclear Information System (INIS)

Slansky, R.

1988-01-01

Highest weight representation theory of finite dimensional and affine Kac-Moody algebras is summarized from a unified point of view. Lattices of discrete additive quantum numbers and the presentation of Lie algebras on Cartan matrices are the central points of departure for the analysis. (author)

Affinity monolith chromatography: A review of general principles and applications.

Science.gov (United States)

Li, Zhao; Rodriguez, Elliott; Azaria, Shiden; Pekarek, Allegra; Hage, David S

2017-11-01

Affinity monolith chromatography, or AMC, is a liquid chromatographic method in which the support is a monolith and the stationary phase is a biological-binding agent or related mimic. AMC has become popular for the isolation of biochemicals, for the measurement of various analytes, and for studying biological interactions. This review will examine the principles and applications of AMC. The materials that have been used to prepare AMC columns will be discussed, which have included various organic polymers, silica, agarose, and cryogels. Immobilization schemes that have been used in AMC will also be considered. Various binding agents and applications that have been reported for AMC will then be described. These applications will include the use of AMC for bioaffinity chromatography, immunoaffinity chromatography, dye-ligand affinity chromatography, and immobilized metal-ion affinity chromatography. The use of AMC with chiral stationary phases and as a tool to characterize biological interactions will also be examined. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of the T cell receptor ligand affinity in T cell activation by bacterial superantigens

DEFF Research Database (Denmark)

Andersen, P S; Geisler, C; Buus, S

2001-01-01

Similar to native peptide/MHC ligands, bacterial superantigens have been found to bind with low affinity to the T cell receptor (TCR). It has been hypothesized that low ligand affinity is required to allow optimal TCR signaling. To test this, we generated variants of Staphylococcus enterotoxin C3...... (SEC3) with up to a 150-fold increase in TCR affinity. By stimulating T cells with SEC3 molecules immobilized onto plastic surfaces, we demonstrate that increasing the affinity of the SEC3/TCR interaction caused a proportional increase in the ability of SEC3 to activate T cells. Thus, the potency...... correlation between ligand affinity and ligand potency indicating that it is the density of receptor-ligand complexes in the T cell contact area that determines TCR signaling strength....

Rational design of peptide affinity ligands for the purification of therapeutic enzymes.

Science.gov (United States)

Trasatti, John P; Woo, James; Ladiwala, Asif; Cramer, Steven; Karande, Pankaj

2018-04-25

Non-mAb biologics represent a growing class of therapeutics under clinical development. Although affinity chromatography is a potentially attractive approach for purification, the development of platform technologies, such as Protein A for mAbs, has been challenging due to the inherent chemical and structural diversity of these molecules. Here, we present our studies on the rapid development of peptide affinity ligands for the purification of biologics using a prototypical enzyme therapeutic in clinical use. Employing a suite of de novo rational and combinatorial design strategies we designed and screened a library of peptides on microarray platforms for their ability to bind to the target with high affinity and selectivity in cell culture fluid. Lead peptides were evaluated on resin in batch conditions and compared with a commercially available resin to evaluate their efficacy. Two lead candidates identified from microarray studies provided high binding capacity to the target while demonstrating high selectivity against culture contaminants and product variants compared to a commercial resin system. These findings provide a proof-of-concept for developing affinity peptide-based bioseparations processes for a target biologic. Peptide affinity ligand design and screening approaches presented in this work can also be easily translated to other biologics of interest. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

Lie algebraic discussion for affinity based information diffusion in social networks

Science.gov (United States)

Shang, Yilun

2017-11-01

In this paper we develop a dynamical information diffusion model which features the affinity of people with information disseminated in social networks. Four types of agents, i.e., susceptible, informed, known, and refractory ones, are involved in the system, and the affinity mechanism composing of an affinity threshold which represents the fitness of information to be propagated is incorporated. The model can be generally described by a time-inhomogeneous Markov chain, which is governed by its master (Kolmogorov) equation. Based on the Wei-Norman method, we derive analytical solutions of the model by constructing a low-dimensional Lie algebra. Numerical examples are provided to illustrate the obtained theoretical results. This study provides useful insights into the closed-form solutions of complex social dynamics models through the Lie algebra method.

Development of an affinity-matured humanized anti-epidermal growth factor receptor antibody for cancer immunotherapy.

Science.gov (United States)

Nakanishi, Takeshi; Maru, Takamitsu; Tahara, Kazuhiro; Sanada, Hideaki; Umetsu, Mitsuo; Asano, Ryutaro; Kumagai, Izumi

2013-02-01

We showed previously that humanization of 528, a murine anti-epidermal growth factor receptor (EGFR) antibody, causes reduced affinity for its target. Here, to improve the affinity of the humanized antibody for use in cancer immunotherapy, we constructed phage display libraries focused on the complementarity-determining regions (CDRs) of the antibody and carried out affinity selection. Two-step selections using libraries constructed in a stepwise manner enabled a 32-fold affinity enhancement of humanized 528 (h528). Thermodynamic analysis of the interactions between the variable domain fragment of h528 (h528Fv) mutants and the soluble extracellular domain of EGFR indicated that the h528Fv mutants obtained from the first selection showed a large increase in negative enthalpy change due to binding, resulting in affinity enhancement. Furthermore, mutants from the second selection showed a decrease in entropy loss, which led to further affinity maturation. These results suggest that a single mutation in the heavy chain variable domain (i.e. Tyr(52) to Trp) enthalpically contributed for overcoming the energetic barrier to the antigen-antibody interaction, which was a major hurdle for the in vitro affinity maturation of h528. We reported previously that the humanized bispecific diabody hEx3 Db, which targets EGFR and CD3, shows strong anti-tumor activity. hEx3 Db mutants, in which the variable domains of h528 were replaced with those of the affinity-enhanced mutants, were prepared and characterized. In a growth inhibition assay of tumor cells, the hEx3 Db mutants showed stronger anti-tumor activity than that of hEx3 Db, suggesting that affinity enhancement of h528Fv enhances the anti-tumor activity of the bispecific diabody.

High affinity calmodulin target sequence in the signalling molecule PI 3-kinase

DEFF Research Database (Denmark)

Fischer, R; Julsgart, J; Berchtold, M W

1998-01-01

M-binding peptide derived from the p110gamma isoform interacts with CaM in a calcium-dependent way. Using gel shift analysis and fluorescence spectrophotometry we discovered that the peptide forms a high affinity complex with CaM. Titration experiments using dansylated CaM gave an affinity constant of 5 n...

Stereoscopic visualization in curved spacetime: seeing deep inside a black hole

International Nuclear Information System (INIS)

Hamilton, Andrew J S; Polhemus, Gavin

2010-01-01

Stereoscopic visualization adds an additional dimension to the viewer's experience, giving them a sense of distance. In a general relativistic visualization, distance can be measured in a variety of ways. We argue that the affine distance, which matches the usual notion of distance in flat spacetime, is a natural distance to use in curved spacetime. As an example, we apply affine distance to the visualization of the interior of a black hole. Affine distance is not the distance perceived with normal binocular vision in curved spacetime. However, the failure of binocular vision is simply a limitation of animals that have evolved in flat spacetime, not a fundamental obstacle to depth perception in curved spacetime. Trinocular vision would provide superior depth perception.

A potential therapy for chordoma via antibody-dependent cell-mediated cytotoxicity employing NK or high-affinity NK cells in combination with cetuximab.

Science.gov (United States)

Fujii, Rika; Schlom, Jeffrey; Hodge, James W

2018-05-01

OBJECTIVE Chordoma is a rare bone tumor derived from the notochord and is resistant to conventional therapies such as chemotherapy, radiotherapy, and targeting therapeutics. Expression of epidermal growth factor receptor (EGFR) in a large proportion of chordoma specimens indicates a potential target for therapeutic intervention. In this study the authors investigated the potential role of the anti-EGFR antibody cetuximab in immunotherapy for chordoma. METHODS Since cetuximab is a monoclonal antibody of the IgG1 isotype, it has the potential to mediate antibody-dependent cell-mediated cytotoxicity (ADCC) employing natural killer (NK) cells as effectors. Polymorphisms in the CD16 allele expressed on NK cells have been shown to influence the degree of ADCC of tumor cells, with the high-affinity valine (V)/V allele being responsible for more lysis than the V/phenylalanine (F) or FF allele. Unfortunately, however, only approximately 10% of the population expresses the VV allele on NK cells. An NK cell line, NK-92, has now been engineered to endogenously express IL-2 and the high-affinity CD16 allele. These irradiated high-affinity (ha)NK cells were analyzed for lysis of chordoma cells with and without cetuximab, and the levels of lysis observed in ADCC were compared with those of NK cells from donors expressing the VV, VF, and FF alleles. RESULTS Here the authors demonstrate for the first time 1) that cetuximab in combination with NK cells can mediate ADCC of chordoma cells; 2) the influence of the NK CD16 polymorphism in cetuximab-mediated ADCC for chordoma cell lysis; 3) that engineered haNK cells-that is, cells transduced to express the CD16 V158 FcγRIIIa receptor-bind cetuximab with similar affinity to normal NK cells expressing the high-affinity VV allele; and 4) that irradiated haNK cells induce ADCC with cetuximab in chordoma cells. CONCLUSIONS These studies provide rationale for the use of cetuximab in combination with irradiated haNK cells for therapy for

Approximate convex hull of affine iterated function system attractors

International Nuclear Information System (INIS)

Mishkinis, Anton; Gentil, Christian; Lanquetin, Sandrine; Sokolov, Dmitry

2012-01-01

Highlights: ► We present an iterative algorithm to approximate affine IFS attractor convex hull. ► Elimination of the interior points significantly reduces the complexity. ► To optimize calculations, we merge the convex hull images at each iteration. ► Approximation by ellipses increases speed of convergence to the exact convex hull. ► We present a method of the output convex hull simplification. - Abstract: In this paper, we present an algorithm to construct an approximate convex hull of the attractors of an affine iterated function system (IFS). We construct a sequence of convex hull approximations for any required precision using the self-similarity property of the attractor in order to optimize calculations. Due to the affine properties of IFS transformations, the number of points considered in the construction is reduced. The time complexity of our algorithm is a linear function of the number of iterations and the number of points in the output approximate convex hull. The number of iterations and the execution time increases logarithmically with increasing accuracy. In addition, we introduce a method to simplify the approximate convex hull without loss of accuracy.

Targeting Anti-Cancer Active Compounds: Affinity-Based Chromatographic Assays

Science.gov (United States)

de Moraes, Marcela Cristina; Cardoso, Carmen Lucia; Seidl, Claudia; Moaddel, Ruin; Cass, Quezia Bezerra

2016-01-01

Affinity-based chromatography assays encompass the use of solid supports containing immobilized biological targets to monitor binding events in the isolation , identification and/or characterization of bioactive compounds. This powerful bioanalytical technique allows the screening of potential binders through fast analyses that can be directly performed using isolated substances or complex matrices. An overview of the recent researches in frontal and zonal affinity-based chromatography screening assays, which has been used as a tool in the identification and characterization of new anti-cancer agents, is discussed. In addition, a critical evaluation of the recently emerged ligands fishing assays in complex mixtures is also discussed. PMID:27306095

Press Advertising – Varieties and Sub-Varieties. Methods of Promoting the Press

OpenAIRE

Mikosz, Joanna

2016-01-01

In the text entitled “Press advertising – varieties and sub-varieties. Methods of promoting the press”, the author discusses press advertising, which is a fast developing mass-media phenomenon. Modernity has granted press advertising a high quality of print and paper, as well as Infinite possibilities of combining various promotional forms with the press. The author argues that press advertising is one of the best ways in which a company can communicate with the market. Its advantage is, abov...

Aspects of affine Toda field theory

International Nuclear Information System (INIS)

Braden, H.W.; Corrigan, E.; Dorey, P.E.; Sasaki, R.

1990-05-01

The report is devoted to properties of the affine Toda field theory, the intention being to highlight a selection of curious properties that should be explicable in terms of the underlying group theory but for which in most cases there are no explanation. The motivation for exploring the ideas contained in this report came principally from the recent work of Zamolodchikov concerning the two dimensional Ising model at critical temperature perturbed by a magnetic field. Hollowood and Mansfield pointed out that since Toda field theory is conformal the perturbation considered by Zamolodchikov might well be best regarded as a perturbation of a Toda field theory. This work made it seem plausible that the theory sought by Zamolodchikov was actually affine E 8 Toda field theory. However, this connection required an imaginary value of the coupling constant. Investigations here concerning exact S-matrices use a perturbative approach based on real coupling and the results differ in various ways from those thought to correspond to perturbed conformal field theory. A further motivation is to explore the connection between conformal and perturbed conformal field theories in other contexts using similar ideas. (N.K.)

Extreme disorder in an ultrahigh-affinity protein complex

DEFF Research Database (Denmark)

Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine

2018-01-01

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions...... with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring...... or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex...

Preparation of Affinity Column Based on Zr{sup 4+} Ion for Phosphoproteins Isolation

Energy Technology Data Exchange (ETDEWEB)

Lee, Seon Mi; Bae, In Ae; Park, Jung Hyen; Kim, Tae Dong; Choi, Seong Ho [Hannam University, Daejeon (Korea, Republic of)

2009-06-15

This paper has described about preparation of Zr{sup 4+} affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr{sup 4+} ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr{sup 4+}-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr{sup 4+} affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr{sup 4+} affinity polymeric microsphere by liquid chromatography. This Zr{sup 4+} affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography.

Development of an aptamer-based affinity purification method for vascular endothelial growth factor

Directory of Open Access Journals (Sweden)

Maren Lönne

2015-12-01

Full Text Available Since aptamers bind their targets with high affinity and specificity, they are promising alternative ligands in protein affinity purification. As aptamers are chemically synthesized oligonucleotides, they can be easily produced in large quantities regarding GMP conditions allowing their application in protein production for therapeutic purposes. Several advantages of aptamers compared to antibodies are described in general within this paper. Here, an aptamer directed against the human Vascular Endothelial Growth Factor (VEGF was used as affinity ligand for establishing a purification platform for VEGF in small scale. The aptamer was covalently immobilized on magnetic beads in a controlled orientation resulting in a functional active affinity matrix. Target binding was optimized by introduction of spacer molecules and variation of aptamer density. Further, salt-induced target elution was demonstrated as well as VEGF purification from a complex protein mixture proving the specificity of protein-aptamer binding.

The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

Directory of Open Access Journals (Sweden)

Fabian König

Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.

Conformational destabilization of Immunoglobulin G increases the low pH-binding affinity with the Neonatal Fc Receptor

DEFF Research Database (Denmark)

Walters, Benjamin T; Jensen, Pernille Foged; Larraillet, Vincent

2016-01-01

Crystallographic evidence suggests that the pH-dependent affinity of IgG molecules for the neonatal Fc receptor (FcRn) receptor primarily arises from salt bridges involving IgG histidine residues, resulting in moderate affinity at mildly acidic conditions. However, this view does not explain the ......H-dependent affinity in IgG-FcRn interactions and exemplify the important and often ignored role of intrinsic conformational dynamics in a protein ligand, to dictate affinity for biologically important receptors.......Crystallographic evidence suggests that the pH-dependent affinity of IgG molecules for the neonatal Fc receptor (FcRn) receptor primarily arises from salt bridges involving IgG histidine residues, resulting in moderate affinity at mildly acidic conditions. However, this view does not explain...... the diversity in affinity found in IgG variants, such as the YTE mutant (M252Y,S254T,T256E), which increases affinity to FcRn by up to 10×. Here we compare hydrogen exchange measurements at pH 7.0 and pH 5.5 with and without FcRn bound with surface plasmon resonance estimates of dissociation constants and Fc...

FOOT ROT DISEASE IDENTIFICATION FOR VELLAIKODI VARIETY OF BETELVINE PLANTS USING DIGITAL IMAGE PROCESSING

Directory of Open Access Journals (Sweden)

J. Vijayakumar

2012-11-01

Full Text Available Betelvine plants are infected variety of diseases in the complete plantation without any premature warning of the diseases. The aim of this paper is to detection of foot rot disease in the vellaikodi variety of betelvine plants using digital image processing techniques. The digital images of the uninfected or normal betelvine leaves and the digital images of the infected in foot rot diseased betelvine leaves at different stages are collected from different Betelvine plants using a high resolution digital camera and collected betelvine images are stored with JPEG format. The digital images of the betelvine leaves analyses are done using the image processing toolbox in MATLAB which gives the normal patterns of the digital images. Using RGB encoding process, the RGB components of the betelvine leaves are separated. The mean and median values for all sample leaves are computed and calculated values are stored in the system. The mean and median values of test leaves are computed and compared with the stored values. As the result of this comparison, it is identified whether test leaves are affected by foot rot disease or not. Finally this analysis helps to recognize the foot rot disease can be identified before it spreads to entire crop.

A soluble, high-affinity, interleukin-4-binding protein is present in the biological fluids of mice

International Nuclear Information System (INIS)

Fernandez-Botran, R.; Vitetta, E.S.

1990-01-01

Cytokines such as interleukin 4 (IL-4) play a key role in the regulation of immune responses, but little is known about how their multiple activities are regulated in vivo. In this report, we demonstrate that an IL-4-binding protein (IL-4BP) is constitutively present in the biological fluids of mice (serum, ascites fluid, and urine). Binding of 125 I-labeled IL-4 to the IL-4BP is specific and saturable and can be inhibited by an excess of unlabeled IL-4 but not IL-2. The IL-4BP binds IL-4 with an affinity similar to that reported for the cellular IL-4 with an affinity similar to that reported for the cellular IL-4 receptor (K d ∼7 x 10 -11 M) and has a molecular mass of 30-40 kDa and pI values of 3.6-4.8. IL-4BP-containing biological fluids or purified IL-4BP competitively inhibit the binding of 125 I-labeled IL-4 to mouse T or B cells and inhibit the biological activity of IL-4 but not IL-2. The serum levels of IL-4BP in severe combined immunodeficiency (SCID) mice are lower than those of normal mice. The above findings suggest that IL-4BP plays an important immunoregulatory role in vivo

Blood O2 affinity of a large polar elasmobranch, the Greenland shark Somniosus microcephalus

DEFF Research Database (Denmark)

Herbert, N.A.; Skov, Peter Vilhelm; Tirsgaard, B.

2017-01-01

The Greenland shark (Somniosus microcephalus. Bloch & Schneider 1801) is a polar elasmobranch that is hypothesised to possess a unique metabolic physiology due to its extreme large size, the cold waters it inhabits and its slow swimming lifestyle. Our results therefore provide the first insight...... into the metabolic physiology of this unique shark, with a focus on blood O2 affinity. An evaluation of blood O2 affinity at 2 °C using tonometry revealed a P50 of 11.7 mmHg at a PCO2 of 2.25 mmHg and a Bohr effect (binding sensitivity of blood to pH, ϕ = Δlog P50/ΔpH) of −0.26. A comparative evaluation of blood O2...... affinity across elasmobranch fishes suggests that S. microcephalus has a high blood O2 affinity (i.e., low P50) and a small Bohr effect but these are common traits in sluggish elasmobranch fishes, with little evidence for any relationship of blood O2 affinity to the low metabolic rates, low environmental...

Ultrasound elastography: efficient estimation of tissue displacement using an affine transformation model

Science.gov (United States)

Hashemi, Hoda Sadat; Boily, Mathieu; Martineau, Paul A.; Rivaz, Hassan

2017-03-01

Ultrasound elastography entails imaging mechanical properties of tissue and is therefore of significant clinical importance. In elastography, two frames of radio-frequency (RF) ultrasound data that are obtained while the tissue is undergoing deformation, and the time-delay estimate (TDE) between the two frames is used to infer mechanical properties of tissue. TDE is a critical step in elastography, and is challenging due to noise and signal decorrelation. This paper presents a novel and robust technique TDE using all samples of RF data simultaneously. We assume tissue deformation can be approximated by an affine transformation, and hence call our method ATME (Affine Transformation Model Elastography). The affine transformation model is utilized to obtain initial estimates of axial and lateral displacement fields. The affine transformation only has six degrees of freedom (DOF), and as such, can be efficiently estimated. A nonlinear cost function that incorporates similarity of RF data intensity and prior information of displacement continuity is formulated to fine-tune the initial affine deformation field. Optimization of this function involves searching for TDE of all samples of the RF data. The optimization problem is converted to a sparse linear system of equations, which can be solved in real-time. Results on simulation are presented for validation. We further collect RF data from in-vivo patellar tendon and medial collateral ligament (MCL), and show that ATME can be used to accurately track tissue displacement.

Self-affine fractal growth front of Aspergillus oryzae

Science.gov (United States)

Matsuura, Shu; Miyazima, Sasuke

1992-12-01

Aspergillus oryzae have been grown in various environmental conditions and analyzed from the viewpoint of self-affinity. The growth behavior can be described by the Eden model in favorable conditions, and by DLA in unfavorable conditions.

Breeding for a low pollen variety of Japanese cedar (Cryptomeria japonica)

International Nuclear Information System (INIS)

Kondo, Teiji

1998-01-01

The number of sufferers of Japanese cedar pollinosis has been increasing recently and this type of pollinosis is a serious allergic disease in Japan, where one of ten persons is suffering it to some extent. Breeding of Japanese cedar trees was attempted to produce less pollen and set fewer male flowers. Because the degree of male flower setting was varied among plus trees, it was thought possible to select the plus trees that set fewer than normal male flowers for use as low pollen varieties. The degree of male flower setting was evaluated under natural conditions and the conditions of gibberellic acid treatment. Since a spontaneous male sterile mutant was previously identified, it was thought possible to induce such mutation. Therefore, the cedars cultivars growing in the γ-field of Institute of Radiation Breeding were examined in respect of male fertility and some abnormal male flowers were obtained. The changes after transplanting these varieties from the γ-field remain to be resolved. Further, it is necessary to monitor the volume and the number of male flowers, and also the allergen content. (M.N.)

7 CFR 51.2112 - Mixed varieties.

Science.gov (United States)

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Mixed varieties. 51.2112 Section 51.2112 Agriculture... FRESH FRUITS, VEGETABLES AND OTHER PRODUCTS 1,2 (INSPECTION, CERTIFICATION, AND STANDARDS) United States Standards for Grades of Shelled Almonds Mixed Varieties § 51.2112 Mixed varieties. Any lot of shelled...

Characterisation of Tmmmian Local Sorghmn Varieties

African Journals Online (AJOL)

Many local varieties of sorghum grown in Tanzania have not been characterised in terms of their end uses. This study was conducted to characterise 14 such varieties. Three improved varieties commonly grown in this country were includedfor comparison. Physical analyses that included 100-grain weight, percent dehulling ...

The role of CH/π interactions in the high affinity binding of streptavidin and biotin.

Science.gov (United States)

Ozawa, Motoyasu; Ozawa, Tomonaga; Nishio, Motohiro; Ueda, Kazuyoshi

2017-08-01

The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10 15 mol -1 ) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of glycation of albumin on its renal clearance in normal and diabetic rats

International Nuclear Information System (INIS)

Layton, G.J.; Jerums, G.

1988-01-01

Two independent techniques have been used to study the renal clearances of nonenzymatically glycated albumin and nonglycated albumin in normal and streptozotocin-induced diabetic rats, 16 to 24 weeks after the onset of diabetes. In the first technique, serum and urinary endogenous glycated and nonglycated albumin were separated using m-aminophenylboronate affinity chromatography and subsequently quantified by radioimmunoassay. Endogenous glycated albumin was cleared approximately twofold faster than nonglycated albumin in normal and diabetic rats. However, no difference was observed in the glycated albumin/nonglycated albumin clearance ratios (Cga/Calb) in normal and diabetic rats, respectively (2.18 +/- 0.39 vs 1.83 +/- 0.22, P greater than 0.05). The second technique measured the renal clearance of injected 125I-labelled glycated albumin and 125I-labelled albumin. The endogenous results were supported by the finding that 125I-labelled glycated albumin was cleared more rapidly than 125I-labelled albumin in normal (P less than 0.01) and diabetic (P less than 0.05) rats. The Cga/Calb ratio calculated for the radiolabelled albumins was 1.4 and 2.0 in normal and diabetic rats, respectively. This evidence suggests that nonenzymatic glycation of albumin increases its renal clearance to a similar degree in normal and diabetic rats

The flow of harmonic applications of a compact variety on a bordered variety

International Nuclear Information System (INIS)

Chen Yunmei; Musina, R.

1989-05-01

If M is a compact riemannian variety and C a riemannian variety closed to border, a weak harmonic application μ:M→C is defined as being a solution of a differential inclusion. We present a theorem of existence and partial regularity for the weak solution of the evolution inclusion for harmonic applications. This solution converges to a weak harmonic application when the time tends appropriately to infinity. 10 refs

Pure homology of algebraic varieties

OpenAIRE

Weber, Andrzej

2003-01-01

We show that for a complete complex algebraic variety the pure component of homology coincides with the image of intersection homology. Therefore pure homology is topologically invariant. To obtain slightly more general results we introduce "image homology" for noncomplete varieties.

Congruence of genomic and ethnolinguistic affinities among five ...

Indian Academy of Sciences (India)

their ethnic and linguistic affinities, we analysed DNA samples of individuals drawn from five tribes with diverse, but ... arisen from admixture between the Gonds (maternal) and ..... nuclear `fossil' of the mitochondrial D-loop and the origin of.

Population Development of Zabrotes subfasciatus (Coleoptera: Chrysomelidae) in Landrace Bean Varieties Occurring in Southwestern Amazonia.

Science.gov (United States)

Lopes, L M; Araújo, A E F; Santos, A C V; Santos, V B; Sousa, A H

2016-02-01

The common bean, Phaseolus vulgaris (L.), is one of the most important sources of protein worldwide, and Latin America is one of the recognized centers of diversity of this species. However, storage of this product after harvest is not feasible because of bruchid attacks. This study determined the accumulated normalized rate of emergence and the daily emergence rate of Zabrotes subfasciatus (Boheman) (Coleoptera: Chrysomelidae:Bruchinae) in five landrace varieties of common bean (BRL 01, SNA 01, RDR 01, RBC 01, and RBC 13) that occurin southwestern Amazonia. These varieties were selected for this study because they are well-distributed throughout the Amazonian communities. Beans of each variety were infested with 50 unsexed adults, and the insects were removed 13 d after beginning the bioassays. The adult progeny obtained from the feeding substrate were counted and removed every other day after the first emergence, until the end of the emergence period. Differences were observed in the calculated rates of development; however, the time required for development and emergence of the insects was independent. Of the five varieties of bean investigated, we observed that the RDR 01, BRL 01, and SNA 01 cultivars are resistant to Z. subfasciatus; the results indicate that the use of these three varieties can reduce problems associated with bruchid attacks and enable storage of the product after harvesting.

Plasma-polymerized films providing selective affinity to the polarity of vaporized organic solvents

International Nuclear Information System (INIS)

Akimoto, Takuo; Ikeshita, Yusuke; Terashima, Ryo; Karube, Isao

2009-01-01

Plasma-polymerized films (PPFs) were fabricated as recognition membranes for a vapor-sensing device, and their affinity to vaporized organic solvents was evaluated with surface plasmon resonance. The affinity we intended to create is the selective sorption of the vaporized organic solvents depending on their polarity. For this purpose, acetonitrile, ethylenediamine (EDA), styrene, hexamethyldisiloxane (HMDSO), and hexamethyldisilazane were used to fabricate PPFs. Vaporized methanol, ethanol, and 1-propanol were used as high-polar solvents to be analyzed. Hexane, toluene, and p-xylene were used as low-polar solvents. As a result, the HMDSO-PPF with 97.3 o of contact angle was found to provide affinity to the low-polar solvents. In contrast, the EDA-PPF with 7.1 o of contact angle provided affinity to the high-polar solvents. Observations of the surface morphology of the HMDSO- and EDA-PPFs with a scanning electron microscope revealed that they are composed of nano-scale islands.

Proadifen-sensitive high affinity binding of /sup 3/H-alaproclate to liver membranes

Energy Technology Data Exchange (ETDEWEB)

Ross, S.B.

1987-01-01

/sup 3/H-alaproclate, a selective 5/sub h/ydroxytryptamine uptake inhibitor, was found to bind to microsomal membranes from the rat liver with high affinity (K/sub D/-=3 nM) and large capacity (B/sub max/ about 2 nmol/g liver). This binding was stereoselective since S-( - )-alaproclate was 30 times more potent than the R-( + )-enantiomer to displace the /sup 3/H-labelled racemate. Proadifen (SKF 525A), an inhibitor of cytochrome P-450, displaced the /sup 3/H-alaproclate binding with the same, high affinity (K/sub i/=3 nM) as alaproclate itself. Repeated treatment with phenobarbital sodium (5x75 mg/kg intraperitoneally) increased the number of alaproclate binding sites 7-8 times without changing the affinity. However, most of the phenobarbital induced /sup 3/H-alaproclate binding was not displaceable by proadifen, showing the presence of at least two different high affinity binding sites. The possible involvement of cytochrome P-450 in the alaproclate binding is discussed.

Affinity for music in Wolf-Hirschhorn syndrome: two case reports.

Science.gov (United States)

Arakawa, Chikako; Fujita, Yukihiko; Fuchigami, Tatsuo; Kawamura, Yuki; Ishii, Wakako; Endo, Ayumi; Kohira, Ryutaro; Takahashi, Shori

2014-10-01

Wolf-Hirschhorn syndrome is a congenital malformation syndrome resulting from deletion of the short arm of chromosome 4. Individuals with Wolf-Hirschhorn syndrome may have a "Greek warrior helmet" appearance, growth retardation, developmental delay, muscular hypotonia, epilepsy, and difficulty with language including verbal communication. An affinity for music has not previously been reported in these patients. We describe two patients with Wolf-Hirschhorn syndrome who both have a strong affinity for music. One patient is a 20-year-old woman who likes to listen to music all day and can hum many tunes. The other patient is a 9-year-old girl who is calmed by music and received music therapy, with subsequent improvement in her communication skills (eye contact, joint attention, and vocalizations to request music). Individuals with Wolf-Hirschhorn syndrome may have a strong affinity for music and may benefit from music therapy. Additional studies are needed to investigate the interest in music in individuals with Wolf-Hirschhorn syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

A Novel Fast and Robust Binary Affine Invariant Descriptor for Image Matching

Directory of Open Access Journals (Sweden)

Xiujie Qu

2014-01-01

Full Text Available As the current binary descriptors have disadvantages of high computational complexity, no affine invariance, and the high false matching rate with viewpoint changes, a new binary affine invariant descriptor, called BAND, is proposed. Different from other descriptors, BAND has an irregular pattern, which is based on local affine invariant region surrounding a feature point, and it has five orientations, which are obtained by LBP effectively. Ultimately, a 256 bits binary string is computed by simple random sampling pattern. Experimental results demonstrate that BAND has a good matching result in the conditions of rotating, image zooming, noising, lighting, and small-scale perspective transformation. It has better matching performance compared with current mainstream descriptors, while it costs less time.

Recombinant spider silk genetically functionalized with affinity domains.

Science.gov (United States)

Jansson, Ronnie; Thatikonda, Naresh; Lindberg, Diana; Rising, Anna; Johansson, Jan; Nygren, Per-Åke; Hedhammar, My

2014-05-12

Functionalization of biocompatible materials for presentation of active protein domains is an area of growing interest. Herein, we describe a strategy for functionalization of recombinant spider silk via gene fusion to affinity domains of broad biotechnological use. Four affinity domains of different origin and structure; the IgG-binding domains Z and C2, the albumin-binding domain ABD, and the biotin-binding domain M4, were all successfully produced as soluble silk fusion proteins under nondenaturing purification conditions. Silk films and fibers produced from the fusion proteins were demonstrated to be chemically and thermally stable. Still, the bioactive domains are concluded to be folded and accessible, since their respective targets could be selectively captured from complex samples, including rabbit serum and human plasma. Interestingly, materials produced from mixtures of two different silk fusion proteins displayed combined binding properties, suggesting that tailor-made materials with desired stoichiometry and surface distributions of several binding domains can be produced. Further, use of the IgG binding ability as a general mean for presentation of desired biomolecules could be demonstrated for a human vascular endothelial growth factor (hVEGF) model system, via a first capture of anti-VEGF IgG to silk containing the Z-domain, followed by incubation with hVEGF. Taken together, this study demonstrates the potential of recombinant silk, genetically functionalized with affinity domains, for construction of biomaterials capable of presentation of almost any desired biomolecule.

Curves and Abelian varieties

CERN Document Server

Alexeev, Valery; Clemens, C Herbert; Beauville, Arnaud

2008-01-01

This book is devoted to recent progress in the study of curves and abelian varieties. It discusses both classical aspects of this deep and beautiful subject as well as two important new developments, tropical geometry and the theory of log schemes. In addition to original research articles, this book contains three surveys devoted to singularities of theta divisors, of compactified Jacobians of singular curves, and of "strange duality" among moduli spaces of vector bundles on algebraic varieties.

The electron affinity of some radiotherapeutic agents used in cancer therapy

International Nuclear Information System (INIS)

Wold, E.; Kaalhus, O.; Johansen, E.S.; Ekse, A.T.

1980-01-01

In order to evaluate whether chemotherapeutic compounds applied in cancer treatment might interact with radiation as anoxic cell sensitizers, the electron-affinic properties of DTIC (5-(3,3-dimethyl-1-triazeno)imidazole-4 carboxamide) AIC 4(5)-aminoimidazole-5(4)-carboxamide, hydroxyurea, busulfan and cyclophosphamide were studied by pulse radiolysis. Reaction rates with hydrated electrons were determined for all these compounds. With the exception of DTIC, they all reacted much more slowly with electrons than do most electron-affinic sensitizers. One-electron reduction potentials were determined for DTIC, AIC and hydroxyurea. The values were all in the region for the onset of sensitization, with hydroxyurea as the most promising (E 7 1 = -0.552 V). For busulfan and cyclophosphamide no value could be determined, but these compounds are probably less electron-affinic than hydroxyurea. A possible application of chemotherapeutic agents as radiosensitizers is discussed. (author)

2017 Louisiana “Ho” nursery variety trials

Science.gov (United States)

In the USDA Sugarcane Research Unit’s sugarcane variety program, promising experimental varieties are assigned permanent numbers three years after selection in the seedling stage. Varieties where both the cross and selection were done in Houma were assigned a prefix of “Ho”. Varieties where a cross...

Craniomandibular morphology and phylogenetic affinities of panthera atrox

DEFF Research Database (Denmark)

Christiansen, Per; Harris, J.M.

2009-01-01

The great North American Pleistocene pantherine felid Panthera atrox has had a turbulent phylogenetic history, and has been claimed to show affinities to both the jaguar and the tiger; currently, it is most often regarded as a subspecies of the extant lion. The cranial, mandibular, and dental...... morphology of Panthera atrox was compared with those of extant lions, jaguars, and tigers using bivariate, multivariate, and shape analyses. Results indicate that the skull of Panthera atrox shows lion affinities, but also deviates from lions in numerous aspects. Mandibular morphology is more similar...... to jaguars and tigers and, as with cranial morphology, the mandible shows a number of traits not present among extant pantherines. Multivariate analyses grouped Panthera atrox separately from other pantherines. Panthera atrox was no lion, and cannot be assigned to any of the extant pantherines...

Structure of Greyhound hemoglobin: origin of high oxygen affinity.

Science.gov (United States)

Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

2011-05-01

This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

Single-cell measurement of red blood cell oxygen affinity.

Science.gov (United States)

Di Caprio, Giuseppe; Stokes, Chris; Higgins, John M; Schonbrun, Ethan

2015-08-11

Oxygen is transported throughout the body by hemoglobin (Hb) in red blood cells (RBCs). Although the oxygen affinity of blood is well-understood and routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of RBC volume and Hb concentration are taken millions of times per day by clinical hematology analyzers, and they are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume, and Hb concentration for individual RBCs in high throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.9%, which corresponds to the maximum slope of the oxygen-Hb dissociation curve. In addition, single-cell oxygen affinity is positively correlated with Hb concentration but independent of osmolarity, which suggests variation in the Hb to 2,3-diphosphoglycerate (2-3 DPG) ratio on a cellular level. By quantifying the functional behavior of a cellular population, our system adds a dimension to blood cell analysis and other measurements of single-cell variability.

Coinheritance of High Oxygen Affinity Hb Helsinki [HBB: c.248A>T; β82(EF6)Lys→Met] with Hb H Disease.

Science.gov (United States)

Lee, Shir-Ying; Goh, Jia-Hui; Tan, Karen M L; Liu, Te-Chih

2017-05-01

Hb Helsinki [HBB: c.248A>T; β82(EF6)Lys→Met] is a high oxygen affinity hemoglobin (Hb) causing polycythemia, whereas Hb H (β4) disease causes mild to severe chronic hemolytic anemia. The clinical characteristics, gel electrophoresis, capillary electrophoresis (CE) and molecular genotyping of a case of Hb Helsinki coinherited with Hb H disease in an ethnic Malay is described, illustrating the interaction between the β-globin variant and coinheritance of three α gene deletions. The proband was asymptomatic, exhibited microcytosis and a normal with Hb value.

Tropical varieties, maps and gossip

NARCIS (Netherlands)

Frenk, B.J.

2013-01-01

Tropical geometry is a relatively new field of mathematics that studies the tropicalization map: a map that assigns a certain type of polyhedral complex, called a tropical variety, to an embedded algebraic variety. In a sense, it translates algebraic geometric statements into combinatorial ones. An

Interaction of albumins and heparinoids investigated by affinity capillary electrophoresis and free flow electrophoresis.

Science.gov (United States)

Mozafari, Mona; El Deeb, Sami; Krull, Friederike; Wildgruber, Robert; Weber, Gerhard; Reiter, Christian G; Wätzig, Hermann

2018-02-01

A fast and precise affinity capillary electrophoresis (ACE) method has been applied to investigate the interactions between two serum albumins (HSA and BSA) and heparinoids. Furthermore, different free flow electrophoresis methods were developed to separate the species which appears owing to interaction of albumins with pentosan polysulfate sodium (PPS) under different experimental conditions. For ACE experiments, the normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. ACE experiments were performed at two different temperatures (23 and 37°C). Both BSA and HSA interact more strongly with PPS than with unfractionated and low molecular weight heparins. For PPS, the interactions can already be observed at low mg/L concentrations (3 mg/L), and saturation is already obtained at approximately 20 mg/L. Unfractionated heparin showed almost no interactions with BSA at 23°C, but weak interactions at 37°C at higher heparin concentrations. The additional signals also appeared at higher concentrations at 37°C. Nevertheless, in most cases the binding data were similar at both temperatures. Furthermore, HSA showed a characteristic splitting in two peaks especially after interacting with PPS, which is probably attributable to the formation of two species or conformational change of HSA after interacting with PPS. The free flow electrophoresis methods have confirmed and completed the ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

Directory of Open Access Journals (Sweden)

Zhiqiang Yan

Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.

7 CFR 932.7 - Variety group 2.

Science.gov (United States)

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Variety group 2. 932.7 Section 932.7 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Regulating Handling Definitions § 932.7 Variety group 2. Variety group 2 means the following varieties and...

7 CFR 932.6 - Variety group 1.

Science.gov (United States)

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Variety group 1. 932.6 Section 932.6 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements... Regulating Handling Definitions § 932.6 Variety group 1. Variety group 1 means the following varieties and...

Rapid and transient stimulation of intracellular reactive oxygen species by melatonin in normal and tumor leukocytes

International Nuclear Information System (INIS)

Radogna, Flavia; Paternoster, Laura; De Nicola, Milena; Cerella, Claudia; Ammendola, Sergio; Bedini, Annalida; Tarzia, Giorgio; Aquilano, Katia; Ciriolo, Maria; Ghibelli, Lina

2009-01-01

Melatonin is a modified tryptophan with potent biological activity, exerted by stimulation of specific plasma membrane (MT1/MT2) receptors, by lower affinity intracellular enzymatic targets (quinone reductase, calmodulin), or through its strong anti-oxidant ability. Scattered studies also report a perplexing pro-oxidant activity, showing that melatonin is able to stimulate production of intracellular reactive oxygen species (ROS). Here we show that on U937 human monocytes melatonin promotes intracellular ROS in a fast (< 1 min) and transient (up to 5-6 h) way. Melatonin equally elicits its pro-radical effect on a set of normal or tumor leukocytes; intriguingly, ROS production does not lead to oxidative stress, as shown by absence of protein carbonylation, maintenance of free thiols, preservation of viability and regular proliferation rate. ROS production is independent from MT1/MT2 receptor interaction, since a) requires micromolar (as opposed to nanomolar) doses of melatonin; b) is not contrasted by the specific MT1/MT2 antagonist luzindole; c) is not mimicked by a set of MT1/MT2 high affinity melatonin analogues. Instead, chlorpromazine, the calmodulin inhibitor shown to prevent melatonin-calmodulin interaction, also prevents melatonin pro-radical effect, suggesting that the low affinity binding to calmodulin (in the micromolar range) may promote ROS production.

Using affinity capillary electrophoresis and computational models for binding studies of heparinoids with p-selectin and other proteins.

Science.gov (United States)

Mozafari, Mona; Balasupramaniam, Shantheya; Preu, Lutz; El Deeb, Sami; Reiter, Christian G; Wätzig, Hermann

2017-06-01

A fast and precise affinity capillary electrophoresis (ACE) method has been developed and applied for the investigation of the binding interactions between P-selectin and heparinoids as potential P-selectin inhibitors in the presence and absence of calcium ions. Furthermore, model proteins and vitronectin were used to appraise the binding behavior of P-selectin. The normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. It was found that P-selectin interacts more strongly with heparinoids in the presence of calcium ions. P-selectin was affected by heparinoids at the concentration of 3 mg/L. In addition, the results of the ACE experiments showed that among other investigated proteins, albumins and vitronectin exhibited strong interactions with heparinoids. Especially with P-selectin and vitronectin, the interaction may additionally induce conformational changes. Subsequently, computational models were applied to interpret the ACE experiments. Docking experiments explained that the binding of heparinoids on P-selectin is promoted by calcium ions. These docking models proved to be particularly well suited to investigate the interaction of charged compounds, and are therefore complementary to ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Growth of some varieties of Lie superalgebras

International Nuclear Information System (INIS)

Zaicev, M V; Mishchenko, S P

2007-01-01

We study numerical characteristics of varieties of Lie superalgebras and, in particular, the growth of codimensions. An example of an insoluble variety of almost polynomial growth is constructed. We prove that the exponent of this variety is equal to three and calculate the growth exponents for two earlier known soluble varieties

Processing quality of NS soybean varieties

Directory of Open Access Journals (Sweden)

Đorđević Vuk

2012-01-01

Full Text Available Current NS soybean varieties are of satisfactory technological quality, and also significant technological diversity. Varieties Triumf and Venera possess higher oil content. Variety Sava has a balanced oil and protein content, and can be used for obtaining different soy products. Variety Rubin has the highest protein content and is suitable for new high protein products. Estimated processing value is a good parameter to describe the processing quality of soybeans. Based on several years and spatial analysis, it is possible to separate the geographic regions with prevailing favourable conditions for obtaining higher protein or oil content.

Molecular basis of a high affinity murine interleukin-5 receptor.

OpenAIRE

Devos, R; Plaetinck, G; Van der Heyden, J; Cornelis, S; Vandekerckhove, J; Fiers, W; Tavernier, J

1991-01-01

The mouse interleukin-5 receptor (mIL-5R) consists of two components one of which, the mIL-5R alpha-chain, binds mIL-5 with low affinity. Recently we demonstrated that monoclonal antibodies (Mabs) recognizing the second mIL-5R beta-chain, immunoprecipitate a p130-140 protein doublet which corresponds to the mIL-3R and the mIL-3R-like protein, the latter chain for which so far no ligand has been identified. In this study we show that a high affinity mIL-5R can be reconstituted on COS1 cells by...

Identification of high- and low-affinity NGF receptors during development of the chicken central nervous system

International Nuclear Information System (INIS)

Escandon, E.; Chao, M.V.

1990-01-01

In order to study regulation of the nerve growth factor (NGF) receptor during embryogenesis in chick brain, we have used affinity crosslinking of tissues with 125 I-NGF. NGF interacts with high- and low-affinity receptors; high-affinity receptors are required for the majority of NGF's actions. Most measurements of receptor levels do not distinguish between high- and low-affinity forms of the receptor. We have used the lipophilic crosslinking agent HSAB to identify the high-affinity, functional receptor during development of the chicken central nervous system. A peak of expression during Embryonic Days 5-10 was detected in all regions of the chicken central nervous system, but, shortly after birth, only the cerebellar region displays significant levels of NGF receptor protein. The time course of expression confirms the dramatic regulation of the NGF receptor gene during defined embryonic periods. The detection of high-affinity NGF receptors in brain and neural retina provides strong evidence that NGF is involved in essential ontogenetic events in the development of the chicken central nervous system

Protease purification and characterization of a serine protease inhibitor from Egyptian varieties of soybean seeds and its efficacy against Spodoptera littoralis

Directory of Open Access Journals (Sweden)

El-latif Ashraf Oukasha Abd

2015-01-01

Full Text Available Serine inhibitors have been described in many plant species and are universal throughout the plant kingdom. Trypsin inhibitors are the most common type. In the present study, trypsin and chymotrypsin inhibitory activity was detected in the seed flour extracts of four Egyptian varieties of soybean (Glycine max. The soybean variety, Giza 22, was found to have higher trypsin and chymotrypsin inhibitory potential compared to other tested soybean varieties. For this reason, Giza 22 was selected for further purification studies which used ammonium sulphate fractionation and DEAE-Sephadex A-25 column. Soybean purified proteins showed a single band on SDS-PAGE corresponding to a molecular mass of 17.9 kDa. The purified inhibitor was stable at temperatures below 60°C and was active at a wide range of pH, from 2 to 12 pH. The kinetic analysis revealed a non-competitive type of inhibition against trypsin and chymotrypsin enzymes. The inhibitor constant (Ki values suggested that the inhibitor has higher affinity toward a trypsin enzyme than to a chymotrypsin enzyme. Purified inhibitor was found to have deep and negative effects on the mean larval weight, larval mortality, pupation, and mean pupal weight of Spodoptera littoralis. It may be concluded, that soybean protease inhibitor gene(s could be potential targets for those future studies which are concerned with developing insect resistant transgenic plants

Characteristics of high affinity and low affinity adenosine binding sites in human cerebral cortex

International Nuclear Information System (INIS)

John, D.; Fox, I.V.

1986-01-01

The binding characteristics of human brain cortical membrane fractions were evaluated to test the hypothesis that there are A 1 and A 2 adenosine binding sites. The ligands used were 2-chloro(8- 3 H) adenosine and N 6 -(adenine-2, 8- 3 H) cyclohexayladenosine. Binding of chloroadenosine to human brain cortical membranes was time dependent, reversible and concentration dependent. The kinetic constant determinations from binding studies of the adenosine receptor are presented. Utilizing tritium-cyclohexyladenosine as ligand the authors observed evidence for a high affinity binding site in human brain cortical membranes with a kd of 5 nM

Transformations Based on Continuous Piecewise-Affine Velocity Fields

DEFF Research Database (Denmark)

Freifeld, Oren; Hauberg, Søren; Batmanghelich, Kayhan

2017-01-01

We propose novel finite-dimensional spaces of well-behaved transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volum...

NUTRITIONAL CHARACTERISTICS OF EMMER WHEAT VARIETIES

Directory of Open Access Journals (Sweden)

Magdaléna Lacko - Bartošová

2015-02-01

Full Text Available The objective of this study was to evaluate the nutritional compounds (fat, sugars, crude protein, soluble fiber, ash and starch of four emmer wheat varieties grown under the conditions of organic farming system. The experiment was established on Scientific Research base Dolná Malanta, near Nitra in Slovakia during 2010 – 2011 and 2011 – 2012 growing seasons. Nutritional parameters, except crude protein content, were not influenced by the variety and weather conditions. Agnone variety had the highest content of fat, crude protein and starch but the lowest content of soluble dietary fiber. The lowest values of fat, crude protein had Molise sel Colli variety; Farvento variety had the lowest sugars and starch content. Emmer wheat as ancient wheat has a unique composition in secondary components, such as starch, which may play a role as functional food ingredients.

Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies.

Science.gov (United States)

Julian, Mark C; Lee, Christine C; Tiller, Kathryn E; Rabia, Lilia A; Day, Evan K; Schick, Arthur J; Tessier, Peter M

2015-10-01

An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Computational estimation of rainbow trout estrogen receptor binding affinities for environmental estrogens

International Nuclear Information System (INIS)

Shyu, Conrad; Cavileer, Timothy D.; Nagler, James J.; Ytreberg, F. Marty

2011-01-01

Environmental estrogens have been the subject of intense research due to their documented detrimental effects on the health of fish and wildlife and their potential to negatively impact humans. A complete understanding of how these compounds affect health is complicated because environmental estrogens are a structurally heterogeneous group of compounds. In this work, computational molecular dynamics simulations were utilized to predict the binding affinity of different compounds using rainbow trout (Oncorhynchus mykiss) estrogen receptors (ERs) as a model. Specifically, this study presents a comparison of the binding affinity of the natural ligand estradiol-17β to the four rainbow trout ER isoforms with that of three known environmental estrogens 17α-ethinylestradiol, bisphenol A, and raloxifene. Two additional compounds, atrazine and testosterone, that are known to be very weak or non-binders to ERs were tested. The binding affinity of these compounds to the human ERα subtype is also included for comparison. The results of this study suggest that, when compared to estradiol-17β, bisphenol A binds less strongly to all four receptors, 17α-ethinylestradiol binds more strongly, and raloxifene has a high affinity for the α subtype only. The results also show that atrazine and testosterone are weak or non-binders to the ERs. All of the results are in excellent qualitative agreement with the known in vivo estrogenicity of these compounds in the rainbow trout and other fishes. Computational estimation of binding affinities could be a valuable tool for predicting the impact of environmental estrogens in fish and other animals.

Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

KAUST Repository

Dai, Hanjun

2017-07-26

Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model (HMM) which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these HMMs into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA data sets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

Science.gov (United States)

Koirala, Deepak; Shelke, Sandip A; Dupont, Marcel; Ruiz, Stormy; DasGupta, Saurja; Bailey, Lucas J; Benner, Steven A; Piccirilli, Joseph A

2018-01-01

Abstract Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3–6 binds to an AAACA RNA pentaloop closed by a GC pair with ∼100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5′-GNGACCC-3′ consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab–RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography. PMID:29309709

Simulating the influence of plasma protein on measured receptor affinity in biochemical assays reveals the utility of Schild analysis for estimating compound affinity for plasma proteins.

Science.gov (United States)

Blakeley, D; Sykes, D A; Ensor, P; Bertran, E; Aston, P J; Charlton, S J

2015-11-01

Plasma protein binding (PPB) influences the free fraction of drug available to bind to its target and is therefore an important consideration in drug discovery. While traditional methods for assessing PPB (e.g. rapid equilibrium dialysis) are suitable for comparing compounds with relatively weak PPB, they are not able to accurately discriminate between highly bound compounds (typically >99.5%). The aim of the present work was to use mathematical modelling to explore the potential utility of receptor binding and cellular functional assays to estimate the affinity of compounds for plasma proteins. Plasma proteins are routinely added to in vitro assays, so a secondary goal was to investigate the effect of plasma proteins on observed ligand-receptor interactions. Using the principle of conservation of mass and the law of mass action, a cubic equation was derived describing the ligand-receptor complex [LR] in the presence of plasma protein at equilibrium. The model demonstrates the profound influence of PPB on in vitro assays and identifies the utility of Schild analysis, which is usually applied to determine receptor-antagonist affinities, for calculating affinity at plasma proteins (termed KP ). We have also extended this analysis to functional effects using operational modelling and demonstrate that these approaches can also be applied to cell-based assay systems. These mathematical models can potentially be used in conjunction with experimental data to estimate drug-plasma protein affinities in the earliest phases of drug discovery programmes. © 2015 The British Pharmacological Society.

Maize variety and method of production

Science.gov (United States)

Pauly, Markus; Hake, Sarah; Kraemer, Florian J

2014-05-27

The disclosure relates to a maize plant, seed, variety, and hybrid. More specifically, the disclosure relates to a maize plant containing a Cal-1 allele, whose expression results in increased cell wall-derived glucan content in the maize plant. The disclosure also relates to crossing inbreds, varieties, and hybrids containing the Cal-1 allele to produce novel types and varieties of maize plants.

From affine Hecke algebras to boundary symmetries

International Nuclear Information System (INIS)

Doikou, Anastasia

2005-01-01

Motivated by earlier works we employ appropriate realizations of the affine Hecke algebra and we recover previously known non-diagonal solutions of the reflection equation for the U q (gl n -bar ) case. The corresponding N site spin chain with open boundary conditions is then constructed and boundary non-local charges associated to the non-diagonal solutions of the reflection equation are derived, as coproduct realizations of the reflection algebra. With the help of linear intertwining relations involving the aforementioned solutions of the reflection equation, the symmetry of the open spin chain with the corresponding boundary conditions is exhibited, being essentially a remnant of the U q (gl n -bar ) algebra. More specifically, we show that representations of certain boundary non-local charges commute with the generators of the affine Hecke algebra and with the local Hamiltonian of the open spin chain for a particular choice of boundary conditions. Furthermore, we are able to show that the transfer matrix of the open spin chain commutes with a certain number of boundary non-local charges, depending on the choice of boundary conditions

Twist on protein microarrays: layering wax-patterned nitrocellulose to create customizable and separable arrays of multiplexed affinity columns.

Science.gov (United States)

de Lange, Victoria; Vörös, János

2014-05-06

We developed the simple and inexpensive FoRe microarray to simultaneously test several 1 μL samples for multiple proteins. By combining forward and reverse phase microarrays into an innovative three-dimensional format, the FoRe array exploits the advantages and eliminates several drawbacks of the traditional approaches (i.e., large sample volumes, protein loss, and cross-reactivity between detection antibodies). Samples are pipetted into an array of separable, multiplexed affinity columns. Several nitrocellulose membranes, each functionalized with a different capture antibody, are stacked to create a customizable affinity column. The nitrocellulose is patterned with wax to form 25 isolated microspots on each layer, allowing us to analyze multiple samples in parallel. After running the immunoassay, the stacks are quickly disassembled, revealing 2D microarrays of different fractions from multiple samples. By combining the stack-and-separate technique with wax patterning, we keep the arrays low cost and easily tailored to a variety of applications. We successfully performed 3D multiplexing using a model system with mouse and rabbit IgG. Binding proved to be independent of the position in the stack, and the limit of detection for a mouse IgG sandwich assay was 7.3 pM in BSA and 15 pM in human plasma. The FoRe microarray makes it possible to identify protein expression patterns across several minute volume samples; for example, it could be used to analyze cell lysate in drug response studies or pricks of blood from small animal studies.

Septide and neurokinin A are high-affinity ligands on the NK-1 receptor: evidence from homologous versus heterologous binding analysis.

Science.gov (United States)

Hastrup, H; Schwartz, T W

1996-12-16

The three main tachykinins, substance P, neurokinin A (NKA), and neurokinin B, are believed to be selective ligands for respectively the NK-1, NK-2 and NK-3 receptors. However, NKA also has actions which cannot be mediated through its normal NK-2 receptor and the synthetic peptide [pGlu6,Pro9]-Substance P9-11--called septide--is known to have tachykinin-like actions despite its apparent lack of binding to any known tachykinin receptor. In the cloned NK-1 receptor expressed in COS-7 cells NKA and septide as expected were poor competitors for radiolabeled substance P. However, by using radiolabeled NKA and septide directly, it was found that both peptides in homologous binding assays as well as in competition against each other in fact bound to the NK-1 receptor with high affinity: Kd values of 0.51 +/- 0.15 nM (NKA) and 0.55 +/- 0.03 nM (septide). It is concluded that NKA and septide are high-affinity ligands for the NK-1 receptor but that they are poor competitors for substance P, which in contrast competes very well for binding with both NKA and septide.

Food variety score is associated with dual burden of malnutrition in Orang Asli (Malaysian indigenous peoples) households: implications for health promotion.

Science.gov (United States)

Saibul, Nurfaizah; Shariff, Zalilah Mohd; Lin, Khor Geok; Kandiah, Mirnalini; Ghani, Nawalyah Abdul; Rahman, Hejar Abdul

2009-01-01

This paper reports on the presence of dual burden households in Orang Asli (OA, indigenous people) communities and its associated factors. A total of 182 OA households in two districts in Selangor with the required criteria (182 non-pregnant women of child bearing age and 284 children aged 2-9 years old) participated in the study. Height and weight of both women and children were measured. Energy intake and food variety score (FVS) were determined using three 24-hour diet recalls. While 58% were underweight and 64% of the children were stunted, the prevalence of overweight and obesity in women were 31% and 20% respectively. The percentage of dual burden households (overweight mother/underweight child) was 25.8% while 14.8% households had normal weight mother/normal weight child. The mean food variety score (FVS) was similar for women (7.0+/-2.1) and children (6.9+/-1.9). Dual burden households were associated with women's employment status (OR: 3.18, 95% CI: 2.65-5.66), FVS of children (OR: 0.71, 95% CI: 0.51-0.95) and FVS of women (OR: 1.39, 95% CI: 1.02- 1.89). The FVS of children (OR: 0.49, 95% CI: 0.25-0.89) and women (OR: 1.92, 95% CI: 1.64-2.77) remained significant even when dual burden households were compared to only households with normal weight mother/normal weight child. In these OA communities, food variety may predict a healthier diet in children, but may increase the risk of overweight and obesity in adults. Efforts to address households with dual burden malnutrition should consider promotion of healthy diets and lifestyle for all members.

[Affine transformation-based automatic registration for peripheral digital subtraction angiography (DSA)].

Science.gov (United States)

Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min

2008-07-01

In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.

Generalized magnification in visual optics. Part 2: Magnification as affine transformation

Directory of Open Access Journals (Sweden)

W. F. Harris

2010-12-01

Full Text Available In astigmatic systems magnification may be different in different directions.  It may also be accompanied by rotation or reflection.  These changes from object to image are examples of generalized magnification.  They are represented by  2 2×  matrices.  Because they are linear transformations they can be called linear magnifications.  Linear magnifications account for a change in appearance without regard to position.  Mathematical structure suggests a natural further generalization to a magnification that is complete in the sense that it accountsfor change in appearance and position.  It is represented by a  3 3×  matrix with a dummy third row. The transformation is called affine in linear algebra which suggests that these generalized magnifica-tions be called affine magnifications.  The purpose of the paper is to define affine magnification in the context of astigmatic optics.  Several examples are presented and illustrated graphically. (S Afr Optom 2010 69(4 166-172

Active fault tolerant control of piecewise affine systems with reference tracking and input constraints

DEFF Research Database (Denmark)

Gholami, M.; Cocquempot, V.; Schiøler, H.

2014-01-01

An active fault tolerant control (AFTC) method is proposed for discrete-time piecewise affine (PWA) systems. Only actuator faults are considered. The AFTC framework contains a supervisory scheme, which selects a suitable controller in a set of controllers such that the stability and an acceptable...... performance of the faulty system are held. The design of the supervisory scheme is not considered here. The set of controllers is composed of a normal controller for the fault-free case, an active fault detection and isolation controller for isolation and identification of the faults, and a set of passive...... fault tolerant controllers (PFTCs) modules designed to be robust against a set of actuator faults. In this research, the piecewise nonlinear model is approximated by a PWA system. The PFTCs are state feedback laws. Each one is robust against a fixed set of actuator faults and is able to track...

Engineered α4β2 nicotinic acetylcholine receptors as models for measuring agonist binding and effect at the orthosteric low-affinity α4-α4 interface

DEFF Research Database (Denmark)

Ahring, Philip K.; Olsen, Jeppe A.; Nielsen, Elsebet O.

2015-01-01

The nicotinic acetylcholine receptor alpha 4 beta 2 is important for normal mammalian brain function and is known to express in two different stoichiometries, (alpha 4)(2)(beta 2)(3) and (alpha 4)(3)(beta 2)(2). While these are similar in many aspects, the (alpha 4)(3)(beta 2)(2) stoichiometry...... differs by harboring a third orthosteric acetylcholine binding site located at the alpha 4-alpha 4 interface. Interestingly, the third binding site has, so far, only been documented using electrophysiological assays, actual binding affinities of nicotinic receptor ligands to this site are not known....... The present study was therefore aimed at determining binding affinities of nicotinic ligands to the alpha 4-alpha 4 interface. Given that epibatidine shows large functional potency differences at alpha 4-beta 2 vs. alpha 4-alpha 4 interfaces, biphasic binding properties would be expected at (alpha 4)(3)(beta...

Yield performance of brassica varieties under rainfed condition

International Nuclear Information System (INIS)

Hassan, M.Z.U.; Wahla, A.J.; Waqar, M.Q.

2014-01-01

A field study was conducted to evaluate crop growth and seed yield performance of Brassica varieties under Rainfed conditions. The varieties, included in the study, were BSA, Zafar-2000, Pakola, Con.1, Con.2, Abaseen, Rainbow, SPS-5, Bard-1, and KJ-119. KJ-119 (2500.0 KG/HA) among Brassica juncea L. varieties and Abaseen (2425.9 kg/ha) among Brassica napusL. Varieties produced with maximum seed yield as compared to rest of varieties. Significantly, minimum seed yield was observed in check variety BSA. The significant difference in seed yield of Brassica varieties, Abaseen and KJ 119, was attributed to improve yield components over other varieties. Maximum pods per plant and seeds per pod led these varieties to attain maximum yield. Inspite of weather variations existence during years 2007-09,the same varieties produced with maximum seed yield. (author)

General super Virasoro construction on affine G

International Nuclear Information System (INIS)

Mohammedi, N.

1990-10-01

We consider a bosonic current algebra and a theory of free fermions and construct a general N = 1 super Virasoro current algebra. We obtain a master-set of equations which comprises the bosonic master equation for general Virasoro construction on affine G. As an illustration we study the case of the group SU(2). (author). 13 refs

Fan Affinity Laws from a Collision Model

Science.gov (United States)

Bhattacharjee, Shayak

2012-01-01

The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

New immunogenic form for vasopressin: production of high-affinity antiserum and RIA for plasmatic AVP

International Nuclear Information System (INIS)

Rougon-Rappuzi, G.; Delaage, M.A.; Conte-Devolx, B.; Millet, Y.

1977-01-01

A highly sensitive and specific radioimmunoassay (RIA) for arginine-vasopressin (AVP) was developped and applied to the measurement of AVP in human plasma. High-affinity antivasopressin antibodies with limited association constant heterogeneity have been induced by immunizing rabbits with Lysine-vasopressine (LVP) coupled to a human immunoglobulin (IgA). Replacing air drying of acetone-petroleum ether extracts by lyophilisation increased significantly the yields of AVP. Equilibrium dialysis was used for separating bound and free antigen, thus reducing the total time required for the assay to 48 hours. Only 1 ml of plasma was required for routine determinations due to a sensitivity threshold better than 0.5 pg/ml. Plasma AVP levels of normal subjects and of patients with inappropriate ADH secretion (SIADH) were determined during different hydratation states and following nicotin of ethanol infusions. (orig.) [de

Solitons, τ-functions and hamiltonian reduction for non-Abelian conformal affine Toda theories

Science.gov (United States)

Ferreira, L. A.; Miramontes, J. Luis; Guillén, Joaquín Sánchez

1995-02-01

We consider the Hamiltonian reduction of the "two-loop" Wess-Zumino-Novikov-Witten model (WZNW) based on an untwisted affine Kac-Moody algebra G. The resulting reduced models, called Generalized Non-Abelian Conformal Affine Toda (G-CAT), are conformally invariant and a wide class of them possesses soliton solutions; these models constitute non-Abelian generalizations of the conformal affine Toda models. Their general solution is constructed by the Leznov-Saveliev method. Moreover, the dressing transformations leading to the solutions in the orbit of the vacuum are considered in detail, as well as the τ-functions, which are defined for any integrable highest weight representation of G, irrespectively of its particular realization. When the conformal symmetry is spontaneously broken, the G-CAT model becomes a generalized affine Toda model, whose soliton solutions are constructed. Their masses are obtained exploring the spontaneous breakdown of the conformal symmetry, and their relation to the fundamental particle masses is discussed. We also introduce what we call the two-loop Virasoro algebra, describing extended symmetries of the two-loop WZNW models.

Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series

Energy Technology Data Exchange (ETDEWEB)

Park, Kichul; Kyun, Nack Sung; Cho, Art E. [Korea Univ., Sejong (Korea, Republic of)

2013-02-15

It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding r{sup 2} = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.

Affinity labeling of the folate-methotrexate transporter from Leishmania donovani

International Nuclear Information System (INIS)

Beck, J.T.; Ullman, B.

1989-01-01

An affinity labeling technique has been developed to identify the folate-methotrexate transporter of Leishmania donovani promastigotes using activated derivatives of the ligands. These activated derivatives were synthesized by incubating folate and methotrexate with a 10-fold excess of 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide (EDC) for 10 min at ambient temperature in dimethyl sulfoxide. When intact wild-type (DI700) Leishmania donovani or preparations of their membranes were incubated with a 0.4 μM concentration of either activated [ 3 H]folate or activated [ 3 H]methotrexate, the radiolabeled ligands were covalently incorporated into a polypeptide with a molecular weight of approximately 46,000, as demonstrated by SDS-polyacrylamide gel electrophoresis. No affinity labeling of a 46,000-dalton protein was observed when equimolar concentrations of activated radiolabeled ligands were incubated with intact cells or membranes prepared from a methotrexate-resistant mutant clone of Leishmania donovani, MTXA5, that is genetically defective in folate-methotrexate transport capability. Time course studies indicated that maximal labeling of the 46,000-dalton protein occurred within 5-10 min of incubation of intact cells with activated ligand. These studies provide biochemical evidence that the folate-methotrexate transporter of Leishmania donovani can be identified in crude extracts by an affinity labeling technique and serve as a prerequisite to further analysis of the transport protein by providing a vehicle for subsequent purification of this membrane carrier. Moreover, these investigations suggest that the affinity labeling technique using EDC-activated ligands may be exploitable to analyze other cell surface binding proteins in Leishmania donovani, as well as in other organisms

Reconstitution of high-affinity opioid agonist binding in brain membranes

Energy Technology Data Exchange (ETDEWEB)

Remmers, A.E.; Medzihradsky, F. (Univ. of Michigan Medical School, Ann Arbor (United States))

1991-03-15

In synaptosomal membranes from rat brain cortex, the {mu} selective agonist ({sup 3}H)dihydromorphine in the absence of sodium, and the nonselective antagonist ({sup 3}H)naltrexone in the presence of sodium, bound to two populations of opioid receptor sites with K{sub d} values of 0.69 and 8.7 nM for dihydromorphine, and 0.34 and 5.5 nM for naltrexone. The addition of 5 {mu}M guanosine 5{prime}-({gamma}-thio)triphosphate (GTP({gamma}S)) strongly reduced high-affinity agonist but not antagonist binding. Exposure of the membranes to high pH reduced the number of GTP({gamma}-{sup 35}S) binding sites by 90% and low K{sub m}, opioid-sensitive GTPase activity by 95%. In these membranes, high-affinity agonist binding was abolished and modulation of residual binding by GTP({gamma}S) was diminished. Alkali treatment of the glioma cell membranes prior to fusion inhibited most of the low K{sub m} GTPase activity and prevented the reconstitution of agonist binding. The results show that high-affinity opioid agonist binding reflects the ligand-occupied receptor - guanine nucleotide binding protein complex.

Affinity membranes for hormone removal from aqueous solutions

NARCIS (Netherlands)

Urmenyi, A.M.; Poot, Andreas A.; Wessling, Matthias; Mulder, M.H.V.

2005-01-01

A novel affinity membrane was prepared by covalent binding of antibodies (against 17--estradiol) to a micro-porous poly(ethylene vinyl alcohol) (EVAL) membrane, taking benefit from the high surface area of EVAL membranes and the large number of reactive groups available for further surface

Diagnostics Strategies with Electrochemical Affinity Biosensors Using Carbon Nanomaterials as Electrode Modifiers

Science.gov (United States)

Campuzano, Susana; Yáñez-Sedeño, Paloma; Pingarrón, José M.

2016-01-01

Early diagnosis is often the key to successful patient treatment and survival. The identification of various disease signaling biomarkers which reliably reflect normal and disease states in humans in biological fluids explain the burgeoning research field in developing new methodologies able to determine the target biomarkers in complex biological samples with the required sensitivity and selectivity and in a simple and rapid way. The unique advantages offered by electrochemical sensors together with the availability of high affinity and specific bioreceptors and their great capabilities in terms of sensitivity and stability imparted by nanostructuring the electrode surface with different carbon nanomaterials have led to the development of new electrochemical biosensing strategies that have flourished as interesting alternatives to conventional methodologies for clinical diagnostics. This paper briefly reviews the advantages of using carbon nanostructures and their hybrid nanocomposites as electrode modifiers to construct efficient electrochemical sensing platforms for diagnosis. The review provides an updated overview of some selected examples involving attractive amplification and biosensing approaches which have been applied to the determination of relevant genetic and protein diagnostics biomarkers. PMID:28035946

In vitro evolution and affinity-maturation with Coliphage qβ display.

Directory of Open Access Journals (Sweden)

Claudia Skamel

Full Text Available The Escherichia coli bacteriophage, Qβ (Coliphage Qβ, offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV. DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets.

Multilayer affinity adsorption of albumin on polymer brushes modified membranes in a continuous-flow system.

Science.gov (United States)

Hu, Meng-Xin; Li, Xiang; Li, Ji-Nian; Huang, Jing-Jing; Ren, Ge-Rui

2018-02-23

Polymer brushes modified surfaces have been widely used for protein immobilization and isolation. Modification of membranes with polymer brushes increases the surface concentration of affinity ligands used for protein binding. Albumin is one of the transporting proteins and shows a high affinity to bile acids. In this work, the modified membranes with cholic acid-containing polymer brushes can be facilely prepared by the immobilization of cholic acid on the poly(2-hydroxyethyl methacrylate) grafted microporous polypropylene membranes (MPPMs) for affinity adsorption of albumin. ATR/FT-IR and X-ray photoelectron spectroscopy were used to characterize the chemical composition of the modified membranes. Water contact angle measurements were used to analyze the hydrophilic/hydrophobic properties of the membrane surface. The modified MPPMs show a high affinity to albumin and have little non-specific adsorption of hemoglobin. The dynamic binding capacity of albumin in the continous-flow system increases with the cycle number and feed rate as the binding degree of cholic acid is moderate. The highest binding capacity of affinity membranes is about 52.49 g/m 2 membrane, which is about 24 times more than the monolayer binding capacity. These results reveal proteins could be captured in multilayers by the polymer brushes containing affinity ligands similar to the polymer brushes containing ion-exchange groups, which open up the potential of the polymer brushes containing affinity ligands in protein or another components separation. And the cholic acid containing polymer brushes modified membranes has the promising potential for albumin separation and purification rapidly from serum or fermented solution in medical diagnosis and bioseparation. Copyright © 2018 Elsevier B.V. All rights reserved.

Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry.

Science.gov (United States)

Krainer, Georg; Keller, Sandro

2015-04-01

Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

Distinguishing plant population and variety with UAV-derived vegetation indices

Science.gov (United States)

Oakes, Joseph; Balota, Maria

2017-05-01

Variety selection and seeding rate are two important choice that a peanut grower must make. High yielding varieties can increase profit with no additional input costs, while seeding rate often determines input cost a grower will incur from seed costs. The overall purpose of this study was to examine the effect that seeding rate has on different peanut varieties. With the advent of new UAV technology, we now have the possibility to use indices collected with the UAV to measure emergence, seeding rate, growth rate, and perhaps make yield predictions. This information could enable growers to make management decisions early in the season based on low plant populations due to poor emergence, and could be a useful tool for growers to use to estimate plant population and growth rate in order to help achieve desired crop stands. Red-Green-Blue (RGB) and near-infrared (NIR) images were collected from a UAV platform starting two weeks after planting and continued weekly for the next six weeks. Ground NDVI was also collected each time aerial images were collected. Vegetation indices were derived from both the RGB and NIR images. Greener area (GGA- the proportion of green pixels with a hue angle from 80° to 120°) and a* (the average red/green color of the image) were derived from the RGB images while Normalized Differential Vegetative Index (NDVI) was derived from NIR images. Aerial indices were successful in distinguishing seeding rates and determining emergence during the first few weeks after planting, but not later in the season. Meanwhile, these aerial indices are not an adequate predictor of yield in peanut at this point.

Production and Characterization of Desmalonichrome Relative Binding Affinity for Uranyl Ions in Relation to Other Siderophores

Energy Technology Data Exchange (ETDEWEB)

Mo, Kai-For; Dai, Ziyu; Wunschel, David S.

2016-06-24

Siderophores are Fe binding secondary metabolites that have been investigated for their uranium binding properties. Much of the previous work has focused on characterizing hydroxamate types of siderophores, such as desferrioxamine B, for their uranyl binding affinity. Carboxylate forms of these metabolites hold potential to be more efficient chelators of uranyl, yet they have not been widely studied and are more difficult to obtain. Desmalonichrome is a carboxylate siderophore which is not commercially available and so was obtained from the ascomycete fungus Fusarium oxysporum cultivated under Fe depleted conditions. The relative affinity for uranyl binding of desmalonichrome was investigated using a competitive analysis of binding affinities between uranyl acetate and different concentrations of iron(III) chloride using electrospray ionization mass spectrometry (ESI-MS). In addition to desmalonichrome, three other siderophores, including two hydroxamates (desferrioxamine B and desferrichrome) and one carboxylate (desferrichrome A) were studied to understand their relative affinities for the uranyl ion at two pH values. The binding affinities of hydroxymate siderophores to uranyl ion were found to decrease to a greater degree at lower pH as the concentration of Fe (III) ion increases. On the other hand, lowering pH has little impact on the binding affinities between carboxylate siderophores and uranyl ion. Desmalonichrome was shown to have the greatest relative affinity for uranyl at any pH and Fe(III) concentration. These results suggest that acidic functional groups in the ligands are critical for strong chelation with uranium at lower pH.

Characterization of Foliage Mutants for Plant Variety Registration

International Nuclear Information System (INIS)

Affrida Abu Hassan; Shuhaimi Shamsuddin; Zaiton Ahmad

2011-01-01

Breeding for new plant varieties requires a substantial investment in terms of skill, labour, material resources and financing. Thus, registration of new plant variety is important to ensure return of revenue and protection of the breeder's right. Before a new variety is registered, it has to comply certain requirements under Plant Variety Protection Act. One of the most important requirements is, the new species/variety must be morphologically distinguishable from existing plant varieties. This paper discusses detailed leaf characteristics of 4 foliage mutants produced by Malaysian Nuclear Agency as part of the requirement for new variety registration. (author)

Definition of percolation thresholds on self-affine surfaces

NARCIS (Netherlands)

Marrink, S.J.; Paterson, Lincoln; Knackstedt, Mark A.

2000-01-01

We study the percolation transition on a two-dimensional substrate with long-range self-affine correlations. We find that the position of the percolation threshold on a correlated lattice is no longer unique and depends on the spanning rule employed. Numerical results are provided for spanning

Complementary three-dimensional quantitative structure-activity relationship modeling of binding affinity and functional potency

DEFF Research Database (Denmark)

Tosco, Paolo; Ahring, Philip K; Dyhring, Tino

2009-01-01

Complementary 3D-QSAR modeling of binding affinity and functional potency is proposed as a tool to pinpoint the molecular features of the ligands, and the corresponding amino acids in the receptor, responsible for high affinity binding vs those driving agonist behavior and receptor activation. Th...

Sensibility of different wheat varieties (strains) to Ar+ implantation

International Nuclear Information System (INIS)

Cui Huanhu; Jing Hua; Ma Aiping; Kang Xiuli; Yang Liping; Huang Mingjing; Ma Buzhou; Shanxi Academy of Agricultural Sciences, Taiyuan

2005-01-01

The sensibility of different wheat varieties (strains) to Ar + implantation was studied. The results showed that the survival rate of 21 wheat varieties (strains) at the dose of 6 x 10 16 Ar + /cm 2 could be divided into five groups: surplus sensitive varieties (strains), sensitive varieties (strains), transitional varieties (strains), obtuse varieties (strains) and surplus obtuse varieties (strains). The sensibility of wheat varieties (strains) to Ar + injection is high-moisture-fertility wheat varieties (strains) > medium-moisture-fertility wheat varieties (strains) > dry land wheat varieties (strains). The study has provided theoretical basis in induced mutation medial lethal dose of different wheat varieties (strains) to Ar + implantation. (authors)

High-affinity α4β2 nicotinic receptors mediate the impairing effects of acute nicotine on contextual fear extinction.

Science.gov (United States)

Kutlu, Munir Gunes; Holliday, Erica; Gould, Thomas J

2016-02-01

Previously, studies from our lab have shown that while acute nicotine administered prior to training and testing enhances contextual fear conditioning, acute nicotine injections prior to extinction sessions impair extinction of contextual fear. Although there is also strong evidence showing that the acute nicotine's enhancing effects on contextual fear conditioning require high-affinity α4β2 nicotinic acetylcholine receptors (nAChRs), it is unknown which nAChR subtypes are involved in the acute nicotine-induced impairment of contextual fear extinction. In this study, we investigated the effects of acute nicotine administration on contextual fear extinction in knock-out (KO) mice lacking α4, β2 or α7 subtypes of nAChRs and their wild-type (WT) littermates. Both KO and WT mice were first trained and tested for contextual fear conditioning and received a daily contextual extinction session for 4 days. Subjects received intraperitoneal injections of nicotine (0.18 mg/kg) or saline 2-4 min prior to each extinction session. Our results showed that the mice that lack α4 and β2 subtypes of nAChRs showed normal contextual fear extinction but not the acute nicotine-induced impairment while the mice that lack the α7 subtype showed both normal contextual extinction and nicotine-induced impairment of contextual extinction. In addition, control experiments showed that acute nicotine-induced impairment of contextual fear extinction persisted when nicotine administration was ceased and repeated acute nicotine administrations alone did not induce freezing behavior in the absence of context-shock learning. These results clearly demonstrate that high-affinity α4β2 nAChRs are necessary for the effects of acute nicotine on contextual fear extinction. Copyright © 2015 Elsevier Inc. All rights reserved.

Simple Methods for Scanner Drift Normalization Validated for Automatic Segmentation of Knee Magnetic Resonance Imaging

DEFF Research Database (Denmark)

Dam, Erik Bjørnager

2018-01-01

Scanner drift is a well-known magnetic resonance imaging (MRI) artifact characterized by gradual signal degradation and scan intensity changes over time. In addition, hardware and software updates may imply abrupt changes in signal. The combined effects are particularly challenging for automatic...... image analysis methods used in longitudinal studies. The implication is increased measurement variation and a risk of bias in the estimations (e.g. in the volume change for a structure). We proposed two quite different approaches for scanner drift normalization and demonstrated the performance...... for segmentation of knee MRI using the fully automatic KneeIQ framework. The validation included a total of 1975 scans from both high-field and low-field MRI. The results demonstrated that the pre-processing method denoted Atlas Affine Normalization significantly removed scanner drift effects and ensured...

Affinity of four polar neurotransmitters for lipid bilayer membranes

DEFF Research Database (Denmark)

Wang, Chunhua; Ye, Fengbin; Valardez, Gustavo F.

2011-01-01

. The simulations suggest that this attraction mainly relies on electrostatic interactions of the amino group of the neurotransmitter and the lipid phosphate. We conclude that moderate attraction to lipid membranes occurs for some polar neurotransmitters and hence that one premise for a theory of bilayer-mediated......Weak interactions of neurotransmitters and the lipid matrix in the synaptic membrane have been hypothesized to play a role in synaptic transmission of nerve signals, particularly with respect to receptor desensitization (Cantor, R. S. Biochemistry 2003, 42, 11891). The strength of such interactions......, however, was not measured, and this is an obvious impediment for further evaluation and understanding of a possible role for desensitization. We have used dialysis equilibrium to directly measure the net affinity of selected neurotransmitters for lipid membranes and analyzed this affinity data...

Extreme disorder in an ultrahigh-affinity protein complex

Science.gov (United States)

Borgia, Alessandro; Borgia, Madeleine B.; Bugge, Katrine; Kissling, Vera M.; Heidarsson, Pétur O.; Fernandes, Catarina B.; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J.; Nettels, Daniel; Kragelund, Birthe B.; Best, Robert B.; Schuler, Benjamin

2018-03-01

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

Momentum conserving defects in affine Toda field theories

Energy Technology Data Exchange (ETDEWEB)

Bristow, Rebecca; Bowcock, Peter [Department of Mathematical Sciences, Durham University,Durham, DH1 3LE (United Kingdom)

2017-05-30

Type II integrable defects with more than one degree of freedom at the defect are investigated. A condition on the form of the Lagrangian for such defects is found which ensures the existence of a conserved momentum in the presence of the defect. In addition it is shown that for any Lagrangian satisfying this condition, the defect equations of motion, when taken to hold everywhere, can be extended to give a Bäcklund transformation between the bulk theories on either side of the defect. This strongly suggests that such systems are integrable. Momentum conserving defects and Bäcklund transformations for affine Toda field theories based on the A{sub n}, B{sub n}, C{sub n} and D{sub n} series of Lie algebras are found. The defect associated with the D{sub 4} affine Toda field theory is examined in more detail. In particular classical time delays for solitons passing through the defect are calculated.

Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

KAUST Repository

Wang, Xiaolei

2014-12-12

Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify

A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent

Directory of Open Access Journals (Sweden)

Lykke Pedersen

2014-01-01

Full Text Available Antisense oligonucleotides complementary to RNA targets promise generality and ease of drug design. The first systemically administered antisense drug was recently approved for treatment and others are in clinical development. Chemical modifications that increase the hybridization affinity of oligonucleotides are reasoned to confer higher potency, i.e., modified oligonucleotides can be dosed at lower concentrations to achieve the same effect. Surprisingly, shorter and less affine oligonucleotides sometimes display increased potency. To explain this apparent contradiction, increased uptake or decreased propensity to form structures have been suggested as possible mechanisms. Here, we provide an alternative explanation that invokes only the kinetics behind oligonucleotide-mediated cleavage of RNA targets. A model based on the law of mass action predicts, and experiments support, the existence of an optimal binding affinity. Exaggerated affinity, and not length per se, is detrimental to potency. This finding clarifies how to optimally apply high-affinity modifications in the discovery of potent antisense oligonucleotide drugs.

Smooth surfaces from bilinear patches: Discrete affine minimal surfaces

KAUST Repository

Kä ferbö ck, Florian; Pottmann, Helmut

2013-01-01

Motivated by applications in freeform architecture, we study surfaces which are composed of smoothly joined bilinear patches. These surfaces turn out to be discrete versions of negatively curved affine minimal surfaces and share many properties

Storage Potential of Local Brazilian Pine Seed Varieties

Directory of Open Access Journals (Sweden)

Cristhyane Garcia Araldi

2018-03-01

Full Text Available ABSTRACT Brazilian pine seeds (Araucaria angustifolia are recalcitrant, and there are no studies evaluating the longevity of their different varieties. Our objective was to evaluate the capacity of different varieties of Brazilian pine seeds to maintain their physiological quality during storage. Seeds of the varieties: sancti josephi (I, angustifolia (II, caiova (III and indehiscens (IV were collected from two populations located in Santa Catarina, and stored under laboratory conditions and in a cold room for 90 days. On average, freshly harvested seeds showed 88% viability, and varieties II and III maintained the greatest viability (with the greatest vigor for variety II after 90 days in storage. Varieties I and II maintained their pre-germinative metabolism for a longer period than the other varieties during storage. Therefore, seeds from the angustifolia variety (II have higher storage potential than the other varieties, maintaining approximately 61% viability at 90 days of storage.

Combining structural modeling with ensemble machine learning to accurately predict protein fold stability and binding affinity effects upon mutation.

Directory of Open Access Journals (Sweden)

Niklas Berliner

Full Text Available Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases.

Combinatorial Vector Fields for Piecewise Affine Control Systems

DEFF Research Database (Denmark)

Wisniewski, Rafal; Larsen, Jesper Abildgaard

2008-01-01

This paper is intended to be a continuation of Habets and van Schuppen (2004) and Habets, Collins and van Schuppen (2006), which address the control problem for piecewise-affine systems on an arbitrary polytope or a family of these. Our work deals with the underlying combinatorics of the underlyi...

An Affine Combination of Adaptive Filters for Channels with Different Sparsity Levels

Directory of Open Access Journals (Sweden)

M. Butsenko

2016-06-01

Full Text Available In this paper we present an affine combination strategy for two adaptive filters. One filter is designed to handle sparse impulse responses and the other one performs better if impulse response is dispersive. Filter outputs are combined using an adaptive mixing parameter and the resulting output shows a better performance than each of the combining filters separately. We also demonstrate that affine combination results in faster convergence than a convex combination of two adaptive filters.

Size and shape dependent deprotonation potential and proton affinity of nanodiamond

International Nuclear Information System (INIS)

Barnard, Amanda S; Per, Manolo C

2014-01-01

Many important reactions in biology and medicine involve proton abstraction and transfer, and it is integral to applications such as drug delivery. Unlike electrons, which are quantum mechanically delocalized, protons are instantaneously localized on specific residues in these reactions, which can be a distinct advantage. However, the introduction of nanoparticles, such as non-toxic nanodiamonds, to this field complicates matters, as the number of possible sites increases as the inverse radius of the particle. In this paper we present >10 4 simulations that map the size- and shape-dependence of the deprotonation potential and proton affinity of nanodiamonds in the range 1.8–2.7 nm in average diameter. We find that while the average deprotonation potential and proton affinities decrease with size, the site-specific values are inhomogeneous over the surface of the particles, exhibiting strong shape-dependence. The proton affinity is strongly facet-dependent, whereas the deprotonation potential is edge/corner-dependent, which creates a type of spatial hysteresis in the transfer of protons to and from the nanodiamond, and provides new opportunities for selective functionalization. (paper)

Size and shape dependent deprotonation potential and proton affinity of nanodiamond

Science.gov (United States)

Barnard, Amanda S.; Per, Manolo C.

2014-11-01

Many important reactions in biology and medicine involve proton abstraction and transfer, and it is integral to applications such as drug delivery. Unlike electrons, which are quantum mechanically delocalized, protons are instantaneously localized on specific residues in these reactions, which can be a distinct advantage. However, the introduction of nanoparticles, such as non-toxic nanodiamonds, to this field complicates matters, as the number of possible sites increases as the inverse radius of the particle. In this paper we present \\gt {{10}4} simulations that map the size- and shape-dependence of the deprotonation potential and proton affinity of nanodiamonds in the range 1.8-2.7 nm in average diameter. We find that while the average deprotonation potential and proton affinities decrease with size, the site-specific values are inhomogeneous over the surface of the particles, exhibiting strong shape-dependence. The proton affinity is strongly facet-dependent, whereas the deprotonation potential is edge/corner-dependent, which creates a type of spatial hysteresis in the transfer of protons to and from the nanodiamond, and provides new opportunities for selective functionalization.

Object matching using a locally affine invariant and linear programming techniques.

Science.gov (United States)

Li, Hongsheng; Huang, Xiaolei; He, Lei

2013-02-01

In this paper, we introduce a new matching method based on a novel locally affine-invariant geometric constraint and linear programming techniques. To model and solve the matching problem in a linear programming formulation, all geometric constraints should be able to be exactly or approximately reformulated into a linear form. This is a major difficulty for this kind of matching algorithm. We propose a novel locally affine-invariant constraint which can be exactly linearized and requires a lot fewer auxiliary variables than other linear programming-based methods do. The key idea behind it is that each point in the template point set can be exactly represented by an affine combination of its neighboring points, whose weights can be solved easily by least squares. Errors of reconstructing each matched point using such weights are used to penalize the disagreement of geometric relationships between the template points and the matched points. The resulting overall objective function can be solved efficiently by linear programming techniques. Our experimental results on both rigid and nonrigid object matching show the effectiveness of the proposed algorithm.

Flower volatiles, crop varieties and bee responses.

Directory of Open Access Journals (Sweden)

Björn K Klatt

Full Text Available Pollination contributes to an estimated one third of global food production, through both the improvement of the yield and the quality of crops. Volatile compounds emitted by crop flowers mediate plant-pollinator interactions, but differences between crop varieties are still little explored. We investigated whether the visitation of crop flowers is determined by variety-specific flower volatiles using strawberry varieties (Fragaria x ananassa Duchesne and how this affects the pollination services of the wild bee Osmia bicornis L. Flower volatile compounds of three strawberry varieties were measured via headspace collection. Gas chromatography showed that the three strawberry varieties produced the same volatile compounds but with quantitative differences of the total amount of volatiles and between distinct compounds. Electroantennographic recordings showed that inexperienced females of Osmia bicornis had higher antennal responses to all volatile compounds than to controls of air and paraffin oil, however responses differed between compounds. The variety Sonata was found to emit a total higher level of volatiles and also higher levels of most of the compounds that evoked antennal responses compared with the other varieties Honeoye and Darselect. Sonata also received more flower visits from Osmia bicornis females under field conditions, compared with Honeoye. Our results suggest that differences in the emission of flower volatile compounds among strawberry varieties mediate their attractiveness to females of Osmia bicornis. Since quality and quantity of marketable fruits depend on optimal pollination, a better understanding of the role of flower volatiles in crop production is required and should be considered more closely in crop-variety breeding.

Yield and competition in barley variety mixtures

Directory of Open Access Journals (Sweden)

Kari Jokinen

1991-09-01

Full Text Available Competition between spring barley varieties and yield performance of two-, three and four-variety mixtures were studied in two replacement series field experiments. In the first experiment, repeated in three successive years (1983 —85 the components were the six-row varieties Agneta, Arra, Hja-673 and Porno. In the second experiment (1984, including two nitrogen doses (50 and 100 kgN/ha, both six-row (Agneta, Pomo and two-row (Ida, Kustaa varieties were used. Arra in the first and Agneta in the second experiment were the most competitive varieties. The results suggested that the fast growth of Arra at the beginning promoted its competitive ability. Increase in available nitrogen usually strengthened the competitiveness of Agneta. The observed competitive differences between varieties were not related to the earliness of a variety, neither to the morphological characters (two- and six-row varieties nor to the grain yield of a variety grown alone. The competitive ability was not always a stable character, the dominant suppression relationship varying from one environment to another (e.g. growing season, nitrogen dose. The observed overyielding was not statistically significant. The ratio of actual to expected yield and the relative yield total of several mixtures exceeded slightly one. As a conclusion, the yield advantage of mixtures was marginal. As a rule, the mixtures were not more stable than monocultures as determined by the coefficient of variation. However, the yield of some mixtures varied less than the yield of the most stable monoculture.

Gravitational Goldstone fields from affine gauge theory

Science.gov (United States)

Tresguerres, Romualdo; Mielke, Eckehard W.

2000-08-01

In order to facilitate the application of standard renormalization techniques, gravitation should be described, in the pure connection formalism, as a Yang-Mills theory of a certain spacetime group, say the Poincaré or the affine group. This embodies the translational as well as the linear connection. However, the coframe is not the standard Yang-Mills-type gauge field of the translations, since it lacks the inhomogeneous gradient term in the gauge transformations. By explicitly restoring this ``hidden'' piece within the framework of nonlinear realizations, the usual geometrical interpretation of the dynamical theory becomes possible, and in addition one can avoid the metric or coframe degeneracy which would otherwise interfere with the integrations within the path integral. We claim that nonlinear realizations provide the general mathematical scheme for the foundation of gauge theories of spacetime symmetries. When applied to construct the Yang-Mills theory of the affine group, tetrads become identified with nonlinear translational connections; the anholonomic metric no longer constitutes an independent gravitational potential, since its degrees of freedom reveal a correspondence to eliminateable Goldstone bosons. This may be an important advantage for quantization.

Morphoagrobiological properties and productivity of new soft winter wheat varieties under the conditions of Kirovohrad variety testing station

Directory of Open Access Journals (Sweden)

О. Л. Уліч

2017-03-01

Full Text Available Purpose. To study morphoagrobiological and adaptive properties, level of yielding capacity of recently registered soft winter wheat varieties of various ecological groups under agroecological conditions of Kirovohrad variety testing station. Methods. Field study, laboratory test, analytical procedure and statistical evaluation. Results. It was established that the yield level of is a key composite indicator of genotype adaptation to agroecological growing conditions. Experimental data indicate significant deviations of yield depending on the genotype and the year of study. During three years of experiments, yield depending of the variety ranged from 4.26 to 9.71 t/ha, such varieties as ‘CN Kombin’, ‘Estivus’, ‘Tradytsiia odeska’, ‘Mudrist odeska’, ‘Lil’ and ‘Fabius’ had higher yields. In case of dry weather conditions and unfavorable agro-ecological factors, the following varieties as ‘Mudrist odeska’, ‘Veteran’, ‘Lil’, ‘Tsentylivka’, ‘Fabius’, ‘Patras’, ‘Montrei’ have demonstrated good adaptive properties. Their yield has decreased by 9,2–19,0%, while in the varieties ‘Mahistral’, ‘Poltavka’, ‘Harantiia odeska’ and ‘Pokrova’ – by 34.4, 42.4, 45.2 and 50.6% accordingly. Conclusions. Investigated soft winter wheat varieties differ in morphoagrobiological characteristics, productivity, height, maturation period, adaptability as well as economic and agronomic value. According to the complex of such indices as productivity, agronomic characters and properties as well as adaptability, in the microzone of Kirovohrad variety testing station it is advisable to grow varie­ties ‘CN Kombi’, ‘Pokrova’, ‘Mudrist odeska’, ‘Veteran’ and ‘Lil’.

Mild desalination demo pilot: New normalization approach to effectively evaluate electrodialysis reversal technology

Directory of Open Access Journals (Sweden)

Roel Bisselink

2016-06-01

Full Text Available Key performance indicators for characterization of nanofiltration performance are well developed, similar key performance indicators for electrodialysis reversal are however underdeveloped. Under the E4Water project Dow Benelux BV and Evides Industriewater BV operate a pilot facility to compare both technologies for their application to mildly desalinate a variety of brackish water streams. Normalized pressure drop, normalized current efficiency and normalized membrane resistance proved to be a useful tool to interpret process performance and to initiate a cleaning procedure if required. The availability of these normalized key performance indicators enables optimization and process monitoring and control of electrodialysis reversal independent of the continuously changing conditions of the feed water.

Epitope structure and binding affinity of single chain llama anti-β-amyloid antibodies revealed by proteolytic excision affinity-mass spectrometry.

Science.gov (United States)

Paraschiv, Gabriela; Vincke, Cécile; Czaplewska, Paulina; Manea, Marilena; Muyldermans, Serge; Przybylski, Michael

2013-01-01

ß-Amyloid (Aß) immunotherapy has become a promising strategy for reducing the level of Aß in brain. New immunological approaches have been recently proposed for rapid, early diagnosis, and molecular treatment of neurodegenerative diseases related to Alzheimer's Disease (AD). The combination of proteolytic epitope excision and extraction and mass spectrometry using digestion with various proteases has been shown to be an efficient tool for the identification and molecular characterization of antigenic determinants. Here, we report the identification of the Aβ epitope recognized by the variable domain of single chain llama anti-Aβ-antibodies, termed Aβ-nanobodies, that have been discovered in the blood of camelids and found to be promising candidates for immunotherapy of AD. The epitope recognized by two Aβ-specific nanobodies was identified by proteolytic epitope extraction- and excision-mass spectrometry using a series of proteases (trypsin, chymotrypsin, GluC-protease, and LysC-protease). Matrix-assisted laser desorption ionization--mass spectrometric analysis of the affinity--elution fraction provided the epitope, Aβ(17-28), in the mid- to carboxy-terminal domain of Aβ, which has been shown to exert an Aß-fibril inhibiting effect. Affinity studies of the synthetic epitope confirmed that the Aβ(17-28) peptide is the minimal fragment that binds to the nanobodies. The interactions between the nanobodies and full length Aβ(1-40) or Aβ-peptides containing or lacking the epitope sequence were further characterized by enzyme linked immunosorbent assay and bioaffinity analysis. Determinations of binding affinities between the Aβ-nanobodies and Aβ(1-40) and the Aβ(17-28) epitope provided K(D) values of approximately 150 and 700 nmol, respectively. Thus, the knowledge of the epitope may be highly useful for future studies of Aβ-aggregation (oligomerization and fibril formation) and for designing new aggregation inhibitors. Copyright © 2012 John Wiley

Export Variety and Country Productivity

OpenAIRE

Feenstra, Robert; Looi Kee, Hiau

2004-01-01

The authors study the link between export product variety and country productivity based on data from 34 industrial and developing countries, from 1982 to 1997. They measure export product variety by the share of U.S. imports on the set of goods exported by each sampled country relative to the world. It is a theoretically sound index which is consistent with within-country GDP maximization...

Affinity-seeking, social loneliness, and social avoidance among Facebook users.

Science.gov (United States)

Lemieux, Robert; Lajoie, Sean; Trainor, Nathan E

2013-04-01

This study explored the relations between use of the social networking site Facebook and scores on affinity-seeking, social loneliness, and social avoidance by 313 college students. Social loneliness and social avoidance, but not affinity-seeking, were positively and statistically significantly related to time spent using Facebook. The number of close Facebook friends was negatively and statistically significantly related to social loneliness and social avoidance. Women perceived Facebook as a more integral part of daily interactions than did men. 38% of the 283 Facebook members indicated their accounts contained information and/or a picture that could embarrass them, with men having significantly more embarrassing content than women. The findings are discussed within the context of social compensation.

Insulin binding and stimulation of hexose and amino acid transport by normal and receptor-defective human fibroblasts

International Nuclear Information System (INIS)

Longo, N.; Nagata, N.; Danner, D.; Priest, J.; Elsas, L.

1986-01-01

The authors analyzed insulin receptors in cells cultured from a sibship of related parents who had two offspring with severe insulin resistance (Leprechaunism). 124 I-Insulin (1 ng/ml) binding to skin fibroblasts from the proband, mother, and father was 9, 60 and 62% of control cells, respectively, at equilibrium, Non-linear regression analysis, utilizing a two receptors model, of curvilinear Scatchard plots indicated a reduced number of high-affinity binding sites in both parents. Influx of L-Proline (System A), L-Serine (ASC) and L-Leucine (L) was similar in control and mutant cells. Similarly, during the depletion of intracellular amino acid pools, there was a release from transinhibition for System A and a decrease of transstimulation of Systems ASC and L in both cell lines. Surprisingly, insulin augmented, normally, A system influx with an ED 50 = 70 ng/ml at 24 0 C and 7 ng/ml at 37 0 C. By contrast insulin failed to simulated 3-0-methyl-D-glucose influx into the proband's cells, while normal cells were stimulated 30% with an ED 50 of 6 ng/ml. These results indicate that defective high-affinity insulin binding is inherited as an autosomal recessive trait; that general membrane functions are intact; that insulin regulates A system amino acid and hexose transport by two different mechanisms; and, that the latter mechanism is impaired by this family's receptor mutation

Acrylamide in potato crisps prepared from 20 UK-grown varieties: Effects of variety and tuber storage time

Science.gov (United States)

Elmore, J. Stephen; Briddon, Adrian; Dodson, Andrew T.; Muttucumaru, Nira; Halford, Nigel G.; Mottram, Donald S.

2015-01-01

Twenty varieties of field-grown potato were stored for 2 months and 6 months at 8 °C. Mean acrylamide contents in crisps prepared from all varieties at both storage times ranged from 131 μg/kg in Verdi to 5360 μg/kg in Pentland Dell. In contrast to previous studies, the longer storage period did not affect acrylamide formation significantly for most varieties, the exceptions being Innovator, where acrylamide formation increased, and Saturna, where it decreased. Four of the five varieties designated as suitable for crisping produced crisps with acrylamide levels below the European Commission indicative value of 1000 μg/kg (Saturna, Lady Rosetta, Lady Claire, and Verdi); the exception was Hermes. Two varieties more often used for French fries, Markies and Fontane, also produced crisps with less than 1000 μg/kg acrylamide. Correlations between acrylamide, its precursors and crisp colour are described, and the implications of the results for production of potato crisps are discussed. PMID:25842300

[CH4 emission features of leading super-rice varieties and their relationships with the varieties growth characteristics in Yangtze Delta of China].

Science.gov (United States)

Yan, Xiao-Jun; Wang, Li-Li; Jiang, Yu; Deng, Ai-Xing; Tian, Yun-Lu; Zhang, Wei-Jian

2013-09-01

A pot experiment was conducted to study the CH4 emission features of fourteen leading super-rice varieties (six Japonica rice varieties and eight Indica hybrid rice varieties) and their relationships with the varieties growth characteristics in Yangtze Delta. Two distinct peaks of CH4 emission were detected during the entire growth period of the varieties, one peak occurred at full-tillering stage, and the other appeared at booting stage. The average total CH4 emission of Japonica rice varieties was 37.6% higher than that of the Indica hybrid rice varieties (Price types occurred at the post-anthesis phase. For all the varieties, there was a significant positive correlation between the total CH4 emission and the maximum leaf area, but the correlations between the CH4 emission and the other growth characteristics varied with variety type. The total CH4 emission of Japonica rice varieties had a significant positive correlation with plant height, while the correlations between the total CH4 emission of Indica hybrid rice varieties and their plant height were not significant. The total CH4 emission of Indica hybrid rice varieties had significant negative correlations with the total aboveground biomass, grain yield, and harvest index, but the correlations were not significant for Japonica rice varieties. The lower CH4 emission of Indica hybrid rice varieties was likely due to their significantly higher root biomass, as compared with Japonica rice varieties.

Preparation and characterization of fluorophenylboronic acid-functionalized affinity monolithic columns for the selective enrichment of cis-diol-containing biomolecules.

Science.gov (United States)

Li, Qianjin; Liu, Zhen

2015-01-01

Boronate affinity monolithic columns have been developed into an important means for the selective recognition and capture of cis-diol-containing biomolecules, such as glycoproteins, nucleosides and saccharides. The ligands of boronic acids are playing an important role in boronate affinity monolithic columns. Although several boronate affinity monoliths with high affinity toward cis-diol-containing biomolecules have been reported, only few publications are focused on their detailed procedures for preparation and characterization. This chapter describes in detail the preparation and characterization of a boronate affinity monolithic column applying 2,4-difluoro-3-formyl-phenylboronic acid (DFFPBA) as a ligand. The DFFPBA-functionalized monolithic column not only exhibited an ultrahigh boronate affinity toward cis-diol-containing biomolecules, but also showed great potential for the selective enrichment of cis-diol-containing biomolecules in real samples.

An affine model of the dynamics of astrophysical discs

Science.gov (United States)

Ogilvie, Gordon I.

2018-06-01

Thin astrophysical discs are very often modelled using the equations of 2D hydrodynamics. We derive an extension of this model that describes more accurately the behaviour of a thin disc in the absence of self-gravity, magnetic fields, and complex internal motions. The ideal fluid theory is derived directly from Hamilton's Principle for a 3D fluid after making a specific approximation to the deformation gradient tensor. We express the equations in Eulerian form after projection on to a reference plane. The disc is thought of as a set of fluid columns, each of which is capable of a time-dependent affine transformation, consisting of a translation together with a linear transformation in three dimensions. Therefore, in addition to the usual 2D hydrodynamics in the reference plane, the theory allows for a deformation of the mid-plane (as occurs in warped discs) and for the internal shearing motions that accompany such deformations. It also allows for the vertical expansions driven in non-circular discs by a variation of the vertical gravitational field around the horizontal streamlines, or by a divergence of the horizontal velocity. The equations of the affine model embody conservation laws for energy and potential vorticity, even for non-planar discs. We verify that they reproduce exactly the linear theories of 3D warped and eccentric discs in a secular approximation. However, the affine model does not rely on any secular or small-amplitude assumptions and should be useful in more general circumstances.

Affinity-tuning leukocyte integrin for development of safe therapeutics

Science.gov (United States)

Park, Spencer

Much attention has been given to the molecular and cellular pathways linking inflammation with cancer and the local tumor environment to identify new target molecules that could lead to improved diagnosis and treatment. Among the many molecular players involved in the complex response, central to the induction of inflammation is intercellular adhesion molecule (ICAM)-1, which is of particular interest for its highly sensitive and localized expression in response to inflammatory signals. ICAM-1, which has been implicated to play a critical role in tumor progression in various types of cancer, has also been linked to cancer metastases, where ICAM-1 facilitates the spread of metastatic cancer cells to secondary sites. This unique expression profile of ICAM-1 throughout solid tumor microenvironment makes ICAM-1 an intriguing molecular target, which holds great potential as an important diagnostic and therapeutic tool. Herein, we have engineered the ligand binding domain, or the inserted (I) domain of a leukocyte integrin, to exhibit a wide range of monovalent affinities to the natural ligand, ICAM-1. Using the resulting I domain variants, we have created drug and gene delivery nanoparticles, as well as targeted immunotherapeutics that have the ability to bind and migrate to inflammatory sites prevalent in tumors and the associated microenvironment. Through the delivery of diagnostic agents, chemotherapeutics, and immunotherapeutics, the following chapters demonstrate that the affinity enhancements achieved by directed evolution bring the affinity of I domains into the range optimal for numerous applications.

Modulating uranium binding affinity in engineered calmodulin EF-hand peptides: effect of phosphorylation.

Directory of Open Access Journals (Sweden)

Romain Pardoux

Full Text Available To improve our understanding of uranium toxicity, the determinants of uranyl affinity in proteins must be better characterized. In this work, we analyzed the contribution of a phosphoryl group on uranium binding affinity in a protein binding site, using the site 1 EF-hand motif of calmodulin. The recombinant domain 1 of calmodulin from A. thaliana was engineered to impair metal binding at site 2 and was used as a structured template. Threonine at position 9 of the loop was phosphorylated in vitro, using the recombinant catalytic subunit of protein kinase CK2. Hence, the T(9TKE(12 sequence was substituted by the CK2 recognition sequence TAAE. A tyrosine was introduced at position 7, so that uranyl and calcium binding affinities could be determined by following tyrosine fluorescence. Phosphorylation was characterized by ESI-MS spectrometry, and the phosphorylated peptide was purified to homogeneity using ion-exchange chromatography. The binding constants for uranyl were determined by competition experiments with iminodiacetate. At pH 6, phosphorylation increased the affinity for uranyl by a factor of ∼5, from K(d = 25±6 nM to K(d = 5±1 nM. The phosphorylated peptide exhibited a much larger affinity at pH 7, with a dissociation constant in the subnanomolar range (K(d = 0.25±0.06 nM. FTIR analyses showed that the phosphothreonine side chain is partly protonated at pH 6, while it is fully deprotonated at pH 7. Moreover, formation of the uranyl-peptide complex at pH 7 resulted in significant frequency shifts of the ν(as(P-O and ν(s(P-O IR modes of phosphothreonine, supporting its direct interaction with uranyl. Accordingly, a bathochromic shift in ν(as(UO(2(2+ vibration (from 923 cm(-1 to 908 cm(-1 was observed upon uranyl coordination to the phosphorylated peptide. Together, our data demonstrate that the phosphoryl group plays a determining role in uranyl binding affinity to proteins at physiological pH.

Modulating uranium binding affinity in engineered Calmodulin EF-hand peptides: effect of phosphorylation

International Nuclear Information System (INIS)

Pardoux, Romain; Sauge-Merle, Sandrine; Lemaire, David; Guilloreau, Luc; Berthomieu, Catherine; Delangle, Pascale; Adriano, Jean-Marc

2012-01-01

To improve our understanding of uranium toxicity, the determinants of uranyl affinity in proteins must be better characterized. In this work, we analyzed the contribution of a phosphoryl group on uranium binding affinity in a protein binding site, using the site 1 EF-hand motif of calmodulin. The recombinant domain 1 of calmodulin from A. thaliana was engineered to impair metal binding at site 2 and was used as a structured template. Threonine at position 9 of the loop was phosphorylated in vitro, using the recombinant catalytic subunit of protein kinase CK2. Hence, the T 9 TKE 12 sequence was substituted by the CK2 recognition sequence TAAE. A tyrosine was introduced at position 7, so that uranyl and calcium binding affinities could be determined by following tyrosine fluorescence. Phosphorylation was characterized by ESI-MS spectrometry, and the phosphorylated peptide was purified to homogeneity using ion-exchange chromatography. The binding constants for uranyl were determined by competition experiments with iminodiacetate. At pH 6, phosphorylation increased the affinity for uranyl by a factor of ∼5, from K d =25±6 nM to K d =5±1 nM. The phosphorylated peptide exhibited a much larger affinity at pH 7, with a dissociation constant in the sub-nanomolar range (K d = 0.25±0.06 nM). FTIR analyses showed that the phospho-threonine side chain is partly protonated at pH 6, while it is fully deprotonated at pH 7. Moreover, formation of the uranyl-peptide complex at pH 7 resulted in significant frequency shifts of the ν as (P-O) and ν s (P-O) IR modes of phospho-threonine, supporting its direct interaction with uranyl. Accordingly, a bathochromic shift in ν as (UO 2 ) 2+ vibration (from 923 cm -1 to 908 cm -1 ) was observed upon uranyl coordination to the phosphorylated peptide. Together, our data demonstrate that the phosphoryl group plays a determining role in uranyl binding affinity to proteins at physiological pH. (authors)

Heparin-binding peptide as a novel affinity tag for purification of recombinant proteins.

Science.gov (United States)

Morris, Jacqueline; Jayanthi, Srinivas; Langston, Rebekah; Daily, Anna; Kight, Alicia; McNabb, David S; Henry, Ralph; Kumar, Thallapuranam Krishnaswamy Suresh

2016-10-01

Purification of recombinant proteins constitutes a significant part of the downstream processing in biopharmaceutical industries. Major costs involved in the production of bio-therapeutics mainly depend on the number of purification steps used during the downstream process. Affinity chromatography is a widely used method for the purification of recombinant proteins expressed in different expression host platforms. Recombinant protein purification is achieved by fusing appropriate affinity tags to either N- or C- terminus of the target recombinant proteins. Currently available protein/peptide affinity tags have proved quite useful in the purification of recombinant proteins. However, these affinity tags suffer from specific limitations in their use under different conditions of purification. In this study, we have designed a novel 34-amino acid heparin-binding affinity tag (HB-tag) for the purification of recombinant proteins expressed in Escherichia coli (E. coli) cells. HB-tag fused recombinant proteins were overexpressed in E. coli in high yields. A one-step heparin-Sepharose-based affinity chromatography protocol was developed to purify HB-fused recombinant proteins to homogeneity using a simple sodium chloride step gradient elution. The HB-tag has also been shown to facilitate the purification of target recombinant proteins from their 8 M urea denatured state(s). The HB-tag has been demonstrated to be successfully released from the fusion protein by an appropriate protease treatment to obtain the recombinant target protein(s) in high yields. Results of the two-dimensional NMR spectroscopy experiments indicate that the purified recombinant target protein(s) exist in the native conformation. Polyclonal antibodies raised against the HB-peptide sequence, exhibited high binding specificity and sensitivity to the HB-fused recombinant proteins (∼10 ng) in different crude cell extracts obtained from diverse expression hosts. In our opinion, the HB-tag provides a

Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

DEFF Research Database (Denmark)

Domanski, Michal; Molloy, Kelly; Jiang, Hua

2012-01-01

An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous...

Studies on lectins. XXXII. Application of affinity electrophoresis to the study of the interaction of lectins and their derivatives with sugars.

Science.gov (United States)

Horejsí, V; Tichá, M; Kocourek, J

1977-09-29

Affinity electrophoresis was used to study the sugar binding heterogeneity of lectins or their derivatives. Commercial and demetallized preparations of concanavalin A could be resolved by affinity electrophoresis into three components with different affinity to immobilized sugar. Similarly the Vicia cracca lectin obtained by affinity chromatography behaved on affinity gels as a mixture of active and inactive molecular species. Affinity electrophoresis has shown that the nonhemagglutinating acetylated lentil lectin and photo-oxidized or sulfenylated pea lectin retain their sugar binding properties; dissociation constants of saccharide complexes of these derivatives are similar to those of native lectins. The presence of specific immobilized sugar in the affinity gel improved the resolution of isolectins from Dolichos biflorus and Ricinus communis seeds.

Consumptive qualities of different potato varieties

Directory of Open Access Journals (Sweden)

М. М. Фурдига

2017-03-01

Full Text Available Purpose. To summarize results of studying consumptive qualities of different varieties of potato and define basic characteristics which allow to subsume them under specific economic categories. Methods. Field study, laboratory test, summarizing, analytical approach. Results. Potato varieties entered in the State register of plant varieties suitable to dissemination in Ukraine and new ones especially to be bred at the Institute of Potato Growing of NAAS were studied during the period of 2005–2016 for such basic economic characters as consumptive quality of tubers, content of starch, dry matters, protein, sugar, vitamins, carotenoids and mineral substances as well as aminoacids, color of flesh, suitability for industrial manufacturing of potato products and for purpose of technology. Attention was paid to the good prospects to use varie­ties with purple, blue and red potato tuber flesh with high antioxidant capacity. Potato varieties with above cha­racteristics and their complex combination were defined and described. The requirements of processing industry for potato as a raw material for manufacturing of potato food were given. Conclusions. The major criterion for consumptive qualities of a potato variety and correspondingly division for the commercial use is consumptive quality of tubers, especially content of essential nutrients and their favorable combination, improved taste and cooking quality, high antioxidant capacity, suitability for potato products manufacturing and use for purpose of technology. Potato varieties can be divided for economic purposes into edible, suitable for potato products manufacturing, technical and multipurpose ones.

2016 Louisiana “Ho” nursery variety trials

Science.gov (United States)

In the Sugarcane Research Unit’s sugarcane variety program, promising experimental varieties are assigned permanent “HoCP” or “Ho” numbers three years after selection in the seedling stage. These varieties are then planted in replicated yield trials at USDA’s Ardoyne Farm in Schriever and at the LS...

Birationally rigid varieties

CERN Document Server

Pukhlikov, Aleksandr

2013-01-01

Birational rigidity is a striking and mysterious phenomenon in higher-dimensional algebraic geometry. It turns out that certain natural families of algebraic varieties (for example, three-dimensional quartics) belong to the same classification type as the projective space but have radically different birational geometric properties. In particular, they admit no non-trivial birational self-maps and cannot be fibred into rational varieties by a rational map. The origins of the theory of birational rigidity are in the work of Max Noether and Fano; however, it was only in 1970 that Iskovskikh and Manin proved birational superrigidity of quartic three-folds. This book gives a systematic exposition of, and a comprehensive introduction to, the theory of birational rigidity, presenting in a uniform way, ideas, techniques, and results that so far could only be found in journal papers. The recent rapid progress in birational geometry and the widening interaction with the neighboring areas generate the growing interest ...

Student Engagement and Neoliberalism: Mapping an Elective Affinity

Science.gov (United States)

Zepke, Nick

2015-01-01

The purpose of this article is to argue that student engagement, an important area for research about learning and teaching in formal higher education, has an elective affinity with neoliberalism, a hegemonic ideology in many countries of the developed world. The paper first surveys an extensive research literature examining student engagement and…

A novel lentiviral scFv display library for rapid optimization and selection of high affinity antibodies.

Science.gov (United States)

Qudsia, Sehar; Merugu, Siva B; Mangukiya, Hitesh B; Hema, Negi; Wu, Zhenghua; Li, Dawei

2018-04-30

Antibody display libraries have become a popular technique to screen monoclonal antibodies for therapeutic purposes. An important aspect of display technology is to generate an optimization library by changing antibody affinity to antigen through mutagenesis and screening the high affinity antibody. In this study, we report a novel lentivirus display based optimization library antibody in which Agtuzumab scFv is displayed on cell membrane of HEK-293T cells. To generate an optimization library, hotspot mutagenesis was performed to achieve diverse antibody library. Based on sequence analysis of randomly selected clones, library size was estimated approximately to be 1.6 × 10 6 . Lentivirus display vector was used to display scFv antibody on cell surface and flow cytometery was performed to check the antibody affinity to antigen. Membrane bound scFv antibodies were then converted to secreted antibody through cre/loxP recombination. One of the mutant clones, M8 showed higher affinity to antigen in flow cytometery analysis. Further characterization of cellular and secreted scFv through western blot showed that antibody affinity was increased by three fold after mutagenesis. This study shows successful construction of a novel antibody library and suggests that hotspot mutagenesis could prove a useful and rapid optimization tool to generate similar libraries with various degree of antigen affinity. Copyright © 2018 Elsevier Inc. All rights reserved.

Morphism of Varieties

Indian Academy of Sciences (India)

Nagaraj, D. S. (IMSc, Chennai)

2011-11-20

Nov 20, 2011 ... a notion of nearness of points in the set is defined. The maps are set maps .... of same degree. X6 + 17X is a degree 6 polynomial in one variable. ..... My current area of research is to study of morphisms of varieties: Given two ...

The variety of complete pairs of zero-dimensional subschemes of length 2 of a smooth three-dimensional variety is singular

International Nuclear Information System (INIS)

Timofeeva, N V

2003-01-01

Equations are obtained that are satisfied by the vectors of the tangent space to the variety X 22 of complete pairs of zero-dimensional subschemes of length 2 of a smooth three-dimensional projective algebraic variety at the most special point of the variety X 22 . It is proved that the system of equations obtained is complete and the variety X 22 is singular

Definite Article Usage across Varieties of English

Science.gov (United States)

Wahid, Ridwan

2013-01-01

This paper seeks to explore the extent of definite article usage variation in several varieties of English based on a classification of its usage types. An annotation scheme based on Hawkins and Prince was developed for this purpose. Using matching corpus data representing Inner Circle varieties and Outer Circle varieties, analysis was made on…

Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

International Nuclear Information System (INIS)

Kang, Un-Beom; Ahn, Younghee; Lee, Jong Won; Kim, Yong-Hak; Kim, Joon; Yu, Myeong-Hee; Noh, Dong-Young; Lee, Cheolju

2010-01-01

Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT) labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD), and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002). BTD levels were lowered in all cancer grades (I-IV) except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940) and progesterone receptor status (p = 0.440) were not associated with the plasma BTD levels. Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer

Isozyme Analysis on Different Varieties of Sugarcane

Directory of Open Access Journals (Sweden)

Johnson M.

2012-05-01

Full Text Available Isozymic and protein diversity among five sugarcane varieties viz., Co 6304, Co 85019, Co 8371, Co 89003 and Co 91010 were studied to understand the varietal interrelationship and to identify the biochemical marker for the disease resistance and stress tolerance. The standard technique of vertical gel electrophoresis PAGE was employed for size separation of isozymes. The gel was stained with different staining solutions for different isozyme systems viz. peroxidase, esterase, acid phosphatase, alkaline phosphatase and proteins. Rf values of the banding profiles, similarity index and variation between the varieties were analysed. Among the four enzyme systems, peroxidase profile reveals the difference between the disease resistant / susceptible and abiotic stress tolerant / non tolerant varieties. The two isoperoxidase bands with Rf values 0.62 and 0.66 showed their presence in disease resistant and abiotic tolerant varieties. The presence of two marker bands (0.62, 0.66 of resistant and stress tolerant varieties suggest that the variety Co 6304 may also be resistant to smut, wilt and moderately resistant to red rot and tolerant to drought.

Biochemical characterization of Tunisian grapevine varieties

Directory of Open Access Journals (Sweden)

Ferjani Ben Abdallah

1998-03-01

The study of GPI, PGM, AAT and peroxydase isozyme banding patterns in combination with berry colour has led to establish a classification of the 61 autochton varieties into 37 groups including 26 varieties definitely differentiated through the results of this biochemical study.

7 CFR 51.348 - One variety.

Science.gov (United States)

2010-01-01

... Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946... Standards for Grades of Apples for Processing Definitions § 51.348 One variety. One variety within the...

Biofortified varieties released under HarvestPlus

African Journals Online (AJOL)

Chapter 5: Annex 1 - Biofortified varieties released under HarvestPlus (as of December 2016). Crop. Micronutrient. Country. Variety. Year of Release. Origin. Type. Baseline. (ppm). Target increment. (ppm). Increment. (ppm). % Target. Increment. (ppm). Micronutrient. Content. (ppm). 11940. BRRI dhan64. 2014. BRRI. Boro.

Staircase Models from Affine Toda Field Theory

CERN Document Server

Dorey, P; Dorey, Patrick; Ravanini, Francesco

1993-01-01

We propose a class of purely elastic scattering theories generalising the staircase model of Al. B. Zamolodchikov, based on the affine Toda field theories for simply-laced Lie algebras g=A,D,E at suitable complex values of their coupling constants. Considering their Thermodynamic Bethe Ansatz equations, we give analytic arguments in support of a conjectured renormalisation group flow visiting the neighbourhood of each W_g minimal model in turn.

A Piecewise Affine Hybrid Systems Approach to Fault Tolerant Satellite Formation Control

DEFF Research Database (Denmark)

Grunnet, Jacob Deleuran; Larsen, Jesper Abildgaard; Bak, Thomas

2008-01-01

In this paper a procedure for modelling satellite formations   including failure dynamics as a piecewise-affine hybrid system is   shown. The formulation enables recently developed methods and tools   for control and analysis of piecewise-affine systems to be applied   leading to synthesis of fault...... tolerant controllers and analysis of   the system behaviour given possible faults.  The method is   illustrated using a simple example involving two satellites trying   to reach a specific formation despite of actuator faults occurring....

Strategies for Developing Drought Tolerant Cowpea varieties for the Semi-Arid regions of Nigeria

International Nuclear Information System (INIS)

Ishiyaku, M. F.

2000-10-01

Drought, meaning the deviation of the total amount and or distribution of precipitation from the normal is an important factor that cause untold human suffering as well as social and economic loss for any nation. Its effects are often felt by places so remote from the area of occurrence. In the agricultural sector, where its effect are most felt, drought risk greatly reduce investment in agriculture. This will no doubt contribute to national food insecurity and social unrest. Of the measures often prescribed to combat the menace of drought include the development and planting of drought resistant/tolerant crop varieties. This paper discusses the strategies for developing drought tolerant cowpea varieties for the drought-prone regions of Nigeria. These strategies include the introduction and screening of candidate drought tolerant cowpea germplasm and their utilization in developing new improved genotypes. The screening of populations will be carried out by adopting novel screening techniques in the lab as well as in the field. In addition to utilizing existing genetic variation to develop varieties with tolerance to drought, new sources of variation will be created artificially for the various traits known to confer tolerance to drought in cowpea. In creating genetic variability for drought tolerance traits artificially, the potential of irradiation induced mutation will be exploited

Generalized Warburg impedance on realistic self-affine fractals ...

Indian Academy of Sciences (India)

Administrator

Generalized Warburg impedance on realistic self-affine fractals: Comparative study of statistically corrugated and isotropic roughness. RAJESH KUMAR and RAMA KANT. Journal of Chemical Sciences, Vol. 121, No. 5, September 2009, pp. 579–588. 1. ( ) c. L. R ω on page 582, column 2, para 2, after eq (8) should read as ...

The Monitoring and Affinity Purification of Proteins Using Dual Tags with Tetracysteine Motifs

Science.gov (United States)

Giannone, Richard J.; Liu, Yie; Wang, Yisong

Identification and characterization of protein-protein interaction networks is essential for the elucidation of biochemical mechanisms and cellular function. Affinity purification in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a very powerful tactic for the identification of specific protein-protein interactions. In this chapter, we describe a comprehensive methodology that uses our recently developed dual-tag affinity purification system for the enrichment and identification of mammalian protein complexes. The protocol covers a series of separate but sequentially related techniques focused on the facile monitoring and purification of a dual-tagged protein of interest and its interacting partners via a system built with tetracysteine motifs and various combinations of affinity tags. Using human telomeric repeat binding factor 2 (TRF2) as an example, we demonstrate the power of the system in terms of bait protein recovery after dual-tag affinity purification, detection of bait protein subcellular localization and expression, and successful identification of known and potentially novel TRF2 interacting proteins. Although the protocol described here has been optimized for the identification and characterization of TRF2-associated proteins, it is, in principle, applicable to the study of any other mammalian protein complexes that may be of interest to the research community.

Breeding of new rice varieties by gamma-rays

International Nuclear Information System (INIS)

Toda, Masayuki

1980-01-01

The breeding procedure for and the agronomic characteristics of some new rice varieties are reported. The seeds of the non-waxy variety ''Toyonishiki'' were exposed to 20 kR of gamma-ray. Two out of 20,000 panicles produced on these plants had waxy grain, and one of these brought forth a new commercial variety, ''Miyuki-mochi''. The yield of the new variety was reduced by 8% as compared with the original variety, but the heading date, culm length, panicle length and the number of panicles of the new variety were almost the same as those of the original variety. If compared with the old leading waxy variety, ''Shinano-mochi'', ''Miyuki-mochi'' is superior in yield by 15% and has high resistance to lodging and to rice blast. Seven other rice varieties were irradiated to obtain waxy mutants, and the frequency of R 1 panicles carrying waxy grains was found to be 1/10,000. There was marked difference in the 1,000 grain weight of these mutants relative to those of the respective original varieties and in amylose content among the waxy mutant strains. A new Saka-mai variety (for Sake brewing), ''Miyamanishiki'', was obtained from ''Takanenishiki'' (30 kR exposure of dry seeds). The most important character for Saka-mai is to have white-core grains. An experiment with several rice varieties showed that the frequency of white core grains was about 0.15% in the control and about 0.21% in the R 1 plants after irradiation. A desirable large grain strain, ''Shinho No. 12'', from ''Todorokiwase'', and a desirable mutant strain suitable as feed for domestic animals, ''Shinho No. 38'', from ''Toyonishiki'' were also obtained by gamma-ray irradiation. (Kaihara, S.)

Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions

DEFF Research Database (Denmark)

Cockburn, Darrell; Wilkens, Casper; Svensson, Birte

2017-01-01

Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate binding modules (CBMs). In recent years, carbohy...

Dynamics behind affinity maturation of an anti-HCMV antibody family influencing antigen binding

KAUST Repository

Di Palma, Francesco; Tramontano, Anna

2017-01-01

The investigation of antibody affinity maturation and its effects on antigen binding is important with respect to understanding the regulation of the immune response. To shed light on this crucial process, we analyzed two Igs neutralizing the human cytomegalovirus: the primary germline antibody M2J1 and its related mature antibody 8F9. Both antibodies target the AD-2S1 epitope of the gB envelope protein and are considered to establish similar interactions with the cognate antigen. We used molecular dynamics simulations to understand the effect of mutations on the antibody–antigen interactions. The results provide a qualitative explanation for the increased 8F9 peptide affinity compared with that of M2J1. The emerging atomistic-detailed description of these complexes reveals the molecular effects of the somatic hypermutations occurring during affinity maturation.

On-bead chemical synthesis and display of phosphopeptides for affinity pull-down proteomics

DEFF Research Database (Denmark)

Malene, Brandt; Madsen, Jens C.; Bunkenborg, Jakob

2006-01-01

We describe a new method for phosphopeptide proteomics based on the solid-phase synthesis of phosphopeptides on beads suitable for affinity pull-down experiments. Peptide sequences containing the Bad Ser112 and Ser136 phosphorylation motifs were used as bait in affinity pull-down experiments...... (aldehyde) at the C terminus for potential activity-based proteomics. The synthetic support-bound Bad phosphopeptides were able to pull down 14-3-3zeta. Furthermore, Bad phosphopeptides bound endogenous 14-3-3 proteins, and all seven members of the 14-3-3 family were identified by mass spectrometry....... In control experiments, none of the unphosphorylated Bad peptides bound transfected 14-3-3zeta or endogenous 14-3-3. We conclude that the combined synthesis and display of phosphopeptides on-bead is a fast and efficient method for affinity pull-down proteomics....

Dynamics behind affinity maturation of an anti-HCMV antibody family influencing antigen binding

KAUST Repository

Di Palma, Francesco

2017-08-03

The investigation of antibody affinity maturation and its effects on antigen binding is important with respect to understanding the regulation of the immune response. To shed light on this crucial process, we analyzed two Igs neutralizing the human cytomegalovirus: the primary germline antibody M2J1 and its related mature antibody 8F9. Both antibodies target the AD-2S1 epitope of the gB envelope protein and are considered to establish similar interactions with the cognate antigen. We used molecular dynamics simulations to understand the effect of mutations on the antibody–antigen interactions. The results provide a qualitative explanation for the increased 8F9 peptide affinity compared with that of M2J1. The emerging atomistic-detailed description of these complexes reveals the molecular effects of the somatic hypermutations occurring during affinity maturation.

Affinity monolith chromatography: A review of principles and recent analytical applications

Science.gov (United States)

Pfaunmiller, Erika L.; Paulemond, Marie Laura; Dupper, Courtney M.; Hage, David S.

2012-01-01

Affinity monolith chromatography (AMC) is a type of liquid chromatography that uses a monolithic support and a biologically-related binding agent as a stationary phase. AMC is a powerful method for the selective separation, analysis or studies of specific target compounds in a sample. This review discusses the basic principles of AMC and recent developments or applications of this method, with particular emphasis being given to work that has appeared in the last five years. Various materials that have been used to prepare columns for AMC are examined, including organic monoliths, silica monoliths, agarose monoliths and cryogels. These supports have been used in AMC for formats that have ranged from traditional columns to disks, microcolumns and capillaries. Many binding agents have also been employed in AMC, such as antibodies, enzymes, proteins, lectins, immobilized metal-ions and dyes. Some applications that have been reported with these binding agents in AMC are bioaffinity chromatography, immunoaffinity chromatography or immunoextraction, immobilized metal-ion affinity chromatography, dye-ligand affinity chromatography, chiral separations and biointeraction studies. Examples are presented from fields that include analytical chemistry, pharmaceutical analysis, clinical testing and biotechnology. Current trends and possible future directions in AMC are also discussed. PMID:23187827

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

Directory of Open Access Journals (Sweden)

Lorenzo Asti

2016-04-01

Full Text Available The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6, outperforming other sequence- and structure-based models.

Investigation of molybdenum-crosslinker interfaces for affinity based electrochemical biosensing applications

Science.gov (United States)

Kamakoti, Vikramshankar; Shanmugam, Nandhinee Radha; Tanak, Ambalika Sanjeev; Jagannath, Badrinath; Prasad, Shalini

2018-04-01

Molybdenum (Mo) has been investigated for implementation as an electrode material for affinity based biosensing towards devloping flexibe electronic biosensors. Treatment of the native oxide of molybdenum was investigated through two surface treatment strategies namely thiol and carbodiimide crosslinking methods. The binding interaction between cross-linker molecules and Mo electrode surface has been characterized using Fourier Transform Infrared Spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and optical microscopy. The efficacy of treatment of Mo with its native oxide using carbodiimide cross linking methodology was established. The carbodiimide cross-linking chemistry was found to possess better surface coverage and binding affinity with Molybdenum electrode surface when compared to thiol cross-linking chemistry.Electrochemical characterization of Mo electrode using Electrochemical Impedance Spectroscopy (EIS) and Cyclic Voltametry (CV) techniques was performed to evaluate the effect of ionic properties of solution buffer on the Mo electrode's performance. Affinity based biosensing of C-Reactive Protein (CRP) has been demonstrated on a flexible nanoporous polymeric substrate with detection threshold of 100 pg/ml in synthetic urine buffer medium. The biosensor has been evaluated to be developed as a dipstick based point of care device for detection of biomarkers in urine.

Low-complexity piecewise-affine virtual sensors: theory and design

Science.gov (United States)

Rubagotti, Matteo; Poggi, Tomaso; Oliveri, Alberto; Pascucci, Carlo Alberto; Bemporad, Alberto; Storace, Marco

2014-03-01

This paper is focused on the theoretical development and the hardware implementation of low-complexity piecewise-affine direct virtual sensors for the estimation of unmeasured variables of interest of nonlinear systems. The direct virtual sensor is designed directly from measured inputs and outputs of the system and does not require a dynamical model. The proposed approach allows one to design estimators which mitigate the effect of the so-called 'curse of dimensionality' of simplicial piecewise-affine functions, and can be therefore applied to relatively high-order systems, enjoying convergence and optimality properties. An automatic toolchain is also presented to generate the VHDL code describing the digital circuit implementing the virtual sensor, starting from the set of measured input and output data. The proposed methodology is applied to generate an FPGA implementation of the virtual sensor for the estimation of vehicle lateral velocity, using a hardware-in-the-loop setting.

The fourth dimension in immunological space: how the struggle for nutrients selects high-affinity lymphocytes.

Science.gov (United States)

Wensveen, Felix M; van Gisbergen, Klaas P J M; Eldering, Eric

2012-09-01

Lymphocyte activation via the antigen receptor is associated with radical shifts in metabolism and changes in requirements for nutrients and cytokines. Concomitantly, drastic changes occur in the expression of pro-and anti-apoptotic proteins that alter the sensitivity of lymphocytes to limiting concentrations of key survival factors. Antigen affinity is a primary determinant for the capacity of activated lymphocytes to access these vital resources. The shift in metabolic needs and the variable access to key survival factors is used by the immune system to eliminate activated low-affinity cells and to generate an optimal high-affinity response. In this review, we focus on the control of apoptosis regulators in activated lymphocytes by nutrients, cytokines, and costimulation. We propose that the struggle among individual clones that leads to the formation of high-affinity effector cell populations is in effect an 'invisible' fourth signal required for effective immune responses. © 2012 John Wiley & Sons A/S.

Cubic systems with invariant affine straight lines of total parallel multiplicity seven

Directory of Open Access Journals (Sweden)

Alexandru Suba

2013-12-01

Full Text Available In this article, we study the planar cubic differential systems with invariant affine straight lines of total parallel multiplicity seven. We classify these system according to their geometric properties encoded in the configurations of invariant straight lines. We show that there are only 17 different topological phase portraits in the Poincar\\'e disc associated to this family of cubic systems up to a reversal of the sense of their orbits, and we provide representatives of every class modulo an affine change of variables and rescaling of the time variable.

From Stein to Weinstein and back symplectic geometry of affine complex manifolds

CERN Document Server

Cieliebak, Kai

2013-01-01

A beautiful and comprehensive introduction to this important field. -Dusa McDuff, Barnard College, Columbia University This excellent book gives a detailed, clear, and wonderfully written treatment of the interplay between the world of Stein manifolds and the more topological and flexible world of Weinstein manifolds. Devoted to this subject with a long history, the book serves as a superb introduction to this area and also contains the authors' new results. -Tomasz Mrowka, MIT This book is devoted to the interplay between complex and symplectic geometry in affine complex manifolds. Affine co

Use of PIXE techniques for food variety differentiation

International Nuclear Information System (INIS)

Alayande, S.O.; Osinkolu, G.A.; Makinde, W.; Ogundele, T.

2011-01-01

Various foods come with varieties; each presents its own uniqueness in term of beneficial nutrients. Differentiation of these varieties will assist to obtain optimum benefit from their consumption, hence PIXE technique was used to differentiate known cowpea varieties in South-west Nigeria. Local names for the varieties were alayin nla, alayin wewe, mala, drum and sakata. The technique detected six major elements (Mg, K, Ca, P, S and CI) and several trace elements (AI, Fe, Ni, Cu, Mn, Sr, Si, Rb and Ti). The concentration of beneficial elements in the varieties differ and comparison with recommended daily allowance value shows consumption of some of the variety is sufficient. This research work will guide health workers in their recommendation of cowpea for nutritional deficiency.

Radionuclide accumulation peculiarities demonstrated by vegetable varieties

International Nuclear Information System (INIS)

Kruk, A.V.; Goncharenko, G.G.; Kilchevsky, A.V.

2004-01-01

This study focused on ecological and genetic aspects of radionuclide accumulation demonstrated by a number of vegetable varieties. The researches resulted in determining the cabbage varieties which were characterised by the minimal level of radionuclide accumulation. It was shown that the above varieties manifested the relation between radionuclide accumulation and morphobiological characteristics such as vegetation period duration and yield criteria. The study specified the genotypes with high ecological stability as regards to radionuclide accumulation: 'Beloruskaya 85' cabbage and 'Dokhodny' tomato showed the best response to Cs 137, while 'Beloruskaya 85', 'Rusinovka', 'Amager 611' cabbage varieties and 'Sprint' tomato showed the minimal level of Sr 90 accumulation. (authors)

Semi-continuous protein fractionating using affinity cross-flow filtration

NARCIS (Netherlands)

Borneman, Zandrie; Zhang, W.; van den Boomgaard, Anthonie; Smolders, C.A.

2002-01-01

Protein purification by means of downstream processing is increasingly important. At the University of Twente a semi-continuous process is developed for the isolation of BSA out of crude protein mixtures. For this purpose an automated Affinity Cross-Flow Filtration, ACFF, process is developed. This

Insulin affects the sodium affinity of the rat adipocyte (Na+,K+)-ATPase

International Nuclear Information System (INIS)

Lytton, J.

1985-01-01

The K0.5 for intracellular sodium of the two forms of (Na + ,K + )-ATPase which exist in rat adipocytes has been determined by incubating the cells in the absence of potassium in buffers of varying sodium concentration; these conditions shut off the Na + pump and allow sodium to equilibrate into the cell. The activity of (Na + ,K + )-ATPase was then monitored with 86 Rb + /K + pumping which was initiated by adding isotope and KCl to 5 mM, followed by a 3-min uptake period. Atomic absorption and 22 Na + tracer equilibration were used to determine the actual intracellular [Na + ] under the different conditions. The K0.5 values thus obtained were 17 mM for alpha and 52 mM for alpha(+). Insulin treatment of rat adipocytes had no effect on the intracellular [Na+] nor on the Vmax of 86 Rb + /K + pumping, but did produce a shift in the sodium ion K0.5 values to 14 mM for alpha and 33 mM for alpha(+). This change in affinity can explain the selective stimulation of alpha(+) by insulin under normal incubation conditions

Detection of Hepatitis C core antibody by dual-affinity yeast chimera and smartphone-based electrochemical sensing.

Science.gov (United States)

Aronoff-Spencer, Eliah; Venkatesh, A G; Sun, Alex; Brickner, Howard; Looney, David; Hall, Drew A

2016-12-15

Yeast cell lines were genetically engineered to display Hepatitis C virus (HCV) core antigen linked to gold binding peptide (GBP) as a dual-affinity biobrick chimera. These multifunctional yeast cells adhere to the gold sensor surface while simultaneously acting as a "renewable" capture reagent for anti-HCV core antibody. This streamlined functionalization and detection strategy removes the need for traditional purification and immobilization techniques. With this biobrick construct, both optical and electrochemical immunoassays were developed. The optical immunoassays demonstrated detection of anti-HCV core antibody down to 12.3pM concentrations while the electrochemical assay demonstrated higher binding constants and dynamic range. The electrochemical format and a custom, low-cost smartphone-based potentiostat ($20 USD) yielded comparable results to assays performed on a state-of-the-art electrochemical workstation. We propose this combination of synthetic biology and scalable, point-of-care sensing has potential to provide low-cost, cutting edge diagnostic capability for many pathogens in a variety of settings. Copyright © 2016 Elsevier B.V. All rights reserved.

New NS varieties of six-rowed winter barley

Directory of Open Access Journals (Sweden)

Pržulj Novo

2009-01-01

Full Text Available The paper describes the characteristics of several new NS varieties of winter six-rowed barley released in Serbia between 2004 and 2007. These are Somborac, Ozren, Javor, Novosadski 773, Sremac and Leotar. In the official variety trials in the country, all six of these varieties outyielded the check variety, and the margins were as follows: Somborac - 3.4%, Ozren - 5.0%, Javor - 7.3%, Novosadski 773 - 3.4%, Sremac - 7.4%, and Leotar - 7.2%. Yield levels in absolute terms depended on the variety as well as year. All six-rowed NS varieties headed earlier than the check and had better resistance to lodging than the check has. The test weight of the new varieties was 70.2-73.8 kg/hl and the 1000-grain weight 33.4-50.2 g. The cellulose content was 4.4-4.8%, the fat content 1.4%, and the protein content 13.3-14.6%. The high variability of the new NS varieties of winter six-rowed barley makes it possible to choose the most suitable genotype for each barley-growing area in the country. .

Affinity for a malignant tumor and organs at the elements in group VIII of the periodic table

International Nuclear Information System (INIS)

Ando, Atsushi; Hisada, Kinichi; Ando, Itsuko.

1975-01-01

In order to investigate the tumor affinity of the radioisotopes, iron(Fe-59), cobalt(Co-58), ruthenium(Ru-103), palladium(Pd-103), osmium(Os-185+191) and iridium(Ir-192), the elements of group VIII in the periodic table were examined, using rats which were subcutaneously transplanted with Yoshida sarcoma. Six preparations, 59 Fe-chloride, 58 Co-chloride, 103 Ru-chloride, 103 Pd-chloride, 185+191 Os-hexachlorosmic acid and 192 Ir-hexachloriridic acid were injected intravenously in to each group of tumor bearing rats. These rats were sacrificed at various periods after injection of each preparation: 3 hours, 24 hours and 48 hours in all preparations, except 59 Fe-chloride with 30 minutes, 3 hours, 24 hours and 48 hours. The radioactivities of the tumor, blood muscle, liver, kidney and spleen were measured by a well-type scintillation counter, and retention values (in every tissue including the tumor were calculated in percent of administered dose per g-tissue weight). 185+191 Os-hexachlorosmic acid had a considerably strong affinity for the malignant tumor. 59 Fe-chloride, 58 Co-chloride, 103 Ru-chloride, 103 Pd-chloride and 192 Ir-hexachloriridic acid did not have any affinity for the malignant tumor. However 59 Fe-chloride had a very strong affinity for blood corpuscles. 103 Pd-chloride had a fairly strong affinity for the kidney and liver, 58 Co-chloride had a fairly affinity for the liver, 103 Ru-chloride, 185+191 Os-hexachlorosmic acid and 192 Ir-hexachloriridic acid had a fairly strong affinity for the kidney. (Evans, J.)

Quiver representations and quiver varieties

CERN Document Server

Jr, Alexander Kirillov

2016-01-01

This book is an introduction to the theory of quiver representations and quiver varieties, starting with basic definitions and ending with Nakajima's work on quiver varieties and the geometric realization of Kac-Moody Lie algebras. The first part of the book is devoted to the classical theory of quivers of finite type. Here the exposition is mostly self-contained and all important proofs are presented in detail. The second part contains the more recent topics of quiver theory that are related to quivers of infinite type: Coxeter functor, tame and wild quivers, McKay correspondence, and representations of Euclidean quivers. In the third part, topics related to geometric aspects of quiver theory are discussed, such as quiver varieties, Hilbert schemes, and the geometric realization of Kac-Moody algebras. Here some of the more technical proofs are omitted; instead only the statements and some ideas of the proofs are given, and the reader is referred to original papers for details. The exposition in the book requ...

Less adaption of newly approved variety Basmati 515 among aromatic basmati rice varieties in Kallar Tract of Punjab, Pakistan

Directory of Open Access Journals (Sweden)

Muhammad Tahir Latif

2017-12-01

Full Text Available A field survey was conducted after harvesting of rice crop 2016 to identify the reasons for less adaption of aromatic rice variety Basmati 515. The rice growers adopting rice-wheat cropping pattern in kallar tract were included in population of research study. Thirty male farmers from each selected district making a total of 180 respondent farmers were interviewed by convenience sampling method. The survey findings showed that the aromatic rice variety Basmati 515 was cultivated on only 2.7% rice area while maximum area (47.3% was under Super basmati variety. The comparison of Basmati 515 was made with Super basmati and PS 2 due to comparatively more cultivated area and declared yield potential of these varieties. Overall the farmers were applying under dosed phosphorus fertilizer (DAP as 0.25, 0.20 and 0.22 bag ha-1 respectively for basmati 515, super basmati and PS-2 varieties. The descriptive analysis showed that the less adaptability of basmati 515 was due to less yield and more attacks of borer (11%, BLB (10% and leaf roller (3.25% in comparison to other aromatic and fine rice varieties. Similarly maximum lodging (16% was recorded on basmati 515. Maximum yield was estimated for PS 2 variety (4.7 t ha-1 followed by super basmati (4.0 t ha-1 and basmati 515 (3.78 t ha-1. The market price of super basmati was still higher due to its natural aroma, long & thin grain and export demand. The research institutes should focus for development of new aromatic high yielding and more qualitative rice varieties to increase the rice production and export.

Classification of rank 2 cluster varieties

DEFF Research Database (Denmark)

Mandel, Travis

We classify rank 2 cluster varieties (those whose corresponding skew-form has rank 2) according to the deformation type of a generic fiber U of their X-spaces, as defined by Fock and Goncharov. Our approach is based on the work of Gross, Hacking, and Keel for cluster varieties and log Calabi...

Microtubule affinity-regulating kinases are potential druggable targets for Alzheimer's disease.

Science.gov (United States)

Annadurai, Narendran; Agrawal, Khushboo; Džubák, Petr; Hajdúch, Marián; Das, Viswanath

2017-11-01

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects normal functions of the brain. Currently, AD is one of the leading causes of death in developed countries and the only one of the top ten diseases without a means to prevent, cure, or significantly slow down its progression. Therefore, newer therapeutic concepts are urgently needed to improve survival and the quality of life of AD patients. Microtubule affinity-regulating kinases (MARKs) regulate tau-microtubule binding and play a crucial role in neurons. However, their role in hyperphosphorylation of tau makes them potential druggable target for AD therapy. Despite the relevance of MARKs in AD pathogenesis, only a few small molecules are known to have anti-MARK activity and not much has been done to progress these compounds into therapeutic candidates. But given the diverse role of MARKs, the specificity of novel inhibitors is imperative for their successful translation from bench to bedside. In this regard, a recent co-crystal structure of MARK4 in association with a pyrazolopyrimidine-based inhibitor offers a potential scaffold for the development of more specific MARK inhibitors. In this manuscript, we review the biological role of MARKs in health and disease, and draw attention to the largely unexplored area of MARK inhibitors for AD.

The high-affinity peptidoglycan binding domain of Pseudomonas phage endolysin KZ144

Energy Technology Data Exchange (ETDEWEB)

Briers, Yves [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium); Schmelcher, Mathias; Loessner, Martin J. [Institute of Food Science and Nutrition, ETH Zuerich, Schmelzbergstrasse 7, CH-8092 Zuerich (Switzerland); Hendrix, Jelle; Engelborghs, Yves [Laboratory of Biomolecular Dynamics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200G, B-3001 Leuven (Belgium); Volckaert, Guido [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium); Lavigne, Rob, E-mail: rob.lavigne@biw.kuleuven.be [Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven (Belgium)

2009-05-29

The binding affinity of the N-terminal peptidoglycan binding domain of endolysin KZ144 (PBD{sub KZ}), originating from Pseudomonas aeruginosa bacteriophage {phi}KZ, has been examined using a fusion protein of PBD{sub KZ} and green fluorescent protein (PBD{sub KZ}-GFP). A fluorescence recovery after photobleaching analysis of bound PBD{sub KZ}-GFP molecules showed less than 10% fluorescence recovery in the bleached area within 15 min. Surface plasmon resonance analysis confirmed this apparent high binding affinity revealing an equilibrium affinity constant of 2.95 x 10{sup 7} M{sup -1} for the PBD{sub KZ}-peptidoglycan interaction. This unique domain, which binds to the peptidoglycan of all tested Gram-negative species, was harnessed to improve the specific activity of the peptidoglycan hydrolase domain KMV36C. The chimeric peptidoglycan hydrolase (PBD{sub KZ}-KMV36C) exhibits a threefold higher specific activity than the native catalytic domain (KMV36C). These results demonstrate that the modular assembly of functional domains is a rational approach to improve the specific activity of endolysins from phages infecting Gram-negatives.

Production and Identification of High Affinity Monoclonal Antibodies Against Pesticide Carbofuran

Institute of Scientific and Technical Information of China (English)

无

2007-01-01

To produce high-affinity monoclonal antibodies against pesticide carbofuran, and the develop immunochemical assays for people's health and environmental protection, the hapten 4-[[(2,3-dihydro-2,2-dimethyl-7-benzofuranyloxy) carbonyl]-amino]-butanoic acid (BFNB) of carbofuran was synthesized and Balb/c mice were immunized by the hapten-carrier (BFNB-bovine serum albumin, BFNB-BSA) conjugates. The splenocytes of immunized mice were fused with Sp2/0 cells and the cultural supernatants of hybridoma cells were screened by the indirect enzyme-linked immunoabsorbent assay (ELISA), based on BFNB-ovoalbumin conjugates (BFNB-OVA). Purified monoclonal antibody (McAb) was obtained from fluids of ascites, deposited by octanoic acid and ammonium sulfate. The affinity and the specificity of McAb were characterized by ELISA or indirect competitive ELISA. A hybridoma cell line (5D3) secreting anti-carbofuran McAb had been established. The titer of culture medium and ascites was up to 1:2.048 × 103 and 1:1.024 × 106, respectively, and the subtype of the McAb was IgG1. The affinity constant of the McAb was about 2.54 × 109 L mol-1, with an IC50 value of 1.18 ng mL-1 and a detection limit of 0.01 ng mL-1. Cross-reactivity studies showed that the McAb was quiet specific for carbofuran, as among the four analogous compounds, they were all hardly recognized (4.59 × 10-4% for 2,3-dihydro-2,2-dimethyl-7-benzofuranol and less than 3.0 × 10-4% for others). The prepared McAb had a very high affinity and specificity,and it could be used to develop ELISA for rapid determination of carbofuran.

Officially released mutant varieties in China

International Nuclear Information System (INIS)

Liu, L.; Van Zanten, L.; Shu, Q.Y.; Maluszynski, M.

2004-01-01

The use of mutation techniques for crop improvement in China has a long and well-established tradition of more than 50 years. As the result of intensive research in many institutes dealing with application of nuclear technologies more than 620 cultivars of 44 crop species have been released. Numerous mutant varieties have been grown on a large scale bringing significant economic impact, sustaining crop production and greatly contributing to increase of food production also in stress prone areas of the country. However, there is still missing information not only on the number of mutant varieties released in particular crop species but also on mutagens applied, selection approaches and on the use of mutants in cross breeding. Numerous Chinese scientists collected and systematized this information. Results of their work were often published in local scientific journals in the Chinese language and as such were unavailable to breeders from other countries. Having this in mind, we requested Dr. Liu Luxiang, the Director of the Department of Plant Mutation Breeding and Genetics, Institute for Application of Atomic Energy, Chinese Academy of Agricultural Sciences in Beijing to help us in finding as much information as possible on mutant varieties officially released in China. The data has been collected in close collaboration with his colleagues from various institutions all over the country and then evaluated, edited and prepared for publication by our team responsible for the FAO/IAEA Database of Officially Released Mutant Varieties. We would like to thank all Chinese colleagues who contributed to this list of Chinese mutant varieties. We hope that this publication will stimulate plant breeders in China to collect more information on released mutant varieties and especially on the use of mutated genes in cross breeding. (author)

Linear codes associated to determinantal varieties

DEFF Research Database (Denmark)

Beelen, Peter; Ghorpade, Sudhir R.; Hasan, Sartaj Ul

2015-01-01

We consider a class of linear codes associated to projective algebraic varieties defined by the vanishing of minors of a fixed size of a generic matrix. It is seen that the resulting code has only a small number of distinct weights. The case of varieties defined by the vanishing of 2×2 minors is ...

Chitinolytic activity of the rumen ciliates Diploplastron affine

Czech Academy of Sciences Publication Activity Database

Belzecki, G.; Miltko, R.; Michalowski, T.; Šimůnek, Jiří; Kopečný, Jan

2008-01-01

Roč. 53, č. 3 (2008), s. 201-203 ISSN 0015-5632 R&D Projects: GA ČR GA525/05/2584 Grant - others:Ministry of Scientific Research and Information Technology Poland(PL) 2 P06Z 052 30 Institutional research plan: CEZ:AV0Z50450515 Keywords : Diploplastron affine Subject RIV: EE - Microbiology, Virology Impact factor: 1.172, year: 2008

A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition

Science.gov (United States)

Junicke, Henrik; Hart, Jonathan R.; Kisko, Jennifer; Glebov, Oleg; Kirsch, Ilan R.; Barton, Jacqueline K.

2003-01-01

A rhodium(III) complex, rac-[Rh(bpy)2phzi]3+ (bpy, 2,2′-bipyridine; phzi, benzo[a]phenazine-5,6-quinone diimine) has been designed as a sterically demanding intercalator targeted to destabilized mismatched sites in double-helical DNA. The complex is readily synthesized by condensation of the phenazine quinone with the corresponding diammine complex. Upon photoactivation, the complex promotes direct strand scission at single-base mismatch sites within the DNA duplex. As with the parent mismatch-specific reagent, [Rh(bpy)2(chrysi)]3+ [chrysene-5,6-quinone diimine (chrysi)], mismatch selectivity depends on the helix destabilization associated with mispairing. Unlike the parent chrysi complex, the phzi analogue binds and cleaves with high affinity and efficiency. The specific binding constants for CA, CC, and CT mismatches within a 31-mer oligonucleotide duplex are 0.3, 1, and 6 × 107 M−1, respectively; site-specific photocleavage is evident at nanomolar concentrations. Moreover, the specificity, defined as the ratio in binding affinities for mispaired vs. well paired sites, is maintained. The increase in affinity is attributed to greater stability in the mismatched site associated with stacking by the heterocyclic aromatic ligand. The high-affinity complex is also applied in the differential cleavage of DNA obtained from cell lines deficient in mismatch repair vs. those proficient in mismatch repair. Agreement is found between photocleavage by the mismatch-specific probes and deficiency in mismatch repair. This mismatch-specific targeting, therefore, offers a potential strategy for new chemotherapeutic design. PMID:12610209

The S-Matrix coupling dependence for a, d and e affine Toda field theory

International Nuclear Information System (INIS)

Braden, H.W.; Sasaki, R.

1990-09-01

Affine Toda field theories are solvable 1+1 dimensional quantum field theories closely related to integrable deformations of conformal field theory. The S-Matrix elements for an affine Toda field theory are known to depend on the coupling constant β through one universal function B(β) which cannot be determined by unitarity, crossing and the bootstrap. From the requirement of nonexistence of extra poles in the physical region its form is conjectured to be B(β) = (2π) -1 ·β 2 /((1+β 2 )/4π). We show that the above conjecture is correct up to one loop order (i.e., β 4 ) of perturbation for simply laced, i.e., a, d and e affine Toda field theories using a general argument which exhibits much of the richness of these theories. (author)

Interest Rates with Long Memory: A Generalized Affine Term-Structure Model

DEFF Research Database (Denmark)

Osterrieder, Daniela

.S. government bonds, we model the time series of the state vector by means of a co-fractional vector autoregressive model. The implication is that yields of all maturities exhibit nonstationary, yet mean-reverting, long-memory behavior of the order d ≈ 0.87. The long-run dynamics of the state vector are driven......We propose a model for the term structure of interest rates that is a generalization of the discrete-time, Gaussian, affine yield-curve model. Compared to standard affine models, our model allows for general linear dynamics in the vector of state variables. In an application to real yields of U...... forecasts that outperform several benchmark models, especially at long forecasting horizons....

The Varieties of Good Design

DEFF Research Database (Denmark)

Ylirisku, Salu; Arvola, Mattias

2018-01-01

This chapter explores the philosopher and logician Georg Henrik von Wright’s metaethical treatise of the varieties of goodness in the context of design. von Wright investigated the use of notion of ‘good’ in language, and he identified six kinds of goodness: namely utilitarian goodness, instrumen......This chapter explores the philosopher and logician Georg Henrik von Wright’s metaethical treatise of the varieties of goodness in the context of design. von Wright investigated the use of notion of ‘good’ in language, and he identified six kinds of goodness: namely utilitarian goodness...

The application of magnetic force differentiation for the measurement of the affinity of peptide libraries

International Nuclear Information System (INIS)

Shang Hao; Kirkham, Perry M.; Myers, Tina M.; Cassell, Gail H.; Lee, Gil U.

2005-01-01

A new method has been developed for measuring the binding affinity of phage displayed peptides and a target protein using magnetic particles. The specific interaction between the phage displayed peptides and the target protein was subject to a force generated by the magnetic particle. The binding affinity was obtained by analyzing the force-bond lifetime