Sequence-influenced interactions of oligoacridines with DNA detected by retarded gel electrophorectic migrations

International Nuclear Information System (INIS)

Nielsen, P.E.; Zhen, W.; Henriksen, U.; Buchardt, O.

1988-01-01

The authors have found that di-, tri-, tetra-, and hexa-9-acridinylamines are so efficiently associated with DNA during electrophoresis in polyacrylamide or agarose gels that they retard its migration. The retardation is roughly proportional to the reagent to base pair ratio, and the magnitude of the retardation indicates that a combined charge neutralization/helix extension mechanism is mainly responsible for the effect. Furthermore, DNA sequence dependent differences are observed. Thus, the pUC 19 restriction fragments (HaeIII or AluI), which in the native state comigrate upon gel electrophoretic analysis, could be separated in the presence of a diacridine, and specific DNA fragments responded differently to different diacridines. These results suggest that the effect also is due to a contribution from the DNA conformation and that the DNA conformation dynamics are influenced differently upon binding of different diacridines. They foresee three applications of this observation: (1) in analytical gel electrophoretic separation of otherwise comigrating DNA molecules, (2) in studies of polyintercalator-DNA interaction, and (3) in measurements of polyintercalator-induced DNA unwinding

Instrumental texture profile analysis of gelatin gel extracted from grouper skin and commercial (bovine and porcine) gelatin gels.

Science.gov (United States)

Rahman, Mohammad Shafiur; Al-Mahrouqi, Abdullah Issa

2009-01-01

Mechanical compression was used to study the gelling characteristics of gelatin gels. Texture profile analysis (TPA) showed that the hardness of fish and mammalian gelatin increased significantly as the concentrations of gels increased. TPA attributes of 10% fish skin gel showed significant differences from those obtained from 20% and 30% gels. In bovine and porcine cases, such generic trends were not observed. Mechanical characteristics of 10% gels of gelatin from fish skin, determined from one cycle compression, were significantly lower than other sources of gelatin gels, while bovine and porcine gels did not show any significant differences. In the case of TPA, hardness of bovine gelatin gel was highest at 41 N for 10% gel, followed by porcine (30 N) then fish skin (5 N) gelatin gels. The gels prepared from different sources did not show any generic trends when all other mechanical attributes were considered.

SCit: web tools for protein side chain conformation analysis.

Science.gov (United States)

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

Science.gov (United States)

Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

2018-05-08

Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

International Nuclear Information System (INIS)

Solieman, A.H.M.

2010-01-01

The conformational analysis of iodinated non-ionic contrast agent, Iobitridol, was carried out using theoretical calculations to explore its conformational space, and to study different aspects connected with application of different search techniques. Monte Carlo (MC), random search (RS) and molecular dynamics (MD) based conformational search techniques were used to extract a reasonable-size sample that adequately represents and has an average behavior of the entire conformational ensemble.While MC is good for quick search for lowest energy conformer, RS is better in obtaining conformational sample that cover the whole conformational space and MD is the best for investigation of isomeric preferences inside the conformational ensemble at thermal equilibrium. Conformational analysis of the produced gas phase samples reveals that RS and MD methods could sufficiently present the 18 distinct isomeric classes that constitute the total conformational space of the Iobitridol. S samples of conformational space of Iobitridol are extensively studied, as it hypothetically cover the total conformational space. They are used to test the suitability of different methods (charge distribution methods, energy calculation methods) for Iobitridol molecular computations and internal structure forces (steric hindrance, resonance interaction), as well as dependences among the internal coordinates (dihedral angles correlations and coincidences). The atomic partial charge distribution is found to greatly affect the energy calculation for the molecular mechanics based conformational energy distributions. Further energy minimization of conformational sample by the quantum molecular orbital methods is crucial to obtain charge independent as well as energy balanced conformational sample.

NMR and modelling techniques in structural and conformation analysis

Energy Technology Data Exchange (ETDEWEB)

Abraham, R J [Liverpool Univ. (United Kingdom)

1994-12-31

The use of Lanthanide Induced Shifts (L.I.S.) and modelling techniques in conformational analysis is presented. The use of Co{sup III} porphyrins as shift reagents is discussed, with examples of their use in the conformational analysis of some heterocyclic amines. (author) 13 refs., 9 figs.

Conformational studies of the (+)-trans, (-)-trans, (+)-cis, and (-)-cis adducts of anti-benzo[a]pyrene diolepoxide to N2-dG in duplex oligonucleotides using polyacrylamide gel electrophoresis and low-temperature fluorescence spectroscopy

NARCIS (Netherlands)

Suh, Myungkoo; Ariese, Freek; Small, Gerald J.; Jankowiak, Ryszard; Liu, Tong Ming; Geacintov, Nicholas E.

1995-01-01

Using polyacrylamide gel electrophoresis (PAGE) and low-temperature, laser-induced fluorescence line narrowing (FLN) and non-line narrowing (NLN) spectroscopic methods, the conformational characteristics of stereochemically defined and site-specific adducts derived from the binding of

A novel conformation of gel grown biologically active cadmium nicotinate

Science.gov (United States)

Nair, Lekshmi P.; Bijini, B. R.; Divya, R.; Nair, Prabitha B.; Eapen, S. M.; Dileep Kumar, B. S.; Nishanth Kumar, S.; Nair, C. M. K.; Deepa, M.; Rajendra Babu, K.

2017-11-01

The elimination of toxic heavy metals by the formation of stable co-ordination compounds with biologically active ligands is applicable in drug designing. A new crystalline complex of cadmium with nicotinic acid is grown at ambient temperature using the single gel diffusion method in which the crystal structure is different from those already reported. Single crystal x-ray diffraction reveals the identity of crystal structure belonging to monoclinic system, P21/c space group with cell dimensions a = 17.220 (2) Å, b = 10.2480 (2) Å, c = 7.229(9) Å, β = 91.829(4)°. Powder x-ray diffraction analysis confirmed the crystallinity of the sample. The unidentate mode of co-ordination between the metal atom and the carboxylate group is supported by the Fourier Transform Infra Red spectral data. Thermal analysis ensures the thermal stability of the complex. Kinetic and thermodynamic parameters are also calculated. The stoichiometry of the complex is confirmed by the elemental analysis. The UV-visible spectral analysis shows the wide transparency window of the complex in the visible region. The band gap of the complex is found to be 3.92 eV. The complex shows excellent antibacterial and antifungal activity.

Extraction of americium (III) by thermosensitive polymer gel copolymerized with acidic phosphorus compound

International Nuclear Information System (INIS)

Takeshita, Kenji; Nakano, Yoshio; Matsumura, Tatsuro

2001-01-01

A new gel-liquid extraction using a thermosensitive gel was proposed. The thermosensitive gel shows the conformational change of polymer network with temperature, which is known as the phase transition phenomena of gel. The extraction rate and equilibrium of Am(III) in an aqueous solution containing nitrate ion were measured batchwise by using a thermosensitive gel, N-isopropylacrylamide (NIPA) copolymerized with 2-methacryloyloxy- ethylacidphosphate (MR). The effects of the conformational change of polymer network on the extraction rate and equilibrium were discussed. The distribution ratio of Am(III) showed a large value at higher than LCST (low critical solution temperature; 34degC) and was decreased by the phase transition of gel from shrinking to swelling with decreasing temperature. The extraction of Am(III) in the aqueous solution and the release of Am(III) extracted in the gel were repeated stably by the temperature swing operation between 40 and 3degC. The extraction mechanism of Am(III) was described simply as Am 3+ + 3R - OH=(R-O) 3 Am + 3H + (R-OH: MR). The equilibrium constant at the shrinking state (40degC) was more than 3 times of that at swelling state (3degC). The gel-phase diffusivity of Eu(III) used as a substitute of Am(III) was evaluated as the order of 10 -12 m 2 /s at either of 3 or 40degC, which was similar to those for practical extraction chromatographic resins. The temperature-response of gel for the extraction of Eu(III) was very excellent without delay even for the rapid temperature change at 10degC/min. These results suggest that the extraction and release of Am(III) in an aqueous solution can be controlled by the conformational change of polymer network of thermosensitive gel. (author)

Conformational analysis of oxa-thio-azolydines through NMR

International Nuclear Information System (INIS)

Val, Amelia Maria Gomes do; Guimaraes, Afonso Celso

1997-01-01

This work presents the conformational analysis of some selected oxa-thio-azolidines. As the chemical properties of such compounds do not depend only upon the chemical structure, but also upon the conformational state which they may present, special emphasis is given to this phenomenon, which can elucidate the compounds properties

Cost Analysis of Treating Neonatal Hypoglycemia with Dextrose Gel.

Science.gov (United States)

Glasgow, Matthew J; Harding, Jane E; Edlin, Richard

2018-04-03

To evaluate the costs of using dextrose gel as a primary treatment for neonatal hypoglycemia in the first 48 hours after birth compared with standard care. We used a decision tree to model overall costs, including those specific to hypoglycemia monitoring and treatment and those related to the infant's length of stay in the postnatal ward or neonatal intensive care unit, comparing the use of dextrose gel for treatment of neonatal hypoglycemia with placebo, using data from the Sugar Babies randomized trial. Sensitivity analyses assessed the impact of dextrose gel cost, neonatal intensive care cost, cesarean delivery rate, and costs of glucose monitoring. In the primary analysis, treating neonatal hypoglycemia using dextrose gel had an overall cost of NZ$6863.81 and standard care (placebo) cost NZ$8178.25; a saving of NZ$1314.44 per infant treated. Sensitivity analyses showed that dextrose gel remained cost saving with wide variations in dextrose gel costs, neonatal intensive care unit costs, cesarean delivery rates, and costs of monitoring. Use of buccal dextrose gel reduces hospital costs for management of neonatal hypoglycemia. Because it is also noninvasive, well tolerated, safe, and associated with improved breastfeeding, buccal dextrose gel should be routinely used for initial treatment of neonatal hypoglycemia. Australian New Zealand Clinical Trials Registry: ACTRN12608000623392. Copyright © 2018 Elsevier Inc. All rights reserved.

Analysis of conformations and ESR spectra of free radicals in carbohydrates

International Nuclear Information System (INIS)

Abaghyan, G.V.; Abaghyan, A.G.; Apresyan, A.S.

1998-01-01

The conformations of free radicals arising when the unpaired electron is localized on carbon atoms in pyranose ring of carbohydrate molecule are considered. On the base of the analysis of expected conformations of radicals a possible contribution of β-protons in hyperfine structure of ESP spectra is predicted. The results of conformational analysis for different types of free radicals are in satisfactory agreement with the corresponding experimental data for the liquid phase. 17 refs

Conformal field theory in conformal space

International Nuclear Information System (INIS)

Preitschopf, C.R.; Vasiliev, M.A.

1999-01-01

We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

Agarose gel electrophoresis for the separation of DNA fragments.

Science.gov (United States)

Lee, Pei Yun; Costumbrado, John; Hsu, Chih-Yuan; Kim, Yong Hoon

2012-04-20

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb(1). Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits(2). During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel's molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight(3). The leading model for DNA movement through an agarose gel is "biased reptation", whereby the leading edge moves forward and pulls the rest of the molecule along(4). The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation(5); 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: Understand the mechanism by which DNA fragments are separated within a gel matrix Understand how conformation of the DNA molecule will determine its mobility through a gel matrix Identify an agarose solution of appropriate

Complex analysis conformal inequalities and the Bieberbach conjecture

CERN Document Server

Kythe, Prem K

2015-01-01

Complex Analysis: Conformal Inequalities and the Bieberbach Conjecture discusses the mathematical analysis created around the Bieberbach conjecture, which is responsible for the development of many beautiful aspects of complex analysis, especially in the geometric-function theory of univalent functions. Assuming basic knowledge of complex analysis and differential equations, the book is suitable for graduate students engaged in analytical research on the topics and researchers working on related areas of complex analysis in one or more complex variables. The author first reviews the theory of analytic functions, univalent functions, and conformal mapping before covering various theorems related to the area principle and discussing Löwner theory. He then presents Schiffer’s variation method, the bounds for the fourth and higher-order coefficients, various subclasses of univalent functions, generalized convexity and the class of a-convex functions, and numerical estimates of the coefficient problem. The boo...

Direct detection of hemophilia B F9 gene mutation using multiplex PCR and conformation sensitive gel electrophoresis

Directory of Open Access Journals (Sweden)

Ki Young Yoo

2010-03-01

Full Text Available Purpose : The F9 gene is known to be the causative gene for hemophilia B, but unfortunately the detection rate for restriction fragment length polymorphism-based linkage analysis is only 55.6%. Direct DNA sequencing can detect 98% of mutations, but this alternative procedure is very costly. Here, we conducted multiplex polymerase chain reactions (PCRs and conformation sensitive gel electrophoresis (CSGE to perform a screened DNA sequencing for the F9 gene, and we compared the results with direct sequencing in terms of accuracy, cost, simplicity, and time consumption. Methods : A total of 27 unrelated hemophilia B patients were enrolled. Direct DNA sequencing was performed for 27 patients by a separate institute, and multiplex PCR-CSGE screened sequencing was done in our laboratory. Results of the direct DNA sequencing were used as a reference, to which the results of the multiplex PCR-CSGE screened sequencing were compared. For the patients whose mutation was not detected by the 2 methods, multiplex ligation-dependent probe amplification (MLPA was conducted. Results : With direct sequencing, the mutations could be identified from 26 patients (96.3%, whereas for multiplex PCR- CSGE screened sequencing, the mutations could be detected in 23 (85.2%. One patient’s mutation was identified by MLPA. A total of 21 different mutations were found among the 27 patients. Conclusion : Multiplex PCR-CSGE screened DNA sequencing detected 88.9% of mutations and reduced costs by 55.7% compared with direct DNA sequencing. However, it was more labor-intensive and time-consuming.

Analysis of Two-Dimensional Electrophoresis Gel Images

DEFF Research Database (Denmark)

Pedersen, Lars

2002-01-01

This thesis describes and proposes solutions to some of the currently most important problems in pattern recognition and image analysis of two-dimensional gel electrophoresis (2DGE) images. 2DGE is the leading technique to separate individual proteins in biological samples with many biological...

Influence of DNA conformation on radiation-induced single-strand breaks

International Nuclear Information System (INIS)

Barone, F.; Belli, M.; Mazzei, F.

1994-01-01

We performed experiments on two DNA fragments of about 300 bp having different conformation to test whether radiation-induced single-strand breakage is dependent on DNA conformation. Breakage analysis was carried out by denaturing polyacrylamide gel electrophoresis, which allows determination of the broken site at single nucleotide resolution. We found uniform cutting patterns in B-form regions. On the contrary, X- or γ-irradiation of curved fragments of kinetoplast DNA showed that the distribution of single-strand breaks was not uniform along the fragment, as the cleavage pattern was modulated in phase with the runs of A-T pairs. This modulation likely reflected the reduced accessibility of the sites which on hydroxyl-radical attack give rise to strand breaks. The cleavage pattern was phased with the runs of A-T pairs. Moreover, the overall yield of strand breaks was considerably lower in curved DNA fragments than in those with extended straight regions. The conformation effect found here indicates that the cleavage pattern reflects the fine structural features of DNA. (orig./MG)

Surface Design Based on Discrete Conformal Transformations

Science.gov (United States)

Duque, Carlos; Santangelo, Christian; Vouga, Etienne

Conformal transformations are angle-preserving maps from one domain to another. Although angles are preserved, the lengths between arbitrary points are not generally conserved. As a consequence there is always a given amount of distortion associated to any conformal map. Different uses of such transformations can be found in various fields, but have been used by us to program non-uniformly swellable gel sheets to buckle into prescribed three dimensional shapes. In this work we apply circle packings as a kind of discrete conformal map in order to find conformal maps from the sphere to the plane that can be used as nearly uniform swelling patterns to program non-Euclidean sheets to buckle into spheres. We explore the possibility of tuning the area distortion to fit the experimental range of minimum and maximum swelling by modifying the boundary of the planar domain through the introduction of different cutting schemes.

Raman Spectroscopy of Irradiated Normoxic Polymethacrylic Acid Gel Dosimeter

Energy Technology Data Exchange (ETDEWEB)

Bong, Ji Hye; Kwon, Soo Il; Cho, Yu Ra; Park, Chae Hee; Park, Hyung Wook [Kyonggi University, Suwon (Korea, Republic of); Choi, Kyu Seok; Yu, Soo Chang [Kunsan National University, Gunsan (Korea, Republic of)

2011-02-15

A quantitative analysis of the decreasing rate of the monomer and increasing rate of the polymerization was made by monitoring radiation level increments using Raman spectroscopy within the therapeutic radiation range for a normoxic polymethacrylic acid gel dosimeter. The gel dosimeter was synthesized by stirring materials such as gelatin, distilled water, methacrylic acid, hydroquinone and tetrakis phosphonium chloride at 50 .deg. C, and the synthesized gel was contained in a 10- mm diameter and 32-mm high vial to conduct measurement. 24 hours after gel synthesis, it was irradiated from 0 Gy to 20 Gy by 2 Gy using a Co-60 radiotherapy unit. With use of the Cryo FE-SEM, structural changes in the 0 Gy and 10 Gy gel dosimeters were investigated. The Raman spectra were acquired using 532-nm laser as the excitation source. In accordance with fitting the changes in C-COOH stretching (801 cm{sup -1}), C=C stretching (1639 cm{sup -1}) and vinyl CH{sub 2} stretching (3114 cm{sup -1}) vibrational modes for monomer and CH{sub 2} bending vibrational mode (1451 cm{sup -1}) for polymer, sensitive parameter S for each mode was calculated. The values of S for monomer bands and polymer band were ranged in 6.0 ± 2.6 Gy and 7.2 ± 2.3 Gy, respectively, which shows a relatively good conformity of the decreasing rate of monomer and the increasing rate of polymerization within the range of error.

Internal structure analysis of particle-double network gels used in a gel organ replica

Science.gov (United States)

Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

2016-04-01

In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

Two-dimensional polyacrylamide gel analysis of Plodia interpunctella granulosis virus

International Nuclear Information System (INIS)

Russell, D.L.; Consigli, R.A.

1986-01-01

The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure

Exploring encapsulation mechanism of DNA and mononucleotides in sol-gel derived silica.

Science.gov (United States)

Kapusuz, Derya; Durucan, Caner

2017-07-01

The encapsulation mechanism of DNA in sol-gel derived silica has been explored in order to elucidate the effect of DNA conformation on encapsulation and to identify the nature of chemical/physical interaction of DNA with silica during and after sol-gel transition. In this respect, double stranded DNA and dAMP (2'-deoxyadenosine 5'-monophosphate) were encapsulated in silica using an alkoxide-based sol-gel route. Biomolecule-encapsulating gels have been characterized using UV-Vis, 29 Si NMR, FTIR spectroscopy and gas adsorption (BET) to investigate chemical interactions of biomolecules with the porous silica network and to examine the extent of sol-gel reactions upon encapsulation. Ethidium bromide intercalation and leach out tests showed that helix conformation of DNA was preserved after encapsulation. For both biomolecules, high water-to-alkoxide ratio promoted water-producing condensation and prevented alcoholic denaturation. NMR and FTIR analyses confirmed high hydraulic reactivity (water adsorption) for more silanol groups-containing DNA and dAMP encapsulated gels than plain silica gel. No chemical binding/interaction occurred between biomolecules and silica network. DNA and dAMP encapsulated silica gelled faster than plain silica due to basic nature of DNA or dAMP containing buffer solutions. DNA was not released from silica gels to aqueous environment up to 9 days. The chemical association between DNA/dAMP and silica host was through phosphate groups and molecular water attached to silanols, acting as a barrier around biomolecules. The helix morphology was found not to be essential for such interaction. BET analyses showed that interconnected, inkbottle-shaped mesoporous silica network was condensed around DNA and dAMP molecules.

Analysis of spatial diffusion of ferric ions in PVA-GTA gel dosimeters through magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Marrale, Maurizio [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); ATeN Center, Università di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Collura, Giorgio [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); Gallo, Salvatore, E-mail: salvatore.gallo05@unipa.it [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Istituto Nazionale di Fisica Nucleare (INFN) – Gruppo V Sezione di Catania, Via Santa Sofia, 64, 95123 Catania (Italy); Dipartimento di Fisica, Universitá di Milano, Via Giovanni Celoria 16, 20133 Milano (Italy); Nici, Stefania [Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Tranchina, Luigi [ATeN Center, Università di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo (Italy); Abbate, Boris Federico [U.O.C. Fisica Sanitaria, A.R.N.A.S., Ospedale Civico Palermo, Piazza Nicola Leotta 4, 90127 Palermo (Italy); Marineo, Sandra; Caracappa, Santo [Istituto Zooprofilattico Sperimentale della Sicilia (IZS), Via Gino Marinuzzi, 3, 90129 Palermo (Italy); and others

2017-04-01

Highlights: • Analysis of ferric ions diffusion throughout the gel matrix in PVA-GTA samples. • Measurements with preclinical 7T MRI scanner with spatial resolution of 200 μm. • Diffusion process is much slower for PVA-GTA gels than for agarose ones. - Abstract: This work focused on the analysis of the temporal diffusion of ferric ions through PVA-GTA gel dosimeters. PVA-GTA gel samples, partly exposed with 6 MV X-rays in order to create an initial steep gradient, were mapped using magnetic resonance imaging on a 7T MRI scanner for small animals. Multiple images of the gels were acquired over several hours after irradiation and were analyzed to quantitatively extract the signal profile. The spatial resolution achieved is 200 μm and this makes this technique particularly suitable for the analysis of steep gradients of ferric ion concentration. The results obtained with PVA-GTA gels were compared with those achieved with agarose gels, which is a standard dosimetric gel formulation. The analysis showed that the diffusion process is much slower (more than five times) for PVA-GTA gels than for agarose ones. Furthermore, it is noteworthy that the diffusion coefficient value obtained through MRI analysis is significantly consistent with that obtained in separate study Marini et al. (Submitted for publication) using a totally independent method such as spectrophotometry. This is a valuable result highlighting that the good dosimetric features of this gel matrix not only can be reproduced but also can be measured through independent experimental techniques based on different physical principles.

Two-dimensional gel electrophoresis analysis of different parts of ...

African Journals Online (AJOL)

Two-dimensional gel electrophoresis analysis of different parts of Panax quinquefolius L. root. ... From these results it was concluded that proteomic analysis method was an effective way to identify the different parts of quinquefolius L. root. These findings may contribute to further understanding of the physiological ...

Theoretical conformational analysis of the bovine adrenal medulla 12 residue peptide molecule

Science.gov (United States)

Akhmedov, N. A.; Tagiyev, Z. H.; Hasanov, E. M.; Akverdieva, G. A.

2003-02-01

The spatial structure and conformational properties of the bovine adrenal medulla 12 residue peptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Arg7-Val8-Gly9-Arg10-Pro11-Glu12 (BAM-12P) molecule were studied by theoretical conformational analysis. It is revealed that this molecule can exist in several stable states. The energy and geometrical parameters for the low-energy conformations are obtained. The conformationally rigid and labile segments of this molecule were revealed.

Deciphering the shape and deformation of secondary structures through local conformation analysis

Directory of Open Access Journals (Sweden)

Camproux Anne-Claude

2011-02-01

Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Deciphering the shape and deformation of secondary structures through local conformation analysis.

Science.gov (United States)

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels

Directory of Open Access Journals (Sweden)

Antonio M. Gonçalves

1990-03-01

Full Text Available A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

Conformational analysis and vibrational studies of ethylenediamine-d4, using DFT method

International Nuclear Information System (INIS)

Catikkas, B.

2010-01-01

In this work, conformational analysis and quantum chemical calculations of ethylenediamine-d4 were carried out. The geometry optimization and the geometric parameters (bond length, bond angle and tortion angle) were calculated. The Infrared and Raman frequencies of fundamental modes of the most stable conformer were determined. Calculations were carried out by using the MPW1PW91/6-311+G(d,p) method and Gaussian03 and GaussView3.0 programs. Populations of the conformers was calculated. Vibrational assignments of the title molecule were calculated by using Scaled Quantum Mechanical (SQM) analysis. Calculated values were compared with the experimental ones.

Conformational analysis of lignin models; Analise conformacional de modelos de lignina

Energy Technology Data Exchange (ETDEWEB)

Santos, Helio F. dos [Juiz de Fora Univ., MG (Brazil). Dept. de Quimica]. E-mail: helius@quimica.ufjf.br

2001-08-01

The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level. (author)

Conformational analysis of some 4‧-substituted 2-(phenylselanyl)- 2-(methoxy)- acetophenones

Science.gov (United States)

Traesel, Henrique J.; Olivato, Paulo R.; Valença, J.; Rodrigues, Daniel N. S.; Zukerman-Schpector, Julio; Colle, Maurizio Dal

2018-04-01

A conformational study of some 4‧-substituited 2-(phenylselanyl)-2-(methoxy)-acetophenones (OMe 1, H 2, and Cl 3) was performed using IR carbonyl stretching band analysis supported by NBO and PCM calculations at the B3LYP/6-31 + G (d,p) level for 1-3 and using X-ray diffraction for 1 and 2. The computational results indicated the existence of three stable conformers for the series (c2, c3, and c1 in order of decreasing stability), whose relative abundance changes with solvent permittivity. The experimental trend observed for the components of the triplet carbonyl band in all solvents matches well with computational results and thus allows for their assignment to distinct conformers. The relative population of the c1 conformer increases in more polar solvents, becoming the most stable conformer in the highest permittivity solvent, acetonitrile, as indicated by IR spectra and PCM calculations. These findings are related to the quasi parallel geometry assumed by the Cδ+ = Oδ- and Cδ+-Oδ- dipoles, which favour stronger solvation. NBO analysis shows that the sum of the energies (ΣE) of the relevant orbital interactions stabilizes the c3 conformer of 1-3 slightly, likely due to the minor contribution of the LPO5→σ*C3sbnd Se10 interaction. However, only the c1 conformer is significantly destabilized by the Oδ-(1)CO … Oδ-(5)OMe short contact electrostatic repulsion, which is also responsible for its highest νCO frequency. In addition, the LPO5→ σ*C2sbnd C3 orbital interaction accounts for the lowest νCO frequency of c3 conformer. X-ray single crystal analysis of compounds 1 and 2 indicates that in the solid state they assume the least stable c1 conformation found in the gas phase. Molecules of these compounds are stabilized in the crystal through a series of Csbnd H⋯O and Csbnd H … π intermolecular interactions.

Manufacture of Regularly Shaped Sol-Gel Pellets

Science.gov (United States)

Leventis, Nicholas; Johnston, James C.; Kinder, James D.

2006-01-01

An extrusion batch process for manufacturing regularly shaped sol-gel pellets has been devised as an improved alternative to a spray process that yields irregularly shaped pellets. The aspect ratio of regularly shaped pellets can be controlled more easily, while regularly shaped pellets pack more efficiently. In the extrusion process, a wet gel is pushed out of a mold and chopped repetitively into short, cylindrical pieces as it emerges from the mold. The pieces are collected and can be either (1) dried at ambient pressure to xerogel, (2) solvent exchanged and dried under ambient pressure to ambigels, or (3) supercritically dried to aerogel. Advantageously, the extruded pellets can be dropped directly in a cross-linking bath, where they develop a conformal polymer coating around the skeletal framework of the wet gel via reaction with the cross linker. These pellets can be dried to mechanically robust X-Aerogel.

Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations.

Science.gov (United States)

Najbauer, Eszter E; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

2015-08-20

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.

Dose response study of PVA-Fx gel for three dimensional dose distribution

International Nuclear Information System (INIS)

Brindha, S.; Ayyangar, Komanduri M.; Shen, Bin; Saw, Cheng B.

2001-01-01

Modern radiotherapy techniques involve complex field arrangements using conformal and intensity modulated radiation that requires three dimensional treatment planning. The verification of these plans poses even more challenge. In 1984, Gore et al., proposed that ferrous gel dosimeters combined with magnetic resonance imaging (MRI) could be used to measure three dimensional radiation dose distributions. Since then, there has been much interest in the development of gel dosimetry to aid the determination of three dimensional dose distributions during field arrangements. In this work, preparation and study of the MR characteristics of a PVA-Fx gel reported in the literature is presented

Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations

Science.gov (United States)

Najbauer, Eszter E.; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

2018-01-01

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, 6 conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-live of (3.7±0.5)·103 s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser induced conversions revealed that the excitation of the stretching overtone of both the side-chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. PMID:26201050

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

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Stella Fabio

2011-05-01

Full Text Available Abstract Background Molecular dynamics (MD simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to

Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

Science.gov (United States)

2011-01-01

Background Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering. Results The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions. Conclusions The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from

The Efficiency of Vascular Embolization Using Alginate Gel : An Experimental Study in Rabbit

International Nuclear Information System (INIS)

Lee, Woo Baek; Kang, Yeong Han; Kim, Jong Ki

2009-01-01

The purpose of this study was to investigate the applicability of poly-L-guluronic alginate (PGA) gel in vascular embolization with angiography simulation. To prepare a gel-forming PGA from no guluronate-rich Laminaria japonica, a new acid hydrolysis method was employed with a lower HCL concentration (0.03 M) and a shorter treatment time (5 min). The obtained PGAs were selected based on gel stability and viscosity. Glass aneurysm model was used to simulate gel embolization in vitro. Then, finally, the PGA was used to embolize the renal vascular system by using a rabbit model and angiography. Glass aneurysm model was made to simulate gel embolization procedure. PGA solution was injected from pump through 2-way catheter. Subsequent injection of CaCl 2 successfully formed gels inside aneurysm model that conforming to its inner contour. In rabbit model, first, renal artery and aorta leading to the right kidney were ligated to block blood flow, then conventional contrast agent was injected through aorta to check the arterial patency to the left kidney. In sequential artery injection method, PGA and CaCl 2 were injected through renal artery sequentially via a single catheter. Re-injection of contrast agent after removing ligated aorta showed blood flow to the right kidney but no flow in the left kidney. This result demonstrated a complete blocking of blood flow due to gel formation in vascular bed of the left kidney. Instillation of calcium alginate into aneurysm model and arterial system in vivo produced an embolization that better fills and conforms to the contour of aneurysms or blocking vascular bed completely. Therefore, PGA was effective endovascular occlusion materials and provide an efficiency of vascular angiography.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

KAUST Repository

Feng, Yitao

2016-10-13

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis

KAUST Repository

Feng, Yitao; Zhang, Lu; Wu, Shaowen; Liu, Zhijun; Gao, Xin; Zhang, Xu; Liu, Maili; Liu, Jianwei; Huang, Xuhui; Wang, Wenning

2016-01-01

The glutamine binding protein (GlnBP) binds l-glutamine and cooperates with its cognate transporters during glutamine uptake. Crystal structure analysis has revealed an open and a closed conformation for apo- and holo-GlnBP, respectively. However, the detailed conformational dynamics have remained unclear. Herein, we combined NMR spectroscopy, MD simulations, and single-molecule FRET techniques to decipher the conformational dynamics of apo-GlnBP. The NMR residual dipolar couplings of apo-GlnBP were in good agreement with a MD-derived structure ensemble consisting of four metastable states. The open and closed conformations are the two major states. This four-state model was further validated by smFRET experiments and suggests the conformational selection mechanism in ligand recognition of GlnBP. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops.

Directory of Open Access Journals (Sweden)

Giovanna Sattin

Full Text Available Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules.

Stimuli-Triggered Sol-Gel Transitions of Polypeptides Derived from α-Amino Acid N-Carboxyanhydride (NCA) Polymerizations.

Science.gov (United States)

He, Xun; Fan, Jingwei; Wooley, Karen L

2016-02-18

The past decade has witnessed significantly increased interest in the development of smart polypeptide-based organo- and hydrogel systems with stimuli responsiveness, especially those that exhibit sol-gel phase-transition properties, with an anticipation of their utility in the construction of adaptive materials, sensor designs, and controlled release systems, among other applications. Such developments have been facilitated by dramatic progress in controlled polymerizations of α-amino acid N-carboxyanhydrides (NCAs), together with advanced orthogonal functionalization techniques, which have enabled economical and practical syntheses of well-defined polypeptides and peptide hybrid polymeric materials. One-dimensional stacking of polypeptides or peptide aggregations in the forms of certain ordered conformations, such as α helices and β sheets, in combination with further physical or chemical cross-linking, result in the construction of three-dimensional matrices of polypeptide gel systems. The macroscopic sol-gel transitions, resulting from the construction or deconstruction of gel networks and the conformational changes between secondary structures, can be triggered by external stimuli, including environmental factors, electromagnetic fields, and (bio)chemical species. Herein, the most recent advances in polypeptide gel systems are described, covering synthetic strategies, gelation mechanisms, and stimuli-triggered sol-gel transitions, with the aim of demonstrating the relationships between chemical compositions, supramolecular structures, and responsive properties of polypeptide-based organo- and hydrogels. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NMR spectroscopy: a tool for conformational analysis

International Nuclear Information System (INIS)

Tormena, Claudio F.; Cormanich, Rodrigo A.; Rittner, Roberto; Freitas, Matheus P.

2011-01-01

The present review deals with the application of NMR data to the conformational analysis of simple organic compounds, together with other experimental methods like infrared spectroscopy and with theoretical calculations. Each sub-section describes the results for a group of compounds which belong to a given organic function like ketones, esters, etc. Studies of a single compound, even of special relevance, were excluded since the main goal of this review is to compare the results for a given function, where different substituents were used or small structural changes were introduced in the substrate, in an attempt to disclose their effects in the conformational equilibrium. Moreover, the huge amount of data available in the literature, on this research field, imposed some limitations which will be detailed in the Introduction, but it can be reminded in advance that these limitations include mostly the period when these results were published. (author)

The Efficiency of Vascular Embolization Using Alginate Gel : An Experimental Study in Rabbit

Energy Technology Data Exchange (ETDEWEB)

Lee, Woo Baek; Kang, Yeong Han [Dept. of Diagnostic Radiology, Daegu Catholic University Hospital, Daegu (Korea, Republic of); Kim, Jong Ki [Dept. of Biomedical Engineering, Daegu Catholic University, Daegu (Korea, Republic of)

2009-03-15

The purpose of this study was to investigate the applicability of poly-L-guluronic alginate (PGA) gel in vascular embolization with angiography simulation. To prepare a gel-forming PGA from no guluronate-rich Laminaria japonica, a new acid hydrolysis method was employed with a lower HCL concentration (0.03 M) and a shorter treatment time (5 min). The obtained PGAs were selected based on gel stability and viscosity. Glass aneurysm model was used to simulate gel embolization in vitro. Then, finally, the PGA was used to embolize the renal vascular system by using a rabbit model and angiography. Glass aneurysm model was made to simulate gel embolization procedure. PGA solution was injected from pump through 2-way catheter. Subsequent injection of CaCl{sub 2} successfully formed gels inside aneurysm model that conforming to its inner contour. In rabbit model, first, renal artery and aorta leading to the right kidney were ligated to block blood flow, then conventional contrast agent was injected through aorta to check the arterial patency to the left kidney. In sequential artery injection method, PGA and CaCl{sub 2} were injected through renal artery sequentially via a single catheter. Re-injection of contrast agent after removing ligated aorta showed blood flow to the right kidney but no flow in the left kidney. This result demonstrated a complete blocking of blood flow due to gel formation in vascular bed of the left kidney. Instillation of calcium alginate into aneurysm model and arterial system in vivo produced an embolization that better fills and conforms to the contour of aneurysms or blocking vascular bed completely. Therefore, PGA was effective endovascular occlusion materials and provide an efficiency of vascular angiography.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

Science.gov (United States)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

DEFF Research Database (Denmark)

Andersen, H; Birkelund, Svend; Christiansen, Gunna

1987-01-01

The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...... isolated variously from genital tract, mouth, blood, upper urinary tract and a wound. These 14 strains shared 76-99% of proteins in SDS-gradient gel analysis and 41-72% in the 2D gels. As expected, the immunoblot analysis likewise revealed the existence of an extensive common protein pattern in M. hominis...

Application of heteronuclear couplings to conformational analysis of oligonucleotides

International Nuclear Information System (INIS)

Zhu, G.; Live, D.; Bax, A.

1994-01-01

The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1' and C1' atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3'-endo and C2'-endo conformations of the sugars and syn and anti bases arrangements

Application of heteronuclear couplings to conformational analysis of oligonucleotides

Energy Technology Data Exchange (ETDEWEB)

Zhu, G. [Univ. of Maryland, College Park, MD (United States); Live, D. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Bax, A. [NIDDK National Institutes of Health, Bethesda, MD (United States)

1994-12-01

The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1{prime} and C1{prime} atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3{prime}-endo and C2{prime}-endo conformations of the sugars and syn and anti bases arrangements.

Conformational Analysis of DNA Repair Intermediates by Time-Resolved Fluorescence Spectroscopy

OpenAIRE

Lin, Su; Horning, David P.; Szostak, Jack W.; Chaput, John C.

2009-01-01

DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of enzymes remains unclear, as small populations of DNA conformations are often difficult to detect by NM...

Conformal symmetry in two-dimensional space: recursion representation of conformal block

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1988-01-01

The four-point conformal block plays an important part in the analysis of the conformally invariant operator algebra in two-dimensional space. The behavior of the conformal block is calculated in the present paper in the limit in which the dimension Δ of the intermediate operator tends to infinity. This makes it possible to construct a recursion relation for this function that connects the conformal block at arbitrary Δ to the blocks corresponding to the dimensions of the zero vectors in the degenerate representations of the Virasoro algebra. The relation is convenient for calculating the expansion of the conformal block in powers of the uniformizing parameters q = i π tau

Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice

Science.gov (United States)

Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan

1991-06-01

Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Kai Wang

Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

Analysis of the retention of water vapor on silica gel; Analisis de la retencion del vapor de agua en silica gel

Energy Technology Data Exchange (ETDEWEB)

Herranz, M.; Pinilla, J. L.; Alegria, N.; Idoeta, R.; Legarda, F.

2011-07-01

Among the various sampling systems tritium content in the atmosphere as water vapor, one of the most basic and, therefore, of widespread use in the environmental field, is the retention on silica gel. However, the behavior of the collection efficiency of silica gel under varying conditions of air temperature and relative humidity makes it difficult to define the amount of this necessary for proper completion of sampling, especially in situations of prolonged sampling. This paper presents partial results obtained in a study on the analysis of these efficiencies under normal conditions of sampling. (Author)

Analysis of non-conformity in continuous quality improvement in a Hospital Radiopharmacy Unit.

Science.gov (United States)

Martinez, T; Contreras, J F

To perform an analysis of non-conformities (NC) registered between 2012 and 2015, as a part of the review process of the Quality Management System of our Radiopharmacy Unit. Non-conformities registered in the Radiopharmacy Unit in the period 2012-2015 are analyzed and sorted by their impact on the process (critical, major, and minor), cause/origin of the non-conformity, and nature of radiopharmaceutical (PET vs. SPECT). A decrease in the NC of 20% per year is observed, especially in PET radiopharmaceuticals. Non-conformities in SPECT make up about 62-84% of the total of the NC, mainly related to the high number of doses prepared and not administered, which is about 1.5-3% in the ratio of non-administered/administered per year. Analysis of the NC can be considered as a useful indicator in assessment of quality assurance, and in our particular case, the decrease in the registration of NC indicates effectiveness in the corrective and preventive actions implemented. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

Heat processing of gels into sintered uranium dioxide modelled by thermal analysis. I

International Nuclear Information System (INIS)

Landspersky, H.; Urbanek, V.

1979-01-01

Thermoanalytical methods were used for investigating the processes of air drying and calcination of gels prepared by internal gelation of uranyl nitrate, urea and urotropine solutions at 90 degC. The gels were dried in air at room temperature, at 220 degC in a controlled atmosphere or by azeotropic distillation with CCl 4 . The course of thermal decomposition of the gel depends not only on the drying method used but also on the medium in which the drying process takes place. If the drying is carried out so as to produce a macroporous structure after the elimination of most of the water, ammonia and possibly other gelation by-products and non-reacted gelating agents, the resulting gels can be further processed by calcination, reduction and sintering, thus obtaining compact undamaged spheres of sintered uranium dioxide. Dilatometric analysis generated of uranium trioxide gels showed that the transformation of UO 3 to U 3 O 8 generated another intermediate thermal decomposition product showing a change in dimensions at temperatures of about 520 degC and a change in colour. This phenomenon is analogous to the decomposition of UO 3 prepared by thermal decomposition of α-UO 3 .2H 2 O involving a change in weight producing the UOsub(3-x) compound or a phase transformation with a change in colour; the structural conversion cannot be identified by X-ray structural analysis. (author)

Histological analysis of effects of 24% EDTA gel for nonsurgical treatment of periodontal tissues.

Science.gov (United States)

de Vasconcellos, Luana Marotta Reis; Ricardo, Lucilene Hernandes; Balducci, Ivan; de Vasconcellos, Luis Gustavo Oliveira; Carvalho, Yasmin Rodarte

2006-12-01

The aim of this study was to investigate, by means of histological and histomorphometric analysis, the effects of 24% ethylenediaminetetraacetic acid (EDTA) gel in periodontal tissue when used in combination with conventional periodontal treatment. Periodontitis was induced in the 2nd upper left permanent molars of 45 male Wistar rats by means of ligature. After 5 weeks, this was removed and debridement was performed. The animals were then randomly divided into 3 groups; group 1: mechanical treatment, group 2: mechanical treatment and EDTA gel application for 2 min, and group 3: mechanical treatment and placebo gel application for 2 min. After the treatment, rinsing was done with 0.9% saline solution for 1 min in all cases, followed by root notching in the deepest part of the pocket. After 4, 10, and 28 days the animals were sacrificed. The averages obtained were evaluated by means of test two-way analysis of variance (ANOVA) and Tukey statistical tests (P 24% EDTA gel did not interfere with periodontal tissue repair when used in combination with conventional periodontal treatment.

Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

Science.gov (United States)

Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

2016-01-01

The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013

Analysis of initial changes in the proteins of soybean root tip under flooding stress using gel-free and gel-based proteomic techniques.

Science.gov (United States)

Yin, Xiaojian; Sakata, Katsumi; Nanjo, Yohei; Komatsu, Setsuko

2014-06-25

Flooding has a severe negative effect on soybean cultivation in the early stages of growth. To obtain a better understanding of the response mechanisms of soybean to flooding stress, initial changes in root tip proteins under flooding were analyzed using two proteomic techniques. Two-day-old soybeans were treated with flooding for 3, 6, 12, and 24h. The weight of soybeans increased during the first 3h of flooding, but root elongation was not observed. Using gel-based and gel-free proteomic techniques, 115 proteins were identified in root tips, of which 9 proteins were commonly detected by both methods. The 71 proteins identified by the gel-free proteomics were analyzed by a hierarchical clustering method based on induction levels during the flooding, and the proteins were divided into 5 clusters. Additional interaction analysis of the proteins revealed that ten proteins belonging to cluster I formed the center of a protein interaction network. mRNA expression analysis of these ten proteins showed that citrate lyase and heat shock protein 70 were down-regulated, whereas calreticulin was up-regulated in initial phase of flooding. These results suggest that flooding stress to soybean induces calcium-related signal transduction, which might play important roles in the early responses to flooding. Flooding has a severe negative effect on soybean cultivation, particularly in the early stages of growth. To better understand the response mechanisms of soybean to the early stages of flooding stress, two proteomic techniques were used. Two-day-old soybeans were treated without or with flooding for 3, 6, 12, and 24h. The fresh weight of soybeans increased during the first 3h of flooding stress, but the growth then slowed and no root elongation was observed. Using gel-based and gel-free proteomic techniques, 115 proteins were identified in root tips, of which 9 proteins were commonly detected by both methods. The 71 proteins identified by the gel-free proteomics were analyzed

Stacking gels: A method for maximising output for pulsed-field gel electrophoresis

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Heng See

2009-01-01

Full Text Available Pulsed field gel electrophoresis (PFGE, the gold standard of molecular typing methods, has a major disadvantage of an unusually long electrophoretic time. From the original protocol of 6 days, it was modified to 3 days and subsequently to a single day. We describe the procedure of stacking five to six gels one on top of another in order to increase and maximize the output in a shorter time without compromising the resolution and reproducibility. All the variables that affect pulsed field gels during electrophoresis were taken into consideration. We firstly optimized the parameters to be used and secondly determined whether stacking of five to six gels had any effect on the molecular separation during electrophoresis in comparison with a single gel run. DNA preparation, restriction, electrophoresis, staining and gel documentation was carried out based on previously published methods. Gels were analysed using BioNumerics and dice coefficient and unweighted pair group methods were used to generate dendrograms based on 1.5% tolerance values. Identical band profiles and band resolution-separation were seen in the PFGE patterns with single gel and multiple stacking gels. Cluster analysis further strengthened the fact that results from stacking gels were reproducible and comparable with a single gel run. This method of stacking gels saves time and maximizes the output at the same time. The run time for a single gel was about 28 hours, but with six stacked gels the run time was 54 hours compared with 28 x 6 = 168 hours if they were run separately as single gels thus saving time of 67.86%. Beside the big factor of saving time, stacking gels save resources (electricity, reagents, water, chemicals and working time by increasing the sample throughput in a shorter time without compromising on quality of data. But optimization of working parameters is vital depending on the PFGE system used.

Cross-protection in Neisseria meningitidis serogroups Y and W polysaccharides: A comparative conformational analysis.

Science.gov (United States)

Kuttel, Michelle M; Timol, Zaheer; Ravenscroft, Neil

2017-06-29

The capsular polysaccharide is the main virulence factor in meningococcus. The capsular polysaccharides for meningococcal serogroups Y and W are almost identical polymers of hexose-sialic acid, suggesting the possibility of cross-protection between group Y and W vaccines. However, early studies indicated that they elicit different levels of cross-protection. Here we explore the conformations of the meningococcal Y and W polysaccharides with molecular dynamics simulations of three repeating unit oligosaccharide strands. We find differences in Y and W antigen conformation: the Y polysaccharide has a single dominant conformation, whereas W exhibits a family of conformations including the Y conformation. This result is supported by our NMR NOESY analysis, which indicates key close contacts for W that are not present in Y. These conformational differences provide an explanation for the different levels of cross-protection measured for the Y and W monovalent vaccines and the high group W responses observed in HibMenCY-TT vaccinees. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Conformation analysis of the N-glycosylation site Asn-X-Thr/Ser in glycoproteins].

Science.gov (United States)

Avanov, A Ia; Lipkind, G M

1990-03-01

Theoretical conformational analysis of oligopeptides CH3CO-Asn-X-Thr-NHCH3 (X = Gly, Ala, Pro), modelling N-glycosylation site, and their glycosylated derivatives CH3CO-(GlcNAc beta 1-4GlcNAc beta 1) Asn-X-Thr-NHCH3 has been carried out. Active conformations of the site are found, corresponding to structural prerequisities of N-glycosylation: Asn residue's position in beta-turn and hydrogen bond formation between side chains of Asn and Thr/Ser residues. In this case the L conformation of the central residue X is most probable. Since Pro residue does not possess this conformation, sequences with X = Pro are not glycosylated. It is shown that glycosylation of the above-mentioned sites is accompanied by reorientation of the Asn residue's side chains.

Thermodynamic analysis of sol-gel transition of gelatin in terms of water activity in various solutions.

Science.gov (United States)

Miyawaki, Osato; Omote, Chiaki; Matsuhira, Keiko

2015-12-01

Sol-gel transition of gelatin was analyzed as a multisite stoichiometric reaction of a gelatin molecule with water and solute molecules. The equilibrium sol-gel transition temperature, Tt , was estimated from the average of gelation and melting temperature measured by differential scanning calorimetry. From Tt and the melting enthalpy, ΔHsol , the equilibrium sol-to-gel ratio was estimated by the van't Hoff equation. The reciprocal form of the Wyman-Tanford equation, which describes the sol-to-gel ratio as a function of water activity, was successfully applied to obtain a good linear relationship. From this analysis, the role of water activity on the sol-gel transition of gelatin was clearly explained and the contributions of hydration and solute binding to gelatin molecules were separately discussed in sol-gel transition. The general solution for the free energy for gel-stabilization in various solutions was obtained as a simple function of solute concentration. © 2015 Wiley Periodicals, Inc.

Study and application of weak gel used for an offshore oilfield

Energy Technology Data Exchange (ETDEWEB)

Tang, X.; Liu, Y.; Bai, B.; Liu, G.; Jiang, R. [Petro-China Research Inst. of Petroleum Exploration and Development, Beijing (China); Xiang, W. [China Offshore Oil Research Center of China National Offshore Oil Co. (China)

2005-07-01

This paper described the profile modification technique which has been used successfully in China's oil fields on land and which has become one of the key techniques to improve the development of mature fields with high heterogeneity and high water cut. One such reservoir is SZ361, an offshore oilfield characterized by thick oil layers, high permeability contrast, high oil viscosity and high water salinity. All injection wells were completed by liner gravel-packing. Water cut of some production wells is above 90 per cent. A large volume of weak gel treatment was proposed to control water conformance. A new weak gel was developed to address the specific features of offshore oil fields, such as small space of platform and high salinity of injection water. The gel properties were presented along with an evaluation of the salinity and temperature on the thermal stability of the gel. The plugging efficiency of the gel was carried out on different permeability cores. Results show that the selected polymer and cross-linkers can be well dispersed and solved within 30 minutes when mixing with sea water or produced water. The gelation time can be controlled by adjusting the gel composition. The novel gel can be applied in the reservoirs with a temperature range of 30-70 degrees C and salinity below 40,000 mg/l. The gel was tested in one injection well and proved to be economically efficient. 7 refs., 3 tabs., 8 figs.

Shape Analysis of Planar Multiply-Connected Objects Using Conformal Welding.

Science.gov (United States)

Lok Ming Lui; Wei Zeng; Shing-Tung Yau; Xianfeng Gu

2014-07-01

Shape analysis is a central problem in the field of computer vision. In 2D shape analysis, classification and recognition of objects from their observed silhouettes are extremely crucial but difficult. It usually involves an efficient representation of 2D shape space with a metric, so that its mathematical structure can be used for further analysis. Although the study of 2D simply-connected shapes has been subject to a corpus of literatures, the analysis of multiply-connected shapes is comparatively less studied. In this work, we propose a representation for general 2D multiply-connected domains with arbitrary topologies using conformal welding. A metric can be defined on the proposed representation space, which gives a metric to measure dissimilarities between objects. The main idea is to map the exterior and interior of the domain conformally to unit disks and circle domains (unit disk with several inner disks removed), using holomorphic 1-forms. A set of diffeomorphisms of the unit circle S(1) can be obtained, which together with the conformal modules are used to define the shape signature. A shape distance between shape signatures can be defined to measure dissimilarities between shapes. We prove theoretically that the proposed shape signature uniquely determines the multiply-connected objects under suitable normalization. We also introduce a reconstruction algorithm to obtain shapes from their signatures. This completes our framework and allows us to move back and forth between shapes and signatures. With that, a morphing algorithm between shapes can be developed through the interpolation of the Beltrami coefficients associated with the signatures. Experiments have been carried out on shapes extracted from real images. Results demonstrate the efficacy of our proposed algorithm as a stable shape representation scheme.

PyElph - a software tool for gel images analysis and phylogenetics

Directory of Open Access Journals (Sweden)

Pavel Ana Brânduşa

2012-01-01

Full Text Available Abstract Background This paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do. Results PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism, AFLP (Amplified Fragment Length Polymorphism, RAPD

The use of static light scattering for the structure analysis of radiosensitive polymer gels: a literature survey

Energy Technology Data Exchange (ETDEWEB)

Bussche, E Vanden [Department of Radiotherapy Nuclear Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium); Deene, Y de [Department of Radiotherapy Nuclear Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium); Dubruel, P [Polymer Material Research Group, Ghent University, Krijgslaan 281, 9000 Ghent (Belgium); Vergote, K [Department of Radiotherapy Nuclear Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium); Schacht, E [Polymer Material Research Group, Ghent University, Krijgslaan 281, 9000 Ghent (Belgium); Wagter, C de [Department of Radiotherapy Nuclear Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent (Belgium)

2004-01-01

Static light scattering (SLS) could be a worthy technique to perform a structure analysis of the polymer structures inside radiation sensitive gels. The information obtained with SLS is a static characterization of the particle structures inside the gel. SLS will be combined with NMR relaxometry and NMR diffusion measurements, which deliver a hydrodynamic characterization of the microstructure of the gels.

The effect of conformational transition of gelatin-polysaccharide polyelectrolyte complex on its functional properties

Directory of Open Access Journals (Sweden)

Tomáš Valenta

2017-01-01

Full Text Available The blends of gelatin and shear-thinning hydrocolloids (guar gum, kappa-carrageenan and xanthan gum were examined to determine the effect of the conformational change on the functional properties of the solutions. The polyelectrolyte complexes of 0.5% gelatin/0.5% polysaccharide in 70 mM KCl or 70 mM NaCl were investigated by the laboratory rheometer and conductivity meter in the temperature range 25 - 45 °C. The rheological data were fitted by the power-law and Herschel-Bulkley model to obtain the flow parameters. The functional properties of the samples were substantially affected by the conformational change of the polysaccharide, as well as by the type of the hydrocolloid and salt solution. There was an evident change of viscosity and conductivity of the solutions upon heating, corresponding to the helix-coil transition of the polysaccharide at temperature about 35 °C. The type of the salt solvent had an effect on the gelation properties of the samples. Gelatin/kappa-carrageenan blend in NaCl provided a gel of high consistency at ambient temperature (20 - 25 °C, whereas the blend in KCl did not gel in the studied temperature range. The potential stability of the blends was determined by zeta-potential analysis. The low values of ζ-potential indicate that the gelatin/polysaccharide blends are electrically unstable systems which tend to coagulate. The mixtures of gelatin/polysaccharide electrostatic complexes may have a great potential in many food applications.

Mixed-substrate (glycerol tributyrate and fibrin) zymography for simultaneous detection of lipolytic and proteolytic enzymes on a single gel.

Science.gov (United States)

Choi, Nack-Shick; Choi, Jong Hyun; Kim, Bo-Hye; Han, Yun-Jon; Kim, Joong Su; Lee, Seung-Goo; Song, Jae Jun

2009-06-01

A new zymography method for simultaneous detection of two different enzymatic activities (lipolytic and proteolytic) using a single SDS-containing or native-conformation gel and a mixed-substrate (glycerol tributyrate and fibrin) (MS)(1) gel was developed. After routine electrophoresis, SDS in the gel was removed by treatment with Triton X-100. Gel proteins were electrotransferred to the MS gel. To visualize lipolytic activity, the MS gel was incubated at 37 degrees C (for 6 or 24 h) until clear bands against an opaque background were observed. To detect proteolytic activity, the same MS gel was stained with Coomassie brilliant blue. Using this method, we show that six lipolytic enzymes from Staphylococcus pasteuri NJ-1 and four proteolytic enzymes from two Bacillus strains, B. licheniformis DJ-2 and B. licheniformis NJ-5, isolated from soil, can be simultaneously detected.

Structural and thermo-rheological analysis of solutions and gels of a β-lactoglobulin fraction isolated from bovine whey.

Science.gov (United States)

Estévez, Natalia; Fuciños, Pablo; Bargiela, Verónica; Pastrana, Lorenzo; Tovar, Clara Asunción; Luisa Rúa, M

2016-05-01

A β-Lactoglobulin fraction (r-βLg) was isolated from milk whey hydrolysates produced with cardosins from Cynara cardunculus. The impact of the technological process on the r-βLg structure and how in turn this determined its heat-induced gelation was investigated. Results were analysed taking pure β-Lg (p-βLg) as control sample. The process induced changes in the r-βLg native conformation causing exposure of hydrophobic groups, lower thermal stability and also, shorter thermal treatments needed to give rise to non-native and aggregated species. At pH 3.2, r-βLg and p-βLg solutions exhibited two gelation steps, with the advantage that r-βLg protein may form stable gels at lower temperature than p-βLg. At pH 7.2, a specific thermo-viscoelastic stability to 73 °C was found, which corresponded to the gel point in both protein solutions. The difference was that while for p-βLg solution in sol state δ45° (fluid-like). Copyright © 2015 Elsevier Ltd. All rights reserved.

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Diffusion structural analysis study of titania films deposited by sol-gel technique on silica glass

Czech Academy of Sciences Publication Activity Database

Balek, V.; Mitsuhashi, T.; Bountseva, I.M.; Haneda, H.; Málek, Z.; Šubrt, Jan

2003-01-01

Roč. 26, 1-3 (2003), s. 185-189 ISSN 0928-0707. [International Workshop on Glasses, Ceramics, Hybrids and Nanocomposites from Gels /11./. Abano Terme, 16.09.2001-21.09.2001] Institutional research plan: CEZ:AV0Z4032918 Keywords : titania film * diffusion structural analysis * sol-gel Subject RIV: CA - Inorganic Chemistry Impact factor: 1.546, year: 2003

Conformal Nets II: Conformal Blocks

Science.gov (United States)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Highly stretchable carbon nanotube transistors enabled by buckled ion gel gate dielectrics

International Nuclear Information System (INIS)

Wu, Meng-Yin; Chang, Tzu-Hsuan; Ma, Zhenqiang; Zhao, Juan; Xu, Feng; Jacobberger, Robert M.; Arnold, Michael S.

2015-01-01

Deformable field-effect transistors (FETs) are expected to facilitate new technologies like stretchable displays, conformal devices, and electronic skins. We previously demonstrated stretchable FETs based on buckled thin films of polyfluorene-wrapped semiconducting single-walled carbon nanotubes as the channel, buckled metal films as electrodes, and unbuckled flexible ion gel films as the dielectric. The FETs were stretchable up to 50% without appreciable degradation in performance before failure of the ion gel film. Here, we show that by buckling the ion gel, the integrity and performance of the nanotube FETs are extended to nearly 90% elongation, limited by the stretchability of the elastomer substrate. The FETs maintain an on/off ratio of >10 4 and a field-effect mobility of 5 cm 2 V −1 s −1 under elongation and demonstrate invariant performance over 1000 stretching cycles

Conformational analysis of phloroglucinols from hypericum Brasiliense by using x-ray diffraction and molecular modeling

Energy Technology Data Exchange (ETDEWEB)

Leal, Katia Z.; Lindgren, Eric B.; Correa, Arthur L., E-mail: kzleal@uol.com.b [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Quimica. Dept. de Fisico-Quimica; Yoneda, Julliane D. [Universidade Federal Fluminense (UFF), Volta Redonda, RJ (Brazil). Polo Universitario de Volta Redonda; Pinheiro, Carlos B. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Fisica; Franca, Hildegardo S. [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Faculdade de Farmacia. Dept. de Tecnologia Farmaceutica

2010-07-01

In this work we intend to verify the applicability of a computational methodology to predict structural features of organic compounds with biological activity. We selected three phloroglucinols and compared their calculated conformational data with their X-ray crystallographic structure. The results showed that conformations obtained by conformational analysis with the AM1 method followed by geometry optimization by using the DFT B3LYP/6-31 G(d,p) basis set are in very good agreement with X-ray data, indicating that the methodology employed here seems to be a very useful tool in order to predict the conformational preference for this class of compounds. (author)

Analysis of third-party certification approaches using an occupational health and safety conformity-assessment model.

Science.gov (United States)

Redinger, C F; Levine, S P

1998-11-01

The occupational health and safety conformity-assessment model presented in this article was developed (1) to analyze 22 public and private programs to determine the extent to which these programs use third parties in conformity-assessment determinations, and (2) to establish a framework to guide future policy developments related to the use of third parties in occupational health and safety conformity-assessment activities. The units of analysis for this study included select Occupational Safety and Health Administration programs and standards, International Organization for Standardization-based standards and guidelines, and standards and guidelines developed by nongovernmental bodies. The model is based on a 15-cell matrix that categorizes first-, second-, and third-party activities in terms of assessment, accreditation, and accreditation-recognition activities. The third-party component of the model has three categories: industrial hygiene/safety testing and sampling; product, equipment, and laboratory certification; and, occupational health and safety management system registration/certification. Using the model, 16 of the 22 programs were found to have a third-party component in their conformity-assessment structure. The analysis revealed that (1) the model provides a useful means to describe and analyze various third-party approaches, (2) the model needs modification to capture aspects of traditional governmental conformity-assessment/enforcement activities, and (3) several existing third-party conformity-assessment systems offer robust models that can guide future third-party policy formulation and implementation activities.

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

Full Text Available Abstract Background Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA, we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM and multiple empirical criteria based method (MECBM hybrided with different force fields. Results Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%. On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational

DFT molecular modeling and NMR conformational analysis of a new longipinenetriolone diester

Science.gov (United States)

Cerda-García-Rojas, Carlos M.; Guerra-Ramírez, Diana; Román-Marín, Luisa U.; Hernández-Hernández, Juan D.; Joseph-Nathan, Pedro

2006-05-01

The structure and conformational behavior of the new natural compound (4 R,5 S,7 S,8 R,9 S,10 R,11 R)-longipin-2-en-7,8,9-triol-1-one 7-angelate-9-isovalerate (1) isolated from Stevia eupatoria, were studied by molecular modeling and NMR spectroscopy. A Monte Carlo search followed by DFT calculations at the B3LYP/6-31G* level provided the theoretical conformations of the sesquiterpene framework, which were in full agreement with results derived from the 1H- 1H coupling constant analysis.

Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.

Science.gov (United States)

Nguyen, Phi-Vu; Ghezal, Ali; Hsueh, Ya-Chih; Boudier, Thomas; Gan, Samuel Ken-En; Lee, Hwee Kuan

2016-08-01

In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the segmentation algorithm. Incorporating this into GelApp, we report a significant enhancement of gel band detection accuracy by 55.9 ± 2.0% for protein polyacrylamide gels, and 35.9 ± 2.5% for DNA SYBR green agarose gels. This implementation is a proof-of-concept in demonstrating MCTS-UCB as a strategy to optimize general image segmentation. The improved version of GelApp-GelApp 2.0-is freely available on both Google Play Store (for Android platform), and Apple App Store (for iOS platform). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-gel casting apparatus for vertical polyacrylamide gels with in-built solution flow system and liquid level detectors.

Science.gov (United States)

Maurye, Praveen; Basu, Arpita; Bandyopadhyay, Tapas Kumar; Biswas, Jayanta Kumar; Mohanty, Bimal Prasana

2017-08-01

PAGE is the most widely used technique for the separation and biochemical analysis of biomolecules. The ever growing field of proteomics and genomics necessitates the analysis of many proteins and nucleic acid samples to understand further about the structure and function of cells. Simultaneous analysis of multiple protein samples often requires casting of many PAGE gels. Several variants of multi-gel casting/electrophoresis apparatuses are frequently used in research laboratories. Requirement of supplementary gels to match the growing demand for analyzing additional protein samples sometimes become a cause of concern. Available apparatuses are not amenable to and therefore, not recommended for any modification to accommodate additional gel casting units other than what is prescribed by the manufacturer. A novel apparatus is described here for casting multiple PAGE gels comprising four detachable components that provide enhanced practicability and performance of the apparatus. This newly modified apparatus promises to be a reliable source for making multiple gels in less time without hassle. Synchronized functioning of unique components broaden the possibilities of developing inexpensive, safe, and time-saving multi-gel casting apparatus. This apparatus can be easily fabricated and modified to accommodate desired number of gel casting units. The estimated cost (∼$300) for fabrication of the main apparatus is very competitive and effortless assembly procedure can be completed within ∼30 min. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly stretchable carbon nanotube transistors enabled by buckled ion gel gate dielectrics

Energy Technology Data Exchange (ETDEWEB)

Wu, Meng-Yin; Chang, Tzu-Hsuan; Ma, Zhenqiang [Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Zhao, Juan [School of Optoelectronic Information, University of Electronic Science and Technology of China, Chengdu 610054 (China); Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Xu, Feng; Jacobberger, Robert M.; Arnold, Michael S., E-mail: michael.arnold@wisc.edu [Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

2015-08-03

Deformable field-effect transistors (FETs) are expected to facilitate new technologies like stretchable displays, conformal devices, and electronic skins. We previously demonstrated stretchable FETs based on buckled thin films of polyfluorene-wrapped semiconducting single-walled carbon nanotubes as the channel, buckled metal films as electrodes, and unbuckled flexible ion gel films as the dielectric. The FETs were stretchable up to 50% without appreciable degradation in performance before failure of the ion gel film. Here, we show that by buckling the ion gel, the integrity and performance of the nanotube FETs are extended to nearly 90% elongation, limited by the stretchability of the elastomer substrate. The FETs maintain an on/off ratio of >10{sup 4} and a field-effect mobility of 5 cm{sup 2} V{sup −1} s{sup −1} under elongation and demonstrate invariant performance over 1000 stretching cycles.

Sol-gel titania-coated needles for solid phase dynamic extraction-GC/MS analysis of desomorphine and desocodeine.

Science.gov (United States)

Su, Chi-Ju; Srimurugan, Sankarewaran; Chen, Chinpiao; Shu, Hun-Chi

2011-01-01

Novel sol-gel titania film coated needles for solid-phase dynamic extraction (SPDE)-GC/MS analysis of desomorphine and desocodeine are described. The high thermal stability of titania film permits efficient extraction and analysis of poorly volatile opiate drugs. The influences of sol-gel reaction time, coating layer, extraction and desorption time and temperature on the SPDE needle performance were investigated. The deuterium labeled internal standard was introduced either during the extraction of analyte or directly injected to GC after the extraction process. The latter method was shown to be more sensitive for the analysis of water and urine samples containing opiate drugs. The proposed conditions provided a wide linear range (from 5-5000 ppb), and satisfactory linearity, with R(2) values from 0.9958 to 0.9999, and prominent sensitivity, LOQs (1.0-5.0 ng/g). The sol-gel titania film coated needle with SPDE-GC/MS will be a promising technique for desomorphine and desocodeine analysis in urine.

Lesion measurement in non-radioactive DNA by quantitative gel electrophoresis

International Nuclear Information System (INIS)

Sutherland, J.C.; Chen, Chun Zhang; Emrick, A.; Hacham, H; Monteleone, D.; Ribeiro, E.; Trunk, J.; Sutherland, B.M.

1989-01-01

The gel electrophoresis method developed during the past ten years in our laboratories makes possible the quantitation of UV induced pyrimidine dimers, gamma ray induced single- and double-strand breaks and many other types of lesions in nanogram quantities of DNA. The DNA does not have to be labeled with radionuclides or of a particular conformation, thus facilitating the use of the method in measuring damage levels and repair rates in the DNA of intact organisms -- including man. The gel method can quantitate any lesion in DNA that either is, or can be converted to a single- or double-strand break. The formation of a strand break produces two shorter DNA molecules for each molecule that existed before the treatment that produced the break. Determining the number of breaks, and hence the number of lesions, becomes a matter of comparing the average lengths of molecules in samples differing only in lesion-induced breaks. This requires that we determine the distribution of mass of DNA on a gel as a function of its distance of migration and also the dispersion function of its distance of migration and also the dispersion function (the relationship between molecular length and distance of migration) in the gel electrophoresis system. 40 refs., 5 figs

Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis.

Science.gov (United States)

Casbarra, Annarita; Birolo, Leila; Infusini, Giuseppe; Dal Piaz, Fabrizio; Svensson, Malin; Pucci, Piero; Svanborg, Catharina; Marino, Gennaro

2004-05-01

A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.

Engineering polyelectrolyte multilayer structure at the nanometer length scale by tuning polymer solution conformation.

Science.gov (United States)

Boddohi, Soheil; Killingsworth, Christopher; Kipper, Matt

2008-03-01

Chitosan (a weak polycation) and heparin (a strong polyanion) are used to make polyelectrolyte multilayers (PEM). PEM thickness and composition are determined as a function of solution pH (4.6 to 5.8) and ionic strength (0.1 to 0.5 M). Over this range, increasing pH increases the PEM thickness; however, the sensitivity to changes in pH is a strong function of ionic strength. The PEM thickness data are correlated to the polymer conformation in solution. Polyelectrolyte conformation in solution is characterized by gel permeation chromatography (GPC). The highest sensitivity of PEM structure to pH is obtained at intermediate ionic strength. Different interactions govern the conformation and adsorption phenomena at low and high ionic strength, leading to reduced sensitivity to solution pH at extreme ionic strengths. The correspondence between PEM thickness and polymer solution conformation offers opportunities to tune polymer thin film structure at the nanometer length scale by controlling simple, reproducible processing conditions.

Microscopic silicon-based lateral high-aspect-ratio structures for thin film conformality analysis

International Nuclear Information System (INIS)

Gao, Feng; Arpiainen, Sanna; Puurunen, Riikka L.

2015-01-01

Film conformality is one of the major drivers for the interest in atomic layer deposition (ALD) processes. This work presents new silicon-based microscopic lateral high-aspect-ratio (LHAR) test structures for the analysis of the conformality of thin films deposited by ALD and by other chemical vapor deposition means. The microscopic LHAR structures consist of a lateral cavity inside silicon with a roof supported by pillars. The cavity length (e.g., 20–5000 μm) and cavity height (e.g., 200–1000 nm) can be varied, giving aspect ratios of, e.g., 20:1 to 25 000:1. Film conformality can be analyzed with the microscopic LHAR by several means, as demonstrated for the ALD Al 2 O 3 and TiO 2 processes from Me 3 Al/H 2 O and TiCl 4 /H 2 O. The microscopic LHAR test structures introduced in this work expose a new parameter space for thin film conformality investigations expected to prove useful in the development, tuning and modeling of ALD and other chemical vapor deposition processes

Theoretical conformational analysis of the tetrasaccharide repeating units of the O-antigenic polysaccharide of Shigella flexneri

International Nuclear Information System (INIS)

Lipkind, G.M.; Kochetkov, N.K.

1986-01-01

A theoretical conformational analysis has been made of the four tetrasaccharide repeating units of the polysaccharide of Shigella flexneri, serotype Y. The interdependence of the conformation states of the neighboring disaccharide units and the oligosaccharides has been investigated. The distribution of the tetrasaccharides over the conformations in solution obtained by calculating the free energies of the optimum structures is given. It has been shown that a substantial correction of the results relating to oligosaccharide chains is achieved when the entropy factors is taken into account

Conformation analysis of oligomeric flavanoids

Science.gov (United States)

Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

1995-01-01

The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

Mass transport of heavy metal ions and radon in gels used as sealing agents in containment technologies

International Nuclear Information System (INIS)

Lakatos, I.; Bauer, K.; Lakatos-Szabo, J.; Kretzschmar, H.J.

1997-01-01

The diffusion and hydrodynamic mass transport of multivalent cations, mostly Cr(III) and Cr(VI) ions and radon in polymer/silicate gels and Montanwax emulsions were studied. It was concluded that the self-conforming gels may decrease the hydrodynamic mass transport in porous and fractured media by 4-6 orders of magnitude. In water saturated systems, however, the diffusion transport can be restricted by hydrogels only to a moderate extent. On the other hand, the high and selective retention capacity of gels towards different diffusing species may open new vistas in the sealing technologies. Similar results were obtained for transport phenomena of radon. The almost perfect quenching process of radon and its nuclides in gels and emulsions further enhances the positive effects of the encapsulation methods. The laboratory experiments provided valuable new information to design the different containment technologies

Mass transport of heavy metal ions and radon in gels used as sealing agents in containment technologies

Energy Technology Data Exchange (ETDEWEB)

Lakatos, I.; Bauer, K.; Lakatos-Szabo, J. [Research Lab. for Mining Chemistry, Miskolc-Egyetemvaros (Hungary); Kretzschmar, H.J. [DBI Gas- und Umwelttechnik GmbH, Feiberg (Germany)

1997-12-31

The diffusion and hydrodynamic mass transport of multivalent cations, mostly Cr(III) and Cr(VI) ions and radon in polymer/silicate gels and Montanwax emulsions were studied. It was concluded that the self-conforming gels may decrease the hydrodynamic mass transport in porous and fractured media by 4-6 orders of magnitude. In water saturated systems, however, the diffusion transport can be restricted by hydrogels only to a moderate extent. On the other hand, the high and selective retention capacity of gels towards different diffusing species may open new vistas in the sealing technologies. Similar results were obtained for transport phenomena of radon. The almost perfect quenching process of radon and its nuclides in gels and emulsions further enhances the positive effects of the encapsulation methods. The laboratory experiments provided valuable new information to design the different containment technologies.

Analysis of charge transport in gels containing polyoxometallates using methods of different sensitivity to migration.

Science.gov (United States)

Caban, Karolina; Lewera, Adam; Zukowska, Grazyna Z; Kulesza, Pawel J; Stojek, Zbigniew; Jeffrey, Kenneth R

2006-08-04

Two methods have been used for examination of transport of charge in gels soaked with DMF and containing dissolved polyoxometallates. The first method is based on the analysis of both Cottrellian and steady-state currents and therefore is capable of giving the concentration of the electroactive redox centres and their transport (diffusion-type) coefficient. The second method provides the real diffusion coefficients, i.e. transport coefficients free of migrational influence, for both the substrate and the product of the electrode reaction. Several gels based on poly(methyl methacrylate), with charged (addition of 1-acrylamido-2-methyl-2-propanesulphonic acid to the polymerization mixture) and uncharged chains, have been used in the investigation. The ratio obtained for the diffusion coefficient (second method) and transport coefficient (first method) was smaller for the gels containing charged polymer chains than for the gels with uncharged chains. In part these changes could be explained by the contribution of migration to the transport of polyoxomatallates in the gels. However, the impact of the changes in the polymer-channel capacity at the electrode surface while the electrode process proceeds was also considered. These structural changes should affect differently the methods based on different time domains.

Dosimetry using radiosensitive gels in radiotherapy: significance and methods

International Nuclear Information System (INIS)

Gibon, D.; Bourel, P.; Castelain, B.; Marchandise, X.; Rousseau, J.

2001-01-01

The goal of conformal radiotherapy is to concentrate the dose in a well-defined volume by avoiding the neighbouring healthy structures. This technique requires powerful treatment planning software and a rigorous control of estimated dosimetry. The usual dosimetric tools are not adapted to visualize and validate complex 3D treatment. Dosimetry by radiosensitive gel permits visualization and measurement of the three-dimensional dose distribution. The objective of this work is to report on current work in this field and, based on our results and our experience, to draw prospects for an optimal use of this technique. Further developments will relate to the realization of new radiosensitive gels satisfying, as well as possible, cost requirements, easy realization and use, magnetic resonance imagery (MRI) sensitivity, tissue equivalence, and stability. Other developments focus on scanning methods, especially in MRI to measure T1 and T2. (author)

Conformational analysis of oligomeric flavanoids

Science.gov (United States)

Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

1995-01-01

The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Even within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio-, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

Conformity index: A review

International Nuclear Information System (INIS)

Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

2006-01-01

We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

Computational investigation and synthesis of a sol-gel imprinted material for sensing application of some biologically active molecules

Energy Technology Data Exchange (ETDEWEB)

Atta, Nada F., E-mail: Nada_fah1@yahoo.com [Department of Chemistry, Faculty of Science, University of Cairo, Post Code 12613, Giza (Egypt); Hamed, Maher M.; Abdel-Mageed, Ali M. [Department of Chemistry, Faculty of Science, University of Cairo, Post Code 12613, Giza (Egypt)

2010-05-14

A hybrid sol-gel material was molecularly imprinted with a group of neurotransmitters. Imprinted material is a sol-gel thin film that is spin coated on the surface of a glassy carbon electrode. Imprinted films were characterized electrochemically using cyclic voltammetry (CV) and the encapsulated molecules were extracted from the films and complementary molecular cavities are formed that enable their rebind. The films were tested in their corresponding template solutions for rebinding using square wave voltammetry (SWV). Computational approach for exploring the primary intermolecular forces between templates and hydrolyzed form of the precursor monomer, tetraethylorthosilicate (TEOS), were carried out using Hartree-Fock method (HF). Interaction energy values were computed for each adduct formed between a monomer and a template. Analysis of the optimized conformations of various adducts could explain the mode of interaction between the templates and the monomer units. We found that interaction via the amino group is the common mode among the studied compounds and the results are in good agreement with the electrochemical measurements.

Conformational stability of calreticulin

DEFF Research Database (Denmark)

Jørgensen, C.S.; Trandum, C.; Larsen, N.

2005-01-01

The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

Electrophoresis gel image processing and analysis using the KODAK 1D software.

Science.gov (United States)

Pizzonia, J

2001-06-01

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

Gel properties and interactions of Mesona blumes polysaccharide-soy protein isolates mixed gel: The effect of salt addition.

Science.gov (United States)

Wang, Wenjie; Shen, Mingyue; Liu, Suchen; Jiang, Lian; Song, Qianqian; Xie, Jianhua

2018-07-15

Effect of different salt ions on the gel properties and microstructure of Mesona blumes polysaccharide (MBP)-soy protein isolates (SPI) mixed gels were investigated. Sodium and calcium ions were chosen to explore their effects on the rheological behavior and gel properties of MBP-SPI mixed gels were evaluated by using rheological, X-ray diffraction, protein solubility determination, and microstructure analysis. Results showed that the addition of salt ions change the crystalline state of gels system, the crystal of gel was enhanced at low ion concentrations (0.005-0.01 M). The two peaks of gel characteristic at 8.9° and 19.9° almost disappeared at high salt ions concentrations (0.015-0.02 M), and new crystallization peaks appeared at around 30° and 45°. The elasticity, viscosity, gel strength, water holding capacity, and thermal stability of gel were increased at low ion concentration. Results showed that the main interactions which promoted gel formation and maintain the three-dimensional structure of the gel were electrostatic interactions, hydrophobic interactions, and disulfide interactions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.

Directory of Open Access Journals (Sweden)

Gómez Marcela

2009-12-01

Full Text Available Abstract Background Expressed sequence tags (ESTs are an important source of gene-based markers such as those based on insertion-deletions (Indels or single-nucleotide polymorphisms (SNPs. Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs, to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. Results A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 × G19833 recombinant inbred line (RIL population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 × 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. Conclusion The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction

Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).

Science.gov (United States)

Galeano, Carlos H; Fernández, Andrea C; Gómez, Marcela; Blair, Matthew W

2009-12-23

Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation

Gauge fixing problem in the conformal QED

International Nuclear Information System (INIS)

Ichinose, Shoichi

1986-01-01

The gauge fixing problem in the conformal (spinor and scalar) QED is examined. For the analysis, we generalize Dirac's manifestly conformal-covariant formalism. It is shown that the (vector and matter) fields must obey a certain mixed (conformal and gauge) type of transformation law in order to fix the local gauge symmetry preserving the conformal invariance in the Lagrangian. (orig.)

Numerical bifurcation analysis of conformal formulations of the Einstein constraints

International Nuclear Information System (INIS)

Holst, M.; Kungurtsev, V.

2011-01-01

The Einstein constraint equations have been the subject of study for more than 50 years. The introduction of the conformal method in the 1970s as a parametrization of initial data for the Einstein equations led to increased interest in the development of a complete solution theory for the constraints, with the theory for constant mean curvature (CMC) spatial slices and closed manifolds completely developed by 1995. The first general non-CMC existence result was establish by Holst et al. in 2008, with extensions to rough data by Holst et al. in 2009, and to vacuum spacetimes by Maxwell in 2009. The non-CMC theory remains mostly open; moreover, recent work of Maxwell on specific symmetry models sheds light on fundamental nonuniqueness problems with the conformal method as a parametrization in non-CMC settings. In parallel with these mathematical developments, computational physicists have uncovered surprising behavior in numerical solutions to the extended conformal thin sandwich formulation of the Einstein constraints. In particular, numerical evidence suggests the existence of multiple solutions with a quadratic fold, and a recent analysis of a simplified model supports this conclusion. In this article, we examine this apparent bifurcation phenomena in a methodical way, using modern techniques in bifurcation theory and in numerical homotopy methods. We first review the evidence for the presence of bifurcation in the Hamiltonian constraint in the time-symmetric case. We give a brief introduction to the mathematical framework for analyzing bifurcation phenomena, and then develop the main ideas behind the construction of numerical homotopy, or path-following, methods in the analysis of bifurcation phenomena. We then apply the continuation software package AUTO to this problem, and verify the presence of the fold with homotopy-based numerical methods. We discuss these results and their physical significance, which lead to some interesting remaining questions to

Further developments and applications of layer gel dosimetry

International Nuclear Information System (INIS)

Gambarini, G; Carrara, M; Colli, V; Gay, S; Tomatis, S

2004-01-01

The method used to perform dosimetry with Fricke-xylenol orange-infused gels in form of layers remains the most reliable method for in-phantom dose profiling and imaging in high fluxes of thermal and epithermal neutrons. Gel-dosimeters in form of layers really give the possibility not only of obtaining spatial dose distributions but also of achieving measurements of each dose contribution in neutron fields. These advantages arise from the layer-geometry thanks to which neutron transport is not sensibly altered, even if the elemental gel composition is changed adding particular isotopes (for example 10 B), as necessary to perform the separation of dose contributions. The gel matrix composition and the experimental procedures, adopted for both dosimeter preparation and analysis, have been already described in previous works. In the present work, the improvements of the method employed for gel analysis, dose imaging and gel applications are illustrated

Applying of isoconversional analysis to calorimetric data on the gel melting

Science.gov (United States)

Dranca, I.; Lupascu, T.; Povar, I.

2012-02-01

The present study is concerned to the thermal stability of gelatin gels that is defined that their resistance to melting or, in other words, to the thermally stimulated transitions from gel to sol. The both sol-gel and gel-sol transitions were followed by regular Mettler-Toledo DSC 823e and stochastically modulated multi-frequency DSC (TOPEM® by Mettler-Toledo). The DSC data have been treated by using an advanced isoconversional method developed by Vyazovkin [1,2]. The method allows revealing a variation in the effective activation energy (Eα) with the extent of conversion (α). It has been discovered that an increase in the concentration of gelatin solutions causes an increase in the energy barrier to melting of non-isothermally prepared gels.

Ion therapy of prostate cancer: daily rectal dose reduction by application of spacer gel

International Nuclear Information System (INIS)

Rucinski, Antoni; Brons, Stephan; Richter, Daniel; Habl, Gregor; Debus, Jürgen; Bert, Christoph; Haberer, Thomas; Jäkel, Oliver

2015-01-01

Ion beam therapy represents a promising approach to treat prostate cancer, mainly due to its high conformity and radiobiological effectiveness. However, the presence of prostate motion, patient positioning and range uncertainties may deteriorate target dose and increase exposure of organs at risk. Spacer gel injected between prostate and rectum may increase the safety of prostate cancer (PC) radiation therapy by separating the rectum from the target dose field. The dosimetric impact of the application of spacer gel for scanned carbon ion therapy of PC has been analyzed at Heidelberg Ion-Beam Therapy Center (HIT). The robustness of ion therapy treatment plans was investigated by comparison of two data sets of patients treated with and without spacer gel. A research treatment planning system for ion therapy was used for treatment plan optimization and calculation of daily dose distributions on 2 to 9 Computed Tomography (CT) studies available for each of the 19 patients. Planning and daily dose distributions were analyzed with respect to target coverage, maximal dose to the rectum (excluding 1 ml of the greatest dose; Dmax-1 ml) and the rectal volume receiving dose greater than 90% of prescribed target dose (V90 Rectum ), respectively. The application of spacer gel did substantially diminish rectum dose. Dmax-1 ml on the treatment planning CT was on average reduced from 100.0 ± 1.0% to 90.2 ± 4.8%, when spacer gel was applied. The robustness analysis performed with daily CT studies demonstrated for all analyzed patient cases that application of spacer gel results in a decrease of the daily V90 Rectum index, which calculated over all patient cases and CT studies was 10.2 ± 10.4 [ml] and 1.1 ± 2.1 [ml] for patients without and with spacer gel, respectively. The dosimetric benefit of increasing the distance between prostate and rectum using spacer gel for PC treatment with carbon ion beams has been quantified. Application of spacer gel substantially reduced rectal

Gel Dosimetry Analysis of Gold Nanoparticle Application in Kilovoltage Radiation Therapy

International Nuclear Information System (INIS)

Marques, T; Schwarcke, M; Garrido, C; Zucolot, V; Baffa, O; Nicolucci, P

2010-01-01

In this work gold nanoparticles (AuNP) were embedded in MAGIC-f gel and irradiated in a 250 kV x-ray clinical beam. The signal of non-irradiated gel samples containing AuNPs showed maximum difference of 0.5% related to gel without nanoparticles. Different AuNPs concentrations were studied: 0.10 mM, 0.05 mM and 0.02 mM, presenting dose enhancements of 106%, 90% and 77% respectively. Monte Carlo spectrometry was performed to quantify theoretical changes in photon energy spectrums due to AuNPs presence. Concordance between simulated dose enhancements and gel dosimetry measurements was better than 97% to all concentrations studied. This study evidences that polymer gel dosimetry as a suitable tool to perform dosimetric investigations of nanoparticle applications in Radiation Therapy.

3D MR gel dosimetry with lung equivalent gel

International Nuclear Information System (INIS)

Scherer, J.; Solleder, M.; Schiessl, I.; Bogner, L.; Herbst, M.

1998-01-01

The MR gel dosimetry is used to verify complex 3D treatment plans. Till now this method served only for dose evaluation in homogeneous phantoms. On the way to build a heterogeneous anthropomorphic gel phantom, a lung equivalent gel with the density 0.4 g/cm 3 was developed. First experiments show a 1.55 times higher dose reponse in the low density gel (LD gel). The comparison of a dose distribution in a gel/LD gel/gel slab phantom with Monte Carlo calculations shows good agreement within 5%. More over the accuray of the measuring device magnetic resonance imager was studied in respect to the now exclusive digital image processing with the software MRD (MR dosimetry). Because of the dimensions of the Fricke gel phantom an artefact correction, based on the data from the unirradiated phantom proved to be essential. (orig.) [de

S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

DEFF Research Database (Denmark)

Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

2002-01-01

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

Influence of colloidal silicon dioxide on gel strength, robustness, and adhesive properties of diclofenac gel formulation for topical application.

Science.gov (United States)

Lu, Zheng; Fassihi, Reza

2015-06-01

The objective of this study is to identify the extent of stiffness, adhesiveness, and thixotropic character of a three-dimensional gel network of a 1% diclofenac sodium topical gel formulation in the presence and absence of colloidal silicon dioxide (CSD) and assess its ease of application and adhesiveness using both objective and subjective analysis. The 1% diclofenac gel was mixed with different amounts of CSD (e.g., 0.5, 1, 2, 3, and 5% w/w) and allowed to equilibrate prior to testing. The texture analyzer in combination with a cone-cap assembly was used to objectively investigate the changes in spreadability and adhesiveness of the gel system before and after addition of CSD. Results indicate that an increase in pliability and adhesiveness at levels ≥2 to ≤5% w/w of CSD dispersed in the gel ensues. For subjective analysis, gels with (2% w/w) CSD and in the absence of CSD were uniformly applied to a 20-cm(2) (5 cm × 4 cm) surface area on the forearms of healthy volunteers and vehicle preferences by the volunteers regarding ease of application, durability on the skin, compliance, and feelings concerning its textural properties were assessed. It appears that changes in the gel formulation with the addition of CSD enhance gel viscosity and bonding to the skin. Results further show that changes in physical and rheological characteristics of gel containing 2% w/w CSD did not significantly change subject preferences for the gel preparations. These findings may help formulators to have additional options to develop more robust and cost-effective formulations.

Hamiltonian analysis of curvature-squared gravity with or without conformal invariance

Science.gov (United States)

KlusoÅ, Josef; Oksanen, Markku; Tureanu, Anca

2014-03-01

We analyze gravitational theories with quadratic curvature terms, including the case of conformally invariant Weyl gravity, motivated by the intention to find a renormalizable theory of gravity in the ultraviolet region, yet yielding general relativity at long distances. In the Hamiltonian formulation of Weyl gravity, the number of local constraints is equal to the number of unstable directions in phase space, which in principle could be sufficient for eliminating the unstable degrees of freedom in the full nonlinear theory. All the other theories of quadratic type are unstable—a problem appearing as ghost modes in the linearized theory. We find that the full projection of the Weyl tensor onto a three-dimensional hypersurface contains an additional fully traceless component, given by a quadratic extrinsic curvature tensor. A certain inconsistency in the literature is found and resolved: when the conformal invariance of Weyl gravity is broken by a cosmological constant term, the theory becomes pathological, since a constraint required by the Hamiltonian analysis imposes the determinant of the metric of spacetime to be zero. In order to resolve this problem by restoring the conformal invariance, we introduce a new scalar field that couples to the curvature of spacetime, reminiscent of the introduction of vector fields for ensuring the gauge invariance.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

International Nuclear Information System (INIS)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian; Roitberg, Adrian E.

2015-01-01

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

Energy Technology Data Exchange (ETDEWEB)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian, E-mail: sfalberti@gmail.com [Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal (Argentina); Roitberg, Adrian E. [Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611 (United States)

2015-06-28

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

Synthesis and application of silica gel modified with alkoxyalcohols. Alkoxyalcohol shushoku silica gel no gosei to riyo

Energy Technology Data Exchange (ETDEWEB)

Moriguchi, T.; Ishiguro, H.; Matsubara, Y.; Yoshihara, M.; Maeshima, T.; Ito, S. (Kinki University, Osaka (Japan). Faculty of Science and Engineering)

1991-08-20

Several kinds of silica gel modified by alkoxyalcohols were synthesized by refluxing and dehyration and the organic reactions were studied when these silica gels were used as the catalyst. It could be confirmed by FT-IR spectra, DTA and elementary analysis that alkoxylalcohols adhere to the surface of silica gels without any decomposition. The acetate was produced by using alkyl halides. It was found that the modified silica gels had clearly the catalytic action for the reaction with n-hexyl bromide and dibromoethane although unmodified silica gels did not show the catalytic action. The reducing reaction of carbonyl compounds was carried out. The reaction proceeded at 25 centigrade for acetophenone, cyclohexanone, 1-indanone and 2-octanone to produce the corresponding reduction products. 11 refs., 5 figs., 4 tabs.

Three-dimensional determination of absorbed dose by spectrophotometric analysis of ferrous-sulphate agarose gel

International Nuclear Information System (INIS)

Gambarini, G.; Gomarasca, G.; Marchesini, R.; Pecci, A.; Pirola, L.; Tomatis, S.

1999-01-01

We describe a technique to obtain three-dimensional (3-D) imaging of an absorbed dose by optical transmittance measurements of phantoms composed by agarose gel in which a ferrous sulphate and xylenol orange solution are incorporated. The analysis of gel samples is performed by acquiring transmittance images with a system based on a CCD camera provided with an interference filter matching the optical absorption peak of interest. The proposed technique for 3-D measurements of an absorbed dose is based on the imaging of phantoms composed of sets of properly piled up gel slices. The slice thickness was optimized in order to obtain a good image contrast as well as a good in-depth spatial resolution. To test the technique, a phantom has been irradiated with a collimated γ-beam and then analysed. Proper software was adapted in order to visualise the images of all slices and to attain the 2-D profiles of the dose absorbed by each slice

Riemann monodromy problem and conformal field theories

International Nuclear Information System (INIS)

Blok, B.

1989-01-01

A systematic analysis of the use of the Riemann monodromy problem for determining correlators (conformal blocks) on the sphere is presented. The monodromy data is constructed in terms of the braid matrices and gives a constraint on the noninteger part of the conformal dimensions of the primary fields. To determine the conformal blocks we need to know the order of singularities. We establish a criterion which tells us when the knowledge of the conformal dimensions of primary fields suffice to determine the blocks. When zero modes of the extended algebra are present the analysis is more difficult. In this case we give a conjecture that works for the SU(2) WZW case. (orig.)

Using Chemicals to Optimize Conformance Control in Fractured Reservoirs; TOPICAL

International Nuclear Information System (INIS)

Seright, Randall S.; Liang, Jenn-Tai; Schrader, Richard; Hagstrom II, John; Wang, Ying; Kumar, Ananad; Wavrik, Kathryn

2001-01-01

This report describes work performed during the third and final year of the project, Using Chemicals to Optimize Conformance Control in Fractured Reservoirs. This research project had three objectives. The first objective was to develop a capability to predict and optimize the ability of gels to reduce permeability to water more than that to oil or gas. The second objective was to develop procedures for optimizing blocking agent placement in wells where hydraulic fractures cause channeling problems. The third objective was to develop procedures to optimize blocking agent placement in naturally fractured reservoirs

Analysis of calcium-induced effects on the conformation of fengycin.

Science.gov (United States)

Nasir, Mehmet Nail; Laurent, Pascal; Flore, Christelle; Lins, Laurence; Ongena, Marc; Deleu, Magali

2013-06-01

Fengycin is a natural lipopeptide with antifungal and eliciting properties and able to inhibit the activity of phospholipase A2. A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate its conformation in a membrane-mimicking environment and to investigate the effect of calcium ions on it. We mainly observed that fengycin adopts a turn conformation. Our results showed that calcium ions are bound by the two charged glutamates. The calcium binding has an influence on the fengycin conformation and more particularly, on the environment of the tyrosine residues. The modulation of the fengycin conformation by the environmental conditions may influence its biological properties. Copyright © 2013 Elsevier B.V. All rights reserved.

Conformable Pressurized Structures : Design and Analysis

NARCIS (Netherlands)

Geuskens, F.J.J.M.M.

2012-01-01

There are many applications where volume needs to be pressurised within a geometrical space for which conventional pressure vessels do not provide suitable solutions. Applications are for example found in pressure cabins for Blended Wing Body Aircraft and conformable pressure vessels for an

Transdermal delivery of paeonol using cubic gel and microemulsion gel

Science.gov (United States)

Luo, Maofu; Shen, Qi; Chen, Jinjin

2011-01-01

Background The aim of this study was to develop new systems for transdermal delivery of paeonol, in particular microemulsion gel and cubic gel formulations. Methods Various microemulsion vehicles were prepared using isopropyl myristate as an oil phase, polyoxyethylated castor oil (Cremophor® EL) as a surfactant, and polyethylene glycol 400 as a cosurfactant. In the optimum microemulsion gel formulation, carbomer 940 was selected as the gel matrix, and consisted of 1% paeonol, 4% isopropyl myristate, 28% Cremophor EL/polyethylene glycol 400 (1:1), and 67% water. The cubic gel was prepared containing 3% paeonol, 30% water, and 67% glyceryl monooleate. Results A skin permeability test using excised rat skins indicated that both the cubic gel and microemulsion gel formulations had higher permeability than did the paeonol solution. An in vivo pharmacokinetic study done in rats showed that the relative bioavailability of the cubic gel and microemulsion gel was enhanced by about 1.51-fold and 1.28-fold, respectively, compared with orally administered paeonol suspension. Conclusion Both the cubic gel and microemulsion gel formulations are promising delivery systems to enhance the skin permeability of paeonol, in particular the cubic gel. PMID:21904450

Pulsed-field gel electrophoresis of bacterial chromosomes.

Science.gov (United States)

Mawer, Julia S P; Leach, David R F

2013-01-01

The separation of fragments of DNA by agarose gel electrophoresis is integral to laboratory life. Nevertheless, standard agarose gel electrophoresis cannot resolve fragments bigger than 50 kb. Pulsed-field gel electrophoresis is a technique that has been developed to overcome the limitations of standard agarose gel electrophoresis. Entire linear eukaryotic chromosomes, or large fragments of a chromosome that have been generated by the action of rare-cutting restriction endonucleases, can be separated using this technique. As a result, pulsed-field gel electrophoresis has many applications, from karyotype analysis of microbial genomes, to the analysis of chromosomal strand breaks and their repair intermediates, to the study of DNA replication and the identification of origins of replication. This chapter presents a detailed protocol for the preparation of Escherichia coli chromosomal DNA that has been embedded in agarose plugs, digested with the rare-cutting endonuclease NotI, and separated by contour-clamped homogeneous field electrophoresis. The principles in this protocol can be applied to the separation of all fragments of DNA whose size range is between 40 kb and 1 Mb.

Harmony of spinning conformal blocks

Energy Technology Data Exchange (ETDEWEB)

Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group; Sobko, Evgeny [Stockholm Univ. (Sweden); Nordita, Stockholm (Sweden); Isachenkov, Mikhail [Weizmann Institute of Science, Rehovoth (Israel). Dept. of Particle Physics and Astrophysics

2016-12-07

Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

Harmony of spinning conformal blocks

Energy Technology Data Exchange (ETDEWEB)

Schomerus, Volker [DESY Hamburg, Theory Group,Notkestraße 85, 22607 Hamburg (Germany); Sobko, Evgeny [Nordita and Stockholm University,Roslagstullsbacken 23, SE-106 91 Stockholm (Sweden); Isachenkov, Mikhail [Department of Particle Physics and Astrophysics, Weizmann Institute of Science,Rehovot 7610001 (Israel)

2017-03-15

Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.

Laser CT evaluation on normoxic PAGAT gel dosimeter

International Nuclear Information System (INIS)

Kumar, D S; Samuel, E J J; Watanabe, Y

2013-01-01

Optical computed tomography has been shown to be a potentially useful imaging tool for the radiation therapy physicists. In radiation therapy, researchers have used optical CT for the readout of 3D dosimeters. The purpose of this paper is to describe the initial evaluation of a newly fabricated laser CT scanner for 3D gel dosimetry which works using the first generation principle. A normoxic PAGAT (Polyacrylamide Gelatin and Tetrakis) gel is used as a dosimeter for this analysis. When a laser passes through the gel phantom, absorption and scattering of photon take place. The optical attenuation coefficient of the laser can be obtained by measuring its intensity after passing through the gel by a sensor. The scanner motion is controlled by a computer program written in Microsoft Visual C++. Reconstruction and data analysis on the irradiated gel phantom is performed by suitable algorithm using Matlab software.

Optical CT evaluation on normoxic polymer gel dosimeter

International Nuclear Information System (INIS)

Samuel, E. James Jebaseelan

2013-01-01

Optical computed tomography has been shown to be a potentially useful imaging tool for the radiation therapy physicists. In radiation therapy, researchers have used optical CT for the readout of 3D dosimeters. The purpose of this paper is to explicate the initial evaluation of a newly fabricated laser CT scanner for '3D gel dosimetry' which works in the first generation principle. The normoxic PAGAT (Polyacrylamide Gelatin and Tetrakis) gel is used as a dosimeter for this analysis. When laser passes through this gel phantom, absorption and scattering of photon take place. The optical attenuation coefficient of the laser can be obtained by measuring its intensity after passing through the gel by a sensor.The scanner motion is controlled by the program written in Microsoft Visual C++. Reconstruction and data analysis on the irradiated gel phantom is performed by suitable algorithm using Matlab software. (author)

Improving reservoir conformance using gelled polymer systems. Final report, September 25, 1992--July 31, 1996

Energy Technology Data Exchange (ETDEWEB)

Green, D.W.; Willhite, G.P.; Buller, C.; McCool, S.; Vossoughi, S.; Michnick, M.

1997-06-01

The objectives of the research program were to (1) identify and develop polymer systems which have potential to improve reservoir conformance of fluid displacement processes, (2) determine the performance of these systems in bulk and in porous media, and (3) develop methods to predict their performance in field applications. The research focused on four types of gel systems--KUSP1 systems that contain an aqueous polysaccharide designated KUSP1, phenolic-aldehyde systems composed of resorcinol and formaldehyde, colloidal-dispersion systems composed of polyacrylamide and aluminum citrate, and a chromium-based system where polyacrylamide is crosslinked by chromium(III). Gelation behavior of the resorcinol-formaldehyde systems and the KUSP1-borate system was examined. Size distributions of aggregates that form in the polyacrylamide-aluminum colloidal-dispersion gel system were determined. Permeabilities to brine of several rock materials were significantly reduced by gel treatments using the KUSP1 polymer-ester (monoethyl phthalate) system, the KUSP1 polymer-boric acid system, and the sulfomethylated resorcinol-formaldehyde system were also shown to significantly reduce the permeability to supercritical carbon dioxide. A mathematical model was developed to simulate the behavior of a chromium redox-polyacrylamide gel system that is injected through a wellbore into a multi-layer reservoir in which crossflow between layers is allowed. The model describes gelation kinetics and filtration of pre-gel aggregates in the reservoir. Studies using the model demonstrated the effect filtration of gel aggregates has on the placement of gel systems in layered reservoirs.

Investigation and analysis of ferrous sulfate polyvinyl alcohol (PVA) gel dosimeter

International Nuclear Information System (INIS)

Hill, Brendan; Baeck, Sven A J; Lepage, Martin; Simpson, John; Healy, Brendan; Baldock, Clive

2002-01-01

Ferrous sulfate (Fe(SO 4 ) 2 ) PVA gels were investigated for a range of absorbed doses up to 20 Gy using both magnetic resonance imaging (MRI) and spectrophotometry to determine R 1 and optical density (OD) dose responses and G values. It was found that R 1 - and OD-dose sensitivities increased with O 2 saturation or by the introduction of a freeze-thaw cycle during preparation of the PVA gel. The storage temperature of the Fe(SO 4 ) 2 PVA gel at -18 deg. C increased R 1 -dose sensitivity above that of gels stored at 5 deg C. The addition of sucrose to the formulation was found to result in the largest increase in both R 1 - and OD-dose sensitivities. Fe(SO 4 ) 2 PVA gel with and without the addition of xylenol orange was demonstrated to have a G value of ∼20 ions/100 eV and with sucrose ∼24 ions/100 eV

Second-order Data by Flow Injection Analysis with Spectrophotometric Diode-array Detection and Incorporated Gel-filtration Chromatographic Column

DEFF Research Database (Denmark)

Bechmann, Iben Ellegaard

1997-01-01

A flow injection analysis (FIA) system furnished with a gel-filtration chromatographic column and with photodiode-array detection was used for the generation of second-order data. The system presented is a model system in which the analytes are blue dextran, potassium hexacyanoferrate(III) and he......A flow injection analysis (FIA) system furnished with a gel-filtration chromatographic column and with photodiode-array detection was used for the generation of second-order data. The system presented is a model system in which the analytes are blue dextran, potassium hexacyanoferrate...

Conformational analysis of 9β,19-cyclopropyl sterols: Detection of the pseudoplanar conformer by nuclear Overhauser effects and its functional implications

International Nuclear Information System (INIS)

Nes, W.D.; Benson, M.; Lundin, R.E.; Le, P.H.

1988-01-01

Nuclear Overhauser difference spectroscopy and variable temperature studies of the 9β,19-cyclopropyl sterols 24,25-dehydropollinastanol (4,4-desmethyl-5α-cycloart-24-en-3β-ol) and cyclolaudenol [(24S)-24-methyl-5α-cycloart-25(27)-en-3β-ol] have shown the solution conformation of the B/C rings to be twist-chair/twist-boat rather than boat/chair as suggested in the literature. This is very similar to the known crystal structure conformation of 9β,19-cyclopropyl sterols. The effect of these conformations on the molecular shape is highly significant; the first conformation orients into a pseudoplanar or flat shape analogous to lanosterol, whereas the latter conformation exhibits a bent shape. The results are interpreted to imply that, for conformational reasons, cyclopropyl sterols can be expected to maintain the pseudoplanar shape in membrane bilayers

Improving reservoir conformance using gelled polymer systems. Annual report, September 25, 1992--September 24, 1993

Energy Technology Data Exchange (ETDEWEB)

Green, D.W.; Willhite, G.P.

1994-08-01

The general objectives of the research program are to (1) identify and develop gelled polymer systems which have potential to improve reservoir conformance of fluid displacement processes, (2) determine the performance of these systems in bulk and in porous media, and (3) develop methods to predict their performance in field applications. The research focuses on three types of gel systems-an aqueous polysaccharide (KUSPI) that gels as a function of pH, polyacrylamide or xanthan crosslinked by CR(III) and a polyacrylamide-aluminum citrate system. Work to date has focused primarily on development of a database, selection of systems, and work to characterize the gel/polymer physical properties and kinetics. The use of ester hydrolysis to control the rate of pH change of a gel system has been investigated and this approach to gel-time control shows promise. Extensive kinetic data were taken on the uptake of CR(III) oligomers by polyacrylamide. A model was developed which describes very well the monomer uptake rates. The model described the dimer uptake data less well and the trimer uptake data poorly. Studies of the flow and gelation in rock materials have been initiated. A mathematical model of rock-fluid interaction during flow of high pH solutions has been developed.

Improving reservoir conformance using gelled polymer systems. Eleventh quarterly report, April 1, 1995--June 30, 1995

Energy Technology Data Exchange (ETDEWEB)

Green, D.W.; Willhite, G.P.; Buller, C.; McCool, S.; Vossoughi, S.; Michnick, M.

1995-07-24

The general objectives are to (1) to identify and develop gelled polymer systems which have potential to improve reservoir conformance of fluid displacement processes, (2) to determine the performance of these systems in bulk and in porous media, and (3) to develop methods to predict the capability of these systems to recover oil from petroleum reservoirs. This work focuses on three types of gel systems -- an aqueous polysaccharide (KUSP1) system that gels as a function of pH, the chromium(III)-polyacrylamide system and the aluminum citrate-polyacrylamide system. Laboratory research is directed at the fundamental understanding of the physics and chemistry of the gelation process in bulk form and in porous media. This knowledge will be used to develop conceptual and mathematical models of the gelation process. Mathematical models will then be extended to predict the performance of gelled polymer treatments in oil reservoirs. Technical progress is described for the following tasks: physical and chemical characterization of gel systems; mechanisms of in situ gelation; and mathematical modelling of the gel systems.

Gel chromatography of sup(99m)Tc-labelled compounds

International Nuclear Information System (INIS)

Vilcek, S.; Machan, V.; Kalincak, M.

1976-01-01

The present state of gel chromatography of sup(99m)Tc-labelled compounds is reviewed. Examples are given of gel chromatography for preparing labelled compounds and for quality control analysis and the development of new types of sup(99m)Tc-labelled compounds. The factors which influence the gel chromatography of these compounds are discussed, i.e., the nature of the elution agent, the duration of the contact of the gel and the preparation the gel type, the nature of the labelled compound. The GCS method (gel chromatography scanning) is briefly described. The advantages of gel chromatography as compared with other chromatographic techniques for sup(99m)Tc-labelled compounds are summarized. (author)

Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

Science.gov (United States)

Tokatli, A.; Ucun, F.; Sütçü, K.; Osmanoğlu, Y. E.; Osmanoğlu, Ş.

2018-02-01

In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6-31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

New insights on mu/delta selectivity of opioid peptides: conformational analysis of deltorphin analogues.

Science.gov (United States)

Tancredi, T; Temussi, P A; Picone, D; Amodeo, P; Tomatis, R; Salvadori, S; Marastoni, M; Santagada, V; Balboni, G

1991-05-01

The message domain of dermorphin (Tyr-D-Ala-Phe), a natural mu-opioid heptapeptide, has long been considered the main cause of the high mu selectivity of this peptide and of its analogues. The recent discovery, in the skin of Phyllomedusa sauvagei (i.e., the same natural source of dermorphin) and of Phyllomedusa bicolor of deltorphins, challenges this belief. Deltorphins, in fact, are three heptapeptides characterized by a message domain typical of mu-selective peptides, but endowed of an extremely high delta selectivity, the highest of all natural opioid peptides. A conformational analysis of dermorphin and deltorphins, based on nmr studies in DMSO and cryoprotective mixtures and internal energy calculations, showed that the enormous differences in receptor selectivity can be interpreted on the basis of receptor models for mu and delta opioids that recognize the same beta-turn in the N-terminal part, but discriminate for the conformation and polarity of the C-terminal part. Here we present the synthesis, biological activity, and conformational analysis in solution of three deltorphin analogues with very similar constitution, but with different net charge, different location of negative residues, or even without negative residues, which confirm these hypotheses and show that His4 can play a specific structural role.

Benchmarking Commercial Conformer Ensemble Generators.

Science.gov (United States)

Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

2017-11-27

We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

Bayesian conformational analysis of ring molecules through reversible jump MCMC

DEFF Research Database (Denmark)

Nolsøe, Kim; Kessler, Mathieu; Pérez, José

2005-01-01

In this paper we address the problem of classifying the conformations of mmembered rings using experimental observations obtained by crystal structure analysis. We formulate a model for the data generation mechanism that consists in a multidimensional mixture model. We perform inference for the p...... for the proportions and the components in a Bayesian framework, implementing an MCMC Reversible Jumps Algorithm to obtain samples of the posterior distributions. The method is illustrated on a simulated data set and on real data corresponding to cyclo-octane structures....

Non-conformal contact mechanical characteristic analysis on spherical components

Energy Technology Data Exchange (ETDEWEB)

Zhen-zhi, G.; Bin, H.; Zheng-ming, G.; Feng-mei, Y.; Jin, Q [The 2. Artillery Engineering Univ., Xi' an (China)

2017-03-15

Non-conformal spherical-contact mechanical problems is a three-dimensional coordination or similar to the coordination spherical contact. Due to the complexity of the problem of spherical-contact and difficulties of solving higher-order partial differential equations, problems of three-dimensional coordination or similar to the coordination spherical-contact is still no exact analytical method for solving. It is based on three-dimensional taper model is proposed a model based on the contour surface of the spherical contact and concluded of the formula of the contact pressure and constructed of finite element model by contact pressure distribution under the non-conformal spherical. The results shows spherical contact model can reflect non-conformal spherical-contacting mechanical problems more than taper-contacting model, and apply for the actual project.

Variable-temperature NMR and conformational analysis of Oenothein B

International Nuclear Information System (INIS)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de

2014-01-01

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

Variable-temperature NMR and conformational analysis of Oenothein B

Energy Technology Data Exchange (ETDEWEB)

Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

2014-02-15

Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

Science.gov (United States)

Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

2017-10-01

Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

A novel method of estimating dose responses for polymer gels using texture analysis of scanning electron microscopy images.

Directory of Open Access Journals (Sweden)

Cheng-Ting Shih

Full Text Available Polymer gels are regarded as a potential dosimeter for independent validation of absorbed doses in clinical radiotherapy. Several imaging modalities have been used to convert radiation-induced polymerization to absorbed doses from a macro-scale viewpoint. This study developed a novel dose conversion mechanism by texture analysis of scanning electron microscopy (SEM images. The modified N-isopropyl-acrylamide (NIPAM gels were prepared under normoxic conditions, and were administered radiation doses from 5 to 20 Gy. After freeze drying, the gel samples were sliced for SEM scanning with 50×, 500×, and 3500× magnifications. Four texture indices were calculated based on the gray level co-occurrence matrix (GLCM. The results showed that entropy and homogeneity were more suitable than contrast and energy as dose indices for higher linearity and sensitivity of the dose response curves. After parameter optimization, an R (2 value of 0.993 can be achieved for homogeneity using 500× magnified SEM images with 27 pixel offsets and no outlier exclusion. For dose verification, the percentage errors between the prescribed dose and the measured dose for 5, 10, 15, and 20 Gy were -7.60%, 5.80%, 2.53%, and -0.95%, respectively. We conclude that texture analysis can be applied to the SEM images of gel dosimeters to accurately convert micro-scale structural features to absorbed doses. The proposed method may extend the feasibility of applying gel dosimeters in the fields of diagnostic radiology and radiation protection.

Fractional order analysis of Sephadex gel structures: NMR measurements reflecting anomalous diffusion

Science.gov (United States)

Magin, Richard L.; Akpa, Belinda S.; Neuberger, Thomas; Webb, Andrew G.

2011-12-01

We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-( bD) α], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4000 s mm -2). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.

[Analysis for Discordance of Positive and Negative Blood Typing by Gel Card].

Science.gov (United States)

Li, Cui-Ying; Xu, Hong; Lei, Hui-Fen; Liu, Juan; Li, Xiao-Wei

2017-08-01

To explore the method of Gel card identifying ABO blood group, determine the inconsistent cause and the distribution of disease affecting factors, and put forward a method of its solutions. To collect 240 positive and negative typing-discordant blood speciments from patients examined by Gel card and send these speciments to blood type reference laboratory for examining with the classic tube method and serological test, such as salivary blood-group substance, in order to performe genotyping method when serologic test can not be determined. Among 240 positive and negative typing-discordant blood speciments from patients examined by Gel card, 107 blood speciments were positive and negative consistent examined by false agglutination test (44.58%), 133 blood specinents were discordent examined by false agglutination (55.42%), out of them, 35 cases (14.58%) with inconsistent cold agglutination test, 22 cases (9.17%) with weakened AB antigenicity, 16 cases (6.67%) with ABO subtyping, 12 cases (5.00%) with positive direct antiglobulin test, 11 cases (4.58%) with reduced or without antibodies, 11 cases (4.58%) with false aggregation caused by drugs or protein, 11 cases (4.58%) with salivary blood-type substances, 8 cases (3.33%) with non-ABO alloantibody, and 7 cases (2.92%) with allogeneic bone marrow transplantation. The distribution of disease were following: blood disease (16.83%), tumor (11.88%), and cardiopulmonary diseases (11.39%); chi-square test results indicated that the distribution significantly different. The analysis of ABO blood grouping shows a variety factors influencing positive and negative blood typing, and the Gel Card identification can produc more false positive blood types. Therefore, more attention should be paid on the high incidence diseases, such as blood disease, tumor, and cardiopulmonary disease.

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

Science.gov (United States)

Sullivan, David C; Lim, Carmay

2006-08-24

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

Operator algebras and conformal field theory

International Nuclear Information System (INIS)

Gabbiani, F.; Froehlich, J.

1993-01-01

We define and study two-dimensional, chiral conformal field theory by the methods of algebraic field theory. We start by characterizing the vacuum sectors of such theories and show that, under very general hypotheses, their algebras of local observables are isomorphic to the unique hyperfinite type III 1 factor. The conformal net determined by the algebras of local observables is proven to satisfy Haag duality. The representation of the Moebius group (and presumably of the entire Virasoro algebra) on the vacuum sector of a conformal field theory is uniquely determined by the Tomita-Takesaki modular operators associated with its vacuum state and its conformal net. We then develop the theory of Mebius covariant representations of a conformal net, using methods of Doplicher, Haag and Roberts. We apply our results to the representation theory of loop groups. Our analysis is motivated by the desire to find a 'background-independent' formulation of conformal field theories. (orig.)

PCR amplification on microarrays of gel immobilized oligonucleotides

Science.gov (United States)

Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

2003-11-04

The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

Improving reservoir conformance using gelled polymer systems. Annual report, September 25, 1994--September 24, 1995

Energy Technology Data Exchange (ETDEWEB)

Green, D.W.; Willhite, G.P.

1996-05-01

The objectives of the research program are to (1) identify and develop polymer systems which have potential to improve reservoir conformance of fluid displacement processes, (2) determine the performance of these systems in bulk and in porous media, and (3) develop methods to predict their performance in field applications. The research focused on four types of gel systems -- KUSP1 systems which contain an aqueous polysaccharide designated KUSP1, phenolic-aldehyde systems composed of resorcinol and formaldehyde, colloidal-dispersion systems composed of polyacrylamide and aluminum citrate, and a chromium-based system where polyacrylamide is crosslinked by chromium(III). Gelation behavior of the resorcinol-formaldehyde systems and the KUSP1-borate system was examined. Size distributions of aggregates that form in the polyacrylamide-aluminum colloidal-dispersion gel system were determined. Permeabilities to brine of several rock materials were significantly reduced by gel treatments using the KUSP1 polymer-ester (monoethylphthalate) system, the KUSP1 polymer-boric acid system, and the sulfomethylated resorcinol-formaldehyde system. The KUSP1 polymer-ester system and the sulfomethylated resorcinol-formaldehyde system were also shown to significantly reduce the permeability to super-critical carbon dioxide. A mathematical model was developed to simulate the behavior of a chromium redox-polyacrylamide gel system that is injected through a wellbore into a multi-layer reservoir in which crossflow between layers is allowed. The model describes gelation kinetics and filtration of pre-gel aggregates in the reservoir. Studies using the model demonstrated the effect filtration of gel aggregates has on the placement of gel systems in layered reservoirs.

Extraction of metal ions using chemically modified silica gel: a PIXE analysis.

Science.gov (United States)

Jal, P K; Dutta, R K; Sudarshan, M; Saha, A; Bhattacharyya, S N; Chintalapudi, S N; K Mishra, B

2001-08-30

Organic ligand with carboxyhydrazide functional group was immobilised on the surface of silica gel and the metal binding capacity of the ligand-embedded silica was investigated. The functional group was covalently bonded to the silica matrix through a spacer of methylene groups by sequential reactions of silica gel with dibromobutane, malonic ester and hydrazine in different media. Surface area value of the modified silica was determined. The changes in surface area were correlated with the structural change of the silica surface due to chemical modifications. A mixture solution of metal ions [K(I),Cr(III),Co(II),Ni(II),Cu(II),Zn(II),Hg(II) and U(VI)] was treated with the ligand-embedded silica in 10(-3) M aqueous solution. The measurement of metal extraction capacity of the silica based ligand was done by multielemental analysis of the metal complexes thus formed by using Proton Induced X-ray Emission (PIXE) technique.

Sol-Gel Glasses

Science.gov (United States)

Mukherjee, S. P.

1985-01-01

Multicomponent homogeneous, ultrapure noncrystalline gels/gel derived glasses are promising batch materials for the containerless glass melting experiments in microgravity. Hence, ultrapure, homogeneous gel precursors could be used to: (1) investigate the effect of the container induced nucleation on the glass forming ability of marginally glass forming compositions; and (2) investigate the influence of gravity on the phase separation and coarsening behavior of gel derived glasses in the liquid-liquid immiscibility zone of the nonsilicate systems having a high density phase. The structure and crystallization behavior of gels in the SiO2-GeO2 as a function of gel chemistry and thermal treatment were investigated. As are the chemical principles involved in the distribution of a second network former in silica gel matrix being investigated. The procedures for synthesizing noncrystalline gels/gel-monoliths in the SiO2-GeO2, GeO2-PbO systems were developed. Preliminary investigations on the levitation and thermal treatment of germania silicate gel-monoliths in the Pressure Facility Acoustic Levitator were done.

Differentiation among isolates of prunus necrotic ringspot virus by transcript conformation polymorphism.

Science.gov (United States)

Rosner, A; Maslenin, L; Spiegel, S

1998-09-01

A method based on differences in electrophoretic mobility of RNA transcripts made from polymerase chain reaction (PCR) products was used for differentiation among virus isolates. A T7 RNA polymerase promoter was attached to amplified prunus necrotic ringspot virus (PNRSV) sequences by PCR. The PCR products then served as a template for transcription. Single-stranded transcripts originated from different PNRSV isolates varied in electrophoretic mobility in polyacrylamide gels, presumably because of transcript conformation polymorphism (TCP). This procedure was applied for the differentiation of PNRSV isolates.

Analysis of glycoprotein-derived oligosaccharides in glycoproteins detected on two-dimensional gel by capillary electrophoresis using on-line concentration method.

Science.gov (United States)

Kamoda, Satoru; Nakanishi, Yasuharu; Kinoshita, Mitsuhiro; Ishikawa, Rika; Kakehi, Kazuaki

2006-02-17

Capillary electrophoresis (CE) is an effective tool to analyze carbohydrate mixture derived from glycoproteins with high resolution. However, CE has a disadvantage that a few nanoliters of a sample solution are injected to a narrow capillary. Therefore, we have to prepare a sample solution of high concentration for CE analysis. In the present study, we applied head column field-amplified sample stacking method to the analysis of N-linked oligosaccharides derived from glycoprotein separated by two-dimensional gel electrophoresis. Model studies demonstrated that we achieved 60-360 times concentration effect on the analysis of carbohydrate chains labeled with 3-aminobenzoic acid (3-AA). The method was applied to the analysis of N-linked oligosaccharides from glycoproteins separated and detected on PAGE gel. Heterogeneity of alpha1-acid glycoprotein (AGP), i.e. glycoforms, was examined by 2D-PAGE and N-linked oligosaccharides were released by in-gel digestion with PNGase F. The released oligosaccharides were derivatized with 3-AA and analyzed by CE. The results showed that glycoforms having lower pI values contained a larger amount of tetra- and tri-antennary oligosaccharides. In contrast, glycoforms having higher pI values contained bi-antennary oligosaccharides abundantly. The result clearly indicated that the spot of a glycoprotein glycoform detected by Coomassie brilliant blue staining on 2D-PAGE gel is sufficient for quantitative profiling of oligosaccharides.

Workers’ Conformism

Directory of Open Access Journals (Sweden)

Nikolay Ivantchev

2013-10-01

Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

Towards conformal loop quantum gravity

International Nuclear Information System (INIS)

Wang, Charles H-T

2006-01-01

A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

International Nuclear Information System (INIS)

Martín-García, Fernando; Mendieta-Moreno, Jesús Ignacio; Mendieta, Jesús; Gómez-Puertas, Paulino

2012-01-01

Highlights: ► Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. ► HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. ► HRS domains of F protein form three single α-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmental pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from β-sheet conformation to an elongated coil and then spontaneously to an α-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

Low Temperature Ferromagnetism and Optical Properties of Fe Doped ZnO Nanoparticles Synthesized by Sol-Gel Method

Directory of Open Access Journals (Sweden)

B. Sathya

2017-06-01

Full Text Available In this present investigation, pure and Fe doped Zinc oxide nanoparticles were successfully synthesized by sol gel method.The structural and optical properties were examined by using X-ray diffraction (XRD, Scanning electron microscope (SEM, Transmission electron microscope (TEM, Ultraviolet spectroscopy and Photoluminescence (PL techniques.The structural characterization of XRD analysis confirmed the phase purity of the samples and crystallite size can be decreased with increasing doping concentrations.SEM image show that nanoparticles in spherical shape. The optical band gap calculated through UV-visible spectroscopy is found to be increasing from 3.48 to 3.57eV. TEM analysis depicted the crystallinity of nanoparticles prepared and chemical composition conformed the EDAX analysis. The PL spectra reveal that, Fe doped ZnO exhibit a decrease in intensity of the band edge emission peak while the intensity of the deep level emission peak increases.The enhancement of low temperature ferromagnetism in ZnO: Fe was achieved.

Conformational Clusters of Phosphorylated Tyrosine.

Science.gov (United States)

Abdelrasoul, Maha; Ponniah, Komala; Mao, Alice; Warden, Meghan S; Elhefnawy, Wessam; Li, Yaohang; Pascal, Steven M

2017-12-06

Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.

Conformational Analysis of Misfolded Protein Aggregation by FRET and Live-Cell Imaging Techniques

Directory of Open Access Journals (Sweden)

Akira Kitamura

2015-03-01

Full Text Available Cellular homeostasis is maintained by several types of protein machinery, including molecular chaperones and proteolysis systems. Dysregulation of the proteome disrupts homeostasis in cells, tissues, and the organism as a whole, and has been hypothesized to cause neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS and Huntington’s disease (HD. A hallmark of neurodegenerative disorders is formation of ubiquitin-positive inclusion bodies in neurons, suggesting that the aggregation process of misfolded proteins changes during disease progression. Hence, high-throughput determination of soluble oligomers during the aggregation process, as well as the conformation of sequestered proteins in inclusion bodies, is essential for elucidation of physiological regulation mechanism and drug discovery in this field. To elucidate the interaction, accumulation, and conformation of aggregation-prone proteins, in situ spectroscopic imaging techniques, such as Förster/fluorescence resonance energy transfer (FRET, fluorescence correlation spectroscopy (FCS, and bimolecular fluorescence complementation (BiFC have been employed. Here, we summarize recent reports in which these techniques were applied to the analysis of aggregation-prone proteins (in particular their dimerization, interactions, and conformational changes, and describe several fluorescent indicators used for real-time observation of physiological states related to proteostasis.

Gel stabilization in chelate sol-gel preparation of Bi-2223 superconductors

Czech Academy of Sciences Publication Activity Database

Rubešová, K.; Jakeš, V.; Hlásek, T.; Vašek, Petr; Matějka, P.

2012-01-01

Roč. 73, č. 3 (2012), s. 448-453 ISSN 0022-3697 Institutional research plan: CEZ:AV0Z10100521 Keywords : superconductors * sol-gel growth * infrared spectroscopy * thermogravimetric analysis (TGA) * X-ray diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.527, year: 2012

Analysis of separation quality of scandium-46 and titanium using silica gel column

International Nuclear Information System (INIS)

Muhamad Basit Febrian; Yanuar Setiadi; Duyeh Setiawan; Titin Sri Mulyati; Nana Suherman

2015-01-01

In this study, quality test of scandium and titanium mixture separation system using a silica gel column has been conducted. This system will be used in the separation of medical radioisotopes of 47 Sc from TiO 2 enriched targets. 20 mg of TiO 2 and 5 mg of Sc 2 O 3 dissolved using 0.5 mL of 50% HF solvent with gentle heating at 60°C - 80°C for 1 hour then 4.5 mL H 2 O was added. Sc and Ti mixture is separated by passing it through a column of silica gel. In the determination of scandium released from silica gel, Sc-46 radiotracer was used. Only 51.60 ± 4.5% of 5 mg of scandium could be retained in the silica gel column. From 51.60% of absorbed scandium in the column, 98.29 ± 3.4% were eluted with 5 mL of H 2 O eluent. During elution of scandium from silica gel column, 2.81 grams of 20 mg of titanium came apart as breakthrough. In determination of recovery of titanium from silica gel, 51.76 ± 5.5% of the 20 mg Ti can be recovered from silica gel column using 5M HCl eluent, whereas remaining Ti were eluted using 40 ml of HCl 5M. Based on those result, it can be concluded that there are still titanium portion in scandium after the separation using a silica gel column. Further purification step using fresh silica gel column, can separate escaped titanium from scandium. (author)

Chemometric, physicomechanical and rheological analysis of the sol-gel dynamics and degree of crosslinking of glycosidic polymers

International Nuclear Information System (INIS)

Choonara, Y E; Pillay, V; Singh, N; Ndesendo, V M K; Khan, R A

2008-01-01

The influence of calcium (Ca 2+ ), zinc (Zn 2+ ) and barium (Ba 2+ ) ions on the sol-gel interconversion dynamics, degree of crosslinking and the matrix resilience of crosslinked alginate gelispheres was determined. The dependent compositional and operational variables of crosslinking make it a challenging task to optimize the degree of crosslinking and the physicomechanical properties of alginate gelispheres. The combinatory approach of textural profiling, assessing pertinent rheological descriptors and chemometric model analysis of the sol-gel interconversion mechanisms and energy paradigms involved during crosslinking, hydration and erosion of gelispheres was explored. Molecular structural modelling of the gelispheres provided a mechanistic understanding of the sol-gel interconversion phenomena and their influence on the degree of crosslinking, the hydrational dynamics and gelisphere formation. Rheological analysis revealed offset yield point values of 6.1 mg ml -1 and 8.0 mg ml -1 were computed from fitted regression curves for determining the crosslinker concentration required for combinatory crosslinkers such as Ca/Zn/Ba ions and Ba/Zn, respectively. The influence of hydration on the erosion was a direct function of the gelispheres physicomechanical strength. Textural profiling characterized the gelisphere matrices for their resilience. The various crosslinkers interacted with monomeric units at varying intensities. Ba-crosslinked gelispheres were brittle with dense polymeric networks. Zn-crosslinked gelispheres produced permeable resilient matrices when hydrated and Ca-crosslinked gelispheres demonstrated intermediate resilience with greater G/M ratio alginate grades. Chemometrical analysis explicated a potential link between several phenomena such as the type of crosslinkers employed, the static shear-rate viscosity attained, the matrix resilience and the associated sol-gel mechanisms and energy paradigms of crosslinked gelispheres

Conformation radiotherapy and conformal radiotherapy

International Nuclear Information System (INIS)

Morita, Kozo

1999-01-01

In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

Static validation of licence conformance policies

DEFF Research Database (Denmark)

Hansen, Rene Rydhof; Nielson, Flemming; Nielson, Hanne Riis

2008-01-01

Policy conformance is a security property gaining importance due to commercial interest like Digital Rights Management. It is well known that static analysis can be used to validate a number of more classical security policies, such as discretionary and mandatory access control policies, as well...... as communication protocols using symmetric and asymmetric cryptography. In this work we show how to develop a Flow Logic for validating the conformance of client software with respect to a licence conformance policy. Our approach is sufficiently flexible that it extends to fully open systems that can admit new...

Conjugates of 1'-Aminoferrocene-1-carboxylic Acid and Proline: Synthesis, Conformational Analysis and Biological Evaluation

Directory of Open Access Journals (Sweden)

Monika Kovačević

2014-08-01

Full Text Available Our previous studies showed that alteration of dipeptides Y-Fca-Ala-OMe (III into Y-Ala-Fca-OMe (IV (Y = Ac, Boc; Fca = 1'-aminoferrocene-1-carboxylic acid significantly influenced their conformational space. The novel bioconjugates Y-Fca-Pro-OMe (1, Y = Ac; 2, Y = Boc and Y-Pro-Fca-OMe (3, Y = Boc; 4, Y = Ac have been prepared in order to investigate the influence of proline, a well-known turn-inducer, on the conformational properties of small organometallic peptides with an exchanged constituent amino acid sequences. For this purpose, peptides 1–4 were subjected to detailed spectroscopic analysis (IR, NMR, CD spectroscopy in solution. The conformation of peptide 3 in the solid state was determined. Furthermore, the ability of the prepared conjugates to inhibit the growth of estrogen receptor-responsive MCF-7 mammary carcinoma cells and HeLa cervical carcinoma cells was tested.

Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis.

Science.gov (United States)

Alakent, Burak; Doruker, Pemra; Camurdan, Mehmet C

2004-09-08

Time series analysis is applied on the collective coordinates obtained from principal component analysis of independent molecular dynamics simulations of alpha-amylase inhibitor tendamistat and immunity protein of colicin E7 based on the Calpha coordinates history. Even though the principal component directions obtained for each run are considerably different, the dynamics information obtained from these runs are surprisingly similar in terms of time series models and parameters. There are two main differences in the dynamics of the two proteins: the higher density of low frequencies and the larger step sizes for the interminima motions of colicin E7 than those of alpha-amylase inhibitor, which may be attributed to the higher number of residues of colicin E7 and/or the structural differences of the two proteins. The cumulative density function of the low frequencies in each run conforms to the expectations from the normal mode analysis. When different runs of alpha-amylase inhibitor are projected on the same set of eigenvectors, it is found that principal components obtained from a certain conformational region of a protein has a moderate explanation power in other conformational regions and the local minima are similar to a certain extent, while the height of the energy barriers in between the minima significantly change. As a final remark, time series analysis tools are further exploited in this study with the motive of explaining the equilibrium fluctuations of proteins. Copyright 2004 American Institute of Physics

Effect of the atmospheric pressure nonequilibrium plasmas on the conformational changes of plasmid DNA

International Nuclear Information System (INIS)

Yan Xu; He Guangyuan; Shi Mengjun; Gao Xuan; Li Yin; Ma Fengyun; Yu Men; Wang Changdong; Wang Yuesheng; Yang Guangxiao; Zou Fei; Lu Xinpei; Xiong Qing; Xiong Zilan

2009-01-01

The cold atmospheric pressure plasma, which has been widely used for biomedical applications, may potentially affect the conformation of DNA. In this letter, an atmospheric pressure plasma plume is used to investigate its effects on the conformational changes of DNA of plasmid pAHC25. It is found that the plasma plume could cause plasmid DNA topology alteration, resulting in the percentage of the supercoiled plasmid DNA form decreased while that of the open circular and linearized form of plasmid DNA increased as detected by agrose gel electrophoresis. On the other hand, further investigation by using polymerase chain reaction method shows that the atmospheric pressure plasma jet treatments under proper conditions does not affect the genes of the plasmid DNA, which may have potential application in increasing the transformation frequency by genetic engineering.

Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D

Directory of Open Access Journals (Sweden)

Matheus Puggina de Freitas

2013-12-01

Full Text Available A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D, a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

Killing tensors and conformal Killing tensors from conformal Killing vectors

International Nuclear Information System (INIS)

Rani, Raffaele; Edgar, S Brian; Barnes, Alan

2003-01-01

Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

Pharmacokinetics of 2 dapivirine vaginal microbicide gels and their safety vs. Hydroxyethyl cellulose-based universal placebo gel.

Science.gov (United States)

Nel, Annalene M; Smythe, Shanique C; Habibi, Sepideh; Kaptur, Paulina E; Romano, Joseph W

2010-10-01

Dapivirine, a nonnucleoside reverse transcriptase inhibitor, is in development as a microbicide for the protection of women against HIV infection. A randomized, double-blind, phase 1 trial was conducted in 36 healthy HIV-negative women to compare the pharmacokinetics of 2 dapivirine vaginal gel formulations (0.05% each) and their safety with the hydroxyethyl cellulose-based universal placebo gel. Gel was self-administered once daily for a total of 11 days. Blood and vaginal fluid samples were collected sequentially over 24 days for pharmacokinetic analysis. Safety was evaluated by pelvic examination, colposcopy, adverse events, and clinical laboratory assessments. Adverse event profiles were similar for the 3 gels. Most events were mild and not related to study gel. Headache and vaginal hemorrhage (any vaginal bleeding) were most common. Plasma concentrations of dapivirine did not exceed 1.1 ng/mL. Steady-state conditions were reached within approximately 10 days. Dapivirine concentrations in vaginal fluids were slightly higher for Gel 4789, but Cmax values on days 1 and 14 were not significantly different. Terminal half-life was 72-73 hours in plasma and 15-17 hours in vaginal fluids. Both formulations of dapivirine gel were safe and well tolerated. Dapivirine was delivered to the lower genital tract at concentrations at least 5 logs greater than in vitro inhibitory concentrations.

Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

DEFF Research Database (Denmark)

Christensen, I T; Jørgensen, Flemming Steen

1997-01-01

. A series of methyl-substituted 1,3-dioxanes were investigated at 1000 K, and the number of chair-chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy......-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method...

GelTouch

DEFF Research Database (Denmark)

Miruchna, Viktor; Walter, Robert; Lindlbauer, David

2015-01-01

We present GelTouch, a gel-based layer that can selectively transition between soft and stiff to provide tactile multi-touch feedback. It is flexible, transparent when not activated, and contains no mechanical, electromagnetic, or hydraulic components, resulting in a compact form factor (a 2mm thin...... touchscreen layer for our prototype). The activated areas can be morphed freely and continuously, without being limited to fixed, predefined shapes. GelTouch consists of a poly(N-isopropylacrylamide) gel layer which alters its viscoelasticity when activated by applying heat (>32 C). We present three different...

Surface analysis and biocorrosion properties of nanostructured surface sol-gel coatings on Ti6Al4V titanium alloy implants.

Science.gov (United States)

Advincula, Maria C; Petersen, Don; Rahemtulla, Firoz; Advincula, Rigoberto; Lemons, Jack E

2007-01-01

Surfaces of biocompatible alloys used as implants play a significant role in their osseointegration. Surface sol-gel processing (SSP), a variant of the bulk sol-gel technique, is a relatively new process to prepare bioreactive nanostructured titanium oxide for thin film coatings. The surface topography, roughness, and composition of sol-gel processed Ti6Al4V titanium alloy coatings was investigated by atomic force microscopy (AFM) and X-ray electron spectroscopy (XPS). This was correlated with corrosion properties, adhesive strength, and bioreactivity in simulated body fluids (SBF). Electroimpedance spectroscopy (EIS) and polarization studies indicated similar advantageous corrosion properties between sol-gel coated and uncoated Ti6Al4V, which was attributed to the stable TiO2 composition, topography, and adhesive strength of the sol-gel coating. In addition, inductive coupled plasma (ICP) and scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) analysis of substrates immersed in SBF revealed higher deposition of calcium and phosphate and low release rates of alloying elements from the sol-gel modified alloys. The equivalent corrosion behavior and the definite increase in nucleation of calcium apatite indicate the potential of the sol-gel coating for enhanced bioimplant applications. 2006 Wiley Periodicals, Inc.

Conformational changes in glycine tri- and hexapeptide

DEFF Research Database (Denmark)

Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.

2006-01-01

conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of the characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods...... also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids....

Sol/gel analysis of poly (acrylamide-co-metacrylic acid) Hydrogels obtained by gamma radiation for biomedical use

International Nuclear Information System (INIS)

Rapado, M.; Altanes, S.; Prado, S.; Chong, B.; Aguilera, Y.; Saldivar, D.

1999-01-01

Sol-Gel analysis of irradiated polymer was carried out and allowed to estimate important radiation parameters as gelation dose, virtual dose , degradation and crosslinking densities and yield of crosslinking and degradation of copolymer according with a modified Charesby-Pinner equation. The degree of copolymer conversion as a function of the absorbed dose of irradiation is presented. These parameters can be correlated with some physical and chemical properties of polymeric network formation and this way be able to design and prepare gels with the desired structure suitable as a drug delivery system

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

Science.gov (United States)

Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

2010-09-01

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

Invariants for minimal conformal supergravity in six dimensions

Energy Technology Data Exchange (ETDEWEB)

Butter, Daniel [Nikhef Theory Group,Science Park 105, 1098 XG Amsterdam (Netherlands); Kuzenko, Sergei M. [School of Physics M013, The University of Western Australia,35 Stirling Highway, Crawley W.A. 6009 (Australia); Novak, Joseph; Theisen, Stefan [Max-Planck-Institut für Gravitationsphysik, Albert-Einstein-Institut,Am Mühlenberg 1, D-14476 Golm (Germany)

2016-12-15

We develop a new off-shell formulation for six-dimensional conformal supergravity obtained by gauging the 6D N=(1,0) superconformal algebra in superspace. This formulation is employed to construct two invariants for 6D N=(1,0) conformal supergravity, which contain C{sup 3} and C◻C terms at the component level. Using a conformal supercurrent analysis, we prove that these exhaust all such invariants in minimal conformal supergravity. Finally, we show how to construct the supersymmetric F◻F invariant in curved superspace.

Replacement between conformity and counter-conformity in consumption decisions.

Science.gov (United States)

Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

2013-02-01

This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

Structural alphabets derived from attractors in conformational space

Directory of Open Access Journals (Sweden)

Kleinjung Jens

2010-02-01

Full Text Available Abstract Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.

Screening of mucoadhesive vaginal gel formulations

Directory of Open Access Journals (Sweden)

Ana Ochoa Andrade

2014-12-01

Full Text Available Rational design of vaginal drug delivery formulations requires special attention to vehicle properties that optimize vaginal coating and retention. The aim of the present work was to perform a screening of mucoadhesive vaginal gels formulated with carbomer or carrageenan in binary combination with a second polymer (carbomer, guar or xanthan gum. The gels were characterised using in vitroadhesion, spreadability and leakage potential studies, as well as rheological measurements (stress and frequency sweep tests and the effect of dilution with simulated vaginal fluid (SVF on spreadability. Results were analysed using analysis of variance and multiple factor analysis. The combination of polymers enhanced adhesion of both primary gelling agents, carbomer and carrageenan. From the rheological point of view all formulations presented a similar behaviour, prevalently elastic and characterised by loss tangent values well below 1. No correlation between rheological and adhesion behaviour was found. Carbomer and carrageenan gels containing the highest percentage of xanthan gum displayed good in vitro mucoadhesion and spreadability, minimal leakage potential and high resistance to dilution. The positive results obtained with carrageenan-xanthan gum-based gels can encourage the use of natural biocompatible adjuvants in the composition of vaginal products, a formulation field that is currently under the synthetic domain.

A method for easily customizable gradient gel electrophoresis.

Science.gov (United States)

Miller, Andrew J; Roman, Brandon; Norstrom, Eric

2016-09-15

Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE. Copyright © 2016 Elsevier Inc. All rights reserved.

Inversion theory and conformal mapping

CERN Document Server

Blair, David E

2000-01-01

It is rarely taught in an undergraduate or even graduate curriculum that the only conformal maps in Euclidean space of dimension greater than two are those generated by similarities and inversions in spheres. This is in stark contrast to the wealth of conformal maps in the plane. The principal aim of this text is to give a treatment of this paucity of conformal maps in higher dimensions. The exposition includes both an analytic proof in general dimension and a differential-geometric proof in dimension three. For completeness, enough complex analysis is developed to prove the abundance of conformal maps in the plane. In addition, the book develops inversion theory as a subject, along with the auxiliary theme of circle-preserving maps. A particular feature is the inclusion of a paper by Carath�odory with the remarkable result that any circle-preserving transformation is necessarily a M�bius transformation, not even the continuity of the transformation is assumed. The text is at the level of advanced undergr...

New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

Science.gov (United States)

Thach, Trung Thanh; Shin, Donghyuk; Han, Seungsu; Lee, Sangho

2016-04-01

The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

Acid-Urea Gel Electrophoresis and Western Blotting of Histones.

Science.gov (United States)

Hazzalin, Catherine A; Mahadevan, Louis C

2017-01-01

Acid-urea gel electrophoresis offers significant advantages over SDS-PAGE for analysis of post-translational protein modifications, being capable of resolving proteins of similar size but varying in charge. Hence, it can be used to separate protein variants with small charge-altering differences in primary sequence, and is particularly useful in the analysis of histones whose charge variation arises from post-translational modification, such as phosphorylation or acetylation. On acid-urea gels, histones that carry multiple modifications, each with a characteristic charge, are resolved into distinct bands, the so-called "histone ladder." Thus, the extent and distribution of different modification states of histones can be visualized. Here, we describe the analysis of histone H3 by acid-urea gel electrophoresis and western blotting.

Cholesterol biosensor based on a plastic optical fibre with sol-gel: structural analysis and sensing properties

Science.gov (United States)

Razo-Medina, D. A.; Trejo-Durán, M.; Alvarado-Méndez, E.

2018-02-01

In this paper, we report the design and characterization of an optical fibre cholesterol biosensor by using sol-gel immobilization technique. The cholesterol enzyme is encapsulated inside of the sol-gel film onto an end of a plastic optical fibre. Two film deposition methods (Dip-Coating and Immersion) were studied. The morphology analysis and sensing properties permit us to determine the best film deposition to sense cholesterol concentration. The range of measured is 4.4-5.2 mM in real time and our results were validated by comparing them with other previously published results. The biosensor is portable, simple cheap, and easy to use.

Pouring and running a protein gel by reusing commercial cassettes.

Science.gov (United States)

Hwang, Alexander C; Grey, Paris H; Cuddy, Katrina; Oppenheimer, David G

2012-02-12

The evaluation of proteins using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is a common technique used by biochemistry and molecular biology researchers. For laboratories that perform daily analyses of proteins, the cost of commercially available polyacrylamide gels (~$10/gel) can be considerable over time. To mitigate this cost, some researchers prepare their own polyacrylamide gels. Traditional methods of pouring these gels typically utilize specialized equipment and glass gel plates that can be expensive and preclude pouring many gels and storing them for future use. Furthermore, handling of glass plates during cleaning or gel pouring can result in accidental breakage creating a safety hazard, which may preclude their use in undergraduate laboratory classes. Our protocol demonstrates how to pour multiple protein gels simultaneously by recycling Invitrogen Nupage Novex minigel cassettes, and inexpensive materials purchased at a home improvement store. This economical and streamlined method includes a way to store the gels at 4°C for a few weeks. By re-using the plastic gel cassettes from commercially available gels, labs that run frequent protein gels can save significant costs and help the environment. In addition, plastic gel cassettes are extremely resistant to breakage, which makes them ideal for undergraduate laboratory classrooms.

Electroactive polymer gels based on epoxy resin

Science.gov (United States)

Samui, A. B.; Jayakumar, S.; Jayalakshmi, C. G.; Pandey, K.; Sivaraman, P.

2007-04-01

Five types of epoxy gels have been synthesized from common epoxy resins and hardeners. Fumed silica and nanoclay, respectively, were used as fillers and butyl methacrylate/acrylamide were used as monomer(s) for making interpenetrating polymer networks (IPNs) in three compositions. Swelling study, tensile property evaluation, dynamic mechanical thermal analysis, thermo-gravimetric analysis, scanning electron microscopy and electroactive property evaluation were done. The gels have sufficient mechanical strength and the time taken for bending to 20° was found to be 22 min for forward bias whereas it was just 12 min for reverse bias.

Preparation and Properties of Polyester-Based Nanocomposite Gel Coat System

Directory of Open Access Journals (Sweden)

P. Jawahar

2006-01-01

Full Text Available Nanocomposite gel coat system is prepared using unsaturated polyester resin with aerosil powder, CaCO3, and organoclay. The influence of organoclay addition on mechanical and water barrier properties of gel coat system is studied for different amount (1, 2, and 3 wt % of organoclay. The nanolevel incorporation of organoclay improves the mechanical and water barrier properties of nanocomposite gel coat system. The nanocomposite gel coat system exhibits 55% improvement in tensile modulus and 25% improvement in flexural modulus. There is a 30% improvement in impact property of nanocomposite gel coat system. The dynamic mechanical analysis shows a slight increase in glass transition temperature for nanocomposite gel coat system.

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

Science.gov (United States)

Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

2017-05-05

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Long-range carbon-proton spin-spin coupling constants in conformational analysis

International Nuclear Information System (INIS)

Spoormaker, T.

1979-01-01

The author has collected a reliable set of data on long range 13 C- 1 H coupling constants in aliphatic compounds and developed the use of long range 13 C- 1 H coupling constants as a tool in the conformational analysis of aliphatic compounds. An empirical determination of the torsion angle dependence of the vicinal 13 C- 1 H coupling constant for model compounds is described and the dependence of long range 13 C- 1 H coupling constants on the electronegativity of substituents attached to the coupling pathway reported for the monohalogen substituted ethanes and propanes. The electronegativity dependence of the vicinal 13 C- 1 H coupling was studied in monosubstituted propanes whose substituents are elements from the first row of the periodic table and it is shown that the vicinal 13 C- 1 H coupling constant in aliphatic systems is a constitutive property. The geminal 13 C- 1 H coupling constants in ethyl, isopropyl and tert-butyl compounds, which have been substituted by an element of the first row of the periodic table or a haline atom, are reported and the influence of electronegative substituents on the vicinal 13 C- 1 H coupling constants in the individual rotamers of 13 CH 3 -C(X)H-C(Y)H- 1 H fragments discussed. The application of long range 13 C- 1 H coupling constants to the conformational analysis of CMP-N-Acetylneuraminic acid and 2,6-dichloro-1,4-oxathiane is described. (Auth.)

Evaluation of wheat by polyacrylamide gel electrophoresis | Shuaib ...

African Journals Online (AJOL)

... polyacrylamide gel electrophoresis (SDS-PAGE). Electrophorogram for each variety were scored and presence or absence of each band noted and was entered in a binary data matrix. Based on the data of SDS-PAGE gels cluster analysis was performed to check the variations among varieties. The overall result shows ...

Energy-Efficient Bioalcohol Recovery by Gel Stripping

Science.gov (United States)

Godbole, Rutvik; Ma, Lan; Hedden, Ronald

2014-03-01

Design of energy-efficient processes for recovering butanol and ethanol from dilute fermentations is a key challenge facing the biofuels industry due to the high energy consumption of traditional multi-stage distillation processes. Gel stripping is an alternative purification process by which a dilute alcohol is stripped from the fermentation product by passing it through a packed bed containing particles of a selectively absorbent polymeric gel material. The gel must be selective for the alcohol, while swelling to a reasonable degree in dilute alcohol-water mixtures. To accelerate materials optimization, a combinatorial approach is taken to screen a matrix of copolymer gels having orthogonal gradients in crosslinker concentration and hydrophilicity. Using a combination of swelling in pure solvents, the selectivity and distribution coefficients of alcohols in the gels can be predicted based upon multi-component extensions of Flory-Rehner theory. Predictions can be validated by measuring swelling in water/alcohol mixtures and conducting h HPLC analysis of the external liquid. 95% + removal of butanol from dilute aqueous solutions has been demonstrated, and a mathematical model of the unsteady-state gel stripping process has been developed. NSF CMMI Award 1335082.

Conformal house

DEFF Research Database (Denmark)

Ryttov, Thomas Aaby; Sannino, Francesco

2010-01-01

fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

Rapid, quantitative analysis of ppm/ppb nicotine using surface-enhanced Raman scattering from polymer-encapsulated Ag nanoparticles (gel-colls).

Science.gov (United States)

Bell, Steven E J; Sirimuthu, Narayana M S

2004-11-01

Rapid, quantitative SERS analysis of nicotine at ppm/ppb levels has been carried out using stable and inexpensive polymer-encapsulated Ag nanoparticles (gel-colls). The strongest nicotine band (1030 cm(-1)) was measured against d(5)-pyridine internal standard (974 cm(-1)) which was introduced during preparation of the stock gel-colls. Calibration plots of I(nic)/I(pyr) against the concentration of nicotine were non-linear but plotting I(nic)/I(pyr) against [nicotine](x)(x = 0.6-0.75, depending on the exact experimental conditions) gave linear calibrations over the range (0.1-10 ppm) with R(2) typically ca. 0.998. The RMS prediction error was found to be 0.10 ppm when the gel-colls were used for quantitative determination of unknown nicotine samples in 1-5 ppm level. The main advantages of the method are that the gel-colls constitute a highly stable and reproducible SERS medium that allows high throughput (50 sample h(-1)) measurements.

Phenylketonuria in The Netherlands : 93% of the mutations are detected by single-strand conformation analysis

NARCIS (Netherlands)

vanderSijsBos, CJM; Diepstraten, CM; Juyn, JA; Plaisier, M; Giltay, JC; vanSpronsen, FJ; Smit, GPA; Berger, R; Smeitink, JAM; PollThe, BT; vanAmstel, JKP

1996-01-01

Single-strand conformational analysis was used to screen for genetic defects in all thirteen exons of the phenylalanine hydroxylase gene (PAH) in phenylketonuria and hyperphenylalaninemia patients in the Netherlands. Exons that showed a bandshift were sequenced directly, In this way, we were able to

Electromyography analysis of natural mastication behavior using varying mouthful quantities of two types of gels.

Science.gov (United States)

Kohyama, Kaoru; Gao, Zhihong; Ishihara, Sayaka; Funami, Takahiro; Nishinari, Katsuyoshi

2016-07-01

The objectives of this study were to examine the effects of mouthful quantities and mechanical properties of gels on natural mastication behaviors using electromyography (EMG). Two types of hydrocolloid gels (A and K) with similar fracture loads but different moduli and fracture strains were served to eleven normal women in 3-, 6-, 12-, and 24-g masses in a randomized order. EMG activities from both masseter muscles were recorded during natural mastication. Because of the similar fracture loads, the numbers of chews, total muscle activities, and entire oral processing times were similar for similar masses of both gel types. Prior to the first swallow, the more elastic K gel with a higher fracture strain required higher muscle activities than the brittle A gel, which had higher modulus. Majority of subjects had preferred sides of chewing, but all subjects with or without preferred sides used both masseters during the consumption of gels. Similar effects of masses and types of gels were observed in EMG activities of both sides of masseters. Contributions of the dominant side of chewing were diminished with increasing masses of gels, and the mass dependency on ratio of the dominant side was more pronounced with K gel. More repetitions of smaller masses required greater muscle activities and longer periods for the consumption of 24-g gel portions. Reduction in the masses with an increased number of repetitions necessitated slower eating and more mastication to consume the gel portions. These observations suggest that chewing using both sides is more effective and unconsciously reduces mastication times during the consumption of gels. Copyright © 2016 Elsevier Inc. All rights reserved.

Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution

Science.gov (United States)

Stellwagen, Nancy C.

2009-01-01

This review describes the electrophoresis of curved and normal DNA molecules in agarose gels, polyacrylamide gels and in free solution. These studies were undertaken to clarify why curved DNA molecules migrate anomalously slowly in polyacrylamide gels but not in agarose gels. Two milestone papers are cited, in which Ferguson plots were used to estimate the effective pore size of agarose and polyacrylamide gels. Subsequent studies on the effect of the electric field on agarose and polyacrylamide gel matrices, DNA interactions with the two gel matrices, and the effect of curvature on the free solution mobility of DNA are also described. The combined results suggest that the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due primarily to preferential interactions of curved DNAs with the polyacrylamide gel matrix; the restrictive pore size of the matrix is of lesser importance. In free solution, DNA mobilities increase with increasing molecular mass until leveling off at a plateau value of (3.17 ± 0.01) × 10-4 cm2/Vs in 40 mM Tris-acetate-EDTA buffer at 20°C. Curved DNA molecules migrate anomalously slowly in free solution as well as in polyacrylamide gels, explaining why the Ferguson plots of curved and normal DNAs containing the same number of base pairs extrapolate to different mobilities at zero gel concentration. PMID:19517510

Revealing time bunching effect in single-molecule enzyme conformational dynamics.

Science.gov (United States)

Lu, H Peter

2011-04-21

In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a

Conformal polishing approach: Tool footprint analysis

Directory of Open Access Journals (Sweden)

José A Dieste

2016-02-01

Full Text Available Polishing process is one of the most critical manufacturing processes during a metal part production because it determines the final quality of the product. Free-form surface polishing is a handmade process with lots of rejected parts, scrap generation and time and energy consumption. Two different research lines are being developed: prediction models of the final surface quality parameters and an analysis of the amount of material removed depending on the polishing parameters to predict the tool footprint during the polishing task. This research lays the foundations for a future automatic conformal polishing system. It is based on rotational and translational tool with dry abrasive in the front mounted at the end of a robot. A tool to part concept is used, useful for large or heavy workpieces. Results are applied on different curved parts typically used in tooling industry, aeronautics or automotive. A mathematical model has been developed to predict the amount of material removed in function of polishing parameters. Model has been fitted for different abrasives and raw materials. Results have shown deviations under 20% that implies a reliable and controllable process. Smaller amount of material can be removed in controlled areas of a three-dimensional workpiece.

Conformal displays: human factor analysis of innovative landing aids

Science.gov (United States)

Schmerwitz, Sven; Lueken, Thomas; Doehler, Hans-Ullrich; Peinecke, Niklas; Ernst, Johannes M.; da Silva Rosa, David L.

2017-05-01

In the past couple of years, research on display content for helicopter operations headed in a new direction. The already reached goals could evolve into a paradigm change for information visualization. Technology advancements allow implementing three-dimensional and conformal content on a helmet-mounted see-through device. This superimposed imagery inherits the same optical flow as the environment. It is supposed to ease switching between display information and environmental cues. The concept is neither pathbreaking nor new, but it has not been successfully established in aviation yet. Nevertheless, there are certainly some advantages to expect-at least from perspective of a human-centered system design. Within the following pages, the next generation displays will be presented and discussed with a focus on human factors. Beginning with recalling some human factor related research facts, an experiment comparing the former two-dimensional research displays will be presented. Before introducing the DLR conformal symbol set and the three experiments about an innovative drift, indication related research activities toward conformal symbol sets will be addressed.

Development in electrophoresis: instrumentation for two-dimensional gel electrophoresis of protein separation and application of capillary electrophoresis in micro-bioanalysis

Energy Technology Data Exchange (ETDEWEB)

Xu, Aoshuang [Iowa State Univ., Ames, IA (United States)

2008-01-01

This dissertation begins with a general introduction of topics related to this work. The following chapters contain three scientific manuscripts, each presented in a separate chapter with accompanying tables, figures, and literature citations. The final chapter summarizes the work and provides some prospective on this work. This introduction starts with a brief treatment of the basic principles of electrophoresis separation, followed by a discussion of gel electrophoresis and particularly polyacrylamide gel electrophoresis for protein separation, a summary of common capillary electrophoresis separation modes, and a brief treatment of micro-bioanalysis application of capillary electrophoresis, and ends with an overview of protein conformation and dynamics.

Novel method based on Fricke gel dosimeters for dose verification in IMRT techniques

International Nuclear Information System (INIS)

Aon, E.; Brunetto, M.; Sansogne, R.; Castellano, G.; Valente, M.

2008-01-01

Modern radiotherapy is becoming increasingly complex. Conformal and intensity modulated (IMRT) techniques are nowadays available for achieving better tumour control. However, accurate methods for 3D dose verification for these modern irradiation techniques have not been adequately established yet. Fricke gel dosimeters consist, essentially, in a ferrous sulphate (Fricke) solution fixed to a gel matrix, which enables spatial resolution. A suitable radiochromic marker (xylenol orange) is added to the solution in order to produce radiochromic changes within the visible spectrum range, due to the chemical internal conversion (oxidation) of ferrous ions to ferric ions. In addition, xylenol orange has proved to slow down the internal diffusion effect of ferric ions. These dosimeters suitably shaped in form of thin layers and optically analyzed by means of visible light transmission imaging have recently been proposed as a method for 3D absorbed dose distribution determinations in radiotherapy, and tested in several IMRT applications employing a homogeneous plane (visible light) illuminator and a CCD camera with a monochromatic filter for sample analysis by means of transmittance images. In this work, the performance of an alternative read-out method is characterized, consisting on visible light images, acquired before and after irradiation by means of a commercially available flatbed-like scanner. Registered images are suitably converted to matrices and analyzed by means of dedicated 'in-house' software. The integral developed method allows performing 1D (profiles), 2D (surfaces) and 3D (volumes) dose mapping. In addition, quantitative comparisons have been performed by means of the Gamma composite criteria. Dose distribution comparisons between Fricke gel dosimeters and traditional standard dosimetric techniques for IMRT irradiations show an overall good agreement, supporting the suitability of the method. The agreement, quantified by the gamma index (that seldom

Evaluation of Topical Gel Bases Formulated with Various Essential ...

African Journals Online (AJOL)

Evaluation of Topical Gel Bases Formulated with Various Essential Oils for Antibacterial Activity against Methicillin- Resistant Staphylococcus Aureus. ... Lemon grass and thyme oils were chosen for further studies, including analysis of their composition by gas chromatography–mass spectrometry (GC/MS). Gels were ...

Prospective analysis of ambiental and weather effects on conform displaying of fireworks

Directory of Open Access Journals (Sweden)

Jitea Ciprian

2017-01-01

Full Text Available The paper presents the results of research on theoretical and practical relating to establishing and analysis of effects of ambiental and weather effects on conform displaying of fireworks used to organizing fireworks. Scientific research highlighted in this article was conducted in the project no. PN 16 43 03 04, study conducted through Nucleu program entitled -„ Research on the influence of microclimate factors on parameters of the products, while testing the functioning of pyrotechnic articles”.

Effect of temperature on internal structure of uranyl gels

International Nuclear Information System (INIS)

Landspersky, H.; Urbanek, V.

1983-01-01

Tempering freshly prepared uranyl gel serves the homogenization of the volume of the individual spheres and the whole volume of the processed material. Tempering is carried out at a temperature of 90 degC in a special countercurrent through-flow column. The tempered gel particles were analyzed for specific surface and porosity using different methods, subjected to phase analysis, and the crystallite mean size was determined. It was found that the quality of the final gel depends on the residence time in the tempering column. Gel recrystallization probably takes place during tempering leading to stress and cracks which in the final stage lead to the disintegration of the xerogel. Maximum permissible gel residence time in the tempering column is 15 mins. (M.D.)

Magneto-dependent stress relaxation of magnetorheological gels

KAUST Repository

Xu, Yangguang; Liu, Taixiang; Liao, G J; Lubineau, Gilles

2017-01-01

The stress relaxation behaviors of magnetorheological (MR) gels under stepwise shear loading are systematically investigated. The particle-enhanced effect, the magneto-induced effect, and the temperature-enhanced effect on the stress relaxation of MR gels are discussed. For further analysis of the magneto-induced stress relaxation mechanism in MR gels, a phenomenological model is established to describe the stress relaxation behavior of the matrix and the magnetic particle chains. All characteristic parameters introduced in the model, i.e. relaxation time, instantaneous modulus, and stable modulus, have well-defined physical meanings and are fitted based on the experimental results. The influence of each parameter on the macroscopic response is discussed and it is found that the relaxation stress induced by the magneto-mechanical coupling effect plays an important role in the stress relaxation process of MR gels.

Magneto-dependent stress relaxation of magnetorheological gels

KAUST Repository

Xu, Yangguang

2017-09-01

The stress relaxation behaviors of magnetorheological (MR) gels under stepwise shear loading are systematically investigated. The particle-enhanced effect, the magneto-induced effect, and the temperature-enhanced effect on the stress relaxation of MR gels are discussed. For further analysis of the magneto-induced stress relaxation mechanism in MR gels, a phenomenological model is established to describe the stress relaxation behavior of the matrix and the magnetic particle chains. All characteristic parameters introduced in the model, i.e. relaxation time, instantaneous modulus, and stable modulus, have well-defined physical meanings and are fitted based on the experimental results. The influence of each parameter on the macroscopic response is discussed and it is found that the relaxation stress induced by the magneto-mechanical coupling effect plays an important role in the stress relaxation process of MR gels.

A PLGA-PEG-PLGA Thermosensitive Gel Enabling Sustained Delivery of Ropivacaine Hydrochloride for Postoperative Pain Relief.

Science.gov (United States)

Fu, Xudong; Zeng, Huilin; Guo, Jiaping; Liu, Hong; Shi, Zhen; Chen, Huhai; Li, Dezong; Xie, Xiangyang; Kuang, Changchun

2017-01-01

Postoperative pain is a complex physiological response to disease and tissue injury. Moderate-to-severe pain typically occurs within 48 h after surgery. Amino amide local anesthetics are widely applied to manage postoperative pain, and they have high efficacy, a low risk for addiction and limited side effects. However, these anesthetics also have short half-lives, often necessitating continuous injection to obtain satisfactory pain relief. In the current work, we used a poly(lactic-co-glycolic acid) (PLGA)-polyethylene glycol (PEG)-PLGA (PLGA-PEG-PLGA) temperature-sensitive gel to deliver a local anesthetic, ropivacaine hydrochloride (RP), to prolong its analgesic effect. We investigated the influence of polymer and drug concentration on gelation temperature and the in vitro drug release rate from the temperature-sensitive gel. RP-loaded PLGA-PEG-PLGA solution is a liquid at room temperature and forms a gel at temperatures slightly lower than body temperature. With regard to the gel's drug release rate, 37.5, 51.3 and 72.6% of RP was released at 12, 24 and 48 h, respectively. This in vitro drug release profile conformed to the Higuchi equation. To assess pain control efficacy when using the gel, we evaluated the mechanical paw withdrawal reflex threshold, thermal pain threshold and incision cumulative pain scores in a rat incisional model. The results showed that the anti-pain effect of a single injection of RP-loaded gel at the incision site lasted for 48 h, which is significantly longer than the effect produced by injection of RP solution alone. The use of RP-loaded thermosensitive gels could provide a promising method for managing postoperative pain.

Neural signatures of social conformity: A coordinate-based activation likelihood estimation meta-analysis of functional brain imaging studies.

Science.gov (United States)

Wu, Haiyan; Luo, Yi; Feng, Chunliang

2016-12-01

People often align their behaviors with group opinions, known as social conformity. Many neuroscience studies have explored the neuropsychological mechanisms underlying social conformity. Here we employed a coordinate-based meta-analysis on neuroimaging studies of social conformity with the purpose to reveal the convergence of the underlying neural architecture. We identified a convergence of reported activation foci in regions associated with normative decision-making, including ventral striatum (VS), dorsal posterior medial frontal cortex (dorsal pMFC), and anterior insula (AI). Specifically, consistent deactivation of VS and activation of dorsal pMFC and AI are identified when people's responses deviate from group opinions. In addition, the deviation-related responses in dorsal pMFC predict people's conforming behavioral adjustments. These are consistent with current models that disagreement with others might evoke "error" signals, cognitive imbalance, and/or aversive feelings, which are plausibly detected in these brain regions as control signals to facilitate subsequent conforming behaviors. Finally, group opinions result in altered neural correlates of valuation, manifested as stronger responses of VS to stimuli endorsed than disliked by others. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis and conformational analysis of new arylated-diphenylurea derivatives related to sorafenib drug via Suzuki-Miyaura cross-coupling reaction

Science.gov (United States)

Al-Masoudi, Najim A.; Essa, Ali Hashem; Alwaaly, Ahmed A. S.; Saeed, Bahjat A.; Langer, Peter

2017-10-01

Sorafenib, is a relatively new cytostatic drug approved for the treatment of renal cell and hepatocellular carcinoma. The development of new sorafenib analogues offers the possibility of generating structures of increased potency. To this end, a series of arylated-diphenylurea analogues 17-31 were synthesized via Suzuki-Miyaura coupling reaction, related to sorafenib by treatment of three diarylureas 2-4 having 3-bromo, 4-chloro and 2-iodo groups with various arylboronic acids. Conformational analysis of the new arylated urea analogues has been investigated using MOPAC 2016 of semi empirical PM7 Hamiltonian computational method. Our results showed that all compounds preferred the trans-trans conformations. Compound 17 has been selected to calculate the torsional energy profiles for rotation around the urea bonds and found to be existed predominantly in the trans-trans conformation with only very minimal fluctuation in conformation.

Transport Phenomena in Gel

Directory of Open Access Journals (Sweden)

Masayuki Tokita

2016-05-01

Full Text Available Gel becomes an important class of soft materials since it can be seen in a wide variety of the chemical and the biological systems. The unique properties of gel arise from the structure, namely, the three-dimensional polymer network that is swollen by a huge amount of solvent. Despite the small volume fraction of the polymer network, which is usually only a few percent or less, gel shows the typical properties that belong to solids such as the elasticity. Gel is, therefore, regarded as a dilute solid because its elasticity is much smaller than that of typical solids. Because of the diluted structure, small molecules can pass along the open space of the polymer network. In addition to the viscous resistance of gel fluid, however, the substance experiences resistance due to the polymer network of gel during the transport process. It is, therefore, of importance to study the diffusion of the small molecules in gel as well as the flow of gel fluid itself through the polymer network of gel. It may be natural to assume that the effects of the resistance due to the polymer network of gel depends strongly on the network structure. Therefore, detailed study on the transport processes in and through gel may open a new insight into the relationship between the structure and the transport properties of gel. The two typical transport processes in and through gel, that is, the diffusion of small molecules due to the thermal fluctuations and the flow of gel fluid that is caused by the mechanical pressure gradient will be reviewed.

Spatially resolved speckle-correlometry of sol-gel transition

Science.gov (United States)

Isaeva, A. A.; Isaeva, E. A.; Pantyukov, A. V.; Zimnyakov, D. A.

2018-04-01

Sol-gel transition was studied using the speckle correlometry method with a localized light source and spatial filtering of backscattered radiation. Water solutions of technical or food gelatin with added TiO2 nanoparticles were used as studied objects. Structural transformation of "sol-gel" system was studied at various temperatures from 25°C to 50°C using analysis of the correlation and structure functions of speckle intensity fluctuations. The characteristic temperatures of "sol - gel" transition were evaluated for studied systems. Obtained results can be used for various applications in biomedicine and food industry.

Sol-gel materials for optofluidics - process and applications

DEFF Research Database (Denmark)

Mikkelsen, Morten Bo Lindholm

2011-01-01

This Ph.D. thesis is concerned with the use of sol-gel materials in optofluidic applications and the physics of DNA molecules in nanoconfinement. The bottom-up formation of solid material, which is provided by the sol-gel process, enables control of the chemical composition and porosity...... of the material. At early stages of gelation, thin gel coatings can be structured by nanoimprint lithography, and purely inorganic silica materials can be obtained by subsequent thermal annealing. The sol-gel process thus constitutes a unique method for nanofabrication of silica materials of special properties....... In this work, sol-gel silica is introduced as a new material class for the fabrication of lab-on-a-chip devices for DNA analysis. An imprint process with a rigid, non-permeable stamp was developed, which enabled fabrication of micro- and nanofluidic silica channels in a single process step without use of any...

The Synthesis of a Novel Cellulose Physical Gel

Directory of Open Access Journals (Sweden)

Jiufang Duan

2014-01-01

Full Text Available Cellulose possessing β-cyclodextrin (β-CD was used as a host molecule and cellulose possessing ferrocene (Fc as a guest polymer. Infrared spectra, differential scanning calorimetry (DSC, ultraviolet spectroscopy (UV, and contact angle analysis were used to characterise the material structure and the inclusion behaviour. The results showed that the β-CD-cellulose and the Fc-cellulose can form inclusion complexes. Moreover, ferrocene oxidation, and reduction of state can be adjusted by sodium hypochlorite (NaClO as an oxidant and glutathione (GSH as a reductant. In this study, a physical gel based on β-CD-cellulose/Fc-cellulose was formed under mild conditions in which autonomous healing between cut surfaces occurred after 24 hours. The physical gel can be controlled in the sol-gel transition. The compressive strength of the Fc-cellulose/β-CD-cellulose gel increased with increased cellulose concentration. The host-guest interaction between the side chains of cellulose could strengthen the gel. The cellulose physical gel may eventually be used as a stimulus-responsive, healing material in biomedical applications.

Conformational analysis of cellobiose by electronic structure theories.

Science.gov (United States)

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis

DEFF Research Database (Denmark)

Garaizar, J.; Lopez-Molina, N.; Laconcha, I.

2000-01-01

Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate...... showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.......0 software, Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance...

Improving reservoir conformance using gelled polymer systems. Quarterly report, September 25--December 24, 1993

Energy Technology Data Exchange (ETDEWEB)

Green, D.W.; Willhite, G.P.; Buller, C.; McCool, S.; Vossoughi, S.; Michnick, M.

1994-01-19

The general objectives are to (1) to identify and develop gelled polymer systems which have potential to improve reservoir conformance of fluid displacement processes, (2) to determine the performance of these systems in bulk and in porous media, and (3) to develop methods to predict the capability of these systems to recover oil from petroleum reservoirs. This work focuses on three types of gel systems -- an aqueous polysaccharide (KUSP1) system that gels as a function of pH, the chromium(III)-polyacrylamide system and the aluminum citrate-polyacrylamide system. Laboratory research is directed at the fundamental understanding of the physics and chemistry of the gelation process in bulk form and in porous media. This knowledge will be used to develop conceptual and mathematical models of the gelation process. Mathematical models will then be extended to predict the performance of gelled polymer treatments in oil reservoirs. Results to date are summarized.

Virtual and solution conformations of oligosaccharides

International Nuclear Information System (INIS)

Cumming, D.A.; Carver, J.P.

1987-01-01

The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

Analysis of the response of PVA-GTA Fricke-gel dosimeters with clinical magnetic resonance imaging

Science.gov (United States)

Collura, Giorgio; Gallo, Salvatore; Tranchina, Luigi; Abbate, Boris Federico; Bartolotta, Antonio; d'Errico, Francesco; Marrale, Maurizio

2018-01-01

Fricke gel dosimeters produced with a matrix of Poly-vinyl alcohol (PVA) cross-linked with glutaraldehyde (GTA) were analyzed with magnetic resonance imaging (MRI). Previous studies based on spectrophotometry showed valuable dosimetric features of these gels in terms of X-ray sensitivity and diffusion of the ferric ions produced after irradiation. In this study, MRI was performed on the gels at 1.5 T with a clinical scanner in order to optimize the acquisition parameters and obtain high contrast between irradiated and non-irradiated samples. The PVA gels were found to offer good linearity in the range of 0-10 Gy and a stable signal for several hours after irradiation. The sensitivity was about 40% higher compared to gels produced with agarose as gelling agent. The effect of xylenol orange (XO) on the MRI signal was also investigated: gel dosimeters made without XO show higher sensitivity to x-rays than those made with XO. The dosimetric accuracy of the 3D gels was investigated by comparing their MRI response to percentage depth dose and transversal dose profile measurements made with an ionization chamber in a water phantom. The comparison of PVA-GTA gels with and without XO showed that the chelating agent reduces the MRI sensitivity of the gels. Depth-dose and transversal dose profiles acquired by PVA-GTA gels without XO are more accurate and consistent with the ionization chamber data. However, diffusion effects hinder accurate measurements in the steep dose gradient regions and they should be further reduced by modifying the gel matrix and/or by minimizing the delay between irradiation and imaging.

Investigation of oral gels breakdown using image analysis

NARCIS (Netherlands)

Tournier, Carole; Devezeaux de Lavergne, Marine; Velde, van de Fred; Stieger, Markus; Salles, Christian; Bertrand, Dominique

2017-01-01

Characterizing the dynamics of food oral breakdown is of interest to understand the temporal perception of food products. The present work aimed at studying the possible contribution of artificial vision for studying bolus formation. Four emulsion-filled gels were prepared from two concentrations

Conformity Assessment in Nuclear Material and Environmental Sample Analysis

International Nuclear Information System (INIS)

Aregbe, Y.; Jakopic, R.; Richter, S.; Venchiarutti, C.

2015-01-01

Safeguards conclusions are based to a large extent on comparison of measurement results between operator and safeguards laboratories. Measurement results must state traceability and uncertainties to be comparable. Recent workshops held at the IAEA and in the frame of the European Safeguards Research and Development Association (ESARDA), reviewed different approaches for Nuclear Material Balance Evaluation (MBE). Among those, the ''bottom-up'' approach requires assessment of operators and safeguards laboratories measurement systems and capabilities. Therefore, inter-laboratory comparisons (ILCs) with independent reference values provided for decades by JRC-IRMM, CEA/CETAMA and US DOE are instrumental to shed light on the current state of practice in measurements of nuclear material and environmental swipe samples. Participating laboratories are requested to report the measurement results with associated uncertainties, and have the possibility to benchmark those results against independent and traceable reference values. The measurement capability of both the IAEA Network of Analytical Laboratories (NWAL) and the nuclear operator's analytical services participating in ILCs can be assessed against the independent reference values as well as against internationally agreed quality goals, in compliance with ISO 13528:2005. The quality goals for nuclear material analysis are the relative combined standard uncertainties listed in the ITV2010. Concerning environmental swipe sample analysis, the IAEA defined measurement quality goals applied in conformity assessment. The paper reports examples from relevant inter-laboratory comparisons, looking at laboratory performance according to the purpose of the measurement and the possible use of the result in line with the IUPAC International Harmonized Protocol. Tendencies of laboratories to either overestimate and/or underestimate uncertainties are discussed using straightforward graphical tools to evaluate

Analysis of coupled mass transfer and sol-gel reaction in a two-phase system

NARCIS (Netherlands)

Castelijns, H.J.; Huinink, H.P.; Pel, L.; Zitha, P.L.J.

2006-01-01

The coupled mass transfer and chemical reactions of a gel-forming compound in a two-phase system were studied in detail. Tetra-methyl-ortho-silicate (TMOS) is often used as a precursor in sol-gel chemistry to produce silica gels in aqueous systems. TMOS can also be mixed with many hydrocarbons

In-depth analysis of subclass-specific conformational preferences of IgG antibodies

Directory of Open Access Journals (Sweden)

Xinsheng Tian

2015-01-01

Full Text Available IgG subclass-specific differences in biological function and in vitro stability are often referred to variations in the conformational flexibility, while this flexibility has rarely been characterized. Here, small-angle X-ray scattering data from IgG1, IgG2 and IgG4 antibodies, which were designed with identical variable regions, were thoroughly analysed by the ensemble optimization method. The extended analysis of the optimized ensembles through shape clustering reveals distinct subclass-specific conformational preferences, which provide new insights for understanding the variations in physical/chemical stability and biological function of therapeutic antibodies. Importantly, the way that specific differences in the linker region correlate with the solution structure of intact antibodies is revealed, thereby visualizing future potential for the rational design of antibodies with designated physicochemical properties and tailored effector functions. In addition, this advanced computational approach is applicable to other flexible multi-domain systems and extends the potential for investigating flexibility in solutions of macromolecules by small-angle X-ray scattering.

Open microfluidic gel electrophoresis: Rapid and low cost separation and analysis of DNA at the nanoliter scale.

Science.gov (United States)

Gutzweiler, Ludwig; Gleichmann, Tobias; Tanguy, Laurent; Koltay, Peter; Zengerle, Roland; Riegger, Lutz

2017-07-01

Gel electrophoresis is one of the most applied and standardized tools for separation and analysis of macromolecules and their fragments in academic research and in industry. In this work we present a novel approach for conducting on-demand electrophoretic separations of DNA molecules in open microfluidic (OM) systems on planar polymer substrates. The approach combines advantages of slab gel, capillary- and chip-based methods offering low consumable costs (<0.1$) circumventing cost-intensive microfluidic chip fabrication, short process times (5 min per analysis) and high sensitivity (4 ng/μL dsDNA) combined with reasonable resolution (17 bases). The open microfluidic separation system comprises two opposing reservoirs of 2-4 μL in volume, a semi-contact written gel line acting as separation channel interconnecting the reservoirs and sample injected into the line via non-contact droplet dispensing and thus enabling the precise control of the injection plug and sample concentration. Evaporation is prevented by covering aqueous structures with PCR-grade mineral oil while maintaining surface temperature at 15°C. The liquid gel line exhibits a semi-circular cross section of adaptable width (∼200-600 μm) and height (∼30-80 μm) as well as a typical length of 15-55 mm. Layout of such liquid structures is adaptable on-demand not requiring time consuming and repetitive fabrication steps. The approach was successfully demonstrated by the separation of a standard label-free DNA ladder (100-1000 bp) at 100 V/cm via in-line staining and laser induced fluorescent end-point detection using an automated prototype. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Growth, morphology, spectral and thermal studies of gel grown diclofenac acid crystals

Science.gov (United States)

Ramachandran, E.; Ramukutty, S.

2014-03-01

The crystal growth of diclofenac acid in silica gel is the first to be reported in literature. The growth parameters were varied to optimize the suitable growth condition. Single crystal X-ray diffraction method was used for the conformation of the crystal structure. Morphology studies showed that the growth is prominent along the b-axis and the prominent face is {002}. Fourier transform infrared spectral study was performed to identify the functional groups present in the crystal. Thermal stability and decomposition of the material were analyzed using thermo calorimetry in the temperature range 30-500 °C.

Comparative gel-based phosphoproteomics in response to signaling molecules

KAUST Repository

Marondedze, Claudius; Lilley, Kathryn S.; Thomas, Ludivine

2013-01-01

The gel-based proteomics approach is a valuable technique for studying the characteristics of proteins. This technique has diverse applications ranging from analysis of a single protein to the study of the total cellular proteins. Further, protein quality and to some extent distribution can be first assessed by means of one-dimensional gel electrophoresis and then more informatively, for comparative analysis, using the two-dimensional gel electrophoresis technique. Here, we describe how to take advantage of the availability of fluorescent dyes to stain for a selective class of proteins on the same gel for the detection of both phospho- and total proteomes. This enables the co-detection of phosphoproteins as well as total proteins from the same gel and is accomplished by utilizing two different fluorescent stains, the ProQ-Diamond, which stains only phosphorylated proteins, and Sypro Ruby, which stains the entire subset of proteins. This workflow can be applied to gain insights into the regulatory mechanisms induced by signaling molecules such as cyclic nucleotides through the quantification and subsequent identification of responsive phospho- and total proteins. © Springer Science+Business Media New York 2013.

Comparative gel-based phosphoproteomics in response to signaling molecules

KAUST Repository

Marondedze, Claudius

2013-09-03

The gel-based proteomics approach is a valuable technique for studying the characteristics of proteins. This technique has diverse applications ranging from analysis of a single protein to the study of the total cellular proteins. Further, protein quality and to some extent distribution can be first assessed by means of one-dimensional gel electrophoresis and then more informatively, for comparative analysis, using the two-dimensional gel electrophoresis technique. Here, we describe how to take advantage of the availability of fluorescent dyes to stain for a selective class of proteins on the same gel for the detection of both phospho- and total proteomes. This enables the co-detection of phosphoproteins as well as total proteins from the same gel and is accomplished by utilizing two different fluorescent stains, the ProQ-Diamond, which stains only phosphorylated proteins, and Sypro Ruby, which stains the entire subset of proteins. This workflow can be applied to gain insights into the regulatory mechanisms induced by signaling molecules such as cyclic nucleotides through the quantification and subsequent identification of responsive phospho- and total proteins. © Springer Science+Business Media New York 2013.

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Science.gov (United States)

Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

2011-01-01

The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

Electrochemical behavior of ionically crosslinked polyampholytic gel electrolytes

International Nuclear Information System (INIS)

Chen Wanyu; Tang Haitao; Ou Ziwei; Wang Hong; Yang Yajiang

2007-01-01

An ionic complex of anionic and cationic monomers was obtained by protonation of (N,N-diethylamino)ethylmethacrylate (DEA) with acrylic acid (AAc). Free radical copolymerization of the ionic complex and acrylamide (AAm), yielded the ionically crosslinked polyampholytic gel electrolytes [poly(AAc-DEA-AAm), designated as PADA] using two types of organic solvents containing a lithium salt. The PADA gel electrolyte exhibited good thermal stability shown by the DSC thermogram. The impedance analysis at temperatures ranging from -30 to 75 deg. C indicated that the ionic conductivities of the PADA gel electrolytes were rather close to those of liquid electrolytes. The temperature dependence of the ionic conductivities was found to be in accord with the Arrhenius equation. Moreover, the ionic conductivities of PADA gel electrolytes increased with an increase of the molar ratios of cationic/anionic monomers. The ionic conductivities of PADA gels prepared in solvent mixtures of propylene carbonate, ethyl methyl ether and dioxolane (3:1:1, v/v) were higher than those of PADA gels prepared in propylene carbonate only. Significantly, the ionic conductivities of two kinds of PADA gel electrolytes were in the range of 10 -3 and 10 -4 S cm -1 even at -30 deg. C. The electrochemical windows of PADA gel electrolytes measured by cyclic voltammetry were in the range from -1 V to 4.5 V

In situ ion-beam analysis and modification of sol-gel zirconia thin films

International Nuclear Information System (INIS)

Levine, T.E.; Mayer, J.W.

1995-01-01

We report the investigation of ion-beam-induced densification of sol-gel zirconia thin films via in situ ion backscattering spectrometry. We have irradiated three regions of a sample with neon, argon, and krypton ions. For each ion species, a series of irradiation and analysis steps were performed using an interconnected 3 MV tandem accelerator. The technique offers the advantages of minimizing the variation of experimental parameters and sequentially monitoring the densification phenomenon with increasing ion dose

Therapeutic effect analysis of three dimensional conformal radiotherapy non-small cell lung cancer

International Nuclear Information System (INIS)

Yao Zhijun; Cao Yongzhen; Zhang Wenxue; Liang Feng

2012-01-01

Objective: To analyse the treatment effect of non-small cell lung cancer of three dimensional conformal radiotherapy (3D-CRT) and to study the effect of patient survival related factors. Methods: Retrospective analysis was mack for 136 cases of non-small cell lung cancer, all accept 3D-CRT, through the case data collection and long-term follow-up, using the single factor and multiple factor analysis survival time and its influencing factors. Results: The recent curative effects of 136 cases of patients with three dimensional conformal radiotherapy: Complete response (CR) 14.7% (20/136), partial response (PR) 60.3 (82/136), stable disease(SD) 19.9% (27/136), progression disease (PD) 5.1% (7/136), total effective rate is 75% (102/136). One, two, three, five year survival rate is 79.4%, 45.4%, 22.1%, 12.5%. Side effects: Class 1 radiated esophagitis 35 cases, Class 2 radiated esophagitis 16 cases, Class 3 and above radiated esophagitis 0 case. Class I radiated pneumonia 20 cases, Class 2 radiated pneumonia 9 cases, Class 3 radiated pneumonia 0 case. Single factor analysis shows the influence of gender, age, pathology, phase, dose, and first-phase curative effect to the survival time are of a statistical significance, Multiple factor analysis showed KPS score, phase, dose, first-phase curative effect are the survival time independent factors. Conclusion: 3D-CRT for patients with non-small cell lung carcinoma is a safe, effective treatment method, Side effects are relatively low, and the patients survival time is long after radiotherapy. (authors)

Molecular dynamics studies of the conformation of sorbitol

Science.gov (United States)

Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

2009-01-01

Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

Thorium inorganic gels

International Nuclear Information System (INIS)

Genet, M.; Brandel, V.

1988-01-01

The optimum pH and concentration values of thorium salts and oxoacids or oxoacid salts which lead to transparent and stable inorganic gels have been determined. The isotherm drying process of the gel at 50 0 C leads successively to a partly dehydrated gel, then, to the formation of an unusual liquid phase and, finally to a dry amorphous solid phase which is still transparent. This kind of transparent inorganic gels and amorphous phase can be used as matrices for spectroscopic studies [fr

Conformational stability and self-association equilibrium in biologics.

Science.gov (United States)

Clarkson, Benjamin R; Schön, Arne; Freire, Ernesto

2016-02-01

Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs energy and can be altered by changes in physical and solution conditions. Some conformations have a tendency to self-associate and aggregate, an undesirable phenomenon in protein therapeutics. Conformational equilibrium and self-association are linked thermodynamic functions. Given that any associative reaction is concentration dependent, conformational stability studies performed at different protein concentrations can provide early clues to future aggregation problems. This analysis can be applied to the selection of protein variants or the identification of better formulation solutions. In this review, we discuss three different aggregation situations and their manifestation in the observed conformational equilibrium of a protein. Copyright © 2015 Elsevier Ltd. All rights reserved.

PREPARATION AND PROPERTIES OF COMPOUND ARNEBIAE RADIX MICROEMULSION GEL.

Science.gov (United States)

Chen, Jing; He, Yanping; Gao, Ting; Zhang, Licheng; Zhao, Yuna

2017-01-01

Compound Arnebiae radix oil has been clinically applied to treat burns and scalds for a long time. However, it is unstable and inconvenient to use. The aim of this study was to prepare a compound Arnebiae radix microemulsion gel for transdermal delivery system and evaluate its characteristics. Based on the solubility of Shikonin, the active component of Arnebiae radix and the results of phase studies, adequate ratio of each component in microemulsion was determined. The optimized microemulsion gel was prepared using Carbomer 940. The gels were characterized in terms of appearance, preliminary stability test and the content of Shikonin in the compound Arnebiae radix microemulsion gel with HPLC analysis. The optimized conditions for preparing microemulsion were Tween-80, glycerin, isopropyl myristate (IPM) with the ratio of 6:3:2. The optimal microemulsion gel was obtained with Carbomer 940 (1.0%). The prepared compound Arnebiae radix microemulsion gel showed good stability over time. It is more convenience in application than the previous used formulations.

A single-step simultaneous protein staining procedure for polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis.

Science.gov (United States)

Pal, Jayanta K; Berwal, Sunil K; Soni, Rupali N

2012-01-01

A simple method for staining of proteins simultaneously on sodium dodecyl sulfate (SDS) polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis is described. A 5% solution of Alta, a commercially available cosmetic preparation, is added in the upper tank buffer during electrophoresis. On completion of electrophoresis, the gel is washed in distilled water and viewed on a white light plate and a transilluminator to photograph the protein profiles. The gel is processed for western blot transfer of proteins onto a nitrocellulose membrane, and upon completion, the protein profiles on the membrane are viewed and photographed as stated above. The membrane can then be processed for immunostaining as per the standard procedure. Thus, the staining procedure using Alta is simple, rapid (without any need of destaining), and cost-effective.

Quantum Conformal Algebras and Closed Conformal Field Theory

CERN Document Server

Anselmi, D

1999-01-01

We investigate the quantum conformal algebras of N=2 and N=1 supersymmetric gauge theories. Phenomena occurring at strong coupling are analysed using the Nachtmann theorem and very general, model-independent, arguments. The results lead us to introduce a novel class of conformal field theories, identified by a closed quantum conformal algebra. We conjecture that they are the exact solution to the strongly coupled large-N_c limit of the open conformal field theories. We study the basic properties of closed conformal field theory and work out the operator product expansion of the conserved current multiplet T. The OPE structure is uniquely determined by two central charges, c and a. The multiplet T does not contain just the stress-tensor, but also R-currents and finite mass operators. For this reason, the ratio c/a is different from 1. On the other hand, an open algebra contains an infinite tower of non-conserved currents, organized in pairs and singlets with respect to renormalization mixing. T mixes with a se...

C-metric solution for conformal gravity with a conformally coupled scalar field

Energy Technology Data Exchange (ETDEWEB)

Meng, Kun, E-mail: mengkun@tjpu.edu.cn [School of Science, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, Liu, E-mail: lzhao@nankai.edu.cn [School of Physics, Nankai University, Tianjin 300071 (China)

2017-02-15

The C-metric solution of conformal gravity with a conformally coupled scalar field is presented. The solution belongs to the class of Petrov type D spacetimes and is conformal to the standard AdS C-metric appeared in vacuum Einstein gravity. For all parameter ranges, we identify some of the physically interesting static regions and the corresponding coordinate ranges. The solution may contain a black hole event horizon, an acceleration horizon, either of which may be cut by the conformal infinity or be hidden behind the conformal infinity. Since the model is conformally invariant, we also discussed the possible effects of the conformal gauge choices on the structure of the spacetime.

A simple gel electrophoresis method for separating polyhedral gold nanoparticles

Science.gov (United States)

Kim, Suhee; Lee, Hye Jin

2015-07-01

In this paper, a simple approach to separate differently shaped and sized polyhedral gold nanoparticles (NPs) within colloidal solutions via gel electrophoresis is described. Gel running parameters for separating efficiently gold NPs including gel composition, added surfactant types and applied voltage were investigated. The plasmonic properties and physical structure of the separated NPs extracted from the gel matrix were then investigated using transmission electron microscopy (TEM) and UV-vis spectrophotometry respectively. Data analysis revealed that gel electrophoresis conditions of a 1.5 % agarose gel with 0.1 % sodium dodecyl sulfate (SDS) surfactant under an applied voltage of 100 V resulted in the selective isolation of ~ 50 nm polyhedral shaped gold nanoparticles. Further efforts are underway to apply the method to purify biomolecule-conjugated polyhedral Au NPs that can be readily used for NP-enhanced biosensing platforms.

Colloid molecular weight estimation by gel chromatography/acrylamide gel electrophoresis

International Nuclear Information System (INIS)

Liberatore, F.A.; Dearborn, C.; Nigam, S.; Poon, C.; Camin, L.; Liteplo, M.

1984-01-01

Size or molecular weight (MW) estimation of radiolabeled collides in aqueous solutions has long been a problem. The authors have prepared several minimicroaggregated albumin colloids (mμAA) by heat denaturation of stannous-containing HSA solutions at pH 7.0, 7.5, and 8.5). The resulting colloids were labeled with Tc-99m and compared with Au-198 colloid and Tc-99m-antimony sulfide colloid (Tc-99m-Sb/sub 2/S3) by gel chromatography and gel electrophoresis. Tc-99mm-mμAA aggregated at pH 7.0 and the Au-198 colloid appeared in the external void volume of a BioRad A5.0 agarose column indicating an apparent MW of > 5 x 10/sup 6/ daltons. The pH7.5 Tc-99m-mμAA, migrated within the filtration range of the column as did a small fraction of Tc-99m-Sb/sub 2/S/sub 3/, suggesting that the MW is between 6 x 10/sup 4/ - 5 x 10/sup 6/ daltons. The Tc-99m-mμAA, aggregated at pH 8.5, had an apparent MW on gel filtration similar to that of untreated albumin, MW 6.6 x 10-/sup 4/ daltons. The mobilities of the colloids, on acrylamide disc gel electrophoresis, were consistent with the results on gel chromatography. The largest colloids, Au-198 colloid and pH 7.0 Tc-99m-mμAA, barely entered the separating gel; intermediate sized colloids, a small fraction of Tc-99m-Sb/sub 2/S/sub 3/ and pH 7.5 Tc-99m-mμAA migrated farther into the separating gel; while pH 8.5 Tc-99m-mμAA had mobility approaching that of untreated albumin. Lymphoscintigraphy studies using these colloids in animals showed the predicted, particle size-related differences in migration and clearance. The authors conclude that gel chromatography and gel electrophoresis are useful methods for estimating the apparent size of the colloidal particles

Native gel analysis for RISC assembly.

Science.gov (United States)

Kawamata, Tomoko; Tomari, Yukihide

2011-01-01

Small-interfering RNAs (siRNAs) and microRNAs (miRNAs) regulate expression of their target mRNAs via the RNA-induced silencing complex (RISC). A core component of RISC is the Argonaute (Ago) protein, which dictates the RISC function. In Drosophila, miRNAs and siRNAs are generally loaded into Ago1-containing RISC (Ago1-RISC) and Ago2-containing RISC (Ago2-RISC), respectively. We developed a native agarose gel system to directly detect Ago1-RISC, Ago2-RISC, and their precursor complexes. Methods presented here will provide powerful tools to biochemically dissect the RISC assembly pathways.

Conformational Study of Taurine in the Gas Phase

Science.gov (United States)

Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

2009-08-01

The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

Non-conformable, partial and conformable transposition

DEFF Research Database (Denmark)

König, Thomas; Mäder, Lars Kai

2013-01-01

and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

Conformal Einstein spaces

International Nuclear Information System (INIS)

Kozameh, C.N.; Newman, E.T.; Tod, K.P.

1985-01-01

Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

Conformal Gravity

International Nuclear Information System (INIS)

Hooft, G.

2012-01-01

The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

The new proposal for harmonised rules for the online sales of tangible goods: conformity, lack of conformity and remedies: in-depth analysis

NARCIS (Netherlands)

Smits, Jan

2016-01-01

Upon request by the JURI Committee, this paper evaluates the European Commission proposal of 9 December 2015 harmonizing certain civil law contractual rules for Online Shopping. The directive's approach concerning conformity, lack of conformity and remedies is analized. It also examines the question

Extracting information from two-dimensional electrophoresis gels by partial least squares regression

DEFF Research Database (Denmark)

Jessen, Flemming; Lametsch, R.; Bendixen, E.

2002-01-01

of all proteins/spots in the gels. In the present study it is demonstrated how information can be extracted by multivariate data analysis. The strategy is based on partial least squares regression followed by variable selection to find proteins that individually or in combination with other proteins vary......Two-dimensional gel electrophoresis (2-DE) produces large amounts of data and extraction of relevant information from these data demands a cautious and time consuming process of spot pattern matching between gels. The classical approach of data analysis is to detect protein markers that appear...... or disappear depending on the experimental conditions. Such biomarkers are found by comparing the relative volumes of individual spots in the individual gels. Multivariate statistical analysis and modelling of 2-DE data for comparison and classification is an alternative approach utilising the combination...

Structural and Electrochemical Analysis of PMMA Based Gel Electrolyte Membranes

Directory of Open Access Journals (Sweden)

Chithra M. Mathew

2015-01-01

Full Text Available New gel polymer electrolytes containing poly(vinylidene chloride-co-acrylonitrile and poly(methyl methacrylate are prepared by solution casting method. With the addition of 60 wt.% of EC to PVdC-AN/PMMA blend, ionic conductivity value 0.398×10-6 S cm−1 has been achieved. XRD and FT-IR studies have been conducted to investigate the structure and complexation in the polymer gel electrolytes. The FT-IR spectra show that the functional groups C=O and C≡N play major role in ion conduction. Thermal stability of the prepared membranes is found to be about 180°C.

A Framework for Online Conformance Checking

DEFF Research Database (Denmark)

Burattin, Andrea; Carmona, Josep

2017-01-01

is quantified after the completion of the process instance. In this paper we propose a framework for online conformance checking: not only do we quantify (non-)conformant behavior as the execution is running, we also restrict the computation to constant time complexity per event analyzed, thus enabling...... the online analysis of a stream of events. The framework is instantiated with ideas coming from the theory of regions, and state similarity. An implementation is available in ProM and promising results have been obtained....

Diagonal Limit for Conformal Blocks in d Dimensions

CERN Document Server

Hogervorst, Matthijs; Rychkov, Slava

2013-01-01

Conformal blocks in any number of dimensions depend on two variables z, zbar. Here we study their restrictions to the special "diagonal" kinematics z = zbar, previously found useful as a starting point for the conformal bootstrap analysis. We show that conformal blocks on the diagonal satisfy ordinary differential equations, third-order for spin zero and fourth-order for the general case. These ODEs determine the blocks uniquely and lead to an efficient numerical evaluation algorithm. For equal external operator dimensions, we find closed-form solutions in terms of finite sums of 3F2 functions.

Tomotherapy dose distribution verification using MAGIC-f polymer gel dosimetry

International Nuclear Information System (INIS)

Pavoni, J. F.; Pike, T. L.; Snow, J.; DeWerd, L.; Baffa, O.

2012-01-01

Purpose: This paper presents the application of MAGIC-f gel in a three-dimensional dose distribution measurement and its ability to accurately measure the dose distribution from a tomotherapy unit. Methods: A prostate intensity-modulated radiation therapy (IMRT) irradiation was simulated in the gel phantom and the treatment was delivered by a TomoTherapy equipment. Dose distribution was evaluated by the R2 distribution measured in magnetic resonance imaging. Results: A high similarity was found by overlapping of isodoses of the dose distribution measured with the gel and expected by the treatment planning system (TPS). Another analysis was done by comparing the relative absorbed dose profiles in the measured and in the expected dose distributions extracted along indicated lines of the volume and the results were also in agreement. The gamma index analysis was also applied to the data and a high pass rate was achieved (88.4% for analysis using 3%/3 mm and of 96.5% using 4%/4 mm). The real three-dimensional analysis compared the dose-volume histograms measured for the planning volumes and expected by the treatment planning, being the results also in good agreement by the overlapping of the curves. Conclusions: These results show that MAGIC-f gel is a promise for tridimensional dose distribution measurements.

Tomotherapy dose distribution verification using MAGIC-f polymer gel dosimetry

Energy Technology Data Exchange (ETDEWEB)

Pavoni, J. F.; Pike, T. L.; Snow, J.; DeWerd, L.; Baffa, O. [Departamento de Fisica, Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto-Universidade de Sao Paulo, Av. Bandeirantes, 3900 - CEP 14040-901 - Bairro Monte Alegre - Ribeirao Preto, SP (Brazil); Medical Radiation Research Center, Department of Medical Physics, University of Wisconsin, 1111 Highland Avenue, B1002 WIMR, Madison, Wisconsin 53705-2275 (United States); Departamento de Fisica, Faculdade de Filosofia Ciencias e Letras de Ribeirao Preto-Universidade de Sao Paulo, Av. Bandeirantes, 3900 - CEP 14040-901 - Bairro Monte Alegre - Ribeirao Preto, SP (Brazil)

2012-05-15

Purpose: This paper presents the application of MAGIC-f gel in a three-dimensional dose distribution measurement and its ability to accurately measure the dose distribution from a tomotherapy unit. Methods: A prostate intensity-modulated radiation therapy (IMRT) irradiation was simulated in the gel phantom and the treatment was delivered by a TomoTherapy equipment. Dose distribution was evaluated by the R2 distribution measured in magnetic resonance imaging. Results: A high similarity was found by overlapping of isodoses of the dose distribution measured with the gel and expected by the treatment planning system (TPS). Another analysis was done by comparing the relative absorbed dose profiles in the measured and in the expected dose distributions extracted along indicated lines of the volume and the results were also in agreement. The gamma index analysis was also applied to the data and a high pass rate was achieved (88.4% for analysis using 3%/3 mm and of 96.5% using 4%/4 mm). The real three-dimensional analysis compared the dose-volume histograms measured for the planning volumes and expected by the treatment planning, being the results also in good agreement by the overlapping of the curves. Conclusions: These results show that MAGIC-f gel is a promise for tridimensional dose distribution measurements.

Polymer gel dosimetry

Energy Technology Data Exchange (ETDEWEB)

Baldock, C [Institute of Medical Physics, School of Physics, University of Sydney (Australia); De Deene, Y [Radiotherapy and Nuclear Medicine, Ghent University Hospital (Belgium); Doran, S [CRUK Clinical Magnetic Resonance Research Group, Institute of Cancer Research, Surrey (United Kingdom); Ibbott, G [Radiation Physics, UT M D Anderson Cancer Center, Houston, TX (United States); Jirasek, A [Department of Physics and Astronomy, University of Victoria, Victoria, BC (Canada); Lepage, M [Centre d' imagerie moleculaire de Sherbrooke, Departement de medecine nucleaire et de radiobiologie, Universite de Sherbrooke, Sherbrooke, QC (Canada); McAuley, K B [Department of Chemical Engineering, Queen' s University, Kingston, ON (Canada); Oldham, M [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Schreiner, L J [Cancer Centre of South Eastern Ontario, Kingston, ON (Canada)], E-mail: c.baldock@physics.usyd.edu.au, E-mail: yves.dedeene@ugent.be

2010-03-07

Polymer gel dosimeters are fabricated from radiation sensitive chemicals which, upon irradiation, polymerize as a function of the absorbed radiation dose. These gel dosimeters, with the capacity to uniquely record the radiation dose distribution in three-dimensions (3D), have specific advantages when compared to one-dimensional dosimeters, such as ion chambers, and two-dimensional dosimeters, such as film. These advantages are particularly significant in dosimetry situations where steep dose gradients exist such as in intensity-modulated radiation therapy (IMRT) and stereotactic radiosurgery. Polymer gel dosimeters also have specific advantages for brachytherapy dosimetry. Potential dosimetry applications include those for low-energy x-rays, high-linear energy transfer (LET) and proton therapy, radionuclide and boron capture neutron therapy dosimetries. These 3D dosimeters are radiologically soft-tissue equivalent with properties that may be modified depending on the application. The 3D radiation dose distribution in polymer gel dosimeters may be imaged using magnetic resonance imaging (MRI), optical-computerized tomography (optical-CT), x-ray CT or ultrasound. The fundamental science underpinning polymer gel dosimetry is reviewed along with the various evaluation techniques. Clinical dosimetry applications of polymer gel dosimetry are also presented. (topical review)

Applications of gel dosimetry

International Nuclear Information System (INIS)

Ibbott, Geoffrey S

2004-01-01

Gel dosimetry has been examined as a clinical dosimeter since the 1950s. During the last two decades, however, a rapid increase in the number of investigators has been seen, and the body of knowledge regarding gel dosimetry has expanded considerably. Gel dosimetry is still considered a research project, and the introduction of this tool into clinical use is proceeding slowly. This paper will review the characteristics of gel dosimetry that make it desirable for clinical use, the postulated and demonstrated applications of gel dosimetry, and some complications, set-backs, and failures that have contributed to the slow introduction into routine clinical use

Analysis of conformational variations of the cricoid cartilages in Thoroughbred horses using computed tomography.

Science.gov (United States)

Dahlberg, J A; Valdes-Martinez, A; Boston, R C; Parente, E J

2011-03-01

Loss of arytenoid abduction is a common post operative complication of laryngoplasty without a definitive cause. It has been a clinical impression during laryngoplasty surgery that there is great conformational variability along the caudal edge of the Thoroughbred cricoid cartilage that could impact post operative retention of suture position. A change in suture position would probably lead to some loss of abduction. Defining any structural variability of the cricoid would be an initial step in determining whether this variability could impact on the retention of suture position. Anatomical variations in the larynx of Thoroughbred horses may be detected and measured using objective analysis and computed tomography. Larynges were harvested from 15 mature Thoroughbred horses. Helical CT scans were performed on each specimen. Three independent observers performed a series of measurements on 2D and 3D reconstruction images using digital software. Measurements included the lateral cricoid angle, the caudal cricoid prominences, the distance to the cricoid slope, the angle of the cricoarytenoid joints (CAJ), the cricoid thickness and the suture angle. Mean, standard deviation, coefficient of variation and linear regression analysis were performed among all observers and all measurements. Notable conformational differences were evident on the 3D reconstructions. The highest degree of variability was found in 3 measurements: the distance to the lateral cricoid slope, the lateral cricoid angle and the cricoid thickness. A larger left CAJ angle directly and significantly correlated with a larger suture angle. There are notable conformational differences among cricoid specimens in the Thoroughbred larynx. The morphometric differences identified may impact on optimal prosthesis placement and long-term retention. Since a larger lateral cricoid angle may facilitate abduction loss secondary to a displaced and loosened suture, alternative techniques for suture placement may be of

Sol-gel-based biosensing applied to medicinal science.

Science.gov (United States)

Moreira, Felismina T C; Moreira-Tavares, Ana P; Sales, M Goreti F

2015-01-01

Biosensors have opened new horizons in biomedical analysis, by ensuring increased assay speed and flexibility, and allowing point-of-care applications, multi-target analyses, automation and reduced costs of testing. This has been a result of many studies merging nanotechnology with biochemistry over the years, thereby enabling the creation of more suitable environments to biological receptors and their substitution by synthetic analogue materials. Sol-gel chemistry, among other materials, is deeply involved in this process. Sol-gel processing allows the immobilization of organic molecules, biomacromolecules and cells maintaining their properties and activities, permitting their integration into different transduction devices, of electrochemical or optical nature, for single or multiple analyses. Sol-gel also allows to the production of synthetic materials mimicking the activity of natural receptors, while bringing advantages, mostly in terms of cost and stability. Moreover, the biocompatibility of sol-gel materials structures of biological nature allowed the use of these materials in emerging in vivo applications. In this chapter, biosensors for biomedical applications based on sol-gel derived composites are presented, compared and described, along with current emerging applications in vivo, concerning drug delivery or biomaterials. Sol-gel materials are shown as a promising tool for current, emerging and future medical applications.

Development of poloxamer gel formulations via hot-melt extrusion technology.

Science.gov (United States)

Mendonsa, Nicole S; Murthy, S Narasimha; Hashemnejad, Seyed Meysam; Kundu, Santanu; Zhang, Feng; Repka, Michael A

2018-02-15

Poloxamer gels are conventionally prepared by the "hot" or the "cold" process. But these techniques have some disadvantages such as high energy consumption, requires expensive equipment and often have scale up issues. Therefore, the objective of this work was to develop poloxamer gels by hot-melt extrusion technology. The model drug selected was ketoprofen. The formulations developed were 30% and 40% poloxamer gels. Of these formulations, the 30% poloxamer gels were selected as ideal gels. DSC and XRD studies showed an amorphous nature of the drug after extrusion. It was observed from the permeation studies that with increasing poloxamer concentration, a decrease in drug permeation was obtained. Other studies conducted for the formulations included in-vitro release studies, texture analysis, rheological studies and pH measurements. In conclusion, the hot-melt extrusion technology could be successfully employed to develop poloxamer gels by overcoming the drawbacks associated with the conventional techniques. Published by Elsevier B.V.

Conformal geometry and quasiregular mappings

CERN Document Server

Vuorinen, Matti

1988-01-01

This book is an introduction to the theory of spatial quasiregular mappings intended for the uninitiated reader. At the same time the book also addresses specialists in classical analysis and, in particular, geometric function theory. The text leads the reader to the frontier of current research and covers some most recent developments in the subject, previously scatterd through the literature. A major role in this monograph is played by certain conformal invariants which are solutions of extremal problems related to extremal lengths of curve families. These invariants are then applied to prove sharp distortion theorems for quasiregular mappings. One of these extremal problems of conformal geometry generalizes a classical two-dimensional problem of O. Teichmüller. The novel feature of the exposition is the way in which conformal invariants are applied and the sharp results obtained should be of considerable interest even in the two-dimensional particular case. This book combines the features of a textbook an...

Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis.

Science.gov (United States)

Bose, Mahuya; Adams, Brian P; Whittal, Randy M; Bose, Himangshu S

2008-02-01

Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.

Removing water from gels

International Nuclear Information System (INIS)

Lane, E.S.; Winter, J.A.

1982-01-01

Water is removed from a gel material by contacting the gel material with an organic liquid and contacting the organic liquid with a gas such that water is taken up by the gas. The invention, in one embodiment, may be used to dry gel materials whilst maintaining an open porous network therein. In one example, the invention is applied to gel precipitated spheres containing uranium and plutonium. (author)

Conformal symmetry and holographic cosmology

NARCIS (Netherlands)

Bzowski, A.W.

2013-01-01

This thesis presents a novel approach to cosmology using gauge/gravity duality. Analysis of the implications of conformal invariance in field theories leads to quantitative cosmological predictions which are in agreement with current data. Furthermore, holographic cosmology extends the theory of

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

Science.gov (United States)

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

Energy Technology Data Exchange (ETDEWEB)

SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

2004-03-24

Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNA populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.

Characterization of alkali silica reaction gels using Raman spectroscopy

International Nuclear Information System (INIS)

Balachandran, C.; Muñoz, J.F.; Arnold, T.

2017-01-01

The ability of Raman spectroscopy to characterize amorphous materials makes this technique ideal to study alkali silica reaction (ASR) gels. The structure of several synthetic ASR gels was thoroughly characterized using Raman Spectroscopy. The results were validated with additional techniques such as Fourier transmission infrared spectroscopy, X-ray powder diffraction and thermogravimetric analysis. The Raman spectra were found to have two broad bands in the 800 to 1200 cm −1 range and the 400 to 700 cm −1 range indicating the amorphous nature of the gel. Important information regarding the silicate polymerization was deduced from both of these spectral regions. An increase in alkali content of the gels caused a depolymerization in the silicate framework which manifested in the Raman spectra as a gradual shift of predominant peaks in both regions. The trends in silicate depolymerization were in agreement with results from a NMR spectroscopy study on similar synthetic ASR gels.

Categorization of rheological scaling models for particle gels applied to casein gels

NARCIS (Netherlands)

Mellema, M.; Opheusden, van J.H.J.; Vliet, van T.

2002-01-01

Rennet-induced casein gels made from skim milk were studied rheologically. A scaling model or framework for describing the rheological behavior of gels is discussed and used for classification of the structure of casein gels. There are two main parameters in the model that describe the number of

Gellan gum fluid gels for topical administration of diclofenac.

Science.gov (United States)

Mahdi, Mohammed H; Conway, Barbara R; Mills, Thomas; Smith, Alan M

2016-12-30

Diclofenac topical formulations are often preferred for drug administration to patients who experience serious GIT problems. Absorption of the drug through the skin, however, can be challenging due to the natural protective feature of the stratum corneum (SC). In this article, fluid gels prepared from gellan gum were explored as a topical drug delivery vehicle. Rheological analysis of the formulations showed that it was possible to produce a topical gel with a viscosity and the mechanical strength similar to that of the commercially available Voltaren ® gel using 1% w/w of a 50:50 low acyl/high acyl (LA/HA) gellan blend. Soft-tribology was used to assess the lubrication properties of gellan fluid gels. The lubrication of the gellan gum fluid gel formulations at high rubbing speeds was similar to the lubrication of the Voltaren ® gel. The use of gellan gum dramatically increased skin permeation of diclofenac when compared with the commercially available formulation and could be controlled by changing the gellan gum concentration and/or sodium ion concentration in the formulation. This study highlights the potential use of fluid gels that can be easily tuned to have physical properties suitable for topical formulations with the added advantage of increasing drug permeation. Copyright © 2016 Elsevier B.V. All rights reserved.

Western Blot of Stained Proteins from Dried Polyacrylamide Gels

Science.gov (United States)

Gruber, Claudia; Stan-Lotter, Helga

1996-01-01

Western blotting of proteins is customarily performed following their separation on polyacrylamide gels, either prior to staining (1) or, as recently reported, following staining (2). We describe here Western blotting with stained gels, which had been dried and some of which had been stored for years. This procedure permits immunological analysis of proteins, to which antisera may have become available only later, or where the application of newly developed sensitive detection methods is desired. Once rehydration of the gels is achieved, proteins can be-transferred to blotting membranes by any appropriate protocol. Proteins stained with Coomassie Blue have to be detected with a non-chromogenic method, such as the film-based enhanced chemiluminescence (ECL)2) procedure (3). Silver stained proteins, which transfer in the colorless form, may be visualized by any detection method, although, because of the usually very low amounts of proteins, detection by ECL is preferable. Blotting of stained proteins from rehydrated gels is as rapid and as quantitative as from freshly prepared gels, in contrast to blotting from wet stained gels, which requires extensive washing and results in low transfer efficiency (2). Together with a photographic record of the gel pattern, unambiguous identification of immunoreactive proteins from complex mixtures is possible. Some further applications of this work are discussed.

Hidden symmetries of integrable conformal mechanical systems

International Nuclear Information System (INIS)

Hakobyan, Tigran; Krivonos, Sergey; Lechtenfeld, Olaf; Nersessian, Armen

2010-01-01

We split the generic conformal mechanical system into a 'radial' and an 'angular' part, where the latter is defined as the Hamiltonian system on the orbit of the conformal group, with the Casimir function in the role of the Hamiltonian. We reduce the analysis of the constants of motion of the full system to the study of certain differential equations on this orbit. For integrable mechanical systems, the conformal invariance renders them superintegrable, yielding an additional series of conserved quantities originally found by Wojciechowski in the rational Calogero model. Finally, we show that, starting from any N=4 supersymmetric 'angular' Hamiltonian system one may construct a new system with full N=4 superconformal D(1,2;α) symmetry.

Open conformal systems and perturbations of transfer operators

CERN Document Server

Pollicott, Mark

2017-01-01

The focus of this book is on open conformal dynamical systems corresponding to the escape of a point through an open Euclidean ball. The ultimate goal is to understand the asymptotic behavior of the escape rate as the radius of the ball tends to zero. In the case of hyperbolic conformal systems this has been addressed by various authors. The conformal maps considered in this book are far more general, and the analysis correspondingly more involved. The asymptotic existence of escape rates is proved and they are calculated in the context of (finite or infinite) countable alphabets, uniformly contracting conformal graph-directed Markov systems, and in particular, conformal countable alphabet iterated function systems. These results have direct applications to interval maps, meromorphic maps and rational functions. Towards this goal the authors develop, on a purely symbolic level, a theory of singular perturbations of Perron--Frobenius (transfer) operators associated with countable alphabet subshifts of finite t...

Disintegration kinetics of food gels during gastric digestion and its role on gastric emptying: an in vitro analysis.

Science.gov (United States)

Guo, Qing; Ye, Aiqian; Lad, Mita; Ferrua, Maria; Dalgleish, Douglas; Singh, Harjinder

2015-03-01

The understanding of the disintegration and gastric emptying of foods in the stomach is important for designing functional foods. In this study, a dynamic stomach model (human gastric simulator, HGS) was employed to investigate the disintegration and subsequent emptying of two differently structured whey protein emulsion gels (soft and hard gels).The gels were mechanically ground into fragments to reproduce the particle size distribution of an in vivo gel bolus. The simulated gel bolus was prepared by mixing gel fragments and artificial saliva, and exposed to 5 hours of simulated gastric digestion in the presence and absence of pepsin. Results showed that regardless of pepsin, the soft gel always disintegrated faster than the hard gel. The presence of pepsin significantly accelerated the disintegration of both gels. In particular, it enhanced abrasion of the soft gel into fine particles (disintegration kinetics in the HGS. In the presence or absence of pepsin, the larger particles of the soft gel emptied slower than the hard one during the first 120 min of process. However, in the presence of pepsin, the soft gel emptied faster than the hard one after 120 min because of a higher level of disintegration. These findings highlight the role of food structure, bolus properties and biochemical effects on the disintegration and gastric emptying patterns of gels during gastric digestion.

Chemical Method to Improve CO{sub 2} Flooding Sweep Efficiency for Oil Recovery Using SPI-CO{sub 2} Gels

Energy Technology Data Exchange (ETDEWEB)

Burns, Lyle D.

2009-04-14

The problem in CO{sub 2} flooding lies with its higher mobility causing low conformance or sweep efficiency. This is an issue in oilfield applications where an injected fluid or gas used to mobilize and produce the oil in a marginal field has substantially higher mobility (function of viscosity and density and relative permeability) relative to the crude oil promoting fingering and early breakthrough. Conformance is particularly critical in CO{sub 2} oilfield floods where the end result is less oil recovered and substantially higher costs related to the CO{sub 2}. The SPI-CO{sub 2} (here after called “SPI”) gel system is a unique silicate based gel system that offers a technically effective solution to the conformance problem with CO{sub 2} floods. This SPI gel system remains a low viscosity fluid until an external initiator (CO{sub 2}) triggers gelation. This is a clear improvement over current technologies where the gels set up as a function of time, regardless of where it is placed in the reservoir. In those current systems, the internal initiator is included in the injected fluid for water shut off applications. In this new research effort, the CO{sub 2} is an external initiator contacted after SPI gel solution placement. This concept ensures in the proper water wet reservoir environment that the SPI gel sets up in the precise high permeability path followed by the CO{sub 2}, therefore improving sweep efficiency to a greater degree than conventional systems. In addition, the final SPI product in commercial quantities is expected to be low cost over the competing systems. This Phase I research effort provided “proof of concept” that SPI gels possess strength and may be formed in a sand pack reducing the permeability to brine and CO{sub 2} flow. This SPI technology is a natural extension of prior R & D and the Phase I effort that together show a high potential for success in a Phase II follow-on project. Carbon dioxide (CO{sub 2}) is a major by-product of

Proteomic Analysis of Bovine Pregnancy-specific Serum Proteins by 2D Fluorescence Difference Gel Electrophoresis

OpenAIRE

Lee, Jae Eun; Lee, Jae Young; Kim, Hong Rye; Shin, Hyun Young; Lin, Tao; Jin, Dong Il

2015-01-01

Two dimensional-fluorescence difference gel electrophoresis (2D DIGE) is an emerging technique for comparative proteomics, which improves the reproducibility and reliability of differential protein expression analysis between samples. The purpose of this study was to investigate bovine pregnancy-specific proteins in the proteome between bovine pregnant and non-pregnant serum using DIGE technique. Serums of 2 pregnant Holstein dairy cattle at day 21 after artificial insemination and those of 2...

[Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

Science.gov (United States)

Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

2016-01-01

It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the

An ill-conditioning conformal radiotherapy analysis based on singular values decomposition

International Nuclear Information System (INIS)

Lefkopoulos, D.; Grandjean, P.; Bendada, S.; Dominique, C.; Platoni, K.; Schlienger, M.

1995-01-01

Clinical experience in stereotactic radiotherapy of irregular complex lesions had shown that optimization algorithms were necessary to improve the dose distribution. We have developed a general optimization procedure which can be applied to different conformal irradiation techniques. In this presentation this procedure is tested on the stereotactic radiotherapy modality of complex cerebral lesions treated with multi-isocentric technique based on the 'associated targets methodology'. In this inverse procedure we use the singular value decomposition (SVD) analysis which proposes several optimal solutions for the narrow beams weights of each isocentre. The SVD analysis quantifies the ill-conditioning of the dosimetric calculation of the stereotactic irradiation, using the condition number which is the ratio of the bigger to smaller singular values. Our dose distribution optimization approach consists on the study of the irradiation parameters influence on the stereotactic radiotherapy inverse problem. The adjustment of the different irradiation parameters into the 'SVD optimizer' procedure is realized taking into account the ratio of the quality reconstruction to the time calculation. It will permit a more efficient use of the 'SVD optimizer' in clinical applications for real 3D lesions. The evaluation criteria for the choice of satisfactory solutions are based on the dose-volume histograms and clinical considerations. We will present the efficiency of ''SVD optimizer'' to analyze and predict the ill-conditioning in stereotactic radiotherapy and to recognize the topography of the different beams in order to create optimal reconstructed weighting vector. The planification of stereotactic treatments using the ''SVD optimizer'' is examined for mono-isocentrically and complex dual-isocentrically treated lesions. The application of the SVD optimization technique provides conformal dose distribution for complex intracranial lesions. It is a general optimization procedure

Acylhydrazone bond dynamic covalent polymer gel monolithic column online coupling to high-performance liquid chromatography for analysis of sulfonamides and fluorescent whitening agents in food.

Science.gov (United States)

Zhang, Chengjiang; Luo, Xialin; Wei, Tianfu; Hu, Yufei; Li, Gongke; Zhang, Zhuomin

2017-10-13

A new dynamic covalent polymer (DCP) gel was well designed and constructed based on imine chemistry. Polycondensation of 4,4'-biphenyldicarboxaldehyde and 1,3,5-benzenetricarbohydrazide via Schiff-base reaction resulted in an acylhydrazone bond gel (AB-gel) DCP. AB-gel DCP had three-dimensional network of interconnected nanoparticles with hierarchically porous structure. AB-gel DCP was successfully fabricated as a monolithic column by an in-situ chemical bonding method for online enrichment and separation purpose with excellent permeability. AB-gel DCP based monolithic column showed remarkable adsorption affinity towards target analytes including sulfonamides (SAs) and fluorescent whitening agents (FWAs) due to its strong π-π affinity, hydrophobic effect and hydrogen bonding interaction. Then, AB-gel DCP based monolithic column was applied for online separation and analysis of trace SAs and FWAs in food samples coupled with high-performance liquid chromatography (HPLC). Sulfathiazole (ST) and sulfadimidine (SM2) in one positive weever sample were actually found and determined with concentrations of 273.8 and 286.3μg/kg, respectively. 2,5-Bis(5-tert-butyl-2-benzoxazolyl) thiophene (FWA184) was actually quantified in one tea infusion sample with the concentration of 268.5ng/L. The spiked experiments suggested the good recoveries in range of 74.5-110% for SAs in weever and shrimp samples with relative standard deviations (RSDs) less than 9.7% and in range of 74.0-113% for FWAs in milk and tea infusion samples with RSDs less than 9.0%. AB-gel DCP monolithic column was proved to be a promising sample preparation medium for online separation and analysis of trace analytes in food samples with complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2000-08-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Conformal Infinity.

Science.gov (United States)

Frauendiener, Jörg

2004-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Metal-silica sol-gel materials

Science.gov (United States)

Stiegman, Albert E. (Inventor)

2002-01-01

The present invention relates to a single phase metal-silica sol-gel glass formed by the co-condensation of a transition metal with silicon atoms where the metal atoms are uniformly distributed within the sol-gel glass as individual metal centers. Any transition metal may be used in the sol-gel glasses. The present invention also relates to sensor materials where the sensor material is formed using the single phase metal-silica sol-gel glasses. The sensor materials may be in the form of a thin film or may be attached to an optical fiber. The present invention also relates to a method of sensing chemicals using the chemical sensors by monitoring the chromatic change of the metal-silica sol-gel glass when the chemical binds to the sensor. The present invention also relates to oxidation catalysts where a metal-silica sol-gel glass catalyzes the reaction. The present invention also relates to a method of performing oxidation reactions using the metal-silica sol-gel glasses. The present invention also relates to organopolymer metal-silica sol-gel composites where the pores of the metal-silica sol-gel glasses are filled with an organic polymer polymerized by the sol-gel glass.

Study of nuclear glasses alteration gel and synthesis of some model gels; Etude du gel d`alteration des verres nucleaires et synthese de gels modeles

Energy Technology Data Exchange (ETDEWEB)

Ricol, S

1995-10-05

This work deals with the general problem of alteration of the reference nuclear glass R7T7. Attention is paid particularly to the altered layer formed at the glass surface during alteration process. In opposition to previous works, related essentially to glass dissolution kinetics based on chemical analyses of lixiviated elements, this thesis deals with alteration problems through structural studies of the reference glass and derived gel. This approach allows the determination of mechanisms for the gel formation and a better understanding of the behaviour of glasses towards lixiviation. Both approaches appeared complementary. Based on several spectroscopic techniques, this work showed the particular role of cations such as calcium, zirconium and iron. Studies of silica-based synthetic gels showed the synergic effect of formers cation and of one highly coordinated cation. The variation of the wavenumber related to Si-O-Si asymmetric stretching vibration can be correlated to O/Si ratio for ternary systems Si/Na/Zr. On the contrary, the Si losses of the materials depend on the number of non-bridging oxygen atoms. In the perspective of long-term behaviour, the alteration gel presents better characteristics than initial glass. It is therefore a highly stable material in static conditions. In the same way, synthetic gels are materials with very low solubilities (much lower than the alteration gel) and could be used as confining matrices. (authors). refs., 71 figs., 37 tabs.

Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis

Science.gov (United States)

Tripathi, Shubhandra; Srivastava, Gaurava; Singh, Aastha; Prakasham, A. P.; Negi, Arvind S.; Sharma, Ashok

2018-03-01

Colchicine site inhibitors are microtubule destabilizers having promising role in cancer therapeutics. In the current study, four such indanone derivatives (t1, t9, t14 and t17) with 3,4,5-trimethoxyphenyl fragment (ring A) and showing significant microtubule destabilization property have been explored. The interaction mechanism and conformational modes triggered by binding of these indanone derivatives and combretastatin at colchicine binding site (CBS) of αβ-tubulin dimer were studied using molecular dynamics (MD) simulation, principle component analysis and free energy landscape analysis. In the MD results, t1 showed binding similar to colchicine interacting in the deep hydrophobic core at the CBS. While t9, t14 and t17 showed binding conformation similar to combretastatin, with ring A superficially binding at the CBS. Results demonstrated that ring A played a vital role in binding via hydrophobic interactions and got anchored between the S8 and S9 sheets, H8 helix and T7 loop at the CBS. Conformational modes study revealed that twisting and bending conformational motions (as found in the apo system) were nearly absent in the ligand bound systems. Absence of twisting motion might causes loss of lateral contacts in microtubule, thus promoting microtubule destabilization. This study provides detailed account of microtubule destabilization mechanism by indanone ligands and combretastatin, and would be helpful for designing microtubule destabilizers with higher activity.

Thoria sol-gel processes

International Nuclear Information System (INIS)

Matthews, R.B.

1978-10-01

Alternate fuel fabrication techniques are being developed at WNRE as part of the thorium fuel cycle program. The sol-gel techniques are attractive and this report assembles and summarizes information relating to thoria sol-gel fuels. Some background information on the behaviour and advantages of sol-gel fuel forms is presented, followed by a review of relevant colloid chemistry and an explanation of the fundamental steps of sol-gel processes. Finally, several variants to the basic process are reviewed and evaluated. (author)

Thermo-physical properties of silica gel for adsorption desalination cycle

KAUST Repository

Thu, Kyaw; Chakraborty, Anutosh; Saha, Bidyut Baran; Ng, Kim Choon

2013-01-01

Thermo-physical properties, surface characteristics and water vapor uptake capacity are key parameters in the selection of adsorbent for an adsorption desalination (AD) cycle. In the AD cycles, silica gel is used as adsorbent due to their high water vapor uptake capacity, reliability, repeatability and inexpensiveness as compared to other adsorbents. Three types of commercially available silica gels (Type-RD 2560,Type-A5BW and Type-A++) are investigated using a surface characteristic analyzer and their thermo-physical properties are evaluated using several analysis methods. The instrument used in this investigation employs the static volumetric method with liquid Nitrogen at 77 K as the filing fluid. The surface area of each adsorbent is studied using Brunauer-Emmett-Teller (BET) method whilst the pore size distribution (PSD) analysis is conducted with the Non-Local Density Functional Theory (NLDFT). It is observed that the Type-A++ silica gel (granular type) possesses the highest surface area of 863.6 m2/g amongst the three parent silica gels studied. It has a two-maxima or bimodal distribution pattern where the pore diameters are distributed mostly between 10 Å and 30 Å. Water vapor uptake capacity of silica gels are studied with water vapor dosage apparatus and the results show that the Type-A++ silica gel exhibits a highest equilibrium uptake at 537 cm3/g. These thermo-physical properties are essential for the design and the numerical simulation of AD cycles. © 2012 Published by Elsevier Ltd.

Thermo-physical properties of silica gel for adsorption desalination cycle

KAUST Repository

Thu, Kyaw

2013-02-01

Thermo-physical properties, surface characteristics and water vapor uptake capacity are key parameters in the selection of adsorbent for an adsorption desalination (AD) cycle. In the AD cycles, silica gel is used as adsorbent due to their high water vapor uptake capacity, reliability, repeatability and inexpensiveness as compared to other adsorbents. Three types of commercially available silica gels (Type-RD 2560,Type-A5BW and Type-A++) are investigated using a surface characteristic analyzer and their thermo-physical properties are evaluated using several analysis methods. The instrument used in this investigation employs the static volumetric method with liquid Nitrogen at 77 K as the filing fluid. The surface area of each adsorbent is studied using Brunauer-Emmett-Teller (BET) method whilst the pore size distribution (PSD) analysis is conducted with the Non-Local Density Functional Theory (NLDFT). It is observed that the Type-A++ silica gel (granular type) possesses the highest surface area of 863.6 m2/g amongst the three parent silica gels studied. It has a two-maxima or bimodal distribution pattern where the pore diameters are distributed mostly between 10 Å and 30 Å. Water vapor uptake capacity of silica gels are studied with water vapor dosage apparatus and the results show that the Type-A++ silica gel exhibits a highest equilibrium uptake at 537 cm3/g. These thermo-physical properties are essential for the design and the numerical simulation of AD cycles. © 2012 Published by Elsevier Ltd.

Review of Fricke gel dosimeters

International Nuclear Information System (INIS)

Schreiner, L J

2004-01-01

The innovation of adding a gel matrix to the traditional Fricke dosimeter to stabilize geometric information established the field of gel dosimetry for radiation therapy. A discussion of Fricke gels provides an overview of the issues that determine the dose response of all gel dosimeters in general. In this paper we review some of the features of Fricke systems to illustrate these issues and, in addition, to motivate renewed clinical interest in Fricke gels

Checking behavioral conformance of artifacts

NARCIS (Netherlands)

Fahland, D.; Leoni, de M.; Dongen, van B.F.; Aalst, van der W.M.P.

2011-01-01

The usefulness of process models (e.g., for analysis, improvement, or execution) strongly depends on their ability to describe reality. Conformance checking is a technique to validate how good a given process model describes recorded executions of the actual process. Recently, artifacts have been

Gel nano-particulates against radioactivity; Des nanoparticules en gel contre la radioactivite

Energy Technology Data Exchange (ETDEWEB)

Deroin, Ph

2004-11-01

The Argonne research center (USA) has developed a 'super-gel' compound, a polymer close to those used in baby's diapers, which can reach a 90% efficiency in the radioactive decontamination of porous materials, like bricks or concrete. The contaminated materials are sprayed with a mixture of polymer gel and wetting agent with nano-particulates in suspension. Under the action of the wetting agent, radioactivity migrates from the pores to the gel and is trapped by the nano-particulates. The drying and recycling of the gel allows to reduce the volume of radioactive wastes. Short paper. (J.S.)

Polymer gel dosimeters with enhanced sensitivity for use in x-ray CT polymer gel dosimetry

International Nuclear Information System (INIS)

Jirasek, A; Hilts, M; McAuley, K B

2010-01-01

A primary limitation of current x-ray CT polymer gel dosimetry is the low contrast, and hence poor dose resolution, of dose images produced by the system. The low contrast is largely due to the low-dose sensitivity of current formulations of polymer gel for x-ray CT imaging. This study reports on the investigation of new dosimeter formulations with improved dose sensitivity for x-ray CT polymer gel dosimetry. We incorporate an isopropanol co-solvent into an N-isopropylacrylamide-based gel formulation in order to increase the total monomer/crosslinker concentration (%T) within the formulation. It is shown that gels of high %T exhibit enhanced dose sensitivity and dose resolutions over traditional formulations. The gels are shown to be temporally stable and reproducible. A single formulation (16%T) is used to demonstrate the capabilities of the x-ray CT polymer gel dosimetry system in measuring known dose distributions. A 1 L gel volume is exposed to three separate irradiations: a single-field percent depth dose, a two-field 'cross' and a three-field 'test case'. The first two irradiations are used to generate a dose calibration curve by which images are calibrated. The calibrated images are compared with treatment planning predictions and it is shown that the x-ray CT polymer gel dosimetry system is capable of capturing spatial and dose information accurately. The proposed new gel formulation is shown to be sensitive, stable and to improve the dose resolution over current formulations so as to provide a feasible gel for clinical applications of x-ray CT polymer gel dosimetry.

Fast and facile preparation of CTAB based gels and their applications in Au and Ag nanoparticles synthesis

Energy Technology Data Exchange (ETDEWEB)

Upadhyay, Ravi Kant, E-mail: rkupadhyay85@gmail.com [Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Gautam Budh Nagar, 201314 Uttar Pradesh (India); Soin, Navneet, E-mail: n.soin@bolton.ac.uk [Knowledge Centre for Materials Chemistry (KCMC), Institute for Materials Research and Innovation (IMRI), University of Bolton, Deane Road, Bolton BL3 5AB (United Kingdom); Saha, Susmita, E-mail: ssaha@bose.res.in [Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India); Barman, Anjan, E-mail: abarman@bose.res.in [Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India); Sinha Roy, Susanta, E-mail: susanta.roy@snu.edu.in [Department of Physics, School of Natural Sciences, Shiv Nadar University, Gautam Budh Nagar, 201314 Uttar Pradesh (India)

2015-04-15

We have demonstrated that the gel-like mesophase of Cetyltrimethylammonium bromide (CTAB) can be synthesized by judicial adjustment of water to surfactant molar ratio (W{sub 0}), without using any additional salts, gelating agents or co-surfactants. Gel formation was found to be highly dependent on the water to surfactant molar ratio (W{sub 0}), with the lowest value of W{sub 0} (41.5) resulting in rapid gel formation. Environmental scanning electron microscope (ESEM) analysis revealed that the gel was comprised of interconnected cylindrical structures. The presence of hydrogen bonding in the gel-like mesophase was confirmed by Fourier Transform Infrared spectroscopy (FTIR) analysis. Rheology measurements revealed that all the gel samples were highly viscoelastic in nature. Furthermore, Au and Ag containing CTAB gels were explored as precursors for the preparation of spherical Gold (Au) and Silver (Ag) nanoparticles using Sodium borohydride (NaBH{sub 4}) as reducing agent. The effects of NaBH{sub 4} concentration on the particle size and morphology of the Au and Ag nanoparticles have also been studied. - Highlights: • A facile synthesis of CTAB based gel-like mesophase is reported. • CTAB gels were obtained by adjusting water to surfactant molar ratio (W{sub 0}). • FTIR analysis revealed that hydrogen bonding plays a key role in gel formation. • Au, Ag nanoparticles were synthesized by using CTAB gel and NaBH{sub 4}.

A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria.

Science.gov (United States)

Javornik, Uroš; Plavec, Janez; Wang, Baifan; Graham, Steven M

2018-01-02

A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca 2+ -release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔH o , ΔS o ) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ + conformer, whereas the A-ring γ-bond was a mixture of the γ + and γ t conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ + conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rotational Spectrum and Conformational Analysis of N-methyl-2-aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Science.gov (United States)

Calabrese, Camilla; Maris, Assimo; Evangelisti, Luca; Piras, Anna; Parravicini, Valentina; Melandri, Sonia

2018-02-01

Abstract We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol’s family, and include 2-aminophenylethanol, 2-methylaminophenylethanol, noradrenaline, adrenaline 2-aminoethanol and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6-18 and 59.6-74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was obtained, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2004-01-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

Energy Technology Data Exchange (ETDEWEB)

Fitzsimmons, Michael

2012-06-01

Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Design of Autonomous Gel Actuators

Directory of Open Access Journals (Sweden)

Shuji Hashimoto

2011-01-01

Full Text Available In this paper, we introduce autonomous gel actuators driven by chemical energy. The polymer gels prepared here have cyclic chemical reaction networks. With a cyclic reaction, the polymer gels generate periodical motion. The periodic motion of the gel is produced by the chemical energy of the oscillatory Belouzov-Zhabotinsky (BZ reaction. We have succeeded in making synthetic polymer gel move autonomously like a living organism. This experimental fact represents the great possibility of the chemical robot.

Twelve massless flavors and three colors below the conformal window

International Nuclear Information System (INIS)

Fodor, Zoltan; Holland, Kieran; Kuti, Julius; Nogradi, Daniel; Schroeder, Chris

2011-01-01

We report new results for a frequently discussed gauge theory with twelve fermion flavors in the fundamental representation of the SU(3) color gauge group. The model, controversial with respect to its conformality, is important in non-perturbative studies searching for a viable composite Higgs mechanism beyond the Standard Model (BSM). In comparison with earlier work, our new simulations apply larger volumes and probe deeper in fermion and pion masses toward the chiral limit. Investigating the controversy, we subject the model to opposite hypotheses with respect to the conformal window. In the first hypothesis, below the conformal window, we test chiral symmetry breaking (χSB) with its Goldstone spectrum, F π , the χSB condensate, and several composite hadron states as analytic functions of the fermion mass when varied in a limited range with our best effort to control finite volume effects. In the second test, for the alternate hypothesis inside the conformal window, we probe conformal behavior driven by a single anomalous mass dimension under the assumption of unbroken chiral symmetry at vanishing fermion mass. Our results at fixed gauge coupling, based on the assumptions of the two hypotheses we define, show low level of confidence in the conformal scenario with leading order scaling analysis. Relaxing the important assumption of leading mass-deformed conformality with its conformal finite size scaling would require added theoretical understanding of the scaling violation terms in the conformal analysis and a comprehensive test of its effects on the confidence level of the fits. Results for the running coupling, based on the force between static sources, and preliminary indications for the finite temperature transition are also presented. Staggered lattice fermions with stout-suppressed taste breaking are used throughout the simulations.

Fibril formation from pea protein and subsequent gel formation.

Science.gov (United States)

Munialo, Claire Darizu; Martin, Anneke H; van der Linden, Erik; de Jongh, Harmen H J

2014-03-19

The objective of this study was to characterize fibrillar aggregates made using pea proteins, to assemble formed fibrils into protein-based gels, and to study the rheological behavior of these gels. Micrometer-long fibrillar aggregates were observed after pea protein solutions had been heated for 20 h at pH 2.0. Following heating of pea proteins, it was observed that all of the proteins were hydrolyzed into peptides and that 50% of these peptides were assembled into fibrils. Changes on a structural level in pea proteins were studied using circular dichroism, transmission electron microscopy, and particle size analysis. During the fibril assembly process, an increase in aggregate size was observed, which coincided with an increase in thioflavin T binding, indicating the presence of β-sheet aggregates. Fibrils made using pea proteins were more branched and curly. Gel formation of preformed fibrils was induced by slow acidification from pH 7.0 to a final pH of around pH 5.0. The ability of pea protein-based fibrillar gels to fracture during an amplitude sweep was comparable to those of soy protein and whey protein-based fibrillar gels, although gels prepared from fibrils made using pea protein and soy protein were weaker than those of whey protein. The findings show that fibrils can be prepared from pea protein, which can be incorporated into protein-based fibrillar gels.

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: A graphical method

International Nuclear Information System (INIS)

Rinkel, L.J.; Altona, C.

1987-01-01

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance

Quantitative two-dimensional gel electrophoresis analysis of human fibroblasts transformed by ras oncogenes.

Science.gov (United States)

Miller, M J; Maher, V M; McCormick, J J

1992-11-01

Quantitative two-dimensional gel electrophoresis was used to compare the cellular protein patterns of a normal foreskin-derived human fibroblasts cell line (LG1) and three immortal derivatives of LG1. One derivative, designated MSU-1.1 VO, was selected for its ability to grow in the absence of serum and is non-tumorigenic in athymic mice. The other two strains were selected for focus-formation following transfection with either Ha-ras or N-ras oncogenes and form high grade malignant tumors. Correspondence and cluster analysis provided a nonbiased estimate of the relative similarity of the different two-dimensional patterns. These techniques separated the gel patterns into three distinct classes: LG1, MSU-1.1 VO, and the ras transformed cell strains. The MSU-1.1 VO cells were more closely related to the parental LG1 than to the ras-transformed cells. The differences between the three classes were primarily quantitative in nature: 16% of the spots demonstrated statistically significant changes (P 2) in the rate of incorporation of radioactive amino acids. The patterns from the two ras-transformed cell strains were similar, and variations in the expression of proteins that occurred between the separate experiments obscured consistent differences between the Ha-ras and N-ras transformed cells. However, while only 9 out of 758 spots were classified as different (1%), correspondence analysis could consistently separate the two ras transformants. One of these spots was five times more intense in the Ha-ras transformed cells than the N-ras.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization and Biocompatibility of Chitosan Gels with Silver and Gold Nanoparticles

Directory of Open Access Journals (Sweden)

C. Sámano-Valencia

2014-01-01

Full Text Available The presence of bacterial resistance to antibiotics is a very important issue and the search of new alternatives is necessary. In this work, a combination of chitosan gel with silver or gold nanoparticles was prepared and characterized using thermal, rheology, bactericide, and biocompatibility analyses. ESEM images were also taken to visualize the incorporation of the nanoparticles into the gel matrix. Thermal analysis showed a better thermal stability in the chitosan-gold nanoparticles gels compared to the chitosan-silver nanoparticles gels. Rheology analyses showed that the viscosity of the gels decreased when velocity increased and there were differences in viscosity when silver and gold nanoparticles concentrations change. ESEM images showed the presence of agglomerates of silver and gold nanoparticles into the gel matrix with a good distribution; in some cases the formation of microstructures was found. Bactericide results show that these materials present an antibacterial activity against S. aureus, S. mutans, and E. coli. The biocompatibility test showed neither negative reaction nor wound healing delay after the application of the gels in an in vivo test. The gels with silver and gold nanoparticles could be used to treat wound infections in oral or skin applications.

Conformal operator product expansion in the Yukawa model

International Nuclear Information System (INIS)

Prati, M.C.

1983-01-01

Conformal techniques are applied to the Yukawa model, as an example of a theory with spinor fields. It is written the partial-wave analysis of the 4-point function of two scalars and two spinors in the channel phi psi → phi psi in terms of spinor tensor representations of the conformal group. Using this conformal expansion, it is diagonalized the Bethe-Salpeter equation, which is reduced to algebraic relations among the partial waves. It is shown that in the γ 5 -invariant model, but not in the general case, it is possible to derive dynamically from the expansions of the 4-point function the vacuum operator product phi psi>

Kefiran-alginate gel microspheres for oral delivery of ciprofloxacin.

Science.gov (United States)

Blandón, Lina M; Islan, German A; Castro, Guillermo R; Noseda, Miguel D; Thomaz-Soccol, Vanete; Soccol, Carlos R

2016-09-01

Ciprofloxacin is a broad-spectrum antibiotic associated with gastric and intestinal side effects after extended oral administration. Alginate is a biopolymer commonly employed in gel synthesis by ionotropic gelation, but unstable in the presence of biological metal-chelating compounds and/or under dried conditions. Kefiran is a microbial biopolymer able to form gels with the advantage of displaying antimicrobial activity. In the present study, kefiran-alginate gel microspheres were developed to encapsulate ciprofloxacin for antimicrobial controlled release and enhanced bactericidal effect against common pathogens. Scanning electron microscopy (SEM) analysis of the hybrid gel microspheres showed a spherical structure with a smoother surface compared to alginate gel matrices. In vitro release of ciprofloxacin from kefiran-alginate microspheres was less than 3.0% and 5.0% at pH 1.2 (stomach), and 5.0% and 25.0% at pH 7.4 (intestine) in 3 and 21h, respectively. Fourier transform infrared spectroscopy (FTIR) of ciprofloxacin-kefiran showed the displacement of typical bands of ciprofloxacin and kefiran, suggesting a cooperative interaction by hydrogen bridges between both molecules. Additionally, the thermal analysis of ciprofloxacin-kefiran showed a protective effect of the biopolymer against ciprofloxacin degradation at high temperatures. Finally, antimicrobial assays of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhymurium, and Staphylococcus aureus demonstrated the synergic effect between ciprofloxacin and kefiran against the tested microorganisms. Copyright © 2016 Elsevier B.V. All rights reserved.

Polymer gel dosimeters with enhanced sensitivity for use in x-ray CT polymer gel dosimetry

Energy Technology Data Exchange (ETDEWEB)

Jirasek, A [Department of Physics and Astronomy, University of Victoria, Victoria BC V8W 3P6 (Canada); Hilts, M [Medical Physics, BC Cancer Agency-Vancouver Island Centre, Victoria BC V6R 2B6 (Canada); McAuley, K B, E-mail: jirasek@uvic.c [Department of Chemical Engineering, Queens University, Kingston, ON K7 L 3N6 (Canada)

2010-09-21

A primary limitation of current x-ray CT polymer gel dosimetry is the low contrast, and hence poor dose resolution, of dose images produced by the system. The low contrast is largely due to the low-dose sensitivity of current formulations of polymer gel for x-ray CT imaging. This study reports on the investigation of new dosimeter formulations with improved dose sensitivity for x-ray CT polymer gel dosimetry. We incorporate an isopropanol co-solvent into an N-isopropylacrylamide-based gel formulation in order to increase the total monomer/crosslinker concentration (%T) within the formulation. It is shown that gels of high %T exhibit enhanced dose sensitivity and dose resolutions over traditional formulations. The gels are shown to be temporally stable and reproducible. A single formulation (16%T) is used to demonstrate the capabilities of the x-ray CT polymer gel dosimetry system in measuring known dose distributions. A 1 L gel volume is exposed to three separate irradiations: a single-field percent depth dose, a two-field 'cross' and a three-field 'test case'. The first two irradiations are used to generate a dose calibration curve by which images are calibrated. The calibrated images are compared with treatment planning predictions and it is shown that the x-ray CT polymer gel dosimetry system is capable of capturing spatial and dose information accurately. The proposed new gel formulation is shown to be sensitive, stable and to improve the dose resolution over current formulations so as to provide a feasible gel for clinical applications of x-ray CT polymer gel dosimetry.

Phenotypic Characterization and Multivariate Analysis to Explain Body Conformation in Lesser Known Buffalo (Bubalus bubalis) from North India

Science.gov (United States)

Vohra, V.; Niranjan, S. K.; Mishra, A. K.; Jamuna, V.; Chopra, A.; Sharma, Neelesh; Jeong, Dong Kee

2015-01-01

Phenotypic characterization and body biometric in 13 traits (height at withers, body length, chest girth, paunch girth, ear length, tail length, length of tail up to switch, face length, face width, horn length, circumference of horn at base, distances between pin bone and hip bone) were recorded in 233 adult Gojri buffaloes from Punjab and Himachal Pradesh states of India. Traits were analysed by using varimax rotated principal component analysis (PCA) with Kaiser Normalization to explain body conformation. PCA revealed four components which explained about 70.9% of the total variation. First component described the general body conformation and explained 31.5% of total variation. It was represented by significant positive high loading of height at wither, body length, heart girth, face length and face width. The communality ranged from 0.83 (hip bone distance) to 0.45 (horn length) and unique factors ranged from 0.16 to 0.55 for all these 13 different biometric traits. Present study suggests that first principal component can be used in the evaluation and comparison of body conformation in buffaloes and thus provides an opportunity to distinguish between early and late maturing to adult, based on a small group of biometric traits to explain body conformation in adult buffaloes. PMID:25656215

Logarithmic conformal field theory through nilpotent conformal dimensions

International Nuclear Information System (INIS)

Moghimi-Araghi, S.; Rouhani, S.; Saadat, M.

2001-01-01

We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFTs such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor

Viscous conformal gauge theories

DEFF Research Database (Denmark)

Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

2017-01-01

We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

Conformational analysis of amide extractants by NMR in organic phase

International Nuclear Information System (INIS)

Berthon, C.

1993-08-01

This study deals with nuclear fuel reprocessing. We have essentially used NMR spectroscopy. We want to understand which kind of conformational parameters control selectivity and efficiency of amide extractant. The symmetric monoamides used are DOBA (C 3 H 7 CON (CH 2 CH(C 2 H 5 ) C 4 H 9 ) 2 ), DOiBA ((CH 3 ) 2 CCHON (CH 2 CH(C 2 H 5 )C 4 H 9 ) 2 ) and DOTA ((CH 3 ) 3 CCH 2 CON(CH 2 CH(C 2 H 5 )C 4 H 9 ) 2 ). Each gives two quasi equivalent conformers (cis and trans) in organic phases. The selected malonamide DMDBTDMA ((C 4 H 9 (CH 3 )NCO) 2 CHC 14 H 29 ) has four conformers because of its twice disymmetric amide functions. Weak interactions between monoamides which yield to dimer formation. The malonamide also gives dimers but forms aggregates too. Nitric acid extraction is due to the competitive formation of six species L, L 2 , L 2 (HNO 3 ), L(HNO 3 ), L(HNO 3 ) 2 , L(HNO 3 ) 3 (L: monoamide). Complexation between lanthanides (III) and monoamides yields to the stoichiometries L 3 Ln(NO 3 ) 3 and L 2 Ln(NO 3 ) 3 . Their ratio depend of steric hindrance on the carbonyl and the metal ionic radius. The same thing is observed of Pu 4+ and Th 4+ extraction in non acidic media. L 2 An(NO 3 ) 4 is the main stoichiometric except for the Th 4+ - DOBA system where the species (DOBA) 3 Th(NO 3 ) 4 appear. Exchange rates between the ligand and the complex are pointed out. The monoamide conformations obtained with lanthanide and plutonium nitrate can explain the difference in extracting power of this molecule between An 4+ and Ln 3+ . (author). 162 refs., 87 figs., 44 tabs., 7 annexes

2 D gel based analysis of biological variability of the human plasma proteome

DEFF Research Database (Denmark)

Rentsch, Maria Louise; Jessen, Flemming

individuals and within an individual changes will also happen over time (e.g. after meal intake). Thus, the aim of the present study was to examine the inter-individual variability of plasma protein levels in humans after meal intake. Five subjects consumed three single meals in a randomised order separated...... by one-week interval. Blood samples were drawn before the meal intake and five times during 24 hours for proteome analysis. Plasma was fractionated by use of IgY-12 spin column depleting the 12 highly abundant proteins and further processed for two-dimensional gel electrophoresis. The plasma proteome...

The limitations of pulsed-field gel electrophoresis for analysis of Yersinia enterocolitica isolates.

Science.gov (United States)

Gilpin, B J; Robson, B; Lin, S; Hudson, J A; Weaver, L; Dufour, M; Strydom, H

2014-09-01

This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed-field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory ability of PFGE was so low as to severely limit its usefulness (DI enterocolitica biotypes 2, 3 and 4, and inferences based on finding indistinguishable PFGE profiles among cases or between cases and sources need to be substantiated using alternative typing tools, or strong epidemiological evidence. © 2013 Blackwell Verlag GmbH.

Conformational kinetics of aliphatic tails

Science.gov (United States)

Ferrarini, Alberta; Moro, Giorgio; Nordio, Pier Luigi

The master equation describing the random walk between sites identified with the stable conformers of a chain molecule, represents the extension to the time domain of the Rotational Isomeric State model. The asymptotic analysis of the multidimensional diffusion equation in the continuous torsional variables subjected to the configurational potential, provides a rigorous justification for the discrete models, and it supplies, without resorting to phenomenological parameters, molecular definitions of the kinetic rates for the conformational transitions occurring at each segment of the chain. The coupling between the torsional variables is fully taken into account, giving rise to cooperative effects. A complete calculation of the specific correlation functions which describe the time evolution of the angular functions probed by N.M.R. and dielectric relaxation measurements, has been performed for alkyl chains attached to a massive core. The resulting behaviour has been compared with the decay of trans and gauche populations of specific bonds, expressed in terms of suitable correlation functions whose time integrals lead quite naturally to the definition of effective kinetic constants for the conformational transitions.

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

Science.gov (United States)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

А new factor effecting gel strength of pectin polysaccharides

Directory of Open Access Journals (Sweden)

S. E. Kholov

2016-01-01

Full Text Available Pectin polysaccharides obtained from various raw materials have a different component composition and form gels with water, sugar and acid or calcium. In this study, an experimental approach the gelation properties of different pectin samples, varied from different sources, using new methods of hydrolysis and purification. Samples were obtained by hydrolysis of accelerated extraction of pectin and purified by diaultrfiltration, have a high gel strength. The highest gel strength have been found in series of high methoxyl (HM- pectin samples of apple, peach, orange and low methoxyl (LM- pectin samples of commercial citrus pectin and apple pectin obtained by new method. It is shown that in addition to the basic parameters (the content of galacturonic acid, degree of esterification, molecular weight and hidrodinamic radius macromolecule to affect gel strength pectins aggregation of macromolecules, which is determined by the z-average molecular weight. There were observed a clear pattern of the influence of the molecular weight on hydrodynamic parameters for both HM- and LM- pectin samples on the gel strength. It were shown that a high values of molecular weight, intrinsic viscosity, and radius of gyration of pectin samples can significantly increase gel strength, while the value of Mz oppositely influenced the gel strength. As a result, a systematic analysis of this parameter and its relationship to the average molecular weight found that indeed the ratio Mz/Mw for pectin’s is an crucial to assess the quality of pectin at the study of gel strength for pectin polysaccharides.

Initial experiments with gel-water: towards MRI-linac dosimetry and imaging.

Science.gov (United States)

Alnaghy, Sarah J; Gargett, Maegan; Liney, Gary; Petasecca, Marco; Begg, Jarrad; Espinoza, Anthony; Newall, Matthew K; Duncan, Mitchell; Holloway, Lois; Lerch, Michael L F; Lazea, Mircea; Rosenfeld, Anatoly B; Metcalfe, Peter

2016-12-01

Tracking the position of a moving radiation detector in time and space during data acquisition can replicate 4D image-guided radiotherapy (4DIGRT). Magnetic resonance imaging (MRI)-linacs need MRI-visible detectors to achieve this, however, imaging solid phantoms is an issue. Hence, gel-water, a material that provides signal for MRI-visibility, and which will in future work, replace solid water for an MRI-linac 4DIGRT quality assurance tool, is discussed. MR and CT images of gel-water were acquired for visualisation and electron density verification. Characterisation of gel-water at 0 T was compared to Gammex-RMI solid water, using MagicPlate-512 (M512) and RMI Attix chamber; this included percentage depth dose, tissue-phantom ratio (TPR 20/10 ), tissue-maximum ratio (TMR), profiles, output factors, and a gamma analysis to investigate field penumbral differences. MR images of a non-powered detector in gel-water demonstrated detector visualisation. The CT-determined gel-water electron density agreed with the calculated value of 1.01. Gel-water depth dose data demonstrated a maximum deviation of 0.7% from solid water for M512 and 2.4% for the Attix chamber, and by 2.1% for TPR 20/10 and 1.0% for TMR. FWHM and output factor differences between materials were ≤0.3 and ≤1.4%. M512 data passed gamma analysis with 100% within 2%, 2 mm tolerance for multileaf collimator defined fields. Gel-water was shown to be tissue-equivalent for dosimetry and a feasible option to replace solid water.

Comparative Evaluation of Pain Scores during Periodontal Probing with or without Anesthetic Gels.

Science.gov (United States)

Mishra, Ashank; Priyanka, Mandapathi; Pradeep, Koppolu; Reddy Pathakota, Krishnajaneya

2016-01-01

Context. The initial periodontal examination which includes full-mouth periodontal probing is one of the discomforting procedures for a patient. Aim. To evaluate the efficacy of two local anesthetic gels in the reduction of pain during periodontal probing using Florida probe in CGP patients in comparison with manual probing. Materials and Methods. Ninety systemically healthy patients with moderate to severe CGP patients were recruited. In each patient, the quadrants were randomly assigned to manual probing with UNC-15 probe, probing with Florida probe, and Florida probing with lidocaine 10% gel and with benzocaine 20% gel. In the quadrants undergoing probing with anesthetic gels, the sites were isolated and the gel was injected using syringe and a blunt-end cannula. Pain was measured using 10 mm horizontal VAS. Statistical Analysis. The analysis was carried out using SPSS version 18. The comparison of mean VAS scores was done using repeated measures ANOVA with post hoc Bonferroni test. Results. Mean VAS for manual probing was significantly more than Florida probing. Further, the mean VAS score for Florida probing was higher than the two gels. Conclusion. It is suggested that the gels might be useful in reducing pain experienced during full-mouth periodontal probing in patients with CGP.

A shear-induced network of aligned wormlike micelles in a sugar-based molecular gel. From gelation to biocompatibility assays.

Science.gov (United States)

Fitremann, Juliette; Lonetti, Barbara; Fratini, Emiliano; Fabing, Isabelle; Payré, Bruno; Boulé, Christelle; Loubinoux, Isabelle; Vaysse, Laurence; Oriol, Luis

2017-10-15

A new low molecular weight hydrogelator with a saccharide (lactobionic) polar head linked by azide-alkyne click chemistry was prepared in three steps. It was obtained in high purity without chromatography, by phase separation and ultrafiltration of the aqueous gel. Gelation was not obtained reproducibly by conventional heating-cooling cycles and instead was obtained by shearing the aqueous solutions, from 2 wt% to 0.25 wt%. This method of preparation favored the formation of a quite unusual network of interconnected large but thin 2D-sheets (7nm-thick) formed by the association side-by-side of long and aligned 7nm diameter wormlike micelles. It was responsible for the reproducible gelation at the macroscopic scale. A second network made of helical fibres with a 10-13nm diameter, more or less intertwined was also formed but was scarcely able to sustain a macroscopic gel on its own. The gels were analysed by TEM (Transmission Electronic Microscopy), cryo-TEM and SAXS (Small Angle X-ray Scattering). Molecular modelling was also used to highlight the possible conformations the hydrogelator can take. The gels displayed a weak and reversible transition near 20°C, close to room temperature, ascribed to the wormlike micelles 2D-sheets network. Heating over 30°C led to the loss of the gel macroscopic integrity, but gel fragments were still observed in suspension. A second transition near 50°C, ascribed to the network of helical fibres, finally dissolved completely these fragments. The gels showed thixotropic behaviour, recovering slowly their initial elastic modulus, in few hours, after injection through a needle. Stable gels were tested as scaffold for neural cell line culture, showing a reduced biocompatibility. This new gelator is a clear illustration of how controlling the pathway was critical for gel formation and how a new kind of self-assembly was obtained by shearing. Copyright © 2017 Elsevier Inc. All rights reserved.

Conformal invariance in supergravity

International Nuclear Information System (INIS)

Bergshoeff, E.A.

1983-01-01

In this thesis the author explains the role of conformal invariance in supergravity. He presents the complete structure of extended conformal supergravity for N <= 4. The outline of this work is as follows. In chapter 2 he briefly summarizes the essential properties of supersymmetry and supergravity and indicates the use of conformal invariance in supergravity. The idea that the introduction of additional symmetry transformations can make clear the structure of a field theory is not reserved to supergravity only. By means of some simple examples it is shown in chapter 3 how one can always introduce additional gauge transformations in a theory of massive vector fields. Moreover it is shown how the gauge invariant formulation sometimes explains the quantum mechanical properties of the theory. In chapter 4 the author defines the conformal transformations and summarizes their main properties. He explains how these conformal transformations can be used to analyse the structure of gravity. The supersymmetric extension of these results is discussed in chapter 5. Here he describes as an example how N=1 supergravity can be reformulated in a conformally-invariant way. He also shows that beyond N=1 the gauge fields of the superconformal symmetries do not constitute an off-shell field representation of extended conformal supergravity. Therefore, in chapter 6, a systematic method to construct the off-shell formulation of all extended conformal supergravity theories with N <= 4 is developed. As an example he uses this method to construct N=1 conformal supergravity. Finally, in chapter 7 N=4 conformal supergravity is discussed. (Auth.)

Optimization of Large Gel 2D Electrophoresis for Proteomic Studies of Skeletal Muscle

Science.gov (United States)

Reed, Patrick W.; Densmore, Allison; Bloch, Robert J.

2013-01-01

We describe improved methods for large format, 2-dimensional gel electrophoresis (2-DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7M urea + 2 M thiourea, instead of 9M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2D-GE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes. PMID:22589104

Astrophysical Tests of Kinematical Conformal Cosmology in Fourth-Order Conformal Weyl Gravity

Directory of Open Access Journals (Sweden)

Gabriele U. Varieschi

2014-12-01

Full Text Available In this work we analyze kinematical conformal cosmology (KCC, an alternative cosmological model based on conformal Weyl gravity (CG, and test it against current type Ia supernova (SNIa luminosity data and other astrophysical observations. Expanding upon previous work on the subject, we revise the analysis of SNIa data, confirming that KCC can explain the evidence for an accelerating expansion of the Universe without using dark energy or other exotic components. We obtain an independent evaluation of the Hubble constant, H0 = 67:53 kms-1 Mpc-1, very close to the current best estimates. The main KCC and CG parameters are re-evaluated and their revised values are found to be close to previous estimates. We also show that available data for the Hubble parameter as a function of redshift can be fitted using KCC and that this model does not suffer from any apparent age problem. Overall,

Silica Sol-Gel Entrapment of the Enzyme Chloro peroxidase

International Nuclear Information System (INIS)

Le, T.; Chan, S.; Ebaid, B.; Sommerhalter, M.

2015-01-01

The enzyme chloro peroxidase (CPO) was immobilized in silica sol-gel beads prepared from tetramethoxysilane. The average pore diameter of the silica host structure (∼3 nm) was smaller than the globular CPO diameter (∼6 nm) and the enzyme remained entrapped after sol-gel maturation. The catalytic performance of the entrapped enzyme was assessed via the pyrogallol peroxidation reaction. Sol-gel beads loaded with 4 μg CPO per mL sol solution reached 9-12% relative activity compared to free CPO in solution. Enzyme kinetic analysis revealed a decrease in K_cat but no changes in K_M or K_I . Product release or enzyme damage might thus limit catalytic performance. Yet circular dichroism and visible absorption spectra of transparent CPO sol-gel sheets did not indicate enzyme damage. Activity decline due to methanol exposure was shown to be reversible in solution. To improve catalytic performance the sol-gel protocol was modified. The incorporation of 5, 20, or 40% methyltrimethoxysilane resulted in more brittle sol-gel beads but the catalytic performance increased to 14% relative to free CPO in solution. The use of more acidic casting buffers (ph 4.5 or 5.5 instead of 6.5) resulted in a more porous silica host reaching up to 18% relative activity

High lane density slab-gel electrophoresis using micromachined instrumentation.

Science.gov (United States)

Papautsky, I; Mohanty, S; Weiss, R; Frazier, A B

2001-10-01

In this paper, micromachined pipette arrays (MPAs) and microcombs were studied as a means of enabling high lane density gel electrophoresis. The MPA provide a miniaturized format to interface sub-microliter volumes of samples between macroscale sample preparation formats and microscale biochemical analysis systems. The microcombs provide a means of creating sample loading wells in the gel material on the same center-to-center spacing as the MPAs. Together, the two micromachined instruments provide an alternative to current combs and pipetting technologies used for creating sample loading wells and sample delivery in gel electrophoresis systems. Using three designs for the microcomb-MPA pair, center-to-center spacings of 1.0 mm, 500 microm, and 250 microm are studied. The results demonstrate an approximate 10-fold increase in lane density and a 10-fold reduction in sample size from 5 microL to 500 pL. As a result, the number of theoretical plates has increased 2.5-fold, while system resolution has increased 1.5-fold over the conventional agarose gel systems. An examination of changes in resolution across the width of individual separation lanes in both systems revealed dependence in the case of the conventional gels and no dependence for the gels loaded with the micromachined instrumentation.

Polymer gels and networks

National Research Council Canada - National Science Library

Osada, Yoshihito; Khokhlov, A. R

2002-01-01

... or magnetic field, etc.). It was realized that not only can polymer gels absorb and hold a considerable volume of liquids, but they can also be forced to expel the absorbed liquid in a controlled manner. Of particular interest are hydrogels, i.e., polymer gels, which swell extensively in water. The most common hydrogels are polyelectrolyte gels: ...

Preparation of continuous alumina gel fibres by aqueous sol–gel ...

Indian Academy of Sciences (India)

Abstract. Continuous alumina gel fibres were prepared by sol–gel method. The spinning sol was prepared by mixing aluminum nitrate, lactic acid and polyvinylpyrrolidone with a mass ratio of 10:3:1·5. Thermogravimetry– differential scanning calorimetry (TG–DSC), Fourier transform infrared (FTIR) spectra, X-ray diffraction ...

The influence of p H and UV visible absorption on hydrolysis stage and gel behavior of glasses synthesized by sol-gel

International Nuclear Information System (INIS)

Khosravi Saghezchi, M.; Sarpoolaky, H.; Heshmatpour, F.

2008-01-01

Lead-containing glass borosilicate was synthesized by Sol-gel technique using metal alkoxide such as tetra ethyleorthosilicate, Al-sec-butoxide and trimethyl borate. The sol containing tetra ethyle ortho silicate converts to gel during drop wise addition of Al-alkoxide while inorganic lead salt was added in the last stage of gelation to prepare the alcogels. The specimens were dried at room temperature to set then heated at 600 d eg C quickly to avoid crystallization preparing a glass containing 63 weight percent lead oxide. The influence of p H on absorption behavior of the sols studied by UV visible technique so the characteristic of the gel, alcogel and xerogel were studied in the different acidic concentrations. The UV spectrums show that the higher the acidity of the hydrolysis stages, the higher the absorbance. The results showed the sample with 63 weight percent lead was found fully amorphous. Microstructure and phase analysis of the glass powders were investigated by X-ray diffraction, X-ray fluorescence and scanning electron microscopy equipped with energy dispersive spectroscopy analysis

Optical fiber smart sensor for conformity analysis of Brazilian gasoline; Sensor inteligente a fibra otica para analise da conformidade da gosolina brasileira

Energy Technology Data Exchange (ETDEWEB)

Possetti, Gustavo R.C.; Camilotti, Emmanuelle; Arruda, Lucia V.R. de; Muller, Marcia; Fabris, Jose L. [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil); Cocco, Lilian C.; Yamamoto, Carlos I. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Falate, Rosane [Universidade Estadual de Ponta Grossa (UEPG), PR (Brazil)

2008-07-01

The conventional techniques employed to monitor the gasoline quality are expensive, time-consuming and demands on specialized workers to its execution. A study about the applicability of a long period grating, a fiber optic device, as an auxiliary tool for the analysis of Brazilian gasoline conformity is presented in this work. The long period grating spectral response was measured with the device immersed in samples of gasoline A with different proportions of hydrated ethyl alcohol fuel. A resolution of 0.23 % was obtained for the concentrations range of commercial interest, between 20 % and 40 %. The device performance was also tested with a set of conform and non-conform gasoline C samples. The device spectral response for these samples, as well as the samples densities and the conformity status were employed to train and to validate an artificial neural network with radial base function. The obtained results show that fiber optic sensors supervised by artificial neural networks can constitute systems for smart measurement with high applicability in the analyses of gasoline conformity, reducing costs and time related to conventional tests. (author)

Gel shift analysis of the empA promoter region in Vibrio anguillarum

Directory of Open Access Journals (Sweden)

Denkin Steven M

2004-10-01

Full Text Available Abstract Background The induction of metalloprotease encoded by empA in Vibrio anguillarum occurs at high cell density in salmon intestinal mucus. Previously we have shown that there are significant differences in empA expression in two strains of V. anguillarum, M93Sm and NB10. It is hypothesized that differences in empA regulation are due to differences in binding of regulatory elements. Results Two strains of V. anguillarum, M93Sm and NB10, were examined and compared for the presence of DNA regulatory proteins that bind to and control the empA promoter region. Gel mobility shift assays, using a digoxigenin (DIG-labeled oligomer containing a lux box-like element and the promoter for empA, were done to demonstrate the presence of a DNA-binding protein. Protein extracts from NB10 cells incubated in Luria Bertani broth + 2% NaCl (LB20, nine salts solution + 200 μg/ml mucus (NSSM, 3M (marine minimal medium, or NSS resulted in a gel mobility shift. No gel mobility shift was seen when protein extracts from either LB20- or NSSM-grown M93Sm cells were mixed with the DIG-labeled empA oligomer. The azocasein assay detected protease activity in all incubation conditions for NB10 culture supernatants. In contrast, protease activity was detected in M93Sm culture supernatants only when incubated in NSSM. Since the luxR homologue in V. anguillarum, vanT, has been cloned, sequenced, and shown to be required for protease activity, we wanted to determine if vanT mutants of NB10 exhibit the same gel shift observed in the wild-type. Site-directed mutagenesis was used to create vanT mutants in V. anguillarum M93Sm and NB10 to test whether VanT is involved with the gel mobility shift. Both vanT mutants, M02 and NB02, did not produce protease activity in any conditions. However, protein extracts from NB02 incubated in each condition still exhibited a gel shift when mixed with the DIG-labeled empA oligomer. Conclusions The data demonstrate that protein extracts of V

Histological Analysis of Intra-Abdominal Adhesions Treated with Sodium Hyaluronate and Carboxymethylcellulose Gel.

Science.gov (United States)

Montalvo-Javé, Eduardo Esteban; Mendoza-Barrera, German Eduardo; García-Pineda, Manuel Alejandro; Jaime Limón, Álvaro Rodrigo; Montalvo-Arenas, César; Castell Rodríguez, Andrés Eliú; Tapia Jurado, Jesús

2016-01-01

To evaluate macro and microscopically the adhesions developed after using the anti-adherence compound sodium hyaluronate and carboxymethylcellulose (SH-CBMC) gel and to determine the volume of the adhesions using a stereological estimation. The study was experimental, random, comparative, and prospective. The subjects of the study were male Wistar rats divided in three groups (n = 10). Group I (control) included rats with no peritoneal injury. Group II rats had a 2 cm diameter injury created bilaterally in the parietal peritoneum at 3 cm from the abdominal midline with electrocautery coated with physiological solution. Group III rats were given the same injuries and coated with SH-CBMC gel. All groups were followed up postoperatively for 30 days, after which a laparotomy was performed to macroscopically determine the presence and type of adhesions. Experimental models were euthanized with anesthetic overdose and biopsies were taken for histopathological examination and stereological estimate of the volume of adhesions. Macroscopic adhesions were 20% less prevalent in Group III compared to Group II, which presented 40% more multiple and firm adhesions, unlike in Group III, in which they were unique and lax. There was a statistically significant decrease in the presence and number of adhesions in rats treated with SH-CBMC gel. Inflammatory infiltrate was significantly lower in rats treated with SH-CBMC gel, but there were no differences in connective tissue, fibrosis, and angiogenesis among groups. There was no statistical difference in the overall volume of adhesions among the treatment groups. SH-CBMC gel reduces macroscopic presence and number of adhesions and the severity of the inflammatory infiltrate.

Factors influencing conformity index in radiotherapy for non-small cell lung cancer.

LENUS (Irish Health Repository)

Brennan, Sinead M

2010-01-01

The radiotherapy conformity index (CI) is a useful tool to quantitatively assess the quality of radiotherapy treatment plans, and represents the relationship between isodose distributions and target volume. A conformity index of unity implies high planning target volume (PTV) coverage and minimal unnecessary irradiation of surrounding tissues. We performed this analysis to describe the CI for lung cancer 3-dimensional conformal radiotherapy (3DCRT) and to identify clinical and technical determinants of CI, as it is not known which factors are associated with good quality 3D conformal radiotherapy treatment planning. Radiotherapy treatment plans from a database of 52 patients with inoperable Stage 1 to 3b lung cancer, on a hypofractionated 3DCRT trial were evaluated. A CI was calculated for all plans using the definition of the ICRU 62:CI = (TV\\/PTV), which is the quotient of the treated volume (TV) and the PTV. Data on patient, tumor, and planning variables, which could influence CI, were recorded and analyzed. Mean CI was 2.01 (range = 1.06-3.8). On univariate analysis, PTV (p = 0.023), number of beams (p = 0.036), medial vs. lateral tumor location (p = 0.016), and increasing tumor stage (p = 0.041) were associated with improved conformity. On multiple regression analysis, factors found to be associated with CI included central vs. peripheral tumor location (p = 0.041) and PTV size (p = 0.058). The term 3DCRT is used routinely in the literature, without any indication of the degree of conformality. We recommend routine reporting of conformity indices. Conformity indices may be affected by both planning variables and tumor factors.

Sealing wells with gel

Energy Technology Data Exchange (ETDEWEB)

Lopez, E C

1967-10-01

A new system is being used in Mexico to temporarily plug producing wells. The temporary seal is a gel with a catalyst. The use of this temporary plug allows gas-lift wells to be taken off production in order to carry out emergency repairs. The gel solidifies by the action of the catalyst to a high temperature (70 - 150/sup 0/C). By locating the bottom of the tubing at the top of the production interval, the gel material will go into the permeable formation, and immediately set. When the gel has solidified, it seals off the horizon that must not be stimulated, and leaves the others exposed to the acid action. When the treatment is finished, the gel, by action of the catalyst, is liquefied and removed from the formation, being produced with the oil.

Images of gel electrophoresis - RGP caps | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us RGP caps Images of gel electrophoresis Data detail Data name Images of gel electrophoresis D...OI 10.18908/lsdba.nbdc00318-05-002 Description of data contents Detailed information and images of gel electrophoresis... of each marker. Data file File name: rgp_caps_electrophoresis_image.zip File URL: ftp://ftp.biosc...iencedbc.jp/archive/rgp-caps/LATEST/rgp_caps_electrophoresis_image.zip File size:... 28.7 MB Simple search URL - Data acquisition method Gel electrophoresis Data analysis method STS markers :

Gel-eletroforese no diagnóstico da varíola Gel-electrophoresis in the smallpox diagnosis

Directory of Open Access Journals (Sweden)

Julio A. Mesquita

1972-01-01

Full Text Available O emprego de gel-eletroforese no diagnóstico da varíola, demonstrou ser ao menos trinta vezes (30X mais sensível que o teste de agar-gel, nas condições descritas (tabela I. Doze (12 espécimes, cujos testes convencionais de inoculação em ovos embrionados e de agar-gel resultaram positivos, foram testados em suas diluições originais congeladas por mais de um ano, sendo seis deles revelados por gel-eletroforese enquanto nenhum o foi por agar-gel (tabela II. Trinta e três (33 amostras isoladas no laboratório, foram testadas com material colhido de membrana cório-alantóica da primeira inoculação para o diagnóstico, conservado em glicerina 50%, resultando 15 positivas em gel-eletroforese e apenas 3 em agar-gel (tabela II. Os últimos 60 espécimes recebidos para diagnóstico, através a Campanha de Erradicação da Varíola, também resultaram negativos em gel-eletroforese, que não mostrou falsos-positivos nas condições descritas.The test of gel-electrophoresis applied to the pox virus group showed to be at least thirth times (30X more sensitive than agar-gel test on the described conditions (Table I. Twelve specimens, which were positives form Smallpox in the conventional tests of egg inoculation and agar-gel difusion test, have been screened in their original dilutions frozen for more than 1 year and six of them were still detectable by gel-eletrophoresis, while by agar-gel test any of them was positive (Table II. Thirty three Smallpox isolates have been tested with material from first egg inoculation (chorioallantoic membranes which have been stored in glycerin 50%, at - 15ºC. Fifteen of them were still positive by gel-electrophoresis and only 3 by agar-gel (Table II. The last 60 specimens received for diagnosis from Smallpox Erradication Campaign (CEV, were negatives by both tests. The gel-electrophoresis, did not show false-positives on described conditions.

Structural Evolution and Stability of Sol-Gel Biocatalysts

International Nuclear Information System (INIS)

Rodgers, L.E.; Foster, L.J.R.; Holden, P.J.; Knott, R.B.; Bartlett, J.B.

2005-01-01

Full text: Immobilisation strategies for catalytic enzymes are important as they allow reuse of the biocatalysts. Sol-gel materials have been used to immobilise Candida antarctica lipase B (CALB), a commonly used industrial enzyme with a known crystal structure. The sol-gel bioencapsulate is produced through the condensation of suitable metal alkoxides in the presence of CALB, yielding materials with controlled pore sizes, volume and surface chemistry. Sol-gel matrices have been shown to prolong the catalytic life and enhance the activity of CALB, although the molecular basis for this effect has yet to be elucidated due to the limitations of analysis techniques applied to date. Small angle neutron scattering (SANS) allows such multicomponent systems to be characterised through contrast matching. In the sol-gel bioencapsulate system, at the contrast match point for silica, residual scattering intensity is due to the CALB and density fluctuations in the matrix. A SANS contrast variation series found the match point for the silica matrix, both with and without enzyme present, to be around 35 percent. The model presented here proposes a mechanism for the interaction between CALB and the surrounding sol-gel matrix, and the observed improvement in enzyme activity and matrix strength. The SANS protocol developed here may be applied more generally to bioencapsulates. (authors)

Additional conformer observed in the microwave spectrum of methyl vinyl ketone

Science.gov (United States)

Wilcox, David S.; Shirar, Amanda J.; Williams, Owen L.; Dian, Brian C.

2011-05-01

A chirped-pulse Fourier transform microwave spectrometer was used to record the rotational spectrum of methyl vinyl ketone (MVK, 3-butene-2-one). Two stable conformations were identified: the previously documented antiperiplanar (ap) conformer and synperiplanar (sp), which is reported for the first time in this microwave study. Methyl torsional analysis resulted in V3 barrier heights of 433.8(1) and 376.6(2) cm-1 for ap- and sp-MVK, respectively. Heavy atom isotopic species of both conformers were detected in natural abundance allowing bond lengths and angles of the molecular frames to be calculated through Kraitchman analysis. A comparison with ab initio calculations is included.

Improved gel electrophoresis matrix for hydrophobic protein separation and identification.

Science.gov (United States)

Tokarski, Caroline; Fillet, Marianne; Rolando, Christian

2011-03-01

We propose an improved acrylamide gel for the separation of hydrophobic proteins. The separation strategy is based on the incorporation of N-alkylated and N,N'-dialkylated acrylamide monomers in the gel composition in order to increase hydrophobic interactions between the gel matrix and the membrane proteins. Focusing on the most efficient monomer, N,N'-dimethylacrylamide, the potentiality of the new matrix was evaluated on membrane proteins of the human colon HCT-116 cell line. Protein analysis was performed using an adapted analytical strategy based on FT-ICR tandem mass spectrometry. As a result of this comparative study, including advanced reproducibility experiments, more hydrophobic proteins were identified in the new gel (average GRAVY: -0.085) than in the classical gel (average GRAVY: -0.411). Highly hydrophobic peptides were identified reaching a GRAVY value up to 1.450, therefore indicating their probable locations in the membrane. Focusing on predicted transmembrane domains, it can be pointed out that 27 proteins were identified in the hydrophobic gel containing up to 11 transmembrane domains; in the classical gel, only 5 proteins containing 1 transmembrane domain were successfully identified. For example, multiple ionic channels and receptors were characterized in the hydrophobic gel such as the sodium/potassium channel and the glutamate or the transferrin receptors whereas they are traditionally detected using specific enrichment techniques such as immunoprecipitation. In total, membrane proteins identified in the classical gel are well documented in the literature, while most of the membrane proteins only identified on the hydrophobic gel have rarely or never been described using a proteomic-based approach. 2010 Elsevier Inc. All rights reserved.

From spinning conformal blocks to matrix Calogero-Sutherland models

Science.gov (United States)

Schomerus, Volker; Sobko, Evgeny

2018-04-01

In this paper we develop further the relation between conformal four-point blocks involving external spinning fields and Calogero-Sutherland quantum mechanics with matrix-valued potentials. To this end, the analysis of [1] is extended to arbitrary dimensions and to the case of boundary two-point functions. In particular, we construct the potential for any set of external tensor fields. Some of the resulting Schrödinger equations are mapped explicitly to the known Casimir equations for 4-dimensional seed conformal blocks. Our approach furnishes solutions of Casimir equations for external fields of arbitrary spin and dimension in terms of functions on the conformal group. This allows us to reinterpret standard operations on conformal blocks in terms of group-theoretic objects. In particular, we shall discuss the relation between the construction of spinning blocks in any dimension through differential operators acting on seed blocks and the action of left/right invariant vector fields on the conformal group.

Single-strand conformation polymorphism analysis of ribosomal DNA for detection of Phytophthora ramorum directly from plant tissues

Science.gov (United States)

Ping Kong; Patricia A. Richardson; Chuanxue Hong; Thomas L. Kubisiak

2006-01-01

At the first Sudden Oak Death Science Symposium, we reported on the use of a single strand conformation polymorphism (SSCP) analysis for rapid identification of Phytophthora ramorum in culture. We have since assessed and improved the fingerprinting technique for detecting this pathogen directly from plant tissues. The improved SSCP protocol uses a...

Gel-aided sample preparation (GASP)--a simplified method for gel-assisted proteomic sample generation from protein extracts and intact cells.

Science.gov (United States)

Fischer, Roman; Kessler, Benedikt M

2015-04-01

We describe a "gel-assisted" proteomic sample preparation method for MS analysis. Solubilized protein extracts or intact cells are copolymerized with acrylamide, facilitating denaturation, reduction, quantitative cysteine alkylation, and matrix formation. Gel-aided sample preparation has been optimized to be highly flexible, scalable, and to allow reproducible sample generation from 50 cells to milligrams of protein extracts. This methodology is fast, sensitive, easy-to-use on a wide range of sample types, and accessible to nonspecialists. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum-chemical study on the bioactive conformation of epothilones.

Science.gov (United States)

Jiménez, Verónica A

2010-12-27

Herein, I report a DFT study on the bioactive conformation of epothilone A based on the analysis of 92 stable conformations of free and bound epothilone to a reduced model of tubulin receptor. The equilibrium structures and relative energies were studied using B3LYP and X3LYP functionals and the 6-31G(d) standard basis set, which was considered appropriate for the size of the systems under study. Calculated relative energies of free and bound epothilones led me to propose a new model for the bioactive conformation of epothilone A, which accounts for several structure-activity data.

Compatibility between weak gel and microorganisms in weak gel-assisted microbial enhanced oil recovery.

Science.gov (United States)

Qi, Yi-Bin; Zheng, Cheng-Gang; Lv, Cheng-Yuan; Lun, Zeng-Min; Ma, Tao

2018-03-20

To investigate weak gel-assisted microbial flooding in Block Wang Long Zhuang in the Jiangsu Oilfield, the compatibility of weak gel and microbe was evaluated using laboratory experiments. Bacillus sp. W5 was isolated from the formation water in Block Wang Long Zhuang. The rate of oil degradation reached 178 mg/day, and the rate of viscosity reduction reached 75.3%. Strain W5 could produce lipopeptide with a yield of 1254 mg/L. Emulsified crude oil was dispersed in the microbial degradation system, and the average diameter of the emulsified oil particles was 18.54 μm. Bacillus sp. W5 did not affect the rheological properties of the weak gel, and the presence of the weak gel did not significantly affect bacterial reproduction (as indicated by an unchanged microbial biomass), emulsification (surface tension is 35.56 mN/m and average oil particles size is 21.38 μm), oil degradation (162 mg/day) and oil viscosity reduction (72.7%). Core-flooding experiments indicated oil recovery of 23.6% when both weak gel and Bacillus sp. W5 were injected into the system, 14.76% when only the weak gel was injected, and 9.78% with strain W5 was injected without the weak gel. The results demonstrate good compatibility between strains W5 and the weak gel and highlight the application potential of weak gel-assisted microbial flooding. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Preliminary study of diffusion effects in Fricke gel dosimeters

International Nuclear Information System (INIS)

Quiroga, A.; Vedelago, J.; Valente, M.

2014-08-01

Diffusion of ferric ions in ferrous sulfate (Fricke) gels represents one of the main drawbacks of some radiation detectors, like Fricke gel dosimeters. In practice, this disadvantage can be overcome by prompt dosimeter analysis, constraining strongly the time between irradiation and analysis. Due to required integral accuracy levels, special dedicated protocols are implemented with the aim of minimizing signal blurring due to diffusion effects. This work presents dedicated analytic modelling and numerical calculations of diffusion coefficients in Fricke gel radiation sensitive material. Samples are optically analysed by means of visible light transmission measurements capturing images with a Ccd camera provided with a monochromatic 585 nm filter corresponding to the X O-infused Fricke solution absorbance peak. Dose distributions in Fricke gels are suitably delivered in order to assess specific initial conditions further studied by periodical sample image acquisitions. In a first analytic approach, experimental data are fit with linear models in order to achieve a value for the diffusion coefficient. The second approach to the problem consists on a group of computational algorithms based on inverse problem formulation, along with suitable 2D diffusion model capable of estimating diffusion coefficients by fitting the obtained algorithm numerical solutions with the corresponding experimental data. Comparisons are performed by introducing an appropriate functional in order to analyse both experimental and numerical values. Solutions to second order diffusion equation are calculated in the framework of a dedicated method that incorporates Finite Element Method. Moreover, optimised solutions can be attained by gradient type minimisation algorithms. Knowledge about diffusion coefficient for Fricke gel radiation detector might be helpful in accounting for effects regarding elapsed time between dosimeter irradiation and further analysis. Hence, corrections might be included

Translational and rotational diffusion of flexible PEG and rigid dendrimer probes in sodium caseinate dispersions and acid gels.

Science.gov (United States)

Salami, Souad; Rondeau-Mouro, Corinne; Barhoum, Myriam; van Duynhoven, John; Mariette, François

2014-09-01

The dynamics of rigid dendrimer and flexible PEG probes in sodium caseinate dispersions and acid gels, including both translational diffusion and rotational diffusion, were studied by NMR. Above the onset of the close-packing limit (C ∼ 10 g/100 g H2 O), translational diffusion of the probe depended on its flexibility and on the fluctuations of the matrix chains. The PEG probe diffused more rapidly than the spherical dendrimer probe of corresponding hydrodynamic radius. The greater conformational flexibility of PEG facilitated its motion through the crowded casein matrix. Rotational diffusion was, however, substantially less hindered than the translational diffusion and depended on the local protein-probe friction which became high when the casein concentration increased. The coagulation of the matrix led to the formation of large voids, which resulted in an increase in the translational diffusion of the probes, whereas the rotational diffusion of the probes was retarded in the gel, which could be attributed to the immobilized environment surrounding the probe. Quantitative information from PFG-NMR and SEM micrographs have been combined for characterizing microstructural details in SC acid gels. © 2014 Wiley Periodicals, Inc.

Causality Constraints in Conformal Field Theory

CERN Multimedia

CERN. Geneva

2015-01-01

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d-dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂φ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinni...

Causality constraints in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Hartman, Thomas; Jain, Sachin; Kundu, Sandipan [Department of Physics, Cornell University,Ithaca, New York (United States)

2016-05-17

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂ϕ){sup 4} coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators.

High transparent shape memory gel

Science.gov (United States)

Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

2014-03-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Book-tax conformity in Polish private companies

Directory of Open Access Journals (Sweden)

Anna Białek-Jaworska

2016-12-01

Full Text Available The purpose of this paper is to identify whether financial income differs significantly from the tax base in Poland and what determines these differences between accounting and taxable results in Polish private entities that are not listed on the stock exchange. In this paper, besides examining the level of book-tax conformity in Poland, we investigate the determinants of book-tax differences in the one-book and twobook accounting systems, with deferred income tax. We use the single factor ANOVA variance analysis, robust fixed effects estimator and the fixed effects linear model with an AR(1 disturbance estimator for panel data of 26,657 private limited liability and non-public joint-stock companies for the period of 2003–2014 (177,667 firm-year observations. The originality of this paper results from the deep quantita-tive analysis of the determinants of book-tax conformity on a novel dataset of Polish private firms. We confirm a strong significant influence of tax law on the shape of the one-book accounting system in Poland. Larger enterprises show fewer book-tax differences. Book-tax conformity is lower in private companies that incur financial losses and in private companies conducting the one-book accounting system. Family-owned companies have higher mean and median book-tax conformity than businessgroups members, due to higher demand for information from their accounts to support stewardship func-tions and to monitor the activities of the management board in the business groups.

Studies on the proteinaceous gel secretion from the skin of the ...

African Journals Online (AJOL)

PRECIOUS

2009-12-15

Dec 15, 2009 ... and SDS-PAGE analysis of the proteinaceous gel of catfish, A. ... SDS–PAGE. One dimensional sodium dodecyl sulphate (SDS) poly acrylamide gel electrophoresis (PAGE) was carried out to estimate the mole- cular weight of the ... 0.2% Triton X-100, was defined as percent hemolysis (Park et al.,. 1997).

Influence of pre-cooking protein paste gelation conditions and post-cooking gel storage conditions on gel texture.

Science.gov (United States)

Paker, Ilgin; Matak, Kristen E

2016-01-15

Gelation conditions affect the setting of myofibrillar fish protein gels. Therefore the impact of widely applied pre-cooking gelation time/temperature strategies and post-cooking period on the texture and color of final protein gels was determined. Four pre-cooking gelation strategies (no setting time, 30 min at 25 °C, 1 h at 40 °C or 24 h at 4 °C) were applied to protein pastes (fish protein concentrate and standard functional additives). After cooking, texture and color were analyzed either directly or after 24 h at 4 °C on gels adjusted to 25 °C. No-set gels were harder, gummier and chewier (P cooking. Gel-setting conditions had a greater (P cooking stored gels in texture and color, depending on the pre-cooking gelation strategy. Pre-cooking gelation conditions will affect final protein gel texture and color, with gel stability benefiting from a gel-setting period. However, post-cooking storage may have a greater impact on final gels, with textural attributes becoming more consistent between all samples. © 2015 Society of Chemical Industry.

Comparative study of nano copper aluminate spinel prepared by sol–gel and modified sol–gel techniques: Structural, electrical, optical and catalytic studies

International Nuclear Information System (INIS)

Kumar, R. Thinesh; Suresh, P.; Selvam, N. Clament Sagaya; Kennedy, L. John; Vijaya, J. Judith

2012-01-01

Highlights: ► A modified sol–gel method for the preparation of nano CuAl 2 O 4 spinel using ethylenediamine was studied. ► Role of ethylenediamine in enhancing the structural, electrical, optical and catalytic properties of copper aluminate is highlighted. ► Effect of preparation method on the activity and selectivity of the samples on the oxidation of benzyl alcohol by CuAl 2 O 4 is studied. - Abstract: The effect of ethylenediamine addition in the sol–gel method for the preparation of nano CuAl 2 O 4 spinel for the enhancement in their structural, electrical, optical and catalytic properties was investigated. The samples were prepared by two different methods: sol–gel and modified sol–gel technique using ethylenediamine. X-ray diffraction (XRD), Fourier transform infrared spectra (FT-IR), scanning electron microscopy (SEM), high resolution-transmission electron microscopy (HR-TEM), energy dispersive X-ray analysis (EDX), nitrogen adsorption/desorption isotherms, temperature dependent conductance measurements, thermoelectric power (TEP) measurements and UV–visible diffuse reflectance (UV–vis-DRS) spectra were used to characterize the samples prepared. CuAl 2 O 4 prepared by modified sol–gel technique was found to possess a higher surface area, lower crystallite size, lower activation energy and high porosity than the one prepared by sol–gel method which in turn lead to the improved performance of it towards the selective oxidation of benzyl alcohol to benzaldehyde. Effect of solvent on the catalytic oxidation of benzyl alcohol by the nano CuAl 2 O 4 prepared by modified sol–gel technique was also investigated.

Controlled release of vancomycin from thin sol-gel films on implant surfaces successfully controls osteomyelitis.

Science.gov (United States)

Adams, Christopher S; Antoci, Valentin; Harrison, Gerald; Patal, Payal; Freeman, Terry A; Shapiro, Irving M; Parvizi, Javad; Hickok, Noreen J; Radin, Shula; Ducheyne, Paul

2009-06-01

Peri-prosthetic infection remains a serious complication of joint replacement surgery. Herein, we demonstrate that a vancomycin-containing sol-gel film on Ti alloy rods can successfully treat bacterial infections in an animal model. The vancomycin-containing sol-gel films exhibited predictable release kinetics, while significantly inhibiting S. aureus adhesion. When evaluated in a rat osteomyelitis model, microbiological analysis indicated that the vancomycin-containing sol-gel film caused a profound decrease in S. aureus number. Radiologically, while the control side showed extensive bone degradation, including abscesses and an extensive periosteal reaction, rods coated with the vancomycin-containing sol-gel film resulted in minimal signs of infection. MicroCT analysis confirmed the radiological results, while demonstrating that the vancomycin-containing sol-gel film significantly protected dense bone from resorption and minimized remodeling. These results clearly demonstrate that this novel thin sol-gel technology can be used for the targeted delivery of antibiotics for the treatment of periprosthetic as well as other bone infections. Copyright 2008 Orthopaedic Research Society

Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

Directory of Open Access Journals (Sweden)

Camilla Calabrese

2018-02-01

Full Text Available We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol's family, and include 2-amino-1-phenylethanol, 2-methylamino-1-phenylethanol, noradrenaline, adrenaline 2-aminoethanol, and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6–18 and 59.6–74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was performed, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

Agar/gelatin bilayer gel matrix fabricated by simple thermo-responsive sol-gel transition method.

Science.gov (United States)

Wang, Yifeng; Dong, Meng; Guo, Mengmeng; Wang, Xia; Zhou, Jing; Lei, Jian; Guo, Chuanhang; Qin, Chaoran

2017-08-01

We present a simple and environmentally-friendly method to generate an agar/gelatin bilayer gel matrix for further biomedical applications. In this method, the thermally responsive sol-gel transitions of agar and gelatin combined with the different transition temperatures are exquisitely employed to fabricate the agar/gelatin bilayer gel matrix and achieve separate loading for various materials (e.g., drugs, fluorescent materials, and nanoparticles). Importantly, the resulting bilayer gel matrix provides two different biopolymer environments (a polysaccharide environment vs a protein environment) with a well-defined border, which allows the loaded materials in different layers to retain their original properties (e.g., magnetism and fluorescence) and reduce mutual interference. In addition, the loaded materials in the bilayer gel matrix exhibit an interesting release behavior under the control of thermal stimuli. Consequently, the resulting agar/gelatin bilayer gel matrix is a promising candidate for biomedical applications in drug delivery, controlled release, fluorescence labeling, and bio-imaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Antimicrobial activity and the mechanism of silver nanoparticle thermosensitive gel

Directory of Open Access Journals (Sweden)

Chen M

2011-11-01

Full Text Available Meiwan Chen1,2,‡, Zhiwen Yang1,‡, Hongmei Wu1, Xin Pan1, Xiaobao Xie3, Chuanbin Wu11Research and Development Center of Pharmaceutical Engineering, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China; 2State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China ‡These authors contributed equally to this workPurpose: The purpose of the present study was to elucidate the antimicrobial activity and mechanism of silver nanoparticles incorporated into thermosensitive gel (S-T-Gel on Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa.Patients and methods: This study investigated the growth, permeability, and morphology of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa cells in order to observe the action of S-T-Gel on the membrane structure of these three bacteria. The cell morphology of normal and treated bacteria cells was assessed by transmission electron microscopy (TEM, and the effects of S-T-Gel on genome DNA of bacterial cells were evaluated by agarose gel electrophoresis.Results: S-T-Gel showed promising activity against Staphylococcus aureus and moderate activity against Escherichia coli and Pseudomonas aeruginosa. The observation with TEM suggested that S-T-Gel may destroy the structure of bacterial cell membranes in order to enter the bacterial cell. S-T-Gel then condensed DNA and combined and coagulated with the cytoplasm of the damaged bacteria, resulting in the leakage of the cytoplasmic component and the eventual death of these three bacteria. In addition, the analysis of agarose gel electrophoresis demonstrated that S-T-Gel could increase the decomposability of genome DNA.Conclusion: These results about promising antimicrobial activity and mechanism of S-T-Gel may be useful for further research

Analysis of rRNA gene methylation in Arabidopsis thaliana by CHEF-Conventional 2D gel electrophoresis

Science.gov (United States)

Mohannath, Gireesha; Pikaard, Craig S.

2017-01-01

Summary Contour-clamped homogenous electric field (CHEF) gel electrophoresis, a variant of Pulsed-field gel electrophoresis (PFGE), is a powerful technique for resolving large fragments of DNA (10 kb to 9 Mb). CHEF has many applications including the physical mapping of chromosomes, artificial chromosomes and sub-chromosomal DNA fragments, etc. Here we describe the use of CHEF and two-dimensional gel electrophoresis to analyze rRNA gene methylation patterns within the two ~ 4 million base pair nucleolus organizer regions (NORs) of Arabidopsis thaliana. The method involves CHEF gel electrophoresis of agarose-embedded DNA following restriction endonuclease digestion to cut the NORs into large but resolvable segments, followed by digestion with methylation-sensitive restriction endonucleases and conventional (or CHEF) gel electrophoresis, in a second dimension. Resulting products are then detected by Southern blotting or PCR analyses capable of discriminating rRNA gene subtypes. PMID:27576719

Chemical Gel for Surface Decontamination

International Nuclear Information System (INIS)

Jung, Chong Hun; Moon, J. K.; Won, H. J.; Lee, K. W.; Kim, C. K.

2010-01-01

Many chemical decontamination processes operate by immersing components in aggressive chemical solutions. In these applications chemical decontamination technique produce large amounts of radioactive liquid waste. Therefore it is necessary to develop processes using chemical gels instead of chemical solutions, to avoid the well-known disadvantages of chemical decontamination techniques while retaining their high efficiency. Chemical gels decontamination process consists of applying the gel by spraying it onto the surface of large area components (floors, walls, etc) to be decontaminated. The gel adheres to any vertical or complex surface due to their thixotropic properties and operates by dissolving the radioactive deposit, along with a thin layer of the gel support, so that the radioactivity trapped at the surface can be removed. Important aspects of the gels are that small quantities can be used and they show thixitropic properties : liquid during spraying, and solid when stationary, allowing for strong adherence to surfaces. This work investigates the decontamination behaviors of organic-based chemical gel for SS 304 metallic surfaces contaminated with radioactive materials

Sol-Gel Manufactured Energetic Materials

Science.gov (United States)

Simpson, Randall L.; Lee, Ronald S.; Tillotson, Thomas M.; Hrubesh, Lawrence W.; Swansiger, Rosalind W.; Fox, Glenn A.

2005-05-17

Sol-gel chemistry is used for the preparation of energetic materials (explosives, propellants and pyrotechnics) with improved homogeneity, and/or which can be cast to near-net shape, and/or made into precision molding powders. The sol-gel method is a synthetic chemical process where reactive monomers are mixed into a solution, polymerization occurs leading to a highly cross-linked three dimensional solid network resulting in a gel. The energetic materials can be incorporated during the formation of the solution or during the gel stage of the process. The composition, pore, and primary particle sizes, gel time, surface areas, and density may be tailored and controlled by the solution chemistry. The gel is then dried using supercritical extraction to produce a highly porous low density aerogel or by controlled slow evaporation to produce a xerogel. Applying stress during the extraction phase can result in high density materials. Thus, the sol-gel method can be used for precision detonator explosive manufacturing as well as producing precision explosives, propellants, and pyrotechnics, along with high power composite energetic materials.

Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

DEFF Research Database (Denmark)

Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

2008-01-01

One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...... and where the aim is to find as many as possible of the group-dependent proteins seems particularly difficult to handle. The present paper investigates such a case regarding the effect of scaling and of prefiltering by univariate nonparametric statistics on the selection of spots. Besides, a modified...

Thixotropic gel for vadose zone remediation

Science.gov (United States)

Rhia, Brian D [Augusta, GA

2011-03-01

A thixotropic gel suitable for use in subsurface bioremediation is provided along with a process of using the gel. The thixotropic gel provides a non-migrating injectable substrate that can provide below ground barrier properties. In addition, the gel components provide for a favorable environment in which certain contaminants are preferentially sequestered in the gel and subsequently remediated by either indigenous or introduced microorganisms.

Meso-Decorated Switching-Knot Gels

Science.gov (United States)

Gong, Jin; Sawamura, Kensuke; Makino, Masato; Kabir, M. H.; Furukawa, Hidemitsu

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry .In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals. The strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Conformal expansions and renormalons

Energy Technology Data Exchange (ETDEWEB)

Rathsman, J.

2000-02-07

The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

Structure of mineral gels

International Nuclear Information System (INIS)

Miranda Salvado, I.M.; Margaca, F.M.A.; Teixeira, J.

1999-01-01

Small Angle Neutron Scattering (SANS) measurements have been performed to investigate the nanoscale structure of materials of the systems xTiO 2 -(1-x)SiO 2 and xZrO 2 -(1-x)SiO 2 with x ≤ 10 mol % at different processing stages. The materials were prepared by sol-gel using the alkoxides method, in strong acidic conditions. Samples were studied as xerogels heat-treated at 120 and 850 deg. C and as wet gels at gel point and after aging. All samples showed identical microstructure at gel point, extended linear chains ∼10 nm long. The aged gel has a mass fractal structure with fractal dimension of 1.7 - 1.9. The 120 deg. C heat-treated xerogels show homogeneous oxide regions with mass fractal structure. For the 850 deg. C heat-treated xerogel the oxide regions average size has reduced and it has densified as compared to 120 deg. C heat-treated sample. (author)

Image registration of BANG[reg] gel dose maps for quantitative dosimetry verification

International Nuclear Information System (INIS)

Meeks, Sanford L.; Bova, Frank J.; Maryanski, Marek J.; Kendrick, Lance A.; Ranade, Manisha K.; Buatti, John M.; Friedman, William A.

1999-01-01

the pixel resolution of the MRI dose maps is 1.56 x 1.56 mm, and the treatment-planning dose distributions were calculated on a 1-mm dose grid. All points within the dose distribution were well within the tolerances set forth for commissioning and quality assurance of stereotactic treatment-planning systems. Moreover, the quantitative evaluation presented here tests the accuracy of the entire treatment-planning and delivery process, including stereotactic frame rigidity, CT localization, CT/MR correlation, dose calculation, and radiation delivery. Conclusion: BANG[reg] polymer gel dosimetry coupled with image correlation provides quantitative verification of the accuracy of 3D dose distributions. Such quantitative evaluation is imperative to ensure the high quality of the 3D dose distributions generated and delivered by stereotactic and other conformal irradiation systems

Quality change of apple slices coated with Aloe vera gel during storage.

Science.gov (United States)

Song, Hye-Yeon; Jo, Wan-Shin; Song, Nak-Bum; Min, Sea C; Song, Kyung Bin

2013-06-01

Fresh-cut apples are easily susceptible to browning and microbial spoilage. In this study, an edible coating prepared from Aloe vera gel containing antibrowning solution was applied to preserve the quality of fresh-cut apples during storage. Fresh-cut apples were treated with both an Aloe vera gel and an Aloe vera gel containing 0.5% cysteine and then stored at 4 °C for 16 d. The color, firmness, weight loss, soluble solid content, titratable acidity, microbial analysis, and sensory evaluation were analyzed during storage. Fresh-cut apples coated with the Aloe vera gel showed delayed browning and reduced weight loss and softening compared to the control. The Aloe vera gel coating was also effective in reducing the populations of the total aerobic bacteria and yeast and molds. In particular, Aloe vera gel containing 0.5% cysteine was most effective in delaying browning and the reduction of microbial populations among the treatments. These results suggest that an Aloe vera gel coating can be used for maintaining the quality of fresh-cut apples. © 2013 Institute of Food Technologists®

Encapsulation of biomaterials in porous glass-like matrices prepared via an aqueous colloidal sol-gel process

Science.gov (United States)

Liu, Dean-Mo; Chen, I-Wei

2001-01-01

The present invention provides a process for the encapsulation of biologically important proteins into transparent, porous silica matrices by an alcohol-free, aqueous, colloidal sol-gel process, and to the biological materials encapsulated thereby. The process is exemplified by studies involving encapsulated cytochrome c, catalase, myoglobin, and hemoglobin, although non-proteinaceous biomaterials, such as active DNA or RNA fragments, cells or even tissues, may also be encapsulated in accordance with the present methods. Conformation, and hence activity of the biomaterial, is successfully retained after encapsulation as demonstrated by optical characterization of the molecules, even after long-term storage. The retained conformation of the biomaterial is strongly correlated to both the rate of gelation and the subsequent drying speed of the encapsulatng matrix. Moreover, in accordance with this process, gelation is accelerated by the use of a higher colloidal solid concentration and a lower synthesis pH than conventional methods, thereby enhancing structural stability and retained conformation of the biomaterials. Thus, the invention also provides a remarkable improvement in retaining the biological activity of the encapsulated biomaterial, as compared with those involved in conventional alkoxide-based processes. It further provides new methods for the quantitative and qualitative detection of test substances that are reactive to, or catalyzed by, the active, encapsulated biological materials.

Mullite fibres preparation by aqueous sol-gel process and activation energy of mullitization

International Nuclear Information System (INIS)

Tan Hongbin; Ding Yaping; Yang Jianfeng

2010-01-01

Mullite fibres were prepared by sol-gel process using aluminum carboxylates (ACs) and silica sol. ACs was synthesized from dissolving aluminum powder in a mixture of formic acid and oxalic acid using aluminum chloride hexahydrate as catalyst. A molar ratio of 1:2:1 for aluminum, formic acid and oxalic acid was optimized to obtain clear solution and viscous ACs sol for fibres synthesis. Thermogravimetry-differential scanning calorimetry (TG-DSC), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM) analysis were used to characterize the properties of the gel and ceramic fibres. The gel fibres completely transformed to mullite at 1200 o C, with a smooth surface and uniform diameter. The activation energy for mullite formation in precursor gel fibres was determined by means of differential thermal analysis. The value obtained, E a = 741.4 kJ/mol, was lower than most data reported in the literatures, which was attributed to the silica-alumina micro-phase separation when organic acids decomposed during gel fibres heating.

Kinetics Study of Gas Pollutant Adsorption and Thermal Desorption on Silica Gel

Directory of Open Access Journals (Sweden)

Rong A

2017-06-01

Full Text Available Silica gel is a typical porous desiccant material. Its adsorption performance for gaseous air pollutants was investigated to determine its potential contribution to reducing such pollutants. Three gaseous air pollutants, toluene, carbon dioxide, and methane, were investigated in this paper. A thermogravimetric analyzer was used to obtain the equilibrium adsorption capacity of gases on single silica gel particles. The silica gel adsorption capacity for toluene is much higher than that for carbon dioxide and methane. To understand gas pollutant thermal desorption from silica gel, the thermogravimetric analysis of toluene desorption was conducted with 609 ppm toluene vapor at 313 K, 323 K, and 333 K. The overall regeneration rate of silica gel was strongly dependent on temperature and the enthalpy of desorption. The gas pollutant adsorption performance and thermal desorption on silica gel material may be used to estimate the operating and design parameters for gas pollutant adsorption by desiccant wheels.

Cyanocobalamin Nasal Gel

Science.gov (United States)

... to supply extra vitamin B12 to people who need unusually large amounts of this vitamin because they are pregnant or have certain diseases. ... Cyanocobalamin nasal gel will supply you with enough vitamin B12 only as ... it regularly. You may need to use cyanocobalamin nasal gel every week for ...

Gels and gel-derived glasses in the system Na2O-B2O3-SiO2

Science.gov (United States)

Mukherjee, S. P.

1983-01-01

The containerless melting of high-purity multicomponent homogeneous gels and gel monoliths offers a unique approach to making ultrapure multicomponent optical glasses in the reduced gravity environment of space. Procedures for preparing and characterizing gels and gel-derived glasses in the system Na2O-B2O3-SiO2 are described. Preparation is based on the polymerization reactions of alkoxysilane with trimethyl borate or boric acid and a suitable sodium compound. The chemistry of the gelling process is discussed in terms of process parameters and the gel compositions. The physicochemical nature of gels prepared by three different procedures was found to be significantly different. Infrared absorption spectra indicate finite differences in the molecular structures of the different gels. The melting of the gel powders and the transformation of porous gel monoliths to transparent 'glass' without melting are described.

The conformal method and the conformal thin-sandwich method are the same

International Nuclear Information System (INIS)

Maxwell, David

2014-01-01

The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign. (paper)

Study of nuclear glasses alteration gel and synthesis of some model gels

International Nuclear Information System (INIS)

Ricol, S.

1995-01-01

This work deals with the general problem of alteration of the reference nuclear glass R7T7. Attention is paid particularly to the altered layer formed at the glass surface during alteration process. In opposition to previous works, related essentially to glass dissolution kinetics based on chemical analyses of lixiviated elements, this thesis deals with alteration problems through structural studies of the reference glass and derived gel. This approach allows the determination of mechanisms for the gel formation and a better understanding of the behaviour of glasses towards lixiviation. Both approaches appeared complementary. Based on several spectroscopic techniques, this work showed the particular role of cations such as calcium, zirconium and iron. Studies of silica-based synthetic gels showed the synergic effect of formers cation and of one highly coordinated cation. The variation of the wavenumber related to Si-O-Si asymmetric stretching vibration can be correlated to O/Si ratio for ternary systems Si/Na/Zr. On the contrary, the Si losses of the materials depend on the number of non-bridging oxygen atoms. In the perspective of long-term behaviour, the alteration gel presents better characteristics than initial glass. It is therefore a highly stable material in static conditions. In the same way, synthetic gels are materials with very low solubilities (much lower than the alteration gel) and could be used as confining matrices. (authors). refs., 71 figs., 37 tabs

Structure and dynamics of spin-labeled insulin entrapped in a silica matrix by the sol-gel method.

Science.gov (United States)

Vanea, E; Gruian, C; Rickert, C; Steinhoff, H-J; Simon, V

2013-08-12

The structure and conformational dynamics of insulin entrapped into a silica matrix was monitored during the sol to maturated-gel transition by electron paramagnetic resonance (EPR) spectroscopy. Insulin was successfully spin-labeled with iodoacetamide and the bifunctional nitroxide reagent HO-1944. Room temperature continuous wave (cw) EPR spectra of insulin were recorded to assess the mobility of the attached spin labels. Insulin conformation and its distribution within the silica matrix were studied using double electron-electron resonance (DEER) and low-temperature cw-EPR. A porous oxide matrix seems to form around insulin molecules with pore diameters in the order of a few nanometers. Secondary structure of the encapsulated insulin investigated by Fourier transform infrared spectroscopy proved a high structural integrity of insulin even in the dried silica matrix. The results show that silica encapsulation can be used as a powerful tool to effectively isolate and functionally preserve biomolecules during preparation, storage, and release.

Analysis of sperm antigens by sodium dodecyl sulfate gel/protein blot radioimmunobinding method

International Nuclear Information System (INIS)

Lee, C.Y.G.; Huang, Y.S.; Hu, P.C.; Gomel, V.; Menge, A.C.

1982-01-01

A radioimmunobinding method based on the blotting of renatured proteins from sodium dodecyl sulfate gels on to nitrocellulose filter papers was developed to analyze the sperm antigens that elicit serum anti-sperm antibodies. In rabbits, serum anti-sperm antibodies were raised by immunization with homologous epididymal spermatozoa mixed with complete Freund's adjuvant. The raised antisera from either male or female rabbits were shown to react with three major sperm protein bands on sodium dodecyl sulfate gels with the corresponding molecular weights of about 70,000 +/- 5000, 14,000, and 13,000, respectively. In humans, the monoclonal antibodies against human sperm were raised by a hybridoma technique. Out of six independent hybrid cell lines that were generated, three of them were shown to secrete immunoglobulins that react with the same two protein bands on sodium dodecyl sulfate gels, which have the approximate molecular weight of 10,000. The same procedure was also used to analyze human serum samples that were shown to contain anti-sperm antibodies by the known techniques. Unique sperm antigens that elicit anti-sperm antibodies in humans were identified and correlated. The results of this study suggest that sodium dodecyl sulfate gel/protein blot radioimmunobinding method may be a sensitive and useful tool for the study of sperm antigens that elicit autoimmune responses and their association with human infertility

Conformational analysis of g protein-coupled receptor signaling by hydrogen/deuterium exchange mass spectrometry.

Science.gov (United States)

Li, Sheng; Lee, Su Youn; Chung, Ka Young

2015-01-01

Conformational change and protein-protein interactions are two major mechanisms of membrane protein signal transduction, including G protein-coupled receptors (GPCRs). Upon agonist binding, GPCRs change conformation, resulting in interaction with downstream signaling molecules such as G proteins. To understand the precise signaling mechanism, studies have investigated the structural mechanism of GPCR signaling using X-ray crystallography, nuclear magnetic resonance (NMR), or electron paramagnetic resonance. In addition to these techniques, hydrogen/deuterium exchange mass spectrometry (HDX-MS) has recently been used in GPCR studies. HDX-MS measures the rate at which peptide amide hydrogens exchange with deuterium in the solvent. Exposed or flexible regions have higher exchange rates and excluded or ordered regions have lower exchange rates. Therefore, HDX-MS is a useful tool for studying protein-protein interfaces and conformational changes after protein activation or protein-protein interactions. Although HDX-MS does not give high-resolution structures, it analyzes protein conformations that are difficult to study with X-ray crystallography or NMR. Furthermore, conformational information from HDX-MS can help in the crystallization of X-ray crystallography by suggesting highly flexible regions. Interactions between GPCRs and downstream signaling molecules are not easily analyzed by X-ray crystallography or NMR because of the large size of the GPCR-signaling molecule complexes, hydrophobicity, and flexibility of GPCRs. HDX-MS could be useful for analyzing the conformational mechanism of GPCR signaling. In this chapter, we discuss details of HDX-MS for analyzing GPCRs using the β2AR-G protein complex as a model system. © 2015 Elsevier Inc. All rights reserved.

Dapsone gel 5% in combination with adapalene gel 0.1%, benzoyl peroxide gel 4% or moisturizer for the treatment of acne vulgaris: a 12-week, randomized, double-blind study.

Science.gov (United States)

Fleischer, Alan B; Shalita, Alan; Eichenfield, Lawrence F; Abramovits, William; Lucky, Anne; Garrett, Steven

2010-01-01

To evaluate the safety and efficacy of dapsone gel 5% in the treatment of acne when used in combination with adapalene gel 0.1%, benzoyl peroxide gel 4% or moisturizer. This was a twelve-week, randomized, double-blind study. Patients aged 12 years and older (n=301) applied dapsone gel twice daily and were randomly assigned (1:1:1) to one of three additional treatments, applied once daily. By week 12, dapsone gel combined with any of the three additional treatments reduced the mean number of inflammatory lesions. However, the authors did not detect a significant difference in the reduction of inflammatory lesions when dapsone was used in combination with adapalene gel or with benzoyl peroxide gel compared to the dapsone plus moisturizer combination group (P=0.052 for both versus moisturizer combination). Patients treated with dapsone gel combined with adapalene showed a significantly better response in reduction in non-inflammatory and total acne lesion count than those who received the moisturizer combination. Local adverse reactions in all three treatment groups were minimal and generally mild in severity. Dapsone gel in combination with adapalene gel or benzoyl peroxide gel is safe and well tolerated for the treatment of acne vulgaris.

Local environment of zirconium in nuclear gels studied by XAS

International Nuclear Information System (INIS)

Pelegrin, E.; Ildefonse, Ph.; Calas, G.; Ricol, St.; Flank, A.M.

1997-01-01

During lixiviation experiments, nuclear gels are formed and heavy metals are retained. In order to understand this retardation mechanisms, we performed an analysis of the local environment of Zr in parent glasses and derived alteration gels both at the Zr-L II,III , and Zr-K edges. Calibration of the method was conducted through the analysis of model compounds with known coordination number (CN): catapleite Na 2 ZrSi 3 O 9 ,2H 2 O (CN=6), baddeleyite ZrO 2 (CN=7) and zircon SiZrO 4 (CN=8). Nuclear glasses (R7T7, and a simplified nuclear glass V 1) and gels obtained at 90 deg C, with leaching times from 7 to 12 months and with solution renewal. were also investigated (GR7T7R and GV1). Zr-L II,III XANES spectra evidenced that zirconium is 6-fold coordinated in R7T7 and V1 nuclear glasses. For GR7T7R and GV1 gels, Zr local environment is significantly changed, and a mixture of CN (6 and 7J has been evidenced. Quantitative structural results were derived from EXAFS analysis at Zr-K edge. In parent glasses, derived Zr-O distance is 2.10±0.01 10 -10 m, and is in the range Zr-O distances for octahedral coordination in model compounds. In both gels studied, Zr-O distances increase significantly up to 2.15 ±0.01 10 -10 m. This distance is close to that known in baddeleyite (2,158 10 -10 m). A better understanding of the Zr retention mechanism has to be made by studying the second neighbors contributions. (authors)

Silver nitrate based gel dosimeter

International Nuclear Information System (INIS)

Titus, D; Samuel, E J J; Srinivasan, K; Roopan, S M; Madhu, C S

2017-01-01

A new radiochromic gel dosimeter based on silver nitrate and a normoxic gel dosimeter was investigated using UV-Visible spectrophotometry in the clinical dose range. Gamma radiation induced the synthesis of silver nanoparticles in the gel and is confirmed from the UV-Visible spectrum which shows an absorbance peak at around 450 nm. The dose response function of the dosimeter is found to be linear upto12Gy. In addition, the gel samples were found to be stable which were kept under refrigeration. (paper)

Self-assembly, Dynamics and Chirality of Conformational Switches on Metal Surfaces Studied by UHV-STM

DEFF Research Database (Denmark)

Nuermaimaiti, Ajiguli

2013-01-01

structures formed by the conformational switches and statistical analysis of conformational states, a detailed study of dynamic processes is performed by acquiring time-resolved STM data. Furthermore, one of the possible applications of conformational switches towards inducing chirality in surface assemblies...

Laser ablation inductively coupled plasma mass spectrometry analysis of agricultural soils using the sol-gel technique of pellet preparation

International Nuclear Information System (INIS)

Hubova, I.; Hola, M.; Vaculovic, T.; Pinkas, J.; Prokes, L.; Stefan, I.; Kanicky, V.

2009-01-01

Full text: Monitoring of metals in agricultural soils is gaining importance as they are accumulated by plants. A LAICPQMS method with Nd:YAG 213 nm laser has been developed for determination of Cr, Ni, Cu, Zn and Pb in soil pellets prepared by the sol-gel technique. LA-ICPMS analysis of archive samples was verified by XRF of wax-soil pellets and ICPMS with nebulization of solutions obtained by total soil decomposition and by analysis of reference materials. Sequention extraction was used for fractionation analysis. (author)

Preliminary study of diffusion effects in Fricke gel dosimeters

Energy Technology Data Exchange (ETDEWEB)

Quiroga, A. [Centro de Investigacion y Estudios de Matematica de Cordoba, Oficina 318 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Vedelago, J. [Laboratorio de Investigaciones e Instrumentacion en Fisica Aplicada a la Medicina e Imagenes por Rayos X, Laboratorio 448 FaMAF - UNC, Ciudad Universitaria, 5000 Cordoba (Argentina); Valente, M., E-mail: aiquiroga@famaf.unc.edu [Instituto de Fisica Enrique Gaviola, Oficina 102 FaMAF - UNC, Av. Luis Medina Allende, Ciudad Universitaria, 5000 Cordoba (Argentina)

2014-08-15

Diffusion of ferric ions in ferrous sulfate (Fricke) gels represents one of the main drawbacks of some radiation detectors, like Fricke gel dosimeters. In practice, this disadvantage can be overcome by prompt dosimeter analysis, constraining strongly the time between irradiation and analysis. Due to required integral accuracy levels, special dedicated protocols are implemented with the aim of minimizing signal blurring due to diffusion effects. This work presents dedicated analytic modelling and numerical calculations of diffusion coefficients in Fricke gel radiation sensitive material. Samples are optically analysed by means of visible light transmission measurements capturing images with a Ccd camera provided with a monochromatic 585 nm filter corresponding to the X O-infused Fricke solution absorbance peak. Dose distributions in Fricke gels are suitably delivered in order to assess specific initial conditions further studied by periodical sample image acquisitions. In a first analytic approach, experimental data are fit with linear models in order to achieve a value for the diffusion coefficient. The second approach to the problem consists on a group of computational algorithms based on inverse problem formulation, along with suitable 2D diffusion model capable of estimating diffusion coefficients by fitting the obtained algorithm numerical solutions with the corresponding experimental data. Comparisons are performed by introducing an appropriate functional in order to analyse both experimental and numerical values. Solutions to second order diffusion equation are calculated in the framework of a dedicated method that incorporates Finite Element Method. Moreover, optimised solutions can be attained by gradient type minimisation algorithms. Knowledge about diffusion coefficient for Fricke gel radiation detector might be helpful in accounting for effects regarding elapsed time between dosimeter irradiation and further analysis. Hence, corrections might be included

Superspace conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2013-07-15

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

Superspace conformal field theory

International Nuclear Information System (INIS)

Quella, Thomas

2013-07-01

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

Surface grafted chitosan gels. Part II. Gel formation and characterization

DEFF Research Database (Denmark)

Liu, Chao; Thormann, Esben; Claesson, Per M.

2014-01-01

Responsive biomaterial hydrogels attract significant attention due to their biocompatibility and degradability. In order to make chitosan based gels, we first graft one layer of chitosan to silica, and then build a chitosan/poly(acrylic acid) multilayer using the layer-by-layer approach. After...... cross-linking the chitosan present in the polyelectrolyte multilayer, poly(acrylic acid) is partly removed by exposing the multilayer structure to a concentrated carbonate buffer solution at a high pH, leaving a surface-grafted cross-linked gel. Chemical cross-linking enhances the gel stability against...... detachment and decomposition. The chemical reaction between gluteraldehyde, the cross-linking agent, and chitosan was followed in situ using total internal reflection Raman (TIRR) spectroscopy, which provided a molecular insight into the complex reaction mechanism, as well as the means to quantify the cross...

Creation of Dosimetric Verification for Implementation of Intensity Modulated Radiation Therapy (IMRT) Validates Using Polymer Gel

International Nuclear Information System (INIS)

Mansour, M.Sh.E.

2015-01-01

Polymer gel dosimeter is a technique that has the ability to map absorbed radiation dose distributions in three dimensions (3D) with high spatial resolution, it offers a number of advantages over traditional dosimeters such as ionization chambers, thermo luminescent dosimeters (TLD) and radiographic film. These gels are reproducible in response and stable 0 n post-irradiation. It is used as the monomer N-iso propyl acryl amide (NIPAM) and N, N- methylene bis acryl amide (Bis) as the cross linker. A historical overview of gel dosimeter was discussed in detail, inside the theses this case; nearly all data met the expected measurement error of 5 % of the maximum dose (50 c Gy). Relative errors were determined to decrease from 25 % at a 2 Gy irradiation to 9.2% for a 10 Gy irradiation The NIPAM polymer gel dosimeter system proved to be an invaluable method for the quantification of the 3-D dose distribution provided by IMRT. A measurement error of less than 5% was achieved. Toxicity and uncertain response to particular environmental characteristics (i.e., temperature and aging) upon the gel are of important concern about the use of the gel at this time. A PAG gel dosimeter is a method verifying dose delivered for prostate cancer radiotherapy treatment, which has been evaluated in this work. A comparison of DVH for PTV between the two treatment plans was verified experimentally. MRI response, the possibility was demonstrated of manufacturing gel dosimeters suitable for 3D dosimeter in the dose range. The results show that IMRT technique not only provides a better conformal dose to the prostate target volume than conventional Seven-field technique, but also reduces doses to the surrounding normal tissues, The aim of this study was to investigate the basic characteristics of the modified gel dosimeter such as temperature effects, magnetic field strength, Ph, aging, energy and dose rate dependence This includes studies of relaxation time dose response, and stability of the

Conformal Infinity

OpenAIRE

Frauendiener, J?rg

2000-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory...

Rheology and structure of milk protein gels

NARCIS (Netherlands)

Vliet, van T.; Lakemond, C.M.M.; Visschers, R.W.

2004-01-01

Recent studies on gel formation and rheology of milk gels are reviewed. A distinction is made between gels formed by aggregated casein, gels of `pure` whey proteins and gels in which both casein and whey proteins contribute to their properties. For casein' whey protein mixtures, it has been shown

A Computing Method to Determine the Performance of an Ionic Liquid Gel Soft Actuator.

Science.gov (United States)

He, Bin; Zhang, Chenghong; Zhou, Yanmin; Wang, Zhipeng

2018-01-01

A new type of soft actuator material-an ionic liquid gel (ILG) that consists of BMIMBF 4 , HEMA, DEAP, and ZrO 2 -is polymerized into a gel state under ultraviolet (UV) light irradiation. In this paper, we first propose that the ILG conforms to the assumptions of hyperelastic theory and that the Mooney-Rivlin model can be used to study the properties of the ILG. Under the five-parameter and nine-parameter Mooney-Rivlin models, the formulas for the calculation of the uniaxial tensile stress, plane uniform tensile stress, and 3D directional stress are deduced. The five-parameter and nine-parameter Mooney-Rivlin models of the ILG with a ZrO 2 content of 3 wt% were obtained by uniaxial tensile testing, and the parameters are denoted as c 10 , c 01 , c 20 , c 11 , and c 02 and c 10 , c 01 , c 20 , c 11 , c 02 , c 30 , c 21 , c 12 , and c 03 , respectively. Through the analysis and comparison of the uniaxial tensile stress between the calculated and experimental data, the error between the stress data calculated from the five-parameter Mooney-Rivlin model and the experimental data is less than 0.51%, and the error between the stress data calculated from the nine-parameter Mooney-Rivlin model and the experimental data is no more than 8.87%. Hence, our work presents a feasible and credible formula for the calculation of the stress of the ILG. This work opens a new path to assess the performance of a soft actuator composed of an ILG and will contribute to the optimized design of soft robots.

Conformation-independent structural comparison of macromolecules with ProSMART

International Nuclear Information System (INIS)

Nicholls, Robert A.; Fischer, Marcus; McNicholas, Stuart; Murshudov, Garib N.

2014-01-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Conformation-independent structural comparison of macromolecules with ProSMART

Energy Technology Data Exchange (ETDEWEB)

Nicholls, Robert A., E-mail: nicholls@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Fischer, Marcus [University of California San Francisco, San Francisco, CA 94158 (United States); McNicholas, Stuart [University of York, Heslington, York YO10 5DD (United Kingdom); Murshudov, Garib N. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom)

2014-09-01

The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing

Breath alcohol of anesthesiologists using alcohol hand gel and the "five moments for hand hygiene" in routine practice.

Science.gov (United States)

Lindsay, Helen A; Hannam, Jacqueline A; Bradfield, Charles N; Mitchell, Simon J

2016-08-01

Appropriate hand hygiene reduces hospital-acquired infections. Anesthesiologists work in environments with numerous hand hygiene opportunities (HHOs). In a prospective observational study, we investigated the potential for an anesthesiologist to return a positive alcohol breath test during routine practice when using alcohol hand gel. We observed ten volunteer anesthesiologists over four hours while they implemented the World Health Organization (WHO) "five moments for hand hygiene" using our hospital's adopted standard 70% ethanol hand gel. We measured the expired alcohol concentration at shift start and every fifteen minutes thereafter with a fuel cell breathalyzer calibrated to measure the percentage of blood alcohol concentration (BAC). Blood alcohol specimens (analyzed with gas chromatography) were collected at shift start and, when possible, immediately after a participant's first positive breathalyzer test. Of the 130 breathalyzer tests obtained, there were eight (6.2%) positive breath alcohol results from six of the ten participants, all within two minutes of a HHO. The highest value breathalyzer BAC recorded was 0.064%, with an overall mean (SD) of 0.023 (0.017)%. Five (62.5%) of the positive breathalyzer tests returned to zero in less than seven minutes. All of three blood specimens obtained immediately after a positive breathalyzer reading tested negative for alcohol. Anesthesia practitioners using alcohol hand gel in a manner that conforms with recommended hand hygiene can test positive for alcohol on a breathalyzer assay. Positive tests probably arose from inhalation of alcohol vapour into the respiratory dead space following gel application. If workplace breath testing for alcohol is implemented, it should be completed more than 15 min after applying alcohol hand gel. Positive results should be verified with a BAC test.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

Antimicrobial efficacy of alcohol-based hand gels.

Science.gov (United States)

Guilhermetti, M; Marques Wiirzler, L A; Castanheira Facio, B; da Silva Furlan, M; Campo Meschial, W; Bronharo Tognim, M C; Botelho Garcia, L; Luiz Cardoso, C

2010-03-01

In recent years, several commercial alcohol-based hand gels have appeared on the market to improve the hand-cleansing compliance of healthcare workers. Although the antimicrobial efficacy of these products has been reported in different countries, few studies have investigated this subject in Brazil. In this study, we assessed the antimicrobial efficacy of 12 alcohol-based hand gels produced in Brazil, containing 70% w/w or v/v ethyl alcohol as the active ingredient, according to the European Standard EN 1500 (EN 1500). The following alcohol gels were tested: Hand Gel, Voga Gel, Solumax Solugel, Doctor Clean, Rio Gel, Clear Gel, Sevengel, Hand CHC, Gel Bac, WBL-50 Gel, Sanigel and Soft Care Gel. In addition, 70% w/w ethyl alcohol and three alcohol-based hand rubs (Sterillium, Sterillium Gel, and Spitaderm), commonly used in Europe and effective according to EN 1500, were also tested. All the products tested, except for two, were approved by the EN 1500 test protocol with a 60s application. The results confirmed the antimicrobial efficacy of the majority of the alcohol gels produced in Brazil for hand hygiene of healthcare workers. Copyright 2009 The Hospital Infection Society. Published by Elsevier Ltd. All rights reserved.

Agarose gel electrophoresis and polyacrylamide gel electrophoresis for visualization of simple sequence repeats.

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Anderson, James; Wright, Drew; Meksem, Khalid

2013-01-01

In the modern age of genetic research there is a constant search for ways to improve the efficiency of plant selection. The most recent technology that can result in a highly efficient means of selection and still be done at a low cost is through plant selection directed by simple sequence repeats (SSRs or microsatellites). The molecular markers are used to select for certain desirable plant traits without relying on ambiguous phenotypic data. The best way to detect these is the use of gel electrophoresis. Gel electrophoresis is a common technique in laboratory settings which is used to separate deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) by size. Loading DNA and RNA onto gels allows for visualization of the size of fragments through the separation of DNA and RNA fragments. This is achieved through the use of the charge in the particles. As the fragments separate, they form into distinct bands at set sizes. We describe the ability to visualize SSRs on slab gels of agarose and polyacrylamide gel electrophoresis.

Theoretical NMR and conformational analysis of solvated oximes for organophosphates-inhibited acetylcholinesterase reactivation

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da Silva, Jorge Alberto Valle; Modesto-Costa, Lucas; de Koning, Martijn C.; Borges, Itamar; França, Tanos Celmar Costa

2018-01-01

In this work, quaternary and non-quaternary oximes designed to bind at the peripheral site of acetylcholinesterase previously inhibited by organophosphates were investigated theoretically. Some of those oximes have a large number of degrees of freedom, thus requiring an accurate method to obtain molecular geometries. For this reason, the density functional theory (DFT) was employed to refine their molecular geometries after conformational analysis and to compare their 1H and 13C nuclear magnetic resonance (NMR) theoretical signals in gas-phase and in solvent. A good agreement with experimental data was achieved and the same theoretical approach was employed to obtain the geometries in water environment for further studies.

Sources of variability among replicate samples separated by two-dimensional gel electrophoresis.

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Bland, Alison M; Janech, Michael G; Almeida, Jonas S; Arthur, John M

2010-04-01

Two-dimensional gel electrophoresis (2DE) offers high-resolution separation for intact proteins. However, variability in the appearance of spots can limit the ability to identify true differences between conditions. Variability can occur at a number of levels. Individual samples can differ because of biological variability. Technical variability can occur during protein extraction, processing, or storage. Another potential source of variability occurs during analysis of the gels and is not a result of any of the causes of variability named above. We performed a study designed to focus only on the variability caused by analysis. We separated three aliquots of rat left ventricle and analyzed differences in protein abundance on the replicate 2D gels. As the samples loaded on each gel were identical, differences in protein abundance are caused by variability in separation or interpretation of the gels. Protein spots were compared across gels by quantile values to determine differences. Fourteen percent of spots had a maximum difference in intensity of 0.4 quantile values or more between replicates. We then looked individually at the spots to determine the cause of differences between the measured intensities. Reasons for differences were: failure to identify a spot (59%), differences in spot boundaries (13%), difference in the peak height (6%), and a combination of these factors (21). This study demonstrates that spot identification and characterization make major contributions to variability seen with 2DE. Methods to highlight why measured protein spot abundance is different could reduce these errors.

Textural Properties of Agarose Gels described by FT-Rheology

NARCIS (Netherlands)

Klein, C.O.; Venema, P.; Sagis, L.M.C.; Linden, van der E.

2008-01-01

Large Amplitude Oscillatory Shear was used to determine the non-linear rheological properties of agarose gels. The analysis was performed with the characteristic functions method based on FT-Rheology, that gives access to a physical interpretation of the non-linear regime. This analysis was then

Self Organizing Maps to efficiently cluster and functionally interpret protein conformational ensembles

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Fabio Stella

2013-09-01

Full Text Available An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the original ensembles can be summarized by using only the representative conformations of the clusters obtained. In addition the network components analysis allows to discover and interpret the dynamic behavior of the conformations won by each neuron. The results showed the ability of this approach to efficiently derive a functional interpretation of the protein dynamics described by the original conformational ensemble, highlighting its potential as a support for protein engineering.

Preparation of zirconium molybdate gel for 99mTc gel generator

International Nuclear Information System (INIS)

Aliludin, Z.; Ohkubo, Masatake; Kushita, Kouhei

1988-09-01

Zirconium molybdate gel has excellent characteristics for use as column matrix material of 99m Tc generators. In this work, zirconium molybdate gels were prepared under different conditions; pH's of molybdate solutions from 2.5 to 7.0, Mo:Zr molar ratios from 0.7:1.0 to 1.3:1.0, drying temperatures from an ambient temperature to 200 deg C, and drying times from 1 h to 25 h. Contents of water, nitrate, molybdenum and zirconium were measured to examine the fundamental conditions in gel preparation. The Mo:Zr molar ratio was 1.0:1.0 for the most of gels obtained. A 99m Tc generator was prepared with an amorphous zirconium molybdate containing a tracer level of 99 Mo as column matrix material. Elution of 99m Tc was rapid and the average elution efficiency was 90 % for 6 ml elutions. Contents of radionuclidic impurities, Zr and Mo in the eluates, were low enough to meet the pharmacopoeia requirements for human use. (author)

Sol-gel niobia sorbent with a positively charged octadecyl ligand providing enhanced enrichment of nucleotides and organophosphorus pesticides in capillary microextraction for online HPLC analysis.

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Kesani, Sheshanka; Malik, Abdul

2018-04-01

A niobia-based sol-gel organic-inorganic hybrid sorbent carrying a positively charged C 18 ligand (Nb 2 O 5 -C 18 (+ve)) was synthesized to achieve enhanced enrichment capability in capillary microextraction of organophosphorus compounds (which include organophosphorus pesticides and nucleotides) before their online analysis by high-performance liquid chromatography. The sorbent was designed to simultaneously provide three different types of molecular level interactions: electrostatic, Lewis acid-base, and van der Waals interactions. To understand relative contributions of various molecular level analyte-sorbent interactions in the extraction process, two other sol-gel niobia sorbents were also created: (a) a purely inorganic sol-gel niobia sorbent (Nb 2 O 5 ) and (b) an organic-inorganic hybrid sol-gel niobia sorbent carrying an electrically neutral-bonded octadecyl ligand (Nb 2 O 5 -C 18 ). The extraction efficiency of the created sol-gel niobia sorbent (Nb 2 O 5 -C 18 (+ve)) was compared with that of analogously designed and synthesized titania-based sol-gel sorbent (TiO 2 -C 18 (+ve)), taking into consideration that titania-based sorbents present state-of-the-art extraction media for organophosphorus compounds. In capillary microextraction with high-performance liquid chromatography analysis, Nb 2 O 5 -C 18 (+ve) had shown 40-50% higher specific extraction values (a measure of extraction efficiency) over that of TiO 2 -C 18 (+ve). Compared to TiO 2 -C 18 (+ve), Nb 2 O 5 -C 18 (+ve) also provided superior analyte desorption efficiency (96 vs. 90%) during the online release of the extracted organophosphorus pesticides from the sorbent coating in the capillary microextraction capillary to the chromatographic column using reversed-phase high-performance liquid chromatography mobile phase. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In-gel detection of esterase-like albumin activity: Characterization of esterase-free sera albumin and its putative role as non-invasive biomarker of hepatic fibrosis

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Areeba Ahmad

2017-07-01

Full Text Available Albumin is a globular and un-glycosylated multifunctional plasma protein and thus correlated with several human diseases. Owing to esterase contamination, albumin levels are usually misleading. In this study, we propose methodical accuracy for albumin estimation taking healthy and fibrotic rats. Liver fibrosis in rats was generated by N′-Nitrosodimethylamine (NDMA (10 mg/kg body weight within three weeks followed by its confirmation through H&E and immunohistochemical staining for α-SMA expression. Animal sera were screened by native polyacrylamide gel electrophoresis (native-PAGE (7.5%. In-gel esterase-like albumin activity was detected using α- and β-naphthyl acetate (5.58 × 10−3 mM; pH 7.5 as substrate. Sera albumin was purified from unstained PA gel-slices through electroelution. Subsequent to conformation of albumin purity by its molecular weight determination using SDS–PAGE (10% and peptide mass fingerprinting by MALDI-TOF-MS, samples were treated with different concentrations of urea. Urea-treated albumins were screened for esterase activity, conformational change and, albumin levels by immunoblotting. Our results demonstrate that esterase-like albumin activity in rat sera albumin is located in domain-III. The esterase-like activity remains detectable up to 4 M urea, which diminishes with increasing urea concentrations. Further, immunoblotting of urea-treated albumin samples displays a significant decline in purified protein bands, indicating hypoalbuminemia during hepatic fibrosis in rats. In conclusion, the present approach of albumin separation and estimation is of potential interest and may be recommended for diagnostic purposes.

Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis

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Hsu Kimberly K

2005-06-01

Full Text Available Abstract Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensional analyses of human erythrocyte membranes, mouse liver membranes, and mouse brain membranes, extracted with buffers that included the zwitterionic detergent MEGA 10 (decanoyl-N-methylglucamide and the zwitterionic lipid LPC (1-lauroyl lysophosphatidylcholine, showed selective improvement over extraction with the common 2-DE detergent CHAPS (3 [(3-cholamidopropyldimethylammonio]-1-propanesulfonate. Mixtures of the three detergents showed additive improvements in spot number, density, and resolution. Substantial improvements in the analysis of a brain membrane proteome were observed. Conclusion This study demonstrates that an optimized detergent mix, coupled with rigorous sample handling and electrophoretic protocols, enables simple and effective analysis of membrane proteomes using two-dimensional electrophoresis.

Conformal superalgebras via tractor calculus

Science.gov (United States)

Lischewski, Andree

2015-01-01

We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

Bacterial analysis of combined periodontal-endodontic lesions by polymerase chain reaction-denaturing gradient gel electrophoresis.

Science.gov (United States)

Xia, Minghui; Qi, Qingguo

2013-01-01

We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.

Preference of small molecules for local minimum conformations when binding to proteins.

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Qi Wang

2007-09-01

Full Text Available It is well known that small molecules (ligands do not necessarily adopt their lowest potential energy conformations when binding to proteins. Analyses of protein-bound ligand crystal structures have reportedly shown that many of them do not even adopt the conformations at local minima of their potential energy surfaces (local minimum conformations. The results of these analyses raise a concern regarding the validity of virtual screening methods that use ligands in local minimum conformations. Here we report a normal-mode-analysis (NMA study of 100 crystal structures of protein-bound ligands. Our data show that the energy minimization of a ligand alone does not automatically stop at a local minimum conformation if the minimum of the potential energy surface is shallow, thus leading to the folding of the ligand. Furthermore, our data show that all 100 ligand conformations in their protein-bound ligand crystal structures are nearly identical to their local minimum conformations obtained from NMA-monitored energy minimization, suggesting that ligands prefer to adopt local minimum conformations when binding to proteins. These results both support virtual screening methods that use ligands in local minimum conformations and caution about possible adverse effect of excessive energy minimization when generating a database of ligand conformations for virtual screening.

Ophthalmic gels: Past, present and future.

Science.gov (United States)

Al-Kinani, Ali A; Zidan, Ghada; Elsaid, Naba; Seyfoddin, Ali; Alani, Adam W G; Alany, Raid G

2018-02-15

Aqueous gels formulated using hydrophilic polymers (hydrogels) along with those based on stimuli responsive polymers (in situ gelling or gel forming systems) continue to attract increasing interest for various eye health-related applications. They allow the incorporation of a variety of ophthalmic pharmaceuticals to achieve therapeutic levels of drugs and bioactives at target ocular sites. The integration of sophisticated drug delivery technologies such as nanotechnology-based ones with intelligent and environment responsive systems can extend current treatment duration to provide more clinically relevant time courses (weeks and months instead of hours and days) which will inevitably reduce dose frequency, increase patient compliance and improve clinical outcomes. Novel applications and design of contact lenses and intracanalicular delivery devices along with the move towards integrating gels into various drug delivery devices like intraocular pumps, injections and implants has the potential to reduce comorbidities caused by glaucoma, corneal keratopathy, cataract, diabetic retinopathies and age-related macular degeneration. This review describes ophthalmic gelling systems with emphasis on mechanism of gel formation and application in ophthalmology. It provides a critical appraisal of the techniques and methods used in the characterization of ophthalmic preformed gels and in situ gelling systems along with a thorough insight into the safety and biocompatibility of these systems. Newly developed ophthalmic gels, hydrogels, preformed gels and in situ gelling systems including the latest in the area of stimuli responsive gels, molecularly imprinted gels, nanogels, 3D printed hydrogels; 3D printed devices comprising ophthalmic gels are covered. Finally, new applications of gels in the production of artificial corneas, corneal wound healing and hydrogel contact lenses are described. Copyright © 2017 Elsevier B.V. All rights reserved.

Strength of interactions between immobilized dye molecules and sol-gel matrices.

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Ismail, Fanya; Schoenleber, Monika; Mansour, Rolan; Bastani, Behnam; Fielden, Peter; Goddard, Nicholas J

2011-02-21

In this paper we present a new theory to re-examine the immobilization technique of dye doped sol-gel films, define the strength and types of possible bonds between the immobilized molecule and sol-gel glass, and show that the immobilized molecule is not free inside the pores as was previously thought. Immobilizing three different pH sensitive dyes with different size and functional groups inside the same sol-gel films revealed important information about the nature of the interaction between the doped molecule and the sol-gel matrix. The samples were characterized by means of ultraviolet-visible spectrophotometer (UV-VIS), thermal gravimetric analysis (TGA), mercury porosimetry (MP), nuclear magnetic resonance spectroscopy ((29)Si NMR) and field-emission environmental scanning electron microscopy (ESEM-FEG). It was found that the doped molecule itself has a great effect on the strength and types of the bonds. A number of factors were identified, such as number and types of the functional groups, overall charge, size, pK(a) and number of the silanol groups which surround the immobilized molecule. These results were confirmed by the successful immobilization of bromocresol green (BCG) after a completely polymerized sol-gel was made. The sol-gel consisted of 50% tetraethoxysilane (TEOS) and 50% methyltriethoxysilane (MTEOS) (w/w). Moreover, the effect of the immobilized molecule on the structure of the sol-gel was studied by means of a leaky waveguide (LW) mode for doped films made before and after polymerization of the sol-gel.

Conformational elasticity can facilitate TALE-DNA recognition.

Science.gov (United States)

Lei, Hongxing; Sun, Jiya; Baldwin, Enoch P; Segal, David J; Duan, Yong

2014-01-01

Sequence-programmable transcription activator-like effector (TALE) proteins have emerged as a highly efficient tool for genome engineering. Recent crystal structures depict a transition between an open unbound solenoid and more compact DNA-bound solenoid formed by the 34 amino acid repeats. How TALEs switch conformation between these two forms without substantial energetic compensation, and how the repeat-variable di-residues (RVDs) discriminate between the cognate base and other bases still remain unclear. Computational analysis on these two aspects of TALE-DNA interaction mechanism has been conducted in order to achieve a better understanding of the energetics. High elasticity was observed in the molecular dynamics simulations of DNA-free TALE structure that started from the bound conformation where it sampled a wide range of conformations including the experimentally determined apo and bound conformations. This elastic feature was also observed in the simulations starting from the apo form which suggests low free energy barrier between the two conformations and small compensation required upon binding. To analyze binding specificity, we performed free energy calculations of various combinations of RVDs and bases using Poisson-Boltzmann surface area (PBSA) and other approaches. The PBSA calculations indicated that the native RVD-base structures had lower binding free energy than mismatched structures for most of the RVDs examined. Our theoretical analyses provided new insight on the dynamics and energetics of TALE-DNA binding mechanism. © 2014 Elsevier Inc. All rights reserved.

Gel electrophoresis of inorganic cations

International Nuclear Information System (INIS)

Schoenhofer, F.; Grass, F.

1978-01-01

In order to be able to separate the largest possible amounts of substance, polyacryl amide gel (PAA) and silica gel are used as carrier for the electrophoresis. Milligramme quantities can easily be separated on PAA gel plates. Electrophoretic ion focussing considerably improves it. Separations of Sr/Y and lanthanoids were carried out. The behaviour of the readily soluble complexing agent acids on silica gel thin layers was minutely investigated and an interpretation of the focussing effect was derived. The conditions for separating radionuclides were optimized. A further improved separation can be achieved by a time sequence combination of normal electrophoresis and ion focussing. Selective isolation methods are advantageous to determine radionuclide traces in environmental samples. The selective adsorption on preformed deposits was transferred to electrophoresis. After pre-investigations on silica gel layers, strontium and barium could also be retained on PAA gel and radium on strontium sulphate in PAA, whereas the disturbing calcium can easily pass through. Cesium can also be retained by prussian blue in the electrophoresis. (orig.) [de

Initial investigation of a novel light-scattering gel phantom for evaluation of optical CT scanners for radiotherapy gel dosimetry

International Nuclear Information System (INIS)

Bosi, Stephen; Naseri, Pourandokht; Puran, Alicia; Davies, Justin; Baldock, Clive

2007-01-01

There is a need for stable gel materials for phantoms used to validate optical computerized tomography (CT) scanners used in conjunction with radiation-induced polymerizing gel dosimeters. Phantoms based on addition of light-absorbing dyes to gelatine to simulate gel dosimeters have been employed. However, to more accurately simulate polymerizing gels one requires phantoms that employ light-scattering colloidal suspensions added to the gel. In this paper, we present the initial results of using an optical CT scanner to evaluate a novel phantom in which radiation-exposed polymer gels are simulated by the addition of colloidal suspensions of varying turbidity. The phantom may be useful as a calibration transfer standard for polymer gel dosimeters. The tests reveal some phenomena peculiar to light-scattering gels that need to be taken into account when calibrating polymer gel dosimeters

Conformal sequestering simplified

International Nuclear Information System (INIS)

Schmaltz, Martin; Sundrum, Raman

2006-01-01

Sequestering is important for obtaining flavor-universal soft masses in models where supersymmetry breaking is mediated at high scales. We construct a simple and robust class of hidden sector models which sequester themselves from the visible sector due to strong and conformally invariant hidden dynamics. Masses for hidden matter eventually break the conformal symmetry and lead to supersymmetry breaking by the mechanism recently discovered by Intriligator, Seiberg and Shih. We give a unified treatment of subtleties due to global symmetries of the CFT. There is enough review for the paper to constitute a self-contained account of conformal sequestering

Chiral supramolecular organization from a sheet-like achiral gel: a study of chiral photoinduction.

Science.gov (United States)

Royes, Jorge; Polo, Víctor; Uriel, Santiago; Oriol, Luis; Piñol, Milagros; Tejedor, Rosa M

2017-05-31

Chiral photoinduction in a photoresponsive gel based on an achiral 2D architecture with high geometric anisotropy and low roughness has been investigated. Circularly polarized light (CPL) was used as a chiral source and an azobenzene chromophore was employed as a chiral trigger. The chiral photoinduction was studied by evaluating the preferential excitation of enantiomeric conformers of the azobenzene units. Crystallographic data and density functional theory (DFT) calculations show how chirality is transferred to the achiral azomaterials as a result of the combination of chiral photochemistry and supramolecular interactions. This procedure could be applied to predict and estimate chirality transfer from a chiral physical source to a supramolecular organization using different light-responsive units.

Condensation of Counterions Gives Rise to Contraction Transitions in a One-Dimensional Polyelectrolyte Gel

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Gerald S. Manning