bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Equalizer™ Technology : The quest for a “democratic proteome”
Authors: Righetti Pier Giorgio , Boschetti Egisto , Lomas Lee , Citterio Attilio 
Published: June 2006

AbstractNo proteome can be considered “democratic”, but rather “oligarchic”, since a few proteins dominate the landscape and often obliterate the signal of the rare ones. This is the reason why most scientists lament that, in proteome analysis, the same set of abundant proteins is seen again and again. A host of pre‐fractionation techniques have been described, but all of them, one way or another, are besieged by problems, in that they are based on a “depletion principle”, i.e. getting rid of the unwanted species. Yet “democracy” calls not for killing the enemy, but for giving “equal rights” to all people. One way to achieve that would be the use of “Protein Equalizer Technology” for reducing protein concentration differences. This comprises a diverse library of combinatorial ligands coupled to spherical porous beads. When these beads come into contact with complex proteomes (e.g. human urine and serum, egg white, and any cell lysate, for that matter) of widely differing protein composition and relative abundances, they are able to “equalize” the protein population, by sharply reducing the concentration of the most abundant components, while simultaneously enhancing the concentration of the most dilute species. It is felt that this novel method could offer a strong step forward in bringing the “unseen proteome” (due to either low abundance and/or presence of interference) within the detection capabilities of current proteomics detection methods. Examples are given of equalization of human urine and serum samples, resulting in the discovery of a host of proteins never reported before. Additionally, these beads can be used to remove host cell proteins from purified recombinant proteins or protein purified from natural sources that are intended for human consumption. These proteins typically reach purities of the order of 98%: higher purities often become prohibitively expensive. Yet, if incubated with “equalizer beads”, these last impurities can be effectively removed at a small cost and with minute losses of the main, valuable product.
Mass spectrometric analysis of formalin‐fixed paraffin‐embedded tissue: Unlocking the proteome within
Authors: Hood Brian L. , Conrads Thomas P. , Veenstra Timothy D. 
Published: June 2006

AbstractThe predominance of tissues stored worldwide in hospitals and clinical laboratories exist in formalin‐fixed paraffin‐embedded (FFPE) blocks that are generated by simple and well‐established protocols. Although generation of FFPE tissues has facilitated their characterization by such techniques as histopathology, they have proven refractory to biomarker discovery investigations using state‐of‐the‐art MS‐based proteomic methodologies. Very recently new methods have been developed that enable proteins extracted from FFPE tissues to be analyzed by MS. This review will highlight and discuss those efforts that have led to this exciting recent progress. Although these developments are quite new, the ability to conduct MS‐based proteomic analyses of FFPE tissues opens heretofore intractable clinical samples for discovery‐based biomarker research.
A high efficiency cloning and expression system for proteomic analysis
Authors: Ding Xuan Z. , Paulsen Ian T. , Bhattacharjee Apurba K. , Nikolich Mikeljon P. , Myers Gary , Hoover David L. 
Published: June 2006

AbstractThe recent description of the complete genomes of the two most pathogenic species of Brucella opens the way for genome‐based analysis of the antigenicity of their proteins. In the present report, we describe a bench‐level high‐efficiency cloning and expression system (HECES) that allow expression of large numbers of Brucella proteins based on genomic sequence information. Purified proteins are produced with high efficiency in a microarray format conducive to analysis of their sero‐reactivity against serum from immunized animals. This method is applicable at either small or large scale of protein processing. While it does not require robotics, the format is amenable to robotic implementation for all aspects of the process and subsequent analysis of protein characteristics. This method will allow selection of new reagents for diagnosis of brucellosis and development of vaccine against Brucella, an important zoonotic disease and biothreat agent.
Preparation and properties of polyhedral oligosilsequioxane tethered aromatic polyamide nanocomposites through Michael addition between maleimide‐containing polyamides and an amino‐functionalized polyhedral oligosilsequioxane
Authors: Liu Ying‐Ling , Lee Hui‐Chen 
Published: June 2006

AbstractPolyhedral oligosilsequioxane (POSS) tethered aromatic polyamide nanocomposites with various POSS fractions were prepared through Michael addition between maleimide‐containing polyamides and amino‐functionalized POSS. The chemical structures of the polyamide–POSS nanocomposites were characterized with Fourier transform infrared and 1H NMR. The polyamide–POSS nanocomposites exhibited good homogeneity in scanning electron microscopy and transmission electron microscopy observations. POSS modification increased the storage modulus and Young's modulus of the polyamides, slightly decreased their glass‐transition temperatures from 312 to 305 °C, and significantly lowered their dielectric constants from 4.45 to 3.35. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4632–4643, 2006
Synthesis, rheology, and morphology of nylon‐11/layered silicate nanocomposite
Authors: Zhang Xikui , Yang Guisheng , Lin Jiaping 
Published: June 2006

AbstractExfoliated nylon‐11/layered silicate nanocomposites were prepared via in situ polymerization by dispersing organoclay in 11‐aminoundecanoic acid monomer. The original clay was modified by a novel method with 11‐aminoundecanoic acid. In situ Fourier transform infrared spectroscopy results show that stronger hydrogen bonds exist between nylon‐11 and organoclay than that of between nylon‐11 and original clay. The linear dynamic viscoelasticity of organoclay nanocomposites was investigated. Before taking rheological measurements, the exfoliated and intercalating structures and the thermal properties were characterized using X‐ray diffraction, transmission electron microscopy, differential scanning calorimetry, and thermogravimetric analysis. The results show that the clay was uniformly distributed in nylon‐11 matrix during in situ polymerization of clay with 4 wt % or less. The presence of clay in nylon‐11 matrix increased the crystallization temperature and the thermal stability of nanocomposites prepared. Rheological properties such as storage modulus, loss modulus, and relative viscosity have close relationship with the dispersion favorably compatible with the organically modified clay. Comparing with neat nylon‐11, the nanocomposites show much higher dynamic modulus and stronger shear thinning behavior. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2161–2172, 2006
In situ FT‐Raman spectroscopic study of the conformational changes occurring in isotactic polypropylene during its melting and crystallization processes
Authors: Khafagy Rasha M. 
Published: June 2006

AbstractThe conformational changes occurring in isotactic polypropylene during the melting and crystallization processes have been carefully investigated using FT‐Raman spectroscopy at temperatures below, at, and above the polymer melting point. Results confirmed the retention of some crystallinity up to +210 °C, which is 50 °C above the melting point. It was found that, at temperatures just above the melting point (1–10 °C), there is still some short range order of at least 12 monomer units long in certain regions of the melt. At 10 °C above the melting point, the short range order drops below 12 monomer units resulting in the disappearance of the Raman band at 841 cm–1. Vice versa, the experimental measurements show that the iPP melt system is stable when the persistence length of helical sequences is less than 12 monomer units. As soon as the helix length exceeds 12 units, the 31 helix conformation extends quickly and then crystallization occurs. These results are discussed in terms of Imai's microphase separation theory and it agreed very well with it. Also, from our observations for correlation splitting, Raman bands related to conformational states were identified. This analysis indicates the existence of three different conformational states at 808, 830, and 841 cm–1. The 808 cm–1 band was assigned to helical chains within crystals (representing crystalline phase). The 841 cm–1 band was shown to be composed of a band at 841 cm–1, assigned to shorter chains in helical conformation with isomeric defects (representing the isomeric defect phase), and a broader band at 830 cm–1 assigned to chains in nonhelical conformation (representing the melt‐like amorphous phase). This indicates the detection of a three‐phase structure in iPP, where a third phase could be due to the presence of defect regions within the crystalline region, or due to the presence of an amorphous–crystal interphase. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2173–2182, 2006
Synthesis, Characterization and Optical Property of Novel Conjugated Polynitrile
Authors: Zhao Xiong‐Yan , Wang Ming‐Zhu , Xiao Ji‐Jun , Wang Zhi 
Published: June 2006

AbstractSummary: A novel conjugated polynitrile, plasma‐polymerized 1‐isoquinolinecarbonitrile (PPIQCN) was prepared by plasma polymerization for the first time. The structure and surface compositions of the deposited PPIQCN thin films were investigated by Fourier Transform Infrared (FTIR), UV‐Visible absorption and X‐ray Photoelectron Spectroscopy (XPS). The results show that extensively conjugated CN double bonds were formed in PPIQCN films during the plasma polymerization of 1‐isoquinolinecarbonitrile. An obvious red shift of more than 120 nm in the maximum absorption wavelength (λmax) for PPIQCN films as compared with the monomer absorption spectrum was observed. To check the possibility of applying the PPIQCN films as optical devices, photoluminescence (PL) measurements were also carried out and a maximum PL emission intensity was observed at about 458 nm.Photoluminescence spectrum of the PPIQCN18 thin film.magnified imagePhotoluminescence spectrum of the PPIQCN18 thin film.
Non Intrusive Mercury Porosimetry: Pyrolysis of Resorcinol‐Formaldehyde Xerogels
Authors: Job Nathalie , Pirard René , Pirard Jean‐Paul , Alié Christelle 
Published: June 2006

AbstractWhen submitted to mercury porosimetry, some materials are penetrated by mercury whereas others, among the most porous, are densified by the isostatic pressure. Notably, this is the case for materials whose structure is made of particles aggregated into filament‐like clusters that are interconnected in a 3‐D array. Indeed, that kind of material undergoes a volume variation due to hierarchical pore collapse. In the case of intrusion, the mercury porosimetry data are classically analyzed by the Washburn equation. In the case of hierarchical pore collapse, data can be correctly analyzed by the collapse model equation. Using an equation that does not correspond to the mechanism leads to large errors in the pore size distribution. Thus, an accurate data analysis requires prior determination of the mechanism leading to the volume variation recorded as a function of the pressure. The present work particularly examines the complex and unusual behavior of partially pyrolyzed resorcinol‐formaldehyde gels when submitted to mercury porosimetry. The unusual behavior encountered complicates the mechanism identification and, therefore, the equation selection. However, the major part of the volume distribution as a function of the pore size can be determined with a good accuracy.
Using Nano‐Cast Model Porous Media and Integrated Gas Sorption to Improve Fundamental Understanding and Data Interpretation in Mercury Porosimetry
Authors: Rigby Sean P. , Evbuomwan Irene O. , Watt‐Smith Matthew J. , Edler Karen , Fletcher Robin S. 
Published: June 2006

AbstractThe mechanisms of entrapment, and the nanoscopic spatial distribution, of the residual mercury within nano‐cast and amorphous porous media (pore sizes ~1–100 nm) following high‐pressure penetration have been studied. It has been shown that, even at the nano‐scale, one of the same two principle mechanisms that have been observed previously in mercury porosimetry experiments on macroscopic glass pore models also occur within a given amorphous, nanoporous solid. Using percolation theory to interpret novel, integrated gas sorption experiments, entrapment was shown to arise, either because of the presence of sufficiently narrow pore necks interspersed between larger voids, or due to non‐random, longer‐range structural heterogeneity. The threshold "snap‐off" ratio parameter for the entrapment process has also been directly measured but found to be considerably smaller than seen previously for macroporous materials. The techniques employed here enable information not previously available for nanoporous systems to be determined, and therefore to be incorporated into simulations of mercury porosimetry on those materials.
Application of Mercury Porosimetry to Predict the Porosity and Strength of Ceramic Catalyst Supports
Authors: Yates Malcolm 
Published: June 2006

AbstractCeramic based monolithic supports are used in many catalytic reactions, especially in environmental remediation to avoid pressure drop limitations that may arise in the treatment of large effluent gas volumes. In these systems, the active phases or their precursors can be incorporated into the paste prior to kneading, extrusion and calcination, in order to achieve a uniform deposition throughout the final structure. However, these types of incorporated monolithic catalysts can suffer from diffusion limitations that necessitate the inclusion of temporary agents, which when removed by thermal treatments, generate a higher porosity. This results in an increase in the interconnectivity of the pore structure of the final material. However, an upper limit is reached since an increased porosity negatively affects the mechanical strength of these ceramic materials. In this paper, the mechanical strength and porosity of ceramic catalyst supports are related to the primary particle size of the raw materials, initial composition and final heat treatment temperature.
Multi‐template approach to modeling engineered disulfide bonds
Authors: Pellequer Jean‐Luc , Chen Shu‐wen W. 
Published: June 2006

AbstractThe key issue for disulfide bond engineering is to select the most appropriate location in the protein. By surveying the structure of experimentally engineered disulfide bonds, we found about half of them that have geometry incompatible with any native disulfide bond geometry. To improve the current prediction methods that tend to apply either ideal geometrical or energetical criteria to single three‐dimensional structures, we have combined a novel computational protocol with the usage of multiple protein structures to take into account protein backbone flexibility. The multiple structures can be selected from either independently determined crystal structures for identical proteins, models of nuclear magnetic resonance experiments, or crystal structures of homology‐related proteins. We have validated our approach by comparing the predictions with known disulfide bonds. The accuracy of prediction for native disulfide bonds reaches 99.6%. In a more stringent test on the reported engineered disulfide bonds, we have obtained a success rate of 93%. Our protocol also determines the oxido‐reduction state of a predicted disulfide bond and the corresponding mutational cost. From the energy ranking, the user can easily choose top predicted sites for mutagenesis experiments. Our method provides information about local stability of the engineered disulfide bond surroundings. Proteins 2006. © 2006 Wiley‐Liss, Inc.
The effect of Echinacea purpurea, Astragalus membranaceus and Glycyrrhiza glabra on CD69 expression and immune cell activation in humans
Authors: Brush Julie , Mendenhall Elissa , Guggenheim Alena , Chan Tracy , Connelly Erin , Soumyanath Amala , Buresh Randal , Barrett Richard , Zwickey Heather 
Published: June 2006

AbstractThe increasing use of medicinal herbs among the general public has piqued the need for scientific‐based research to determine the mechanism of action of herbs administered orally in human subjects. The ability of three herbs, Echinacea purpurea, Astragalus membranaceus and Glycyrrhiza glabra, to activate immune cells in human subjects was assessed in this pilot study. The effect of these herbs when ingested for 7 days was measured both when administered singly, and in combination, using flow cytometry. The primary cell activation marker measured was CD69. The results demonstrate that Echinacea, Astragalus and Glycyrrhiza herbal tinctures stimulated immune cells as quantified by CD69 expression on CD4 and CD8 T cells. This activation took place within 24 h of ingestion, and continued for at least 7 days. In addition, these three herbs had an additive effect on CD69 expression when used in combination. Copyright © 2006 John Wiley & Sons, Ltd.
Excitation of the a1Πg and B3Πg electronic states of the nitrogen molecule by electron impact
Authors: Da Costa R. F. , Lima M. A. P. 
Published: June 2006

AbstractAb initio calculations were performed for the excitations of the a1Πg and B3Πg electronic states of the N2 molecule by impact of low‐energy electrons. The scattering amplitudes were obtained by means of the Schwinger multichannel method within the scope of the minimal orbital basis for the single configuration interactions (MOB‐SCI) approach. Through the use of the MOB‐SCI strategy, we have investigated the coupling effects among ground state, first singlet, and first triplet excited states of the Πg symmetry. Integral and differential cross sections are shown for impact energies from near threshold up to 30 eV. Present results are compared with SMC two‐state calculations and also with available theoretical and experimental data. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Electronic structure study of the reaction C2H → C2H + H2
Authors: Costa Fabio 
Published: June 2006

AbstractThe photoionization of ethylene (C2H4) and the behavior of the molecular ion (C2H) in its diverse electronic states have been subject of numerous experimental and theoretical studies. The first ethylene cation fragments from the dissociative process; i.e., acetylene cation (C2H) and vinyl cation (C2H), appear on the second ionization band. The papers in literature, though enlightening, leave behind some unclarified points and doubts about the C2H → C2H + H2 dissociative process. As for example: whether some energetic barriers exist or not along the steps followed. Hence, the main goal of this paper is to carry out a systematic research on the C2H → C2H + H2 dissociative process using quality electronic structure calculations to determine the least energy pertinent pathway and to characterize the stationary points along this pathway. Geometry optimization and vibrational frequencies calculations were carried out at the B3LYP, MP2 and CCSD (T) using the 6‐311G(d,p) basis set. To establish the stationary points connectivity in the transitional states, characterized as the first order saddle point, intrinsic reaction coordinate (IRC) calculations were performed. In order to obtain more accurate electronic energies, single point calculations were performed at the CCSD(T)/6‐311++G(3d,2p) theoretical level in the CCSD(T)/6‐311G(d,p) optimized geometries. All energies were corrected for zero point energy (ZPE) contributions, calculated at the CCSD)(T)/6‐311G(d,p) level. Calculated AE at high theoretical level, CCSD(T)/6‐311++G(3df,2p)//CCSD(T)/6‐311 G(d,p), presents an excellent concurrence with the experimental values. More accurate barrier energies are established using CCSD(T)/6‐311++G(3df,2p)//CCSD(T)/6‐311G(d,p) level. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Falciform Ligament in the Management of the Residual Cavity for Liver Hydatidosis: New Surgical Technique
Authors: Ozmen M. Mahir , Coskun Faruk , Ziraman Ipek 
Published: June 2006

AbstractIntroductionHydatid disease is a common condition worldwide and continues to be a significant societal problem in many countries of all continents. Alhough other treatment options are also available, surgery remains the cornerstone of therapy for hepatic hydatid disease. Omentoplasty seems to be an efficient technique for managing the residual cavity, but it has some shortcomings and might be difficult in secondary cases. Therefore we describe a new technique using the falciform ligament as a flap instead of omentum for managing the residual cavity, as it is more anatomic and a better option for liver cysts.MethodsFrom April 2004 to October 2005, a total of 20 patients (11 women) with a median age of 43 years (range 23–66 years) underwent partial cystectomy‐falciformoplasty for hydatid liver disease. The falciform ligament was prepared as a flap in all patients during the initial step of the operation and, after partial cystectomy and evacuation of the cystic components, the flap was inserted into the cystic cavity and fixed with sutures. A single drain was inserted into the subhepatic area.ResultsCysts were located in the right lobe of the liver in 14 patients and mean diameter of the cyst was 10 cm (range 7–25 cm). The mean duration of the operation was 40 minutes (range 35–69 minutes), and the mean postoperative hospital stay was 4 days (range 3–7 days). None of the patients had any major complications. Only two patients had persistent drainage for 7 days, which stopped spontaneously. The median follow‐up was 9 months (range 2–19 months). Patients underwent duplex ultrasonography (US) to check the viability of the flap and the residual cavity at 1 week, 1 month, and 3 months postoperatively. US did not reveal any collection, the cavities were fully collapsed, and blood flow to the falciform ligaments was seen to be viable.ConclusionsUsing the falciform ligament as a flap for management of the residual cavity is an easy, safe, effective new technique with few complications. It might be a good choice in patients with hydatid liver disease.