bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo‐Electron Tomography for Structural Characterization of Macromolecular Complexes
Authors: Cope Julia , Heumann John , Hoenger Andreas 
Published: August 2011

AbstractCryo‐electron tomography (cryo‐ET) is an emerging 3‐D reconstruction technology that combines the principles of tomographic 3‐D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo‐ET is particularly suited to investigating cell‐biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging‐based 3‐D reconstruction procedures. This unit aims to make cryo‐ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo‐ET. Protocols describe specimen preparation, data recording and 3‐D data reconstruction for cryo‐ET, with a special focus on macromolecular complexes. A step‐by‐step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt‐series acquisition for cryo‐ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo‐tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal‐to‐noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. Curr. Protoc. Protein Sci. 65:17.13.1‐17.13.31. © 2011 by John Wiley & Sons, Inc.
Identification of Protein‐Protein Interactions by Surface Plasmon Resonance followed by Mass Spectrometry
Authors: Madeira Alexandra , Vikeved Elisabet , Nilsson Anna , Sjögren Benita , Andrén Per E. , Svenningsson Per 
Published: August 2011

AbstractElucidation of the function and meaning of the protein networks can be useful in the understanding of many pathological processes and the identification of new therapeutic targets. This unit describes an approach to discover protein‐protein interactions by coupling surface plasmon resonance to mass spectrometry. Briefly, a protein is covalently bound to a sensor chip, which is then exposed to brain extracts injected over the surface via a microfluidic system. This allows the monitoring in real‐time of the interactions between the immobilized ligand and the extracts. Interacting proteins from the extracts are then recovered, trypsinized, and identified using mass spectrometry. The data obtained are searched against a sequence database using the Mascot software. To exclude nonspecific interactors, control experiments using blank sensor chips, and/or randomized peptides, are performed. The protocol presented here does not require specific labeling or modification of proteins and can be performed in <4 days. Curr. Protoc. Protein Sci. 65:19.21.1‐19.21.9. © 2011 by John Wiley & Sons, Inc.
Peptide Extraction from Formalin‐Fixed Paraffin‐Embedded Tissue
Authors: Heaton Katherine J. , Master Stephen R. 
Published: August 2011

AbstractThis unit describes how to extract tryptic peptides from formalin‐fixed, paraffin‐embedded (FFPE) tissues for analysis using nano‐reverse‐phase liquid chromatography/tandem mass spectrometry (nRPLC‐MS/MS). The tissues are deparaffinized in the first protocol. Following deparaffinization, the cells are harvested via one of two methods: needle dissection or laser capture microdissection (LCM). Needle dissection is performed using hydrated, unstained tissue, whereas LCM is performed with dehydrated, hematoxylin‐stained tissue. Heat is applied to the collected cells to reverse the cross‐links that have formed during the formalin fixation process. Finally, the cells are digested using filter‐aided sample preparation, in which buffers are exchanged throughout the process. An alternate protocol using commercially available Liquid Tissue is also described. These samples are then ready for mass spectrometric analysis. Curr. Protoc. Protein Sci. 65:23.5.1‐23.5.19. © 2011 by John Wiley & Sons, Inc.
Fast Relaxation Imaging in Living Cells
Authors: Dhar Apratim , Gruebele Martin 
Published: August 2011

AbstractThis protocol describes the technique of Fast Relaxation Imaging (FReI) as applied to protein folding inside living cells. The required modifications of a fluorescence microscope by addition of a diode laser temperature jump source, a yellow/blue switchable light‐emitting diode source, and a two‐color CCD camera to collect movies of protein dynamics inside cells are discussed. A description of how proteins are labeled for imaging, how cells are prepared for imaging, and how imaging of kinetics inside cells with millisecond time resolution is obtained, along with the complementary in vitro experiments, is also provided. The ability to carry out comparative in vitro and “in‐cell” measurements on the same setup allows for direct comparison of the features distinguishing cellular protein folding (or other biomolecular processes) from studies performed in dilute solution. Curr. Protoc. Protein Sci. 65:28.1.1‐28.1.19. © 2011 by John Wiley & Sons, Inc.
Strain Mismatch Induced Tilted Heteroepitaxial (000l) Hexagonal ZnO Films on (001) Cubic Substrates
Authors: Kang Bo Soo , Stan Liliana , Usov Igor O. , Lee Jung‐Kun , Harriman Tres A. , Lucca Don A. , DePaula Raymond F. , Arendt Paul N. , Nastasi Michael , MacManus‐Driscoll Judith L. , Park Bae Ho , Jia Quanxi 
Published: August 2011

AbstractA novel strain mismatch induced tilted epitaxy method has been demonstrated for producing high quality (000l) hexagonal films on (001) cubic substrates. Highly oriented hexagonal (000l) ZnO films are grown on cubic (001) MgO substrates using Sm0.28Zr0.72O2−δ (SZO) as a template. The large lattice mismatch of >13% between the obvious crystallographic matching directions of the template and substrate means that cube‐on‐cube epitaxy is energetically unfavorable, leading to growth instead of two high index, low energy compact planes, close to the {111} orientation. These planes give three different in‐plane orientations resulting from coincidence site lattice matching (12 in‐plane orientations in total) and provide a pseudo‐hexagonal symmetry surface for the ZnO to grow on. The texture of the ensuing (000l) ZnO layer is markedly improved over the template. The work opens up both a new avenue for growing technologically important hexagonal structures on a range of readily available, (001) cubic substrates, as well as showing that there are wide possibilities for heteroepitaxial growth of a range of dissimilar materials.
A New Variant Selection Criterion for Twin Variants in Titanium Alloys (Part 1)
Authors: Schuman Christophe , Bao Lei , Sébastien Lecomte Jean , Zhang Yudong , Marc Raulot Jean , Jeanne Philippe Marie , Esling Claude 
Published: August 2011

AbstractA new selection criterion to explain the activation of the twinning variant is proposed based on the calculation of the deformation energy to create a primary twin. The calculation takes into account the effect of the grain size using a Hall‐Petch type relation. This criterion allows to obtain a very good prediction for the variant selection. The calculations are compared with the experimental results obtained on T40 deformed by Channel Die compression.
Elevated serum free light chains are associated with inferior event free and overall survival in Hodgkin lymphoma
Authors: Thompson Carrie A. , Maurer Matthew J. , Cerhan James R. , Katzmann Jerry A. , Ansell Stephen M. , Habermann Thomas M. , Macon William R. , Weiner George J. , Link Brian K. , Witzig Thomas E. 
Published: August 2011

AbstractThe serum free light chain (FLC) assay quantitates free immunoglobulin kappa and lambda light chains, which has prognostic value in plasma cell dyscrasias. However, there is limited data on serum FLC in lymphoid malignancies. We analyzed the association of pretreatment FLC with event‐free survival (EFS) and overall survival (OS) in 100 patients with Hodgkin lymphoma (HL). Elevated polyclonal FLC were present in 30% of patients; these patients had an inferior EFS (HR = 4.84; 95% CI: 1.84–12.7) and OS (HR = 8.87; 95% CI: 2.35–33.52) compared to patients with normal FLC. Further studies of FLC in HL are warranted. Am. J. Hematol., 2011. © 2011 Wiley‐Liss, Inc.
A mutation in sigma‐1 receptor causes juvenile amyotrophic lateral sclerosis
Authors: Al‐Saif Amr , Al‐Mohanna Futwan , Bohlega Saeed 
Published: August 2011

AbstractObjective:Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by loss of motor neurons in the brain and spinal cord, leading to muscle weakness and eventually death from respiratory failure. ALS is familial in about 10% of cases, with SOD1 mutations accounting for 20% of familial cases. Here we describe a consanguineous family segregating juvenile ALS in an autosomal recessive pattern and describe the genetic variant responsible for the disorder.Methods:We performed homozygosity mapping and direct sequencing to detect the genetic variant and tested the effect of this variant on a motor neuron‐like cell line model (NSC34) expressing the wild‐type or mutant gene.Results:We identified a shared homozygosity region in affected individuals that spans ∼120kbp on chromosome 9p13.3 containing 9 RefSeq genes. Sequencing the SIGMAR1 gene revealed a mutation affecting a highly conserved amino acid located in the transmembrane domain of the encoded protein, sigma‐1 receptor. The mutated protein showed an aberrant subcellular distribution in NSC34 cells. Furthermore, cells expressing the mutant protein were less resistant to apoptosis induced by endoplasmic reticulum stress.Interpretation:Sigma‐1 receptors are known to have neuroprotective properties, and recently Sigmar1 knockout mice have been described to have motor deficiency. Our findings emphasize the role of sigma‐1 receptors in motor neuron function and disease. ANN NEUROL 2011;
Cocontinuous phase morphology for an asymmetric composition of polypropylene/polyamide 6 blend by melt mixing of polypropylene with premelted polyamide 6/organoclay masterbatch
Authors: Wang Li , Guo Zhao‐Xia , Yu Jian 
Published: August 2011

AbstractCocontinuous morphology was obtained for an asymmetric composition of polypropylene/polyamide 6 (70/30 w/w) blend by controlling melt compounding sequence of PP, PA6, and organoclay. Three different compounding sequences were tested: direct melt mixing of all the components, melt mixing of PP with PA6/organoclay masterbatch, and melt mixing of PP with premelted PA6/organoclay masterbatch. Only the third method promotes cocontinuous morphology. In all three cases, organoclay locates preferentially in the PA6 phase and at the interface, although the level of organoclay dispersion is poorer in the case of direct mixing than in the two‐masterbatch approaches. The morphology evolution processes of the three different compounding sequences were investigated and revealed that the main reason for the formation of cocontinuous morphology in the third method is the inhibiting effect of organoclay preincluded in the premelted PA6 phase on phase inversion. The viscosity of PA6 phase and the barrier effect of organoclay were confirmed to be two key factors in promoting cocontinuous structure. Dynamic mechanical analysis shows that the blend having cocontinuous morphology displays higher storage modulus than those having matrix‐dispersed morphology at the same organoclay loading. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
PWA/silica doped sulfonated poly(ether sulfone) composite membranes for direct methanol fuel cells
Authors: Chen Chien‐Chung , Tsi Hung‐Yi , Tsen Wen‐Chin , Chuang Fu‐Sheng , Jang Shin‐Cheng , Shu Yao‐Chi , Wen Sheng , Gong Chunli 
Published: August 2011

AbstractA novel sulfonated poly(ether sulfone) (SPES)/phosphotungstic acid (PWA)/silica composite membranes for direct methanol fuel cells (DMFCs) application were prepared. The structure and performance of the obtained membranes were characterized by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), water uptake, proton conductivity, and methanol permeability. Compared to a pure SPES membrane, PWA and SiO2 doped membranes had a higher thermal stability and glass transition temperature (Tg) as revealed by TGA‐FTIR and DSC. The morphology of the composite membranes indicated that SiO2 and PWA were uniformly distributed throughout the SPES matrix. Proper PWA and silica loadings in the composite membranes showed high proton conductivity and sufficient methanol permeability. The selectivity (the ratio of proton conductivity to methanol permeability) of the SPES‐P‐S 15% composite membrane was almost five times than that of Nafion 112 membrane. This excellent selectivity of SPES/PWA/silica composite membranes indicate a potential feasibility as a promising electrolyte for DMFC. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Structure and toughness of polyethersulfone (PESU)‐modified anhydride‐cured tetrafunctional epoxy resin: Effect of PESU molecular mass
Authors: Grishchuk S. , Gryshchuk O. , Weber M. , Karger‐Kocsis J. 
Published: August 2011

AbstractA tetrafunctional, anhydride hardened epoxy resin (EP) was modified with polyethersulfones (PESU) of different molecular mass (MM) without using additional solvent in 10 wt %. The morphology, thermal, and fracture mechanical properties of the EP/PESU systems were determined. PESU was present as dispersed phase in the EP matrix. The final morphology of EP/PESU depended on MM of PESU. PESU of low and medium MM formed submicron scale spherical droplets, whereas PESU of high MM was present in micron scale inclusions of complex (sea‐island) structure. With increasing MM of PESU, the fracture mechanical properties, and especially the fracture energy, were increased. This was traced to differences in the morphology (dispersion of PESU) of the EP/PESU systems triggering different failure mechanisms. The onset of thermal degradation was slightly reduced, whereas the char yield enhanced by PESU modification compared with the reference EP. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Privacy dictionary: A new resource for the automated content analysis of privacy
Authors: Vasalou Asimina , Gill Alastair J. , Mazanderani Fadhila , Papoutsi Chrysanthi , Joinson Adam 
Published: August 2011

AbstractThis article presents the privacy dictionary, a new linguistic resource for automated content analysis on privacy‐related texts. To overcome the definitional challenges inherent in privacy research, the dictionary was informed by an inclusive set of relevant theoretical perspectives. Using methods from corpus linguistics, we constructed and validated eight dictionary categories on empirical material from a wide range of privacy‐sensitive contexts. It was shown that the dictionary categories are able to measure unique linguistic patterns within privacy discussions. At a time when privacy considerations are increasing and online resources provide ever‐growing quantities of textual data, the privacy dictionary can play a significant role not only for research in the social sciences but also in technology design and policymaking.
Industry and regulatory experience of the glycosylation of monoclonal antibodies
Authors: Read Erik K. , Park Jun T. , Brorson Kurt A. 
Published: August 2011

AbstractWe surveyed 23 antibody‐related marketing applications for glycoform analytical and functional information. Our database analysis shows a clear trend of increasing sophistication of analytical methods used to identify and quantify glycans. These have revealed a high degree of complexity and heterogeneity of glycans attached to antibody products. The nature of the complexity is influenced by product type and expression system, and may be associated with functional consequences in some but not all cases.
Generation of an enriched pool of DNA aptamers for an HER2‐overexpressing cell line selected by Cell SELEX
Authors: Dastjerdi Kazem , Tabar Gholamreza Hashemi , Dehghani Hesam , Haghparast Alireza 
Published: August 2011

AbstractOverexpression of human epidermal growth factor receptor 2 (HER2) occurs in a large percentage of breast cancers. Monoclonal antibodies targeting HER2 are vastly used for both diagnostic and therapeutic aims. However, identifying a new molecular probe against HER2 with improved diagnostic and therapeutic features is of great importance. In this report, we have applied the cell systematic evolution of ligands by exponential enrichment (SELEX) strategy for 16 selection rounds to generate an enriched pool of aptamers that specifically recognize the HER2 positive cell line. During the Cell SELEX procedure, a human HER2‐overexpressing breast cancer cell line and a human HER2 negative breast cancer cell line were used. Our results reveal that polymerase chain reaction (PCR) amplification of random DNA libraries and the selected single‐stranded DNA pool in different Cell SELEX rounds are different from what we expect from PCR amplification of homologous DNA. Our results also confirmed previous studies describing positive HER2 status of SK‐BR3 and the absence of the HER2 expression in the MDA‐MB468. We also developed a new method, Cell enzyme‐linked assay, to monitor the enrichment of aptamers in a given round of Cell SELEX. This method would also be useful in other experiments using live cell enzyme‐linked immunosorbent assay on adherent cells.
Probing of some compounds as anti‐aggregatory additives in the protein refolding process from Escherichia coli inclusion bodies
Authors: Zilinskas Albinas , Sereikaite Jolanta 
Published: August 2011

AbstractFive compounds of different chemical structure were tested for aggregation suppression during the refolding of porcine and mink growth hormones as model proteins from Escherichia coli inclusion bodies by the dilution method. Of all compounds tested in this work, 3‐guanidinopropionic acid (GPA) containing a guanidinium group was the most effective additive for aggregation suppression. Anti‐aggregatory properties of GPA were compared with the ones of l‐arginine.
Graph‐Framing Effects in Decision Making
Authors: Sun Yan , Li Shu , Bonini Nicolao , Su Yin 
Published: August 2011

ABSTRACTThis study manipulated the graphical representation of options by framing the physical characters in figures and found that preferences could be affected even when the words and numbers of the problem were constant. Based on attribute substitution theory and an equate‐to‐differentiate approach, we proposed a two‐process model of graph‐framing effects. In the first mental process, the graph‐editing process, the physical features (e.g., distance, size) represented in the graph are visually edited, and the perceived numerical difference between the options is judged based on its physical features. The second mental process, the preferential choice process, occurs by an equate‐to‐differentiate approach in which people seek to equate the difference between options on the dimension on which the difference is smaller, thus leaving the greater other‐dimensional difference to be the determinant of the final choice. Four experiments were tested for graph‐framing effects. Experiment 1 found a graph‐framing effect in coordinate graphs resting on the (de)compression of the scales employed in the figures. Experiment 2 revealed additional graph‐framing effects in other question scenarios and showed that preference changes were mediated by perceived numerical distances. Experiment 3 further confirmed the presence of graph‐framing effects in sector graphs similar to those found in coordinate ones. Experiment 4 suggested that such graph‐framing effects could be eliminated when logical processing (e.g., introducing a mathematical operation before a choice task) was encouraged. This paper discusses related research and a possible substrate basis for graph‐framing effects. Copyright © 2011 John Wiley & Sons, Ltd.
Social Discounting and Cigarette Smoking During Pregnancy
Authors: Bradstreet Matthew P. , Higgins Stephen T. , Heil Sarah H. , Badger Gary J. , Skelly Joan M. , Lynch Mary Ellen , Trayah Molly C. 
Published: August 2011

ABSTRACTIn this study, we examined the association between social discounting and smoking status in a cohort of pregnant cigarette smokers (n = 91), quitters (n = 27), or never‐smokers (n = 30). The smokers and quitters were participants in clinical trials on smoking cessation and relapse prevention, whereas the never‐smokers were controls in a study on nicotine withdrawal during pregnancy. Social discounting was assessed using a paper‐and‐pencil task that assesses the amount of hypothetical money a person is willing to forgo in order to share with individuals in their social network ranging from the person who is emotionally closest to them to a mere acquaintance. The amount that women were willing to forgo in order to share decreased hyperbolically as a function of social distance, with smokers exhibiting steeper discounting functions (i.e., less generosity) than quitters or never‐smokers; discounting functions of quitters and never‐smokers did not differ significantly. In multivariate analyses controlling for potential sociodemographic and other confounds, social discounting remained a significant predictor of smoking status among smokers versus quitters. Overall, these results suggest that individual differences in social discounting may be a factor influencing the choices that women make about quitting smoking upon learning of a pregnancy. Copyright © 2011 John Wiley & Sons, Ltd.
Head exposure system for a human provocation study to assess the possible influence of UMTS‐like electromagnetic fields on cerebral blood circulation using near‐infrared imaging
Authors: Lehmann Hugo , Pollara Laurent , Spichtig Sonja , Kühn Sven , Wolf Martin 
Published: August 2011

AbstractA head exposure setup for efficient and precisely defined exposure of human subjects equipped with a near‐infrared imaging (NIRI) sensor is presented. In a partially shielded anechoic chamber the subjects were exposed to Universal Mobile Telecommunications System (UMTS)‐like electromagnetic fields (EMF) by using a patch antenna at a distance of 4 cm from the head. The non‐contact design of the exposure setup enabled NIRI sensors to easily attach to the head. Moreover, different regions of the head were chosen for localised exposure and simultaneous NIRI investigation. The control software enabled the simple adaptation of the test parameters during exploratory testing as well as the performance of controlled, randomised, crossover and double‐blind provocation studies. Four different signals with a carrier frequency of 1900 MHz were chosen for the exposure: a simple continuous wave signal and three different UMTS signals. Furthermore, three exposure doses were available: sham, low (spatial peak specific absorption rate (SAR) = 0.18 W/kg averaged over 10 g) and high (spatial peak SAR = 1.8 W/kg averaged over 10 g). The SAR assessment was performed by measurement and simulation. Direct comparison of measurement and numerical results showed good agreement in terms of spatial peak SAR and SAR distribution. The variability analysis of the spatial peak SAR over 10 g was assessed by numerical simulations. Maximal deviations of −22% and +32% from the nominal situation were observed. Compared to other exposure setups, the present setup allows for low exposure uncertainty, combined with high SAR efficiency, easy access for the NIRI sensor and minimal impairment of test subjects. Bioelectromagnetics 33:124–133, 2012. © 2011 Wiley Periodicals, Inc.