bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cylinder‐to‐rod‐to‐sphere evolution of complex micelles in solution and their corresponding solvent‐induced crystallization process
Authors: Huang Weihuan , Luo Chunxia , Wang Hanfu , Han Yanchun 
Published: April 2010

AbstractIn a previous paper, we investigated the solvent‐induced crystallization of films made up of spherical micelles, which were prepared by mixing polystyrene‐block‐poly(acrylic acid) and polystyrene‐block‐poly(2‐vinylpyridine)‐block‐poly(ethylene oxide) in the neutral solvent N,N‐dimethylformamide (DMF). In the work reported in the present paper, we further studied the cylinder‐to‐rod‐to‐sphere evolution of complex micelles in solution and their corresponding solvent‐induced crystallization process. The initial morphology of the micelles in the solution was cylindrical due to a rapid growth of micelles with high unimer concentration, and spheres became the dominant form after storage at room temperature for a longer time. Regular square platelets can form after a certain period of treatment for all micelles in DMF vapor for sufficient time. However, the kinetics of their solvent‐induced crystallization process is quite different. The aggregation and subsequent nucleation of poly(ethylene oxide) blocks are determined by the distribution of crystallizable poly(ethylene oxide) blocks in the films. Copyright © 2010 Society of Chemical Industry
Biomaterials‐based organic electronic devices
Authors: Bettinger Christopher J , Bao Zhenan 
Published: April 2010

AbstractOrganic electronic devices have demonstrated tremendous versatility in a wide range of applications including consumer electronics, photovoltaics and biotechnology. The traditional interface of organic electronics with biology, biotechnology and medicine occurs in the general field of sensing biological phenomena. For example, the fabrication of hybrid electronic structures using both organic semiconductors and bioactive molecules has led to enhancements in the sensitivity and specificity within biosensing platforms, which in turn has a potentially wide range of clinical applications. However, the interface of biomolecules and organic semiconductors has also recently explored the potential use of natural and synthetic biomaterials as structural components of electronic devices. The fabrication of electronically active systems using biomaterials‐based components has the potential to produce a large set of unique devices including environmentally biodegradable systems and bioresorbable temporary medical devices. This article reviews recent advances in the implementation of biomaterials as structural components in organic electronic devices with a focus on potential applications in biotechnology and medicine. Copyright © 2010 Society of Chemical Industry
Using controlled radical polymerisation techniques for the synthesis of functional polymers containing amino acid moieties
Authors: O'Reilly Rachel K 
Published: April 2010

AbstractThere is great current interest in bridging the gap between robust synthetic polymers and complex biological polymers to allow for the preparation of novel functional, well‐defined, biocompatible and tailorable materials. In this mini‐review recent reports on the preparation of functional amino acid polymers using controlled radical polymerisation techniques are discussed. The future potential applications of these materials as well as the proposed further directions in the field are also highlighted. Copyright © 2010 Society of Chemical Industry
2‐D DIGE reveals changes in wheat xylanase inhibitor protein families due to Fusarium graminearum ΔTri5 infection and grain development
Authors: Dornez Emmie , Croes Evi , Gebruers Kurt , Carpentier Sebastien , Swennen Rony , Laukens Kris , Witters Erwin , Urban Martin , Delcour Jan A. , Courtin Christophe M. 
Published: April 2010

AbstractWheat contains three different classes of proteinaceous xylanase inhibitors (XIs), i.e. Triticum aestivum xylanase inhibitors (TAXIs) xylanase‐inhibiting proteins (XIPs), and thaumatin‐like xylanase inhibitors (TLXIs) which are believed to act as a defensive barrier against phytopathogenic attack. In the absence of relevant data in wheat kernels, we here examined the response of the different members of the XI protein population to infection with a ΔTri5 mutant of Fusarium graminearum, the wild type of which is one of the most important wheat ear pathogens, in early developing wheat grain. Wheat ears were inoculated at anthesis, analyzed using 2‐D DIGE and multivariate analysis at 5, 15, and 25 days post anthesis (DPA), and compared with control samples. Distinct abundance patterns could be distinguished for different XI forms in response to infection with F. graminearum ΔTri5. Some (iso)forms were up‐regulated, whereas others were down‐regulated. This pathogen‐specific regulation of proteins was mostly visible at five DPA and levelled off in the samples situated further from the inoculation point. Furthermore, it was shown that most identified TAXI‐ and XIP‐type XI (iso)forms significantly increased in abundance from the milky (15 DPA) to the soft dough stages (25 DPA) on a per kernel basis, although the extent of increase differed greatly. Non‐glycosylated XIP forms increased more strongly than their glycosylated counterparts.
Estimating false discovery rates for peptide and protein identification using randomized databases
Authors: Hather Gregory , Higdon Roger , Bauman Andrew , von Haller Priska D. , Kolker Eugene 
Published: April 2010

AbstractMS‐based proteomics characterizes protein contents of biological samples. The most common approach is to first match observed MS/MS peptide spectra against theoretical spectra from a protein sequence database and then to score these matches. The false discovery rate (FDR) can be estimated as a function of the score by searching together the protein sequence database and its randomized version and comparing the score distributions of the randomized versus nonrandomized matches. This work introduces a straightforward isotonic regression‐based method to estimate the cumulative FDRs and local FDRs (LFDRs) of peptide identification. Our isotonic method not only performed as well as other methods used for comparison, but also has the advantages of being: (i) monotonic in the score, (ii) computationally simple, and (iii) not dependent on assumptions about score distributions. We demonstrate the flexibility of our approach by using it to estimate FDRs and LFDRs for protein identification using summaries of the peptide spectra scores. We reconfirmed that several of these methods were superior to a two‐peptide rule. Finally, by estimating both the FDRs and LFDRs, we showed for both peptide and protein identification, moderate FDR values (5%) corresponded to large LFDR values (53 and 60%).
Quantitative cortical synapse proteomics of a transgenic migraine mouse model with mutated CaV2.1 calcium channels
Authors: Klychnikov Oleg I. , Li Ka Wan , Sidorov Igor A. , Loos Maarten , Spijker Sabine , Broos Ludo A. M. , Frants Rune R. , Ferrari Michel D. , Mayboroda Oleg A. , Deelder André M. , Smit August B. , van den Maagdenberg Arn M. J. M. 
Published: April 2010

AbstractFamilial hemiplegic migraine type 1 (FHM1) is caused by missense mutations in the CACNA1A gene that encodes the α1A pore‐forming subunit of CaV2.1 Ca2+ channels. Knock‐in (KI) transgenic mice expressing CaV2.1 Ca2+ channels with a human pathogenic FHM1 mutation reveal enhanced glutamatergic neurotransmission in the cortex. In this study, we employed an iTRAQ‐based LC‐LC MS/MS approach to identify differentially expressed proteins in cortical synapse proteomes of Cacna1a R192Q KI and wild‐type mice. All expression differences determined were subtle and in the range of 10–30%. Observed upregulated proteins in the mutant mice are involved in processes, such as neurite outgrowth and actin dynamics, vesicle turnover, and glutamate transporters. Our data support the view that in Cacna1a R192Q KI mice, several compensatory mechanisms counterbalancing a dysregulated glutamatergic signaling have come into effect. We propose that such adaptation mechanisms at the synapse level may play a role in the pathophysiology of FHM and possibly in the common forms of migraine.
A domain level interaction network of amyloid precursor protein and Aβ of Alzheimer's disease
Authors: Perreau Victoria M. , Orchard Sandra , Adlard Paul A. , Bellingham Shayne A. , Cappai Roberto , Ciccotosto Giuseppe D. , Cowie Tiffany F. , Crouch Peter J. , Duce James A. , Evin Genevieve , Faux Noel G. , Hill Andrew F. , Hung Ya Hui , James Simon A. , Li Qiao‐Xin , Mok Su San , Tew Deborah J. , White Anthony R. , Bush Ashley I. , Hermjakob Henning , Masters Colin L. 
Published: April 2010

AbstractThe primary constituent of the amyloid plaque, β‐amyloid (Aβ), is thought to be the causal “toxic moiety” of Alzheimer's disease. However, despite much work focused on both Aβ and its parent protein, amyloid precursor protein (APP), the functional roles of APP and its cleavage products remain to be fully elucidated. Protein–protein interaction networks can provide insight into protein function, however, high‐throughput data often report false positives and are in frequent disagreement with low‐throughput experiments. Moreover, the complexity of the CNS is likely to be under represented in such databases. Therefore, we curated the published work characterizing both APP and Aβ to create a protein interaction network of APP and its proteolytic cleavage products, with annotation, where possible, to the level of APP binding domain and isoform. This is the first time that an interactome has been refined to domain level, essential for the interpretation of APP due to the presence of multiple isoforms and processed fragments. Gene ontology and network analysis were used to identify potentially novel functional relationships among interacting proteins.
2‐Picoline‐borane: A non‐toxic reducing agent for oligosaccharide labeling by reductive amination
Authors: Ruhaak L. Renee , Steenvoorden Evelyne , Koeleman Carolien A. M. , Deelder André M. , Wuhrer Manfred 
Published: April 2010

AbstractAnalysis of N‐glycans is often performed by LC coupled to fluorescence detection. The N‐glycans are usually labeled by reductive amination with a fluorophore containing a primary amine to allow fluorescence detection. Moreover, many of the commonly applied labels also allow improved mass spectrometric detection of oligosaccharides. For reductive amination, the amine group of the label reacts with the reducing‐end aldehyde group of the oligosaccharide to form a Schiff base, which is reduced to a secondary amine. Here, we propose the use of 2‐picoline‐borane as the reducing agent, as a non‐toxic alternative to the extensively used, but toxic sodium cyanoborohydride. Using dextran oligosaccharides and plasma N‐glycans, we demonstrate similar labeling efficacies for 2‐picoline‐borane and sodium cyanoborohydride. Therefore, 2‐picoline‐borane is a non‐toxic alternative to sodium cyanoborohydride for the labeling of oligosaccharides.
Identifying secreted proteins of Marssonina brunnea by degenerate PCR
Authors: Cheng Qiang , Cao Youzhi , Jiang Cong , Xu Li'an , Wang Mingxiu , Zhang Shougong , Huang Minren 
Published: April 2010

AbstractMarssonina brunnea is an important fungal pathogen of the Populus genus. To further our understanding of the pathogenesis of M. brunnea, we initiated a proteome‐level study of the fungal secretome. Using de novo peptide sequencing by MS/MS, we obtained peptide sequences for 32 protein spots. Four proteins were identified by sequence homology to conserved proteins in public databases using MS‐driven BLAST. To identify additional protein spots, we combined a degenerate PCR method, based on the Consensus–DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) method, and a rapid amplification of cDNA ends method to clone the full‐length cDNA fragments encoding the proteins identified in the gel. Using this method, we cloned the full‐length cDNA fragments encoding 11 M. brunnea‐specific proteins. This method provides an efficient approach to identification of species‐specific proteins of non‐sequenced organisms. Furthermore, we analyzed the expression patterns of these genes during infection. We found that most of the identified secreted proteins could be induced in artificial medium after hyphae entered poplar apoplast spaces. We propose that for the host‐specialized M. brunnea, the elongation of hyphae has evolved closely with the secretion of apoplastic proteins.
Genome‐wide profiling of humoral immune response to Coxiella burnetii infection by protein microarray
Authors: Vigil Adam , Ortega Rocio , Nakajima‐Sasaki Rie , Pablo Jozelyn , Molina Douglas M. , Chao Chien‐Chung , Chen Hua‐Wei , Ching Wei‐Mei , Felgner Philip L. 
Published: April 2010

AbstractComprehensive evaluation of the humoral immune response to Coxiella burnetii may identify highly needed diagnostic antigens and potential subunit vaccine candidates. Here we report the construction of a protein microarray containing 1901 C. burnetii ORFs (84% of the entire proteome). This array was probed with Q‐fever patient sera and naïve controls in order to discover C. burnetii‐specific seroreactive antigens. Among the 21 seroreactive antigens identified, 13 were significantly more reactive in Q‐fever cases than naïve controls. The remaining eight antigens were cross‐reactive in both C. burnetii infected and naïve patient sera. An additional 64 antigens displayed variable seroreactivity in Q‐fever patients, and underscore the diversity of the humoral immune response to C. burnetii. Nine of the differentially reactive antigens were validated on an alternative immunostrip platform, demonstrating proof‐of‐concept development of a consistent, safe, and inexpensive diagnostic assay alternative. Furthermore, we report here the identification of several new diagnostic antigens and potential subunit vaccine candidates for the highly infectious category B alphaproteobacteria, C. burnetii.
Endobronchial atypical mycobacteria in an immunocompetent child
Authors: del Rio Camacho G. , Soriano Guillén L. , Flandes Aldeyturriaga J. , Hernández García B. , Bernácer Borja M. 
Published: April 2010

AbstractEndobronchial granulomas in children are mainly caused by mycobacterial infections. In addition to Mycobacterium tuberculosis, other organisms such as nontuberculous mycobacteria (NTM) have emerged. These organisms cause a broad spectrum of pulmonary diseases. An isolated endobronchial NTM infection in a child is reported. After bronchoscopic removal, a decision not to add drug treatment was made, with satisfactory results. Treatment options are not well established in children and remain a source of controversy. Different options are discussed. Pediatr Pulmonol. 2010; 45:511–513. © 2010 Wiley‐Liss, Inc.
Accuracy of three transcutaneous carbon dioxide monitors in critically ill children
Authors: Urbano Javier , Cruzado Verónica , López‐Herce Jesús , del Castillo Jimena , Bellón José María , Carrillo Ángel 
Published: April 2010

AbstractObjectivesTo study the accuracy of three devices for measuring transcutaneous CO2 tension in critically ill children.MethodsA prospective study comparing the values from three transcutaneous CO2 monitors (SenTec®, TOSCA 500®, and TINA TCM3®) with simultaneous arterial CO2 (PaCO2) and end‐tidal CO2 (EtCO2) values. Clinical data were collected from the patients. Influence of core‐skin temperature gradient and doses of inotropic drugs was evaluated.ResultsThere were 62 samples from 41 critically ill children with ages between 2 and 192 months (median, 18.5 months) and weights between 3.1 and 72 kg (median, 9 kg). The median PaCO2 was 42.5 mmHg (range, 28–85 mmHg). Transcutaneous CO2 (PtcCO2) values correlated better with PaCO2 than with EtCO2. The correlation coefficient between PaCO2 and PtCO2 was 0.833 with the TINA TCM3® monitor, 0.931 with the SenTec® monitor, and 0.765 with the TOSCA 500® monitor. The mean (SD) differences between the PaCO2 and PtcCO2 were 4.5 (3.7) mmHg, 4.3 (3.8) mmHg, and 5.6 (5.1) mmHg, respectively, with the three monitors, and the differences between the PaCO2 and PtcCO2 were less than 7.5 mmHg in 77.7%, 81.2%, and 67.7% of the samples. Bland–Altman analysis showed a precision of ±11.5 mmHg for TINA TCM3® monitor, ±10.6 mmHg for SenTec® monitor, and ±14.8 mmHg for TOSCA® monitor. No influence of core‐skin temperature gradient and inotropic index on the differences between PaCO2 and PtcCO2 was observed.ConclusionsThe three transcutaneous CO2 monitors have an acceptable correlation with arterial CO2 tension and can be useful in critically ill children. Pediatr Pulmonol. 2010; 45:481–486. © 2010 Wiley‐Liss, Inc.
Vocal cord function and bispectral index in pediatric bronchoscopy patients emerging from propofol anesthesia
Authors: Schroeck Hedwig , Fecho Karamarie , Abode Kathleen , Bailey Ann 
Published: April 2010

AbstractObjectiveIn children undergoing bronchoscopy for evaluation of stridor or respiratory symptoms, movement of the vocal cords is routinely assessed at the conclusion of flexible bronchoscopy with children still anesthetized. The effect of anesthesia on vocal cord function is not well described. This study aimed to characterize the relationship between depth of propofol anesthesia, as measured by Bispectral Index (BIS), and vocal cord movement in pediatric patients.MethodsChildren between 6 months and 12 years of age presenting for diagnostic flexible bronchoscopy were enrolled in this prospective observational study. Anesthesia was maintained with a propofol infusion which was discontinued upon completion of the lower airway evaluation. An independent observer recorded the BIS score every 15 sec from discontinuation of propofol whereas the pulmonologist continued to observe vocal cord motion. BIS scores were also recorded for each observed clinical endpoint (paradoxical and normal vocal cord movement, complete vocal cord closure, and volitional movement).ResultsData were analyzed for 47 subjects. The BIS values increased significantly from the conclusion of the lower airway evaluation with return of normal vocal cord movement, complete vocal cord closure, and volitional movement (P < 0.0005). BIS readings were higher for patients younger than 2 years. Paradoxical vocal cord movement was documented in 10.6% of subjects, but resolved in all subjects.ConclusionsOur findings suggest that return of vocal cord function during emergence from propofol anesthesia is related to decreasing anesthetic depth with complete vocal cord closure occurring at BIS values near those associated with volitional movement. Pediatr Pulmonol. 2010; 45:494–499. © 2010 Wiley‐Liss, Inc.
A non‐invasive method based on saliva to characterize transthyretin in familial amyloidotic polyneuropathy patients using FT‐ICR high‐resolution MS
Authors: da Costa Gonçalo , Guerreiro Ana , Correia Catarina F. , Gomes Ricardo J. , Freire António , Monteiro Estela , Barroso Eduardo , Coelho Ana V. , Outeiro Tiago F. , Freire Ana Ponces , Cordeiro Carlos 
Published: April 2010

AbstractPurpose: To identify, characterize and perform a relative quantification of human transthyretin (TTR) variants in human saliva.Experimental design: Serum and saliva samples were collected from healthy and familial amyloidotic polyneuropathy (FAP) patients, proteins separated by SDS‐PAGE, TTR bands excised, in‐gel digested and analyzed by MALDI‐FTICR.Results: We identified and performed a relative quantification of mutated and native TTR forms in human saliva, based on FTICR‐MS. The results are quantitatively identical to the ones obtained with human serum. In FAP patients subjected to cadaveric liver transplant, the TTR mutant form is no longer detected in saliva, while in patients receiving a domino liver from a FAP donor the mutant form of TTR becomes detectable in saliva, thus demonstrating the serum origin of TTR in saliva.Conclusions and clinical relevance: Saliva TTR originates in serum and the ratio of mutant to native TTR is preserved. The method provides a non‐invasive detection of mutated TTR and a relative quantification of TTR forms. Diagnostic and disease prognosis of FAP is crucial at early stages of the disease and after liver transplantation, the only curative therapy. A suitable non‐invasive method was developed for monitoring the most important FAP biomarker in human saliva.
The use of native cation‐exchange chromatography to study aggregation and phase separation of monoclonal antibodies
Authors: Chen Shuang , Lau Hollis , Brodsky Yan , Kleemann Gerd R. , Latypov Ramil F. 
Published: April 2010

AbstractThis study introduces a novel analytical approach for studying aggregation and phase separation of monoclonal antibodies (mAbs). The approach is based on using analytical scale cation‐exchange chromatography (CEX) for measuring the loss of soluble monomer in the case of individual and mixed protein solutions. Native CEX outperforms traditional size‐exclusion chromatography in separating complex protein mixtures, offering an easy way to assess mAb aggregation propensity. Different IgG1 and IgG2 molecules were tested individually and in mixtures consisting of up to four protein molecules. Antibody aggregation was induced by four different stress factors: high temperature, low pH, addition of fatty acids, and rigorous agitation. The extent of aggregation was determined from the amount of monomeric protein remaining in solution after stress. Consequently, it was possible to address the role of specific mAb regions in antibody aggregation by co‐incubating Fab and Fc fragments with their respective full‐length molecules. Our results revealed that the relative contribution of Fab and Fc regions in mAb aggregation is strongly dependent on pH and the stress factor applied. In addition, the CEX‐based approach was used to study reversible protein precipitation due to phase separation, which demonstrated its use for a broader range of protein–protein association phenomena. In all cases, the role of Fab and Fc was clearly dissected, providing important information for engineering more stable mAb‐based therapeutics.
Physical–chemical determinants of coil conformations in globular proteins
Authors: Perskie Lauren L. , Rose George D. 
Published: April 2010

AbstractWe present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α‐helices and/or β‐strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two‐, three‐, and four‐residue turns from X‐ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash‐free conformers in which no backbone polar group lacks a hydrogen‐bond partner. Further, at least 90% of longer coil segments, ranging from 5‐ to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database‐derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database‐derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue.