bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Wheat 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

MS‐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

Familial 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

The 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

Analysis 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

Marssonina 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

Comprehensive 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

Endobronchial 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

Objectives

To study the accuracy of three devices for measuring transcutaneous CO2 tension in critically ill children.

Methods

A 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.

Results

There 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.

Conclusions

The 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

Objective

In 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.

Methods

Children 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).

Results

Data 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.

Conclusions

Our 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

Purpose: 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

This 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

We 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.
Dissecting the cAMP‐inducible allosteric switch in protein kinase A RIα
Authors: Sjoberg Timothy J. , Kornev Alexandr P. , Taylor Susan S.
Published: April 2010

The regulatory subunits of cAMP‐dependent protein kinase (PKA) are the major receptors of cAMP in most eukaryotic cells. As the cyclic nucleotide binding (CNB) domains release cAMP and bind to the catalytic subunit of PKA, they undergo a major conformational change. The change is mediated by the B/C helix in CNB‐A, which extends into one long helix that now separates the two CNB domains and docks onto the surface of the catalytic subunit. We explore here the role of three key residues on the B/C helix that dock onto the catalytic subunit, Arg226, Leu233, and Met 234. By replacing each residue with Ala, we show that each contributes significantly to creating the R:C interface. By also deleting the second CNB domain (CNB‐B), we show furthermore that CNB‐B is a critical part of the cAMP‐induced conformational switch that dislodges the B/C helix from the surface of the catalytic subunit. Without CNB‐B the Ka for activation by cAMP increases from 80 to 1000 nM. Replacing any of the key interface residues with Ala reduces the Ka to 25–40 nM. Leu233 and M234 contribute to a hydrophobic latch that binds the B/C helix onto the large lobe of the C‐subunit, while Arg226 is part of an electrostatic switch that couples the B/C helix to the phosphate binding cassette where the cAMP docks.
On the fermion spectrum of spontaneously generated fuzzy extra dimensions with fluxes
Authors: Chatzistavrakidis A. , Steinacker H. , Zoupanos G.
Published: April 2010

We consider certain vacua of four‐dimensional SU(N) gauge theory with the same field content as the 𝒩 = 4 supersymmetric Yang‐Mills theory, resulting from potentials which break the 𝒩 = 4 supersymmetry as well as its global SO(6) symmetry down to SO(3) × SO(3). We show that the theory behaves at intermediate scales as Yang‐Mills theory on M4 × SL2 × SR2, where the extra dimensions are fuzzy spheres with magnetic fluxes. We determine in particular the structure of the zero modes due to the fluxes, which leads to low‐energy mirror models.
Photoinduced magnetization of magnetic polarons in Cd0.8Mn0.2Te under high‐density resonant excitation of free exciton
Authors: Katayama K.
Published: April 2010

The pump‐probe Kerr rotation measurement of Cd0.8Mn0.2Te has revealed that the resonant excitation of free excitons is a more suitable method for angular momentum transfer from laser pulse to the exciton magnetic polaron than the band‐to‐band excitation. In the case of band‐to‐band excitation, a formation of macroscopic spin alignment of exciton magnetic polarons is suppressed by heat originating from excess energy of hot electron‐hole pairs and scatterings among the electron‐hole pairs. By contrast, in the case of the resonant excitation, the angular momentum of the laser is transferred to the spins of the exciton magnetic polarons even though the excitation density is higher than the Mott density. These results are consistent and supportive for our suggestion that the selective excitation of localized excitons with energy lower than that of free exciton leads to the high‐spin state of the high‐density exciton magnetic polaron. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interface phonons and polaron effect in II‐VI quantum wells
Authors: Maslov Alexander Yu. , Proshina Olga V.
Published: April 2010

The theory of large radius polaron in II‐VI quantum wells is developed. The analytic expressions for polaron binding energy are obtained for the electron, the hole and the exciton polarons. The numerical results obtained show that the strong electron‐phonon interaction conditions can be realized in the quantum wells based on a number of II‐VI compounds. The influence of the interface optical phonons on the polaron states is accounted for. The extent of interface phonon influence depends on the properties both of the quantum well and of the barrier materials. It is shown that the interaction of charge particles with the interface phonons can lead to the enhancement as well as to the reduction of the polaron effects. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of Shockley‐Read recombination center parameters in MBE p‐Hg1‐xCdxTe/GaAs via photoconductivity in magnetic field
Authors: Protasov D. Yu. , Kostuchenko V. Ya. , Varavin V. S. , Dvoretsky S. A. , Mikhailov N. N.
Published: April 2010

A new method for determination of parameters of recombination centres is developed. This method is based on measurements of steady‐state photoconductivity in magnetic field for Faradey's geometry (magnetophotoconductivity). The method was used for investigation of the parameters of recombination centres into MBE p‐HgCdTe with x=0.22. It was obtained, that the energy of recombination centres is lies near to midgap. The ratio between electrons and holes capture coefficients exceeds earlier published data by an order of magnitude. The concentration of recombination centres does not depends on hole concentration in range (4÷8)×1021 m‐3. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
MBE overgrowth of ex‐situ prepared CdSe colloidal nanocrystals
Authors: Rashad M. , Paluga M. , Pawlis A. , Lischka K. , Schikora D. , Artemyev M. V. , Woggon U.
Published: April 2010

We present a growth technique, which combines molecular beam epitaxy of ZnSe and externally wet‐chemically prepared, colloidal NCs of CdSe to achieve fully integrated monolithic epitaxial heterostructures. Our results show that wet‐chemically prepared semiconductor nanocrystals can be incorporated in an epitaxally grown crystalline cap layer. We investigated CdSe core, CdSe/ZnSe and CdSe/ZnS core/shell nanocrystals (NCs) overgrown with cap layers of ZnSe, where the thickness was varied between 20‐40 nm.

In this paper we discuss PL measurements of overgrown NCs as a function of the cap layer thickness and compare the results with the PL of NCs in solution. A distinct blue shift of the PL is observed when the core/shell dots are overgrown by ZnSe. We present a model which explains this blue shift as resulting from dissolution of the shell of the dots during the overgrowth (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
ZnSe‐based laser structures for electron‐beam pumping with graded index waveguide
Authors: Gronin S. V. , Sorokin S. V. , Sedova I. V. , Ivanov S. V. , Zdanova E. V. , Zverev M. M.
Published: April 2010

Electron beam pumped (EBP) laser heterostructures with graded index waveguide (GIW) have been grown by molecular beam epitaxy and studied in detail. The maximum achieved output pulse power per facet is as high as 8.5 W at an electron beam energy of 16 kV. No saturation of output power with the increase of electron beam current as well as no suitable degradation of GIW EBP laser structures have been observed. The ways for further optimizations of GIW heterostructures are discussed. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Early evolution of the largest‐sized droplets in maritime cumulus clouds
Authors: Lowenstein Jason H. , Blyth Alan M. , Lawson R. Paul
Published: April 2010

Droplet size distributions (DSDs) measured within a distance of approximately 1 km above the base of shallow maritime cumulus clouds during the Rain in Cumulus over the Ocean (RICO) field campaign are compared with results of a condensation and stochastic coalescence model, run in the framework of a closed parcel. New measurements of cloud droplets in the critical size range of 30 to 100 µm are presented from the 2D‐S probe. Observations are also presented of the large‐size tail of the sub‐cloud aerosol size distribution measured by the forward‐scattering spectrometer probe. Results show that droplet growth in this region is dominated by condensation, and the large‐size tail of the observed DSDs can be explained with the observed sub‐cloud particles, including giant and ultra‐giant aerosols. Copyright © 2010 Royal Meteorological Society
Science education as a contributor to adequate yearly progress and accountability programs
Authors: Judson Eugene
Published: April 2010

The No Child Left Behind (NCLB) Act requires states to measure the adequate yearly progress (AYP) of each public school and local educational agency (LEA) and to hold schools and LEAs accountable for failing to make AYP. Although it is required that science be assessed in at least three grades, the achievement results from science examinations are not required to be used when calculating AYP. A history of attempts to include science into AYP calculations and the role of science education within state accountability programs is provided here. An examination of National Assessment of Educational Progress science achievement data revealed that those states that opted to make schools accountable for students' science achievement had significantly higher fourth‐grade mean scale scores when compared to states that did not include science in this manner. However, a significant difference was not found between these groups of states when analyzing eighth‐grade data. Specific recommendations are provided to include science into accountability programs and to ameliorate existing requirements of NCLB. © 2010 Wiley Periodicals, Inc. Sci Ed 94:888–902, 2010
Study of the deposition of Ti/TiN multilayers by magnetron sputtering
Authors: Saoula N. , Djerourou S. , Yahiaoui K. , Henda K. , Kesri R. , Erasmus R. M. , Comins J. D.
Published: April 2010

In this study, we present the effect of the plasma deposition parameters on the electrical and structural properties of Ti/TiN multilayers. The films were formed by r.f. magnetron sputtering (13.56 MHz) under nitrogen and argon reactive plasma at low pressure. The first step of our study was the optimization of the deposition conditions in order to obtain good‐quality films. The total pressure was set between 2 and 10 mTorr. The primary result is that the self‐bias voltage plays a major role in the structural evolution of TiN films by changing the preferred film orientation and their hardness. The variation of the resistivity as the function of substrate bias was also investigated. The deposited multilayers were characterized by X‐ray diffraction (XRD), energy dispersive spectroscopy (EDS), and Raman scattering analysis, as well as by the standard four‐probe technique. Copyright © 2010 John Wiley & Sons, Ltd.
Differential toxicity of Disperse Red 1 and Disperse Red 13 in the Ames test, HepG2 cytotoxicity assay, and Daphnia acute toxicity test
Authors: Ferraz E. R. A. , Umbuzeiro G. A. , de‐Almeida G. , Caloto‐Oliveira A. , Chequer F. M. D. , Zanoni M. V. B. , Dorta D. J. , Oliveira D. P.
Published: April 2010

Azo dyes are of environmental concern due to their degradation products, widespread use, and low‐removal rate during conventional treatment. Their toxic properties are related to the nature and position of the substituents with respect to the aromatic rings and amino nitrogen atom. The dyes Disperse Red 1 and Disperse Red 13 were tested for Salmonella mutagenicity, cell viability by annexin V, and propidium iodide in HepG2 and by aquatic toxicity assays using daphnids. Both dyes tested positive in the Salmonella assay, and the suggestion was made that these compounds induce mainly frame‐shift mutations and that the enzymes nitroreductase and O‐acetyltransferase play an important role in the observed effect. In addition, it was shown that the presence of the chlorine substituent in Disperse Red 13 decreased the mutagenicity about 14 times when compared with Disperse Red 1, which shows the same structure as Disperse Red 13, but without the chlorine substituent. The presence of this substituent did not cause cytotoxicity in HepG2 cells, but toxicity to the water flea Daphnia similis increased in the presence of the chlorine substituent. These data suggest that the insertion of a chlorine substituent could be an alternative in the design of dyes with low‐mutagenic potency, although the ecotoxicity should be carefully evaluated. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2010.
The cytotoxic effects of synthetic 6‐hydroxylated and 6‐methoxylated polybrominated diphenyl ether 47 (BDE47)
Authors: An Jing , Li Shuhui , Zhong Yufang , Wang Yipei , Zhen Kewen , Zhang Xinyu , Wang Yangjun , Wu Minghong , Yu Zhiqiang , Sheng Guoying , Fu Jiamo , Huang Yuecheng
Published: April 2010

Polybrominated diphenyl ethers (PBDE) have been widely applied as flame retardants in plastics, polyurethane foam, paints, and synthetic fabrics. The rising PBDE level in human tissues and environment has led to concern about the health impact of exposure to PBDE. The 2,2′,4,4′‐tetrabromodiphenyl ether (BDE47), the dominant PBDE congener found in the environment and human tissues, has been shown to be an endocrine disruptor. It has also been reported to cause liver and neurodevelopmental toxicity. BDE47 can be metabolized to 6‐OH‐BDE47 and 6‐MeO‐BDE47. So far little has been reported on the cytotoxicity of the metabolites. In the present study, the cytotoxicity of the two metabolites was investigated by exposing human hepatoma cell line HepG2 to different doses of 6‐OH‐BDE47 and 6‐MeO‐BDE47. The cell viability, cell cycle, apoptosis, DNA damage, micronucleus levels, and oxidative stress response were studied. The results indicated that both metabolites could markedly inhibit the proliferation of HepG2 cells with 6‐OH‐BDE47 showing a stronger effect, and significantly increase the micronucleus level and apoptosis rate in a dose‐dependant manner. Moreover, treatment with 6‐OH‐BDE47 (≥0.5 μM) resulted in a marked cell cycle block. The SCGE experiments revealed that both metabolites could cause DNA damage in a dose‐dependant manner. Analysis of the oxidative stress response showed that 6‐OH‐BDE47 treatment (≥2.0 μM) significantly increased intracellular ROS levels as indicated by GSH depletion and elevation of SOD level, whereas 6‐MeO‐BDE47 showed a weaker effect, suggesting that oxidative stress might play a role in the cytotoxic effects. We concluded that 6‐OH‐BDE47 or 6‐MeO‐BDE47 exposure was able to induce inhibition of cell viability, increase of apoptosis rate, cell cycle block, and DNA damages, which might involve the alterated oxidative stress response due to the elevated free radicals and impaired antioxidative system. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Subcellular partitioning links BLM‐based toxicokinetics for assessing cadmium toxicity to rainbow trout
Authors: Liao Chung‐Min , Ju Yun‐Ru , Chen Wei‐Yu
Published: April 2010

The purpose of this article was to develop an integrated‐scale toxicological model to investigate the impact of cadmium (Cd) toxicity on rainbow trout (Oncorhynchus mykiss) based on recent published experimental data. This model was generated from three different types of functional relationship: biotic ligand model (BLM), damage assessment model (DAM), and subcellular partitioning model (SPM), both of key toxicological determinants involved and of functional connections between them. Toxicokinetic parameters of uptake rate constant (k1) and elimination rate constant (k2) in gill, liver, and subcellular fractions were derived. A negative correlation between gill binding fraction of Cd and bioaccumulation factor was found. Detoxifying ability (% detoxified in liver metabolically detoxified pool (MDP)) and k2 were negatively correlated, indicating that increasing % detoxified in MDP can compensate for lower k2. This finding suggests a potential tradeoff between the abilities of elimination and detoxification for Cd. Yet, compensation between the ability to eliminate Cd and the ability to recover Cd‐induced damage was not found. However, changes in k2 and recovery rate constant (kr) can shift the dynamics of Cd susceptibility probability. This analysis implicates that once k2 is determined experimentally, the values of kr and % detoxified in MDP can be predicted by the proposed k2−kr and k2−% detoxified relationships. This study suggests that the mechanistic linking of BLM‐based DAM and SPM can incorporate the organ‐ and cell‐scale exposure experimental data to investigate the mechanisms of ecophysiological response for aquatic organisms exposed to metal stressors. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Effects of 17α‐ethynylestradiol and nonylphenol on liver and gonadal apoptosis and histopathology in Chalcalburnus tarichi
Authors: Kaptaner Burak , Ünal Güler
Published: April 2010

Chalcalburnus tarichi is an endemic cyprinid fish living in the Lake Van basin located in the Eastern Turkey. Fish (3+ ages) were exposed to 17α‐ethynylestradiol (EE2; 1, 10, 100 ng L−1; nominal concentrations) and nonylphenol (NP; 10, 60, 200 μg L−1; nominal concentrations) for 32 days under semistatic daily renewal conditions. The exposure period was followed by an evaluation of liver and gonadal apoptosis and gonad histopathology in males and females. Exposure to the highest concentrations of EE2 (100 ng L−1) and NP (200 μg L−1) caused significant increases in the extent of apoptosis in liver and gonads. Treatment with 100 ng L−1 of EE2 and 200 μg L−1 NP increased the number of TUNEL positive hepatocytes significantly in both sexes compared to controls. The rates of apoptosis in testicular germ cells and ovarian follicular cells were significantly greater at the same concentrations. Exposure to EE2 (100 ng L−1) and NP (60 and 200 μg L−1) caused thickening of interstitial connective tissue (fibrosis) in the seminiferous tubule wall and testis‐ova formation in males. In females treated with 100 ng L−1 EE2, increased percentage of atretic ooctytes and fibrotic areas in the ovarian somatic stromal tissue were found in the ovaries. Increase in atresia, without a statistical significance, and fibrotic stromal tissue were also noted in 60 and 200 μg L−1 NP treatments. Results suggest that EE2‐ and NP‐dependent hepatotoxicity and gonadotoxicity are causally related to the increase in apoptosis in C. tarichi. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2011.
Analytical modeling and resource planning for cognitive radio systems
Authors: Cavdar Derya , Yilmaz H. Birkan , Tugcu Tuna , Alagöz Fatih
Published: April 2010

Cognitive radio heralds the next step in the evolution of wireless communications. In this paper, an analytical model for infrastructure based cognitive radio systems is proposed, and its performance is evaluated under bursty traffic scenarios in a multiple cell environment. Performance metrics like probabilities of dropping and blocking for primary and secondary users as well as forced termination and forced frequency handoff for secondary users are investigated, and the analytical model is verified with simulations. In addition to the analytical model, a new resource planning method is proposed to compensate for uneven traffic load distribution. The proposed method considers offered traffic, hop count to the heavily loaded cell, and velocity of mobile users during resource planning and performs better in terms of probability of blocking, dropping, and forced termination. The proposed method is promising in balancing the system performance measures, yet there is room for further improvement for finding a closed formula for the proposed analytical model. Copyright © 2010 John Wiley & Sons, Ltd.
Building a push-button RESOLVE verifier: Progress and challenges
Authors: Sitaraman Murali , Adcock Bruce , Avigad Jeremy , Bronish Derek , Bucci Paolo , Frazier David , Friedman Harvey M. , Harton Heather , Heym Wayne , Kirschenbaum Jason , Krone Joan , Smith Hampton , Weide Bruce W.
Published: April 2010

A central objective of the verifying compiler grand challenge is to develop a push-button verifier that generates proofs of correctness in a syntax-driven fashion similar to the way an ordinary compiler generates machine code. The software developer’s role is then to provide suitable specifications and annotated code, but otherwise to have no direct involvement in the verification step. However, the general mathematical developments and results upon which software correctness is based may be established through a separate formal proof process in which proofs might be mechanically checked, but not necessarily automatically generated. While many ideas that could conceivably form the basis for software verification have been known “in principle” for decades, and several tools to support an aspect of verification have been devised, practical fully automated verification of full software behavior remains a grand challenge. This paper explains how RESOLVE takes a step towards addressing this challenge by integrating foundational and practical elements of software engineering, programming languages, and mathematical logic into a coherent framework. Current versions of the RESOLVE verifier generate verification conditions (VCs) for the correctness of component-based software in a modular fashion—one component at a time. The VCs are currently verified using automated capabilities of the Isabelle proof assistant, the SMT solver Z3, a minimalist rewrite prover, and some specialized decision procedures. Initial experiments with the tools and further analytic considerations show both the progress that has been made and the challenges that remain.
Expression of MUC5AC, an early marker of pancreatobiliary cancer, is regulated by DNA methylation in the distal promoter region in cancer cells
Authors: Yamada Norishige , Nishida Yukari , Yokoyama Seiya , Tsutsumida Hideaki , Houjou Izumi , Kitamoto Sho , Goto Masamichi , Higashi Michiyo , Yonezawa Suguru
Published: April 2010

Background and purpose

High de novo expression of MUC5AC (a gastric‐type secreted mucin) is observed in many types of pancreatobiliary neoplasms, including precursor lesions. In this study, we show that the DNA methylation pattern is intimately correlated with MUC5AC expression in ten cancer cell lines (breast, lung, pancreas, and colon).

Methods

The CpG methylation status of theMUC5AC promoter from −3855 to +321 was mapped using MassARRAY analysis, which utilizes base‐specific cleavage of nucleic acids. ChIP assays and micro‐RNA (miRNA) microarray expression profiling were also carried out in both MUC5AC‐positive cells and in those with no or low MUC5AC expression.

Results

In the distal region from −3718 to −3670 of the promoter, MUC5AC‐negative cancer cells (e.g., MDA‐MB‐453) were highly methylated, whereas MUC5AC‐positive cells (e.g., MCF‐7) had low methylation levels. The modification status of histone H3 lysine 9 (H3‐K9) was also closely related toMUC5AC expression. Expression levels of miRNAs in the cancer cells were not correlated with MUC5AC expression.

Conclusion

Our results indicate thatMUC5AC is regulated by CpG methylation and histone H3‐K9 modification of theMUC5AC promoter distal region, but not by miRNAs. An understanding of the epigenetic regulation ofMUC5AC may be of importance for the diagnosis of carcinogenic risk in the pancreatobiliary system.
Arbuscular mycorrhizal fungi species‐specifically affect induced plant responses to a spider mite
Authors: Nishida Takaaki , Katayama Noboru , Izumi Naoyuki , Ohgushi Takayuki
Published: April 2010

It is widely recognized that arbuscular mycorrhizal fungi (AMF) improve plant growth and nutrient conditions, but their effects can vary from negative to positive depending on AMF species. Since the performance of herbivorous arthropods varies with plant quality, different AMF species should differently affect the density of herbivorous arthropods on plants and the herbivore‐induced plant responses. We examined the indirect effects of AMF on the number of spider mites (Tetranychus urticae) and the number of damaged leaves in an outdoor glass‐chamber experiment, using Lotus japonicus plants inoculated with one of four different AMF species (Gigaspora margarita, Glomus etunicatum, Gl. intraradices, and Acaulospora longula). Plants with Gi. margarita and A. longula had significantly fewer female mites than plants with Gl. etunicatum and Gl. intraradices, and plants with Gi. margarita had the fewest damaged leaves, followed by plants with A. longula,Gl. intraradices, and Gl. etunicatum. To examine species‐specific effects of AMF on herbivore‐induced plant responses, we carried out a bioassay with eggs laid by spider mites, and analyses of leaf chemicals (carbon, nitrogen, phosphorus, and total phenolics) using plants subjected or not subjected to herbivory. The bioassay showed that mite egg production and its changes following mite herbivory changed depending on the AMF species. In addition, Principal component analysis for leaf chemicals revealed not only mite‐induced changes in leaf chemical composition, but also AMF effects on the herbivore‐induced response in a species‐specific way. Thus, we need to pay more attention to the species identity of AMF as an important factor in determining the strength of effects of belowground AMF on the performance and/or preferences of aboveground herbivores.
A New Microsphere-Based Immunoassay for Measuring the Activity of Transcription Factors
Authors: Lin Yu-Ling , Lai Yun-Ju , Tsai Nu-Man , Peng Tai-Chu , Liu Yen-Ku , Lee Ru-Ping , Tsai Chueh-Jen , Liao Kuang-Wen
Published: April 2010

There are several traditional and well-developed methods for analyzing the activity of transcription factors, such as EMSA, enzyme-linked immunosorbent assay, and reporter gene activity assays. All of these methods have their own distinct disadvantages, but none can analyze the changes in transcription factors in the few cells that are cultured in the wells of 96-well titer plates. Thus, a new microsphere-based immunoassay to measure the activity of transcription factors (MIA-TF) was developed. In MIA-TF, NeutrAvidin-labeled microspheres were used as the solid phase to capture biotin-labeled double-strand DNA fragments which contain certain transcription factor binding elements. The activity of transcription factors was detected by immunoassay using a transcription factor-specific antibody to monitor the binding with the DNA probe. Next, analysis was performed by flow cytometry. The targets hypoxia-inducible factor-1α (HIF-1α) and nuclear factor-kappa B (NF-κB) were applied and detected in this MIA-TF method; the results that we obtained demonstrated that this method could be used to monitor the changes of NF-κB or HIF within 50 or 100 ng of nuclear extract. Furthermore, MIA-TF could detect the changes in NF-κB or HIF in cells that were cultured in wells of a 96-well plate without purification of the nuclear protein, an important consideration for applying this method to high-throughput assays in the future. The development of MIA-TF would support further progress in clinical analysis and drug screening systems. Overall, MIA-TF is a method with high potential to detect the activity of transcription factors.
The molecular signature of oncofusion proteins in acute myeloid leukemia
Authors: Martens Joost H.A. , Stunnenberg Henk G.
Published: April 2010

Acute myeloid leukemia (AML) associated translocations often cause gene fusions that encode oncofusion proteins. Although many of the breakpoints involved in chromosomal translocations have been cloned, in most cases the role of the chimeric proteins in tumorigenesis is not elucidated. Here we will discuss the fusion proteins of the 4 most common translocations associated with AML as well as the common molecular mechanisms that these four and other fusion proteins utilize to transform progenitor cells. Intriguingly, although the individual partners within the fusion proteins represent a wide variety of cellular functions, at the molecular level many commodities can be found.