bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transforming growth factor‐β1 in bronchoalveolar lavage fluid from children with cystic fibrosis
Authors: Harris William T. , Muhlebach Marianne S. , Oster Robert A. , Knowles Michael R. , Noah Terry L. 
Published: October 2009

AbstractRationaleTransforming factor β1 (TGF‐β1) genetic polymorphisms have been identified as a modifier of cystic fibrosis (CF) lung disease severity. However, few data link TGF‐β1 protein levels and clinical markers of CF lung disease severity.ObjectivesTo determine the association between protein levels of TGF‐β1 in pediatric CF bronchoalveolar lavage fluid (BALF) and clinical parameters of CF lung disease severity.MethodsTotal TGF‐β1 was measured in BALF from 30 pediatric CF patients and 12 non‐CF disease controls undergoing clinically indicated flexible bronchoscopy, and compared to four indicators of clinical disease: infection, inflammation, pulmonary function, and recent/recurrent hospitalization.ResultsTGF‐β1 was elevated in CF BALF compared to non‐CF controls (135 ± 15 pg/ml vs. 57 ± 10 pg/ml, P < 0.01). In CF BALF, increased TGF‐β1 was associated with elevated BALF PMN % (r = 0.67, P < 0.01). BALF TGF‐β1 was increased in CF subjects whose FEV1 after the completion of antibiotic therapy remained below CF age‐normative median values (205.9 ± 20.5 pg/ml vs. 106.4 ± 24.0, P = 0.01). BALF TGF‐β1 was increased in CF children hospitalized in the previous year compared to those not recently hospitalized (169.9 ± 21.6 pg/ml vs. 107.5 ± 17.5 pg/ml, P = 0.04). Neither the presence of a bacterial pathogen nor bacterial quantity was associated with BALF TGF‐β1.ConclusionsIn CF, BALF TGF‐β1 is elevated compared to non‐CF controls. Increased BALF TGF‐β1 is associated with neutrophilic inflammation, diminished lung function and recent hospitalization. Further investigation is needed to address mechanisms behind these associations. Pediatr Pulmonol. 2009; 44:1057–1064. ©2009 Wiley‐Liss, Inc.
Superoxide dismutase and catalase activity in naturally derived commercial surfactants
Authors: Dani Carlo , Buonocore Giuseppe , Longini Mariangela , Felici Cosetta , Rodriguez Antonello , Corsini Iuri , Rubaltelli Firmino F. 
Published: October 2009

AbstractDespite the role of reactive oxygen species in the development of respiratory distress syndrome (RDS) and bronchopulmonary dysplasia (BPD) in preterm infants, the anti‐oxidant properties of commercial surfactants have never been studied. We measured the superoxide dismutase (SOD) and catalase (CAT) activity, the scavenger activity against hydrogen peroxide (H2O2), and its changes after the addition of SOD and CAT in four natural surfactants, namely Infasurf, Curosurf, Survanta, and Alveofact. We found that they contain measurable amount of SOD and CAT. Curosurf and Survanta seem to have higher antioxidant effect than Infasurf and Alveofact. Moreover, the highest phospholipid concentration and recommended dose of Curosurf imply that its scavenger activity for each treatment dose in preterm infants is likely higher than that of Survanta. Finally, the supplementation with SOD and CAT induced a remarkable increase of antioxidant action in all studied surfactants. Pediatr Pulmonol. 2009; 44:1125–1131. ©2009 Wiley‐Liss, Inc.
The use of phosphate‐affinity SDS‐PAGE to measure the cardiac troponin I phosphorylation site distribution in human heart muscle
Authors: Messer Andrew E. , Gallon Clare E. , McKenna William J. , Dos Remedios Cristobal G. , Marston Steven B. 
Published: October 2009

AbstractWe have used phosphate affinity SDS‐PAGE to separate the phosphorylated species of cardiac troponin I (cTnI). To test the method we phosphorylated pure cTnI with protein kinase A catalytic subunit and observed up to six bands corresponding to 0, 1P, 2P, 3P, 4P and 5P phospho‐species. We examined the phospho‐species of cTnI in human heart myofibrillar extracts by phosphate affinity SDS‐PAGE and Western blotting with a non‐specific troponin I (TnI) antibody. In donor heart samples the bis‐phosphorylated species of cTnI predominated and no more highly phosphorylated species were not detectable (0P was 10.3±1.9%, 1P, 17.5±3.5%, 2P, 72.2±4.7%, 11 samples). Total phosphorylation was 1.62±0.06 molsPi/mol TnI. In myofibrils from end‐stage failing hearts, the unphosphorylated cTnI species predominated (0P was 78.5±1.8%, 1P, 17.5±1.9%, 2P, 4.0±0.7%, total phosphorylation 0.26±0.02 molsPi/mol TnI, five samples). Muscle from patients with hypertrophic obstructive cardiomyopathy was also largely unphosphorylated (0P was 76.6±3.1%, 1P, 17.5±2.7%, 2P, 5.9±0.8%, total phosphorylation 0.29±0.04 molsPi/mol TnI, 19 samples). Using a range of phospho‐specific antibodies we demonstrated that 3/4 of the bis‐phosphorylated band of donor heart cTnI is phosphorylated at Ser22 and Ser23 in approximately equal amounts and that phosphorylation of Ser43 and Thr142 was not detected.
Bioimaging of geographically adjacent proteins in a single cell by quantum dot‐based fluorescent resonance energy transfer
Authors: Kang Won Jun , Ko Mee Hyang , Lee Dong Soo , Kim Soonhag 
Published: October 2009

AbstractThousands of proteins are simultaneously involved in the maintenance of a single cancer cell. Fluorescent resonance energy transfer (FRET) is one of the most general techniques for imaging biologically interacting molecules in a cell. Here, we applied FRET to image the co‐localization of two proteins that do not interact biologically (nucleolin and integrin αvβ3), both of which are highly expressed in the plasma membrane of cancer cells. AS1411 aptamer, which targets nucleolin, was labeled by Cy3 (Cy3‐AS1411) and arginine–glycine–aspartic acid (RGD) peptide, which targets integrin αvβ3, was conjugated with quantum dot (525 nm, Qd) Qd arginine–glycine–aspartic acid (Qd‐RGD). FRET activities between Cy3‐AS1411 and Qd‐RGD were measured in HeLa cells, a human cervical cancer cell line. FRET phenomena between Qd and Cy3 showed good compatibility according to proximity. The fluorescence signature using Qd‐RGD and Cy3‐AS1411 showed that nucleolin and integrin αvβ3 proteins were highly expressed in HeLa cells. Co‐incubation of Qd‐RGD and Cy3‐AS1411 in a single HeLa cell demonstrated that the fluorescence overlay by FRET was quantitatively and geographically quite different from that of individual confocal images. These results suggest that Qd‐based FRET analysis can provide information on geographical co‐localization of proteins in naïve cells, which is very important for determining the molecular and cellular functions of genes involved in cancers and other clinical diseases.
Mining mammalian genomes for folding competent proteins using Tat‐dependent genetic selection in Escherichia coli
Authors: Lim Hyung‐Kwon , Mansell Thomas J. , Linderman Stephen W. , Fisher Adam C. , Dyson Michael R. , DeLisa Matthew P. 
Published: October 2009

AbstractRecombinant expression of eukaryotic proteins in Escherichia coli is often limited by poor folding and solubility. To address this problem, we employed a recently developed genetic selection for protein folding and solubility based on the bacterial twin‐arginine translocation (Tat) pathway to rapidly identify properly folded recombinant proteins or soluble protein domains of mammalian origin. The coding sequences for 29 different mammalian polypeptides were cloned as sandwich fusions between an N‐terminal Tat export signal and a C‐terminal selectable marker, namely β‐lactamase. Hence, expression of the selectable marker and survival on selective media was linked to Tat export of the target mammalian protein. Since the folding quality control feature of the Tat pathway prevents export of misfolded proteins, only correctly folded fusion proteins reached the periplasm and conferred cell survival. In general, the ability to confer growth was found to relate closely to the solubility profile and molecular weight of the protein, although other features such as number of contiguous hydrophobic amino acids and cysteine content may also be important. These results highlight the capacity of Tat selection to reveal the folding potential of mammalian proteins and protein domains without the need for structural or functional information about the target protein.
Optimizing atom interferometry on atom chips
Authors: Hohenester U. , Grond J. , Schmiedmayer J. 
Published: October 2009

AbstractWe theoretically investigate the performance of atom interferometers based on ultracold atoms and atom chips. Within the framework of the Gross‐Pitaevskii equation, we simulate the splitting and trapping of a condensate. Within the two‐mode model and the multi‐configurational Hartree method for Bosons, we investigate number squeezing and its impact on the interferometer performance. We show that optimized control strategies allow for efficient condensate trapping and number squeezing on short time scales.
Minimal motif peptide structure of metzincin clan zinc peptidases in micelles
Authors: Onoda Akira , Suzuki Takako , Ishizuka Hiroaki , Sugiyama Rumiko , Ariyasu Shinya , Yamamura Takeshi 
Published: October 2009

AbstractIt is well known that the functions of metalloproteins generally originate from their metal‐binding motifs. However, the intrinsic nature of individual motifs remains unknown, particularly the details about metal‐binding effects on the folding of motifs; the converse is also unknown, although there is no doubt that the motif is the core of the reactivity for each metalloprotein. In this study, we focused our attention on the zinc‐binding motif of the metzincin clan family, HEXXHXXGXXH; this family contains the general zinc‐binding sequence His–Glu–Xaa–Xaa–His (HEXXH) and the extended GXXH region. We adopted the motif sequence of stromelysin‐1 and investigated the folding properties of the Trp‐labeled peptides WAHEIAHSLGLFHA (STR‐W1), AWHEIAHSLGLFHA (STR‐W2), AHEIAHSLGWFHA (STR‐W11), and AHEIAHSLGLFHWA (STR‐W14) in the presence and absence of zinc ions in hydrophobic micellar environments by circular dichroism (CD) measurements. We accessed successful incorporation of these zinc peptides into micelles using quenching of Trp fluorescence. Results of CD studies indicated that two of the Trp‐incorporated peptides, STR‐W1 and STR‐W14, exhibited helical folding in the hydrophobic region of cetyltrimethylammonium chloride micelle. The NMR structural analysis of the apo STR‐W14 revealed that the conformation in the C‐terminus GXXH region significantly differred between the apo state in the micelle and the reported Zn‐bound state of stromelysin‐1 in crystal structures. The structural analyses of the qualitative Zn‐binding properties of this motif peptide provide an interesting Zn‐binding mechanism: the minimum consensus motif in the metzincin clan, a basic zinc‐binding motif with an extended GXXH region, has the potential to serve as a preorganized Zn binding scaffold in a hydrophobic environment. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
High frequency behaviour of low temperature sintered polycrystalline NiCuZn ferrites and their composite thick films
Authors: Dimri Mukesh C. , Kashyap Subhash C. , Dube D. C. 
Published: October 2009

AbstractNiCuZn ferrite nanopowders and polycrystalline bulk samples were prepared by wet chemical (citrate) method followed by sintering at temperatures lower than those for conventional solid‐state ceramic route. The citrate method results in nanopowders. The addition of copper promotes sintering, and results in grain‐growth during sintering, even at a low temperature. Composite thick films of desired thickness were prepared by die casting the ferrite mixed with a polymer in different weight ratios. The dielectric properties of the polycrystalline NiCuZn ferrite and their composite thick films were investigated at radio‐ and X‐band microwave frequencies. Dielectric and magnetic losses are estimated to be appreciably low, even at microwave frequencies.
Faceting of twin grain boundaries in polysilicon films
Authors: Nakhodkin Nikolay , Kulish Nikolay , Rodionova Tatyana 
Published: October 2009

AbstractThe faceting of grain boundaries (GB) under annealing in phosphorus‐doped polysilicon films, produced by low‐pressure chemical vapor deposition, has been investigated by transmission electron microscopy. It has been shown that the facet types and facet density depend on annealing temperature. It has been found that GB facets are generally parallel with close‐packed planes in coincidence site lattice. A correlation between GB faceting and grain‐growth mechanisms has been considered. It has been shown that faceting takes place both under normal and abnormal grain growth. It is revealed that twinning plays the key role for GB faceting under normal grain growth.
In memory of Dr. Maurizio Biasini
Authors: Alam M. Ashraf 
Published: October 2009

AbstractMaurizio Biasini was a member of the positron/positronium community over a period of some 25 years and made substantial contributions to the science in this community and beyond. Tragically, Maurizio's association with us and his family and friends was cut short by a freak accident on the 29th of November 2008 during a family outing. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Doppler‐broadening (DB) measurement of ionic liquids using a monoenergetic positron beam
Authors: Pikart Philip , Hugenschmidt Christoph , Schreckenbach Klaus 
Published: October 2009

AbstractA positron beam is applied to investigate 1‐Butyl‐3‐methyl‐imidazolium‐hexafluorphosphat (BMIm‐PF6) by Doppler broadening (DB) measurements. A liquid is principally free of lateral inhomogeneities while its depth dependent structure is influenced by the surface. This structure is studied in‐situ and non‐destructively by the use of a monoenergetic positron beam.In a second measurement, the ionic liquid performs different phase changes during heating and cooling. Temperature dependent DB measurements of the 511 keV photopeak show very clear influence of phase transitions (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A new method to measure the ortho‐positronium quenching rate in low vapor‐pressure gases
Authors: Wada Ken , Saito Fuminori , Hyodo Toshio 
Published: October 2009

AbstractA new method to measure the ortho‐positronium collisional quenching rate for low vapor‐pressure gases is described. The value of the normalized positronium quenching rate, 1Zeff, for CH3Br, measured by this method, is 0. 70 ± 0.04 (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparison of Contemporary Feature Selection Algorithms: Application to the Classification of ABC‐Transporter Substrates
Authors: Demel Michael A. , Janecek Andreas G. K. , Gansterer Wilfried N. , Ecker Gerhard F. 
Published: October 2009

AbstractMultidrug ABC‐transporters are highly polyspecific in their substrate recognition pattern and influence the pharmacokinetics of a broad variety of structurally diverse compounds. Thus, prediction of ABC‐transporter substrate properties of compound libraries is of major interest. In this study, we use k‐nearest neighbor (kNN) classification in combination with five different feature subset selection (FS) algorithms to create predictive models for classification of ABCB1, ABCC1, and ABCG2 substrates. Our results show that FS methods that incorporate the classification algorithm give the best results and contain only a small subset of descriptors. For ABCB1 and ABCG2 cross validated accuracies of higher than 80% were achieved. The interpretation of the best performing feature subsets showed that descriptors consisting of simple counts as well as of projections of physicochemical properties on subdivided surface areas have highest contribution to the models.
Regression test suite reduction based on SDL models of system requirements
Authors: Chen Yanping , Probert Robert L. , Ural Hasan 
Published: October 2009

AbstractThis paper proposes a model‐based regression test suite reduction method. The proposed method considers an SDL model representing the requirements of a system under test and a set of modifications on this model, applies dependence analysis to identify interaction patterns related to each type of modifications, i.e., adding, deleting, and changing transitions in the SDL model, and reduces the size of a given regression test suite by examining interaction patterns covered by each test case in the test suite. Results of empirical studies are reported. Copyright © 2009 John Wiley & Sons, Ltd.
Clinical application of fetal urine production rate in unexplained polyhydramnios
Authors: Touboul C. , Picone O. , Levaillant J. M. , Boithias C. , Frydman R. , Boulvain M. , Senat M. V. 
Published: October 2009

AbstractObjectiveTo evaluate the clinical use of hourly fetal urine production rate (HFUPR) in polyhydramnios.MethodsThis was a retrospective review of 33 singleton pregnancies with polyhydramnios, 30 of them unexplained and three due to gastrointestinal atresia. HFUPR was estimated using three‐dimensional ultrasound and was compared with recently established nomograms. Abnormal midterm outcome, defined as diagnosis or persistence of pathology after the neonatal period until the age of 2 years, was analyzed according to prenatal HFUPR measurements and other polyhydramnios characteristics.ResultsSeventeen of the 30 fetuses with unexplained polyhydramnios had an HFUPR above the 95th centile, and five (29.4%) of them developed midterm disorders. None of the 13 with normal HFUPR developed midterm disorders. The HFUPR was 1.9 (SD, 0.7) multiples of the median (MoM) in fetuses with an adverse childhood outcome and 1.4 (SD, 1.2) in fetuses with normal childhood outcome (P = 0.34). In the three fetuses with gastrointestinal atresia, the HFUPR was significantly lower than in those with unexplained polyhydramnios (P = 0.003).ConclusionHFUPR was associated with the mechanism of polyhydramnios but failed to help in the prognosis of unexplained polyhydramnios because of lack of power. Children with prenatal unexplained polyhydramnios and HFUPR above the 95th centile should nevertheless receive detailed pediatric follow‐up. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Efficient mapping of multiple VoIP vocoders in WiMAX systems
Authors: Kitroser I. , Chai E. , Ben‐Shimol Y. 
Published: October 2009

AbstractThis paper addresses the problem of efficient mapping and allocation of voice over IP (VoIP) traffic with multiple VoIP vocoders in WiMAX systems. We show that by taking advantage of the periodicity of VoIP frames, generated by multiple vocoder types, and by applying semi‐fixed allocations in the existing resource allocation process, the mapping overhead can be reduced substantially. We present a system model that allows the evaluation of the proposed solutions for the problem at hand. Using this model, we show that the problem is NP hard and present a set of observations on the resource allocation process leading to good mapping decisions from the perspective of mapping overhead. We present a new mapping algorithm that implement the decisions and show by extensive simulations that the proposed mapping algorithm can reduce the overhead down to 25% of the overhead experienced in orthogonal frequency division multiple access (OFDMA)‐based systems such as WiMAX and IEEE802.16, while retaining a low computational complexity. Copyright © 2009 John Wiley & Sons, Ltd.
Detection of minerals by scattered x‐ray radiation
Authors: Kitov B. I. , Mukhachev Yu. S. 
Published: October 2009

AbstractA new procedure of detecting minerals by their scattered x‐ray radiation has been developed. The paper presents a methodology of calculating conditions in which analytical signals of minerals with different compositions differ from each other considerably.The scattered x‐ray radiation of the mineral is registered against the background of scattered radiation from an additional screen made of a material with a low atomic number. The screen is set up behind the mineral in such a way that the mineral's x‐ray shadow falls on it, on the way of primary radiation's spreading.It has been experimentally shown that the suggested method allows to separate natural diamonds from their accompanying minerals with a high precision. Copyright © 2009 John Wiley & Sons, Ltd.
Study of the possibility of the theoretical account for the microabsorption heterogeneity effect of emitters in X‐ray fluorescence
Authors: Smagunova A. N. , Korzhova E. N. , Stavitskaya M. V. , Potapova L. A. , Kozlov V. A. 
Published: October 2009

AbstractIt is shown in the literature that there are two radically different models that describe the microabsorption heterogeneity (MAH) effect in the X‐ray fluorescence (XRF) analysis of powder materials. One of these models is valid when there is a covering of coarse analyte‐containing particles with fine filler particles (II type) and the other one is valid when the covering is absent (I type). For some materials, the magnitude and sign of this effect change depending on its type. It has been experimentally found that the covering is a multifactor process, which is dependent on the strength of particles of a material ground, its humidity, and the presence of other phases, which make its prediction difficult. The variation in the chemical composition of different granulometric fractions of the ground material was quantitatively estimated. The above‐mentioned facts make the theoretical calculation of MAH effect hardly probable when conducting a routine XRF of powder materials. Copyright © 2009 John Wiley & Sons, Ltd.
From voice to agency: Guiding principles for participatory action research with youth
Authors: Rodríguez Louie F. , Brown Tara M. 
Published: October 2009

AbstractThis article begins by examining current crises facing historically marginalized youth, which necessitate more critical approaches to youth development and empirical investigations into the challenges that young people face. This requires not only listening to their voices, but actively engaging them in investigations of and interventions into social problems that affect their lives. Researching with youth raises particular dilemmas, however. The authors discuss strategies, within three guiding principles, that they found effective in conducting participatory action research with marginalized youth for the purposes of social and educational transformation.
Contextualizing black boys' use of a street identity in high school
Authors: Payne Yasser Arafat , Starks Brian Chad , Gibson LaMar Rashad 
Published: October 2009

AbstractThis participatory action research project worked with four street‐life‐oriented black men to document how a community sample of street‐life‐oriented black adolescents between the ages of sixteen and nineteen frame street life as a site of resiliency inside schools based on 156 surveys, 10 individual interviews, and 1 group interview. Data collection took place primarily in Paterson, New Jersey, and Harlem, New York City. Findings reveal that the adolescents overall hold negative attitudes about their educational experiences within two dominant themes: student‐teacher interactions and preparation for economic and educational opportunities. Results can be used to understand how the adolescents' street identities are adaptive inside schools.
A social justice epistemology and pedagogy for Latina/o students: Transforming public education with participatory action research
Authors: Cammarota Julio , Romero Augustine F. 
Published: October 2009

AbstractThe article reports on Latina/o high school students who conducted participatory action research (PAR) on problems that circumscribe their possibilities for self‐determination. The intention is to legitimize student knowledge to develop effective educational policies and practices for young Latinas/os. PAR is engaged through the Social Justice Education Project, which provides students with all social science requirements for their junior and senior years. The mandated curriculum is supplemented with advanced‐level readings from Chicana/o studies, critical race theory, critical pedagogy, and, most important, PAR. The intention is for students to meet the requirements for graduation and to develop sophisticated critical analyses to address problems in their own social contexts.