bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lung function decline from adolescence to young adulthood in cystic fibrosis
Authors: VandenBranden Stacy L. , McMullen Ann , Schechter Michael S. , Pasta David J. , Michaelis Rory L. , Konstan Michael W. , Wagener Jeffrey S. , Morgan Wayne J. , McColley Susanna A. ,   for the Investigators and Coordinators of the Epidemiologic Study of Cystic Fibrosis
Published: September 2011

AbstractBackgroundDespite improving survival in cystic fibrosis (CF) patients, there is a mortality peak in early adulthood. Defining risk factors that predict significant worsening of lung disease in young adulthood may identify opportunities to improve outcomes in adults.MethodsWe identified 4,680 patients in the Epidemiologic Study of Cystic Fibrosis 1994–2005 with data in both adolescence (age 14.0–17.4 years) and young adulthood (age 18.5–22.0 years) and analyzed 2,267 who had ≥5 encounters and ≥5 measurements of forced expiratory volume in 1 second (FEV1) spanning ≥1 year during both adolescence and young adulthood, and ≥1 encounter with weight and height and ≥1 FEV1 measurement age 17.5–18.5 years. We compared the annualized rates of decline in FEV1 during adolescence and young adulthood stratified by best FEV1 around age 18. Logistic regression was used to identify risk factors associated with substantial decline (>20 points) in FEV1% predicted in young adulthood.ResultsAnnual rate of decline was greater in young adulthood than in adolescence. Risk factors for substantial decline included slower rate of FEV1 decline, greater FEV1 variability, faster body mass index (BMI) decline, male sex, chronic inhaled antibiotics, Haemophilus influenzae detection, and absence of multidrug‐resistant Pseudomonas aeruginosa in adolescence, and lower than expected FEV1 and BMI around age 18.ConclusionsDecline in lung function accelerates in young adults with CF, especially in those with early stage lung disease. Adolescents at risk for substantial decline in lung function in young adulthood have higher FEV1 and worse nutritional status, among other identifiable risk factors. Pediatr Pulmonol. 2012; 47:135–143. © 2011 Wiley Periodicals, Inc.
Surviving the Sun: Repair and bypass of DNA UV lesions
Authors: Yang Wei 
Published: September 2011

AbstractStructural studies of UV‐induced lesions and their complexes with repair proteins reveal an intrinsic flexibility of DNA at lesion sites. Reduced DNA rigidity stems primarily from the loss of base stacking, which may manifest as bending, unwinding, base unstacking, or flipping out. The intrinsic flexibility at UV lesions allows efficient initial lesion recognition within a pool of millions to billions of normal DNA base pairs. To bypass the damaged site by translesion synthesis, the specialized DNA polymerase η acts like a molecular “splint” and reinforces B‐form DNA by numerous protein–phosphate interactions. Photolyases and glycosylases that specifically repair UV lesions interact directly with UV lesions in bent DNA via surface complementation. UvrA and UvrB, which recognize a variety of lesions in the bacterial nucleotide excision repair pathway, appear to exploit hysteresis exhibited by DNA lesions and conduct an ATP‐dependent stress test to distort and separate DNA strands. Similar stress tests are likely conducted in eukaryotic nucleotide excision repair.
Increased expression of putative cancer stem cell markers in primary prostate cancer is associated with progression of bone metastases
Authors: Colombel Marc , Eaton Colby L. , Hamdy Freddy , Ricci Estelle , van der Pluijm Gabri , Cecchini Marco , Mege‐Lechevallier Florence , Clezardin Philippe , Thalmann George 
Published: September 2011

AbstractBACKGROUNDA number of putative stem cell markers have been associated with aggressiveness of prostate cancer, including alpha 2 and alpha 6 integrin and c‐met. The study aimed to test the hypothesis that the development of bone metastasis correlates with the proportion of prostate cancer stem cell‐like cells present in the primary tumor.METHODSProstate tissue samples were obtained from patients with high‐risk prostatic adenocarcinoma. Prostate cancer tumor tissue samples underwent immunohistochemical staining for alpha 2 and alpha 6 integrin and c‐met; positive and negative controls were included. Samples were scored as positive if >5% of cells within the sample stained positively. Survival and bone metastasis‐free survival curves on the patient cohort were estimated by the actuarial method of Kaplan–Meier.RESULTSA total of 62 patients were included in the study. Bone metastases progression rate was 46% at 105 months with a median time of 46 months (95% CI: 1–62.5 months); prostate cancer‐specific survival was 33% at 122 months with a median survival time of 69.4 months (95% CI: 63.5–109.4 months). Survival curves show that c‐met‐, alpha 2, and alpha 6 integrin‐positive tumors were positively associated with the occurrence of bone metastasis‐free survival. There was a higher level of significance when at least c‐met and either alpha 2 or alpha 6 integrin was positive.CONCLUSIONIt can be concluded that percentage of stem cell‐like prostate cancer cells has a prognostic impact especially on the risk of metastatic bone progression. Prostate 72:713–720, 2012. © 2011 Wiley Periodicals, Inc.
Identification of prostatic acid phosphatase (PAP) specific HLA‐DR1‐restricted t‐cell epitopes
Authors: Johnson Laura E. , McNeel Douglas G. 
Published: September 2011

AbstractBACKGROUNDProstatic acid phosphatase (PAP) is a prostate cancer tumor antigen and is an immunological target in several active immunotherapy clinical trials for the treatment of prostate cancer. We and others have demonstrated that PAP‐specific T‐cell responses can be elicited and augmented following antigen‐specific immunization in both humans and animal models. We have previously reported that prostate cancer patients immunized with a DNA vaccine encoding PAP (pTVG‐HP) developed both CD4+ and CD8+ T‐cell responses. PAP‐specific, CD4+ T‐cell proliferative responses were generated in three out of four HLA‐DRB1*0101 patients suggesting the possibility that DR1‐restricted epitopes exist.METHODSTo identify PAP‐specific HLA‐DRB1*0101 restricted epitopes, we immunized HLA‐A2.01/HLA‐DRB1*0101 (A2/DR1) transgenic mice with the pTVG‐HP DNA vaccine. To map DRB1*0101‐restricted epitopes, splenocytes from immunized mice were screened against a library of overlapping 15‐residue, PAP‐derived peptides using an IFNγ ELISPOT assay.RESULTSWe identified four HLA‐DRB1*0101 epitopes for PAP in A2/DR1 mice (PAP161–175, PAP181–195, PAP191–205, and PAP 351–365). T cells specific for one epitope (PAP181–195) were found to be augmented after immunization in a HLA‐DRB1*0101+ prostate cancer patient.CONCLUSIONSThe identification of MHC class II epitopes may provide tools to directly monitor immune responses after vaccination and may be important for the design of future prostate cancer vaccines. Prostate 72:730–740, 2012. © 2011 Wiley Periodicals, Inc.
How many ionizable groups can sit on a protein hydrophobic core?
Authors: Garcia‐Seisdedos Hector , Ibarra‐Molero Beatriz , Sanchez‐Ruiz Jose M. 
Published: September 2011

AbstractFull or partial burial of ionizable groups in the hydrophobic interior of proteins underlies the large modulation in group properties (modified pK value, high nucleophilicity, enhanced capability of interaction with chemical moieties of the substrate, etc.) linked to biological function. Indeed, the few internal ionizable residues found in proteins are known to play important functional roles in catalysis and, in general, in energy transduction processes. However, ionizable‐group burial is expected to be seriously disruptive and, it is important to note, most functional sites contain not just one, but several ionizable residues. Hence, the adaptations involved in the development of function in proteins (through in vitro engineering or during the course of natural evolution) are not fully understood. Here, we explore experimentally how proteins respond to the accumulation of hydrophobic‐to‐ionizable residue substitutions. For this purpose, we have constructed a combinatorial library targeting a hydrophobic cluster in a consensus‐engineered, stabilized form of a small model protein. Contrary to naïve expectation, half of the variants randomly selected from the library are soluble, folded, and active, despite including up to four mutations. Furthermore, for these variants, the dependence of stability with the number of mutations is not synergistic and catastrophic, but smooth and approximately linear. Clearly, stabilized protein scaffolds may be robust enough to withstand many disruptive hydrophobic‐to‐ionizable residue mutations, even when they are introduced in the same region of the structure. These results should be relevant for protein engineering and may have implications for the understanding of the early evolution of enzymes. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Simulation of movement of pesticides towards drains with a preferential flow version of PEARL
Authors: Tiktak Aaldrik , Hendriks Rob FA , Boesten Jos JTI 
Published: September 2011

AbstractBACKGROUND: As part of the Dutch authorisation procedure for pesticides, an assessment of the effects on aquatic organisms in surface waters adjacent to agricultural fields is required. The peak concentration is considered to be the most important exposure endpoint for the ecotoxicological effect assessment. Macropore flow is an important driver for the peak concentration, so the leaching model PEARL was extended with a macropore module. The new model has two macropore domains: a bypass domain and an internal catchment domain. The model was tested against data from a field leaching study on a cracking clay soil in the Netherlands.RESULTS: Most parameters of the model could be obtained from site‐specific measurements, pedotransfer functions and general soil structural knowledge; only three macropore‐flow‐related parameters needed calibration. The flow‐related macropore parameters could not be calibrated without using the concentration in drain water. Sequential calibration strategies, in which firstly the water flow model and then the pesticide fate model are calibrated, may therefore be less suitable for preferential flow models.CONCLUSION: After calibration, PEARL could simulate well the observed rapid movement towards drains of two pesticides with contrasting sorption and degradation rate properties. The calibrated value for the fraction of the internal catchment domain was high (90%). This means that a large fraction of water entering the macropores infiltrates into the soil matrix, thus reducing the fraction of rapid flow. Copyright © 2011 Society of Chemical Industry
The mechanism of Pt films to suppress the electron emission of grid in TWTs
Authors: Li TianJun , Feng Tao , Jiang BingYao , Liu XiangHuai , Chen YiWei , Sun Zhuo 
Published: September 2011

AbstractPt films were deposited onto molybdenum grids by ion‐beam‐assisted deposition (IBAD) method. Electron‐emission characteristics of molybdenum, with and without Pt films, contaminated by active electron‐emission substances (Ba and BaO) were measured by analogous diode method. X‐ray diffraction (XRD) and combined thermogravimetry/differential thermal analysis/mass spectrometry (TG‐DTA‐MS) were used to study the reaction between Pt and BaO in simulation experiments. The results showed that the emission current from an Mo grid coated with a Pt film is much less than that from Mo grid without a film, and the mechanism for electron emission suppression of the molybdenum grid coated with Pt films was discussed (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tunnelling magnetoresistance effects in FeCoGd(t)/AlO/FeCo multilayers
Authors: Bai X. J. , Yang M. , Ge J. J. , You B. , Zhang W. , Zhao X. R. , Cao C. D. , Du J. 
Published: September 2011

AbstractFeCoGd(t)/AlO/FeCo magnetic tunneling junctions (MTJs) have been fabricated using a shadow mask by magnetron sputtering system on SiO2 wafer, with a simple oxidation in the atmosphere to the bottom electrode FeCoGd layer. From the transmission electron microscopy (TEM) with element content analysis, we found a serious oxidation of the Gd element at the FeCoGd/AlO interface. At room temperature, inverse/normal TMR effects and normal TMR effects were observed simultaneously in the low and high magnetic field region, respectively. The high field curves show superparamagnetic behaviour, which are difficult to be saturated. The saturation field increases with the increase of t. The low field normal or inverse TMR effect is mainly resulted from the existence of the compensation thickness of the FeCoGd layer at room temperature. However, the normal TMR effect in high field region mainly origins from the existence of a granular layer at the FeCoGd/AlO interface consists of FeCo‐rich particles embedded in GdO insulating matrix. With the increase of the external magnetic field, the magnetic moments of the FeCo‐rich particles in the granular layer gradually rotate to the field direction (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Atomic and electronic structure of Mn‐delta doped GaN (1\bar 100) film from first‐principles calculations
Authors: Wang JiXia , Huang GuiQin 
Published: September 2011

AbstractThe atomic and electronic structure of Mn‐delta doped GaN (1\bar 100) nonpolar films are investigated using first‐principles calculations. The geometric relaxation is analyzed. When Mn is doped in the interior layer of the film, the atomic relaxation around it is small, the Mn‐N bond length is elongated slightly. But when Mn is doped at the surface layer of the film, the Mn‐N bond length is reduced as the Ga‐N bond at the surface, but the phenomena of the buckling of Ga‐N bond is not observed for Mn‐N bond. The calculations of Mn formation energy show that the site closest to the surface is favored. The results of electronic structure calculation indicate that spin polarized Mn impurity bands appear in the gap of the host film, which is in favor of spin injection (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The ferromagnetic and ferroelectric properties of (Bi0.9La0.1)(Fe0.95Co0.05)O3
Authors: Xu Qingyu , Wen Zheng , Gao Jinlong , Liu Xiao , Wu Di , Tang Shaolong , Yang Bin 
Published: September 2011

Abstract(Bi0.9La0.1)(Fe0.95Co0.05)O3 films were deposited onto LaNiO3‐coated Si substrates by chemical solution deposition. The X‐ray diffraction pattern shows pure R3c structure of the film without any impurity phase, which has been further confirmed by the Raman measurements. Weak room temperature ferromagnetism has been observed with saturate magnetization of 4 emu/cm3. The ferroelectricity of the film was confirmed by the voltage dependent converse piezoelectric coefficient d33 hysteresis loop. The both observation of the magnetic domain and ferroelectric domain patterns indicate the potential multiferroic applications. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nitrates: A new class of electrolytes for the rapid anodic growth of self‐ordered oxide nanopore layers on Ti and Ta
Authors: Wei Wei , Kirchgeorg Robin , Lee Kiyoung , So Seulgi , Schmuki Patrik 
Published: September 2011

AbstractIn the present work, we demonstrate that anodization in a nitrate containing organic electrolyte, under specific conditions, can be used to achieve highly aligned nanoporous oxide layers on Ti and Ta substrates. These layers after formation consist of amorphous TiO2 and Ta2O5, respectively, with regular pore sizes in the range of 20 to 30 nm. The amorphous layers can easily be crystallized by annealing. A main geometric feature of the layers is that they show a through‐hole morphology which is considered to be of high interest for various types of membrane applications.magnified image(© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical studies of Aum and PtAun clusters and their N2 and O2 adsorption complexes
Authors: Chen Ya Kun , Tian Wei Quan , Wang Yan Alexander 
Published: September 2011

AbstractSmall homonuclear Aum (m ≤ 5) and bimetallic PtAun (n ≤ 4) clusters were studied using density functional theory. Both homonuclear and bimetallic clusters tend to form compact two‐dimensional structures. All the low‐lying Aum clusters have delocalized highest occupied molecular orbitals (HOMOs), whereas all the PtAun clusters have more localized HOMOs on the Pt atom. The localized HOMO makes the PtAun clusters more regioselective toward electrophilic reactions than the Aum clusters. Adsorptions of N2 and O2 onto these metal clusters were further studied. In N2 adsorption, the metal clusters donate their electrons primarily to the σ* orbitals of N2 to form end‐on complexes preferably. In O2 adsorption, complicated π orbital interactions between the cluster and O2 dominate to form side‐on complexes with relatively larger binding energies. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical calculation of the pKa values of some drugs in aqueous solution
Authors: Ghalami‐Choobar Bahram , Dezhampanah Hamid , Nikparsa Paria , Ghiami‐Shomami Ali 
Published: September 2011

AbstractIn this work, calculations of pKa values have been performed on benzoic acid and its para‐substituted derivatives and some drugs by using Gaussian 98 software package. Gas‐phase energies were calculated with HF/6‐31 G** and B3LYP/6‐31 G** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor‐like PCM (CPCM), and the integral equation formalism‐PCM at the same levels which have been used for geometry determination in the gas‐phase. The results that show the calculated pKa values using the B3LYP are better than those using the corresponding HF. In comparison to the other models, the results obtained indicate that the PCM model is a suitable solvation model for calculating pKa values. For the investigated compounds, a good agreement between the experimental and the calculated pKa values was also observed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The benchmark of Gutzwiller density functional theory in hydrogen systems
Authors: Yao Y. X. , Wang C. Z. , Ho K. M. 
Published: September 2011

AbstractWe propose an approximate form of the exchange‐correlation energy functional for the Gutzwiller density functional theory. It satisfies certain physical constraints in both weak and strong electron correlation limits. We benchmark the Gutzwiller density functional approximation in the hydrogen systems, where the static correlation error is shown to be negligible. The good transferability is demonstrated by applications to the hydrogen molecule and some crystal structures. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
H ∞  sliding mode observer design for a class of nonlinear discrete time‐delay systems: A delay‐fractioning approach
Authors: Hu Jun , Wang Zidong , Niu Yugang , Stergioulas Lampros K. 
Published: September 2011

SUMMARYIn this paper, the H ∞  sliding mode observer (SMO) design problem is investigated for a class of nonlinear discrete time‐delay systems. The nonlinear descriptions quantify the maximum possible derivations from a linear model, and the system states are allowed to be immeasurable. Attention is focused on the design of a discrete‐time SMO such that the asymptotic stability as well as the H ∞  performance requirement of the error dynamics can be guaranteed in the presence of nonlinearities, time delay and external disturbances. Firstly, a discrete‐time discontinuous switched term is proposed to make sure that the reaching condition holds. Then, by constructing a new Lyapunov–Krasovskii functional based on the idea of ‘delay fractioning’ and by introducing some appropriate free‐weighting matrices, a sufficient condition is established to guarantee the desired performance of the error dynamics in the specified sliding mode surface by solving a minimization problem. Finally, an illustrative example is given to show the effectiveness of the designed SMO design scheme. Copyright © 2011 John Wiley & Sons, Ltd.
Giant components in Kronecker graphs
Authors: Horn Paul , Radcliffe Mary 
Published: September 2011

AbstractLet
\documentclass{article} \usepackage{mathrsfs} \usepackage{amsmath, amssymb} \pagestyle{empty} \begin{document} \begin{align*}n\in\mathbb{N}\end{align*} \end{document}, 0 <α,β,γ< 1. Define the random Kronecker graph K(n,α,γ,β) to be the graph with vertex set
\documentclass{article} \usepackage{mathrsfs} \usepackage{amsmath, amssymb} \pagestyle{empty} \begin{document} \begin{align*}\mathbb{Z}_2^n\end{align*} \end{document}, where the probability that u is adjacent to v is given by pu,v =α u⋅vγ(1‐u)⋅(1‐v)βn‐u⋅v‐(1‐u)⋅(1‐v). This model has been shown to obey several useful properties of real‐world networks. We establish the asymptotic size of the giant component in the random Kronecker graph.© 2011 Wiley Periodicals, Inc. Random Struct. Alg.,2011
Towards a better understanding of software evolution: an empirical study on open‐source software
Authors: Neamtiu Iulian , Xie Guowu , Chen Jianbo 
Published: September 2011

SUMMARYSoftware evolution is a fact of life. Over the past 30 years, researchers have proposed hypotheses on how software changes and provided evidence that both supports and refutes these hypotheses. To paint a clearer image of the software evolution process, we performed an empirical study on long spans in the lifetime of nine open‐source projects. Our analysis covers 705 official releases and a combined 108 years of evolution. We first tried to confirm Lehman's eight laws of software evolution on these projects using statistical hypothesis testing. Our findings indicate that only the laws of continuing change and continuing growth are confirmed for all programs, whereas the other six laws are violated by some programs, or can be both confirmed and invalidated, depending on the laws' operational definitions. Second, we analyze the growth rate for projects' development and maintenance branches, and the distribution of software changes. We find similarities in the evolution patterns of the programs we studied, which brings us closer to constructing rigorous models for software evolution. Copyright © 2011 John Wiley & Sons, Ltd.
A JAVA application framework for scientific software development
Authors: Fdez‐Riverola F. , Glez‐Peña D. , López‐Fernández H. , Reboiro‐Jato M. , Méndez J.R. 
Published: September 2011

SUMMARYThis paper presents AIBench (SING group, Ourense, Spain), a JAVA desktop application framework mainly focused on scientific software development, with the goal of improving the productivity of research groups. Following the MVC design pattern, the programmer is able to develop applications using only three types of concepts: operations, data‐typesand views. The framework provides the rest of the functionality present in typical scientific applications, including user parameter requests, logging facilities, multithreading execution, experiment repeatability and graphic user interface generation, among others. The proposed framework is implemented following a plugin‐based architecture, which also allows assembling new applications by the reuse of modules from past development projects. Copyright © 2011 John Wiley & Sons, Ltd.
Combination of acid‐demineralization and enzymatic desizing of cotton fabrics by using industrial acid stable glucoamylases and α‐amylases
Authors: Dehabadi Vahid Ameri , Opwis Klaus , Gutmann Jochen 
Published: September 2011

AbstractIn this study, the possibility of simultaneous acid‐demineralization and enzymatic desizing of cotton fabric in acidic conditions (pH 2) by using industrial acid stable enzymes has been investigated. Acid‐demineralization is necessary to remove undesired cationic metals and earth alkalis. Our experiments showed that by use of a mixture of two appropriate enzymes, a glucoamylase (Multifect GA 10L) and an α‐amylase (Optisize Next) in a solution of citric acid and presence of a chelating agent, enzymatic desizing, and acid‐demineralization can be successfully carried out at the same time. Therefore, two processes of pretreatment were integrated into a single process, which can effectively reduce time and costs for textile industry.